Isolated polynucleotides and polypeptides and methods of using same for increasing plant yield, biom

专利摘要:
Provided are isolated polynucleotides comprising a nucleic acid sequence encoding a polypeptide at least 80 % identical to SEQ ID NO: 422, 362-421, 423-601, 2429-4085 and 4086, such as a polynucleotide which is at least 80% identical to SEQ ID NO: 260, 1-259, 261-361, 602-2427 and 2428, nucleic acid constructs comprising same, plant cells comprising same, transgenic plants expressing same, and methods of generating thereof for increasing the yield, biomass, growth rate, vigor, oil content, fiber yield, fiber quality, nitrogen use efficiency and/or abiotic stress tolerance of a plant.
公开号:AU2013227247A1
申请号:U2013227247
申请日:2013-02-27
公开日:2014-09-18
发明作者:Hagai Karchi；Noa Matarasso
申请人:Evogene Ltd；
IPC主号:A01H5-00

专利说明:
WO 2013/128448 PCT/IL2013/050172 1 ISOLATED POLYNUCLEOTIDES AND POLYPEPTIDES AND METHODS OF USING SAME FOR INCREASING PLANT YIELD, BIOMASS, GROWTH RATE, VIGOR, OIL CONTENT, ABIOTIC STRESS TOLERANCE OF PLANTS AND NITROGEN USE EFFICIENCY 5 FIELD AND BACKGROUND OF THE INVENTION The present invention, in some embodiments thereof, relates to isolated polypeptides and polynucleotides, nucleic acid constructs comprising same, transgenic cells comprising same, transgenic plants exogenously expressing same and more 10 particularly, but not exclusively, to methods of using same for increasing yield (e.g., seed yield, oil yield), biomass, growth rate, vigor, oil content, fiber yield, fiber quality, fertilizer use efficiency (e.g., nitrogen use efficiency) and/or abiotic stress tolerance of a plant. Yield is affected by various factors, such as, the number and size of the plant 15 organs, plant architecture (for example, the number of branches), grains set length, number of filled grains, vigor (e.g. seedling), growth rate, root development, utilization of water, nutrients (e.g., nitrogen) and fertilizers, and stress tolerance. Crops such as, corn, rice, wheat, canola and soybean account for over half of total human caloric intake, whether through direct consumption of the seeds themselves 20 or through consumption of meat products raised on processed seeds or forage. Seeds are also a source of sugars, proteins and oils and metabolites used in industrial processes. The ability to increase plant yield, whether through increase dry matter accumulation rate, modifying cellulose or lignin composition, increase stalk strength, enlarge meristem size, change of plant branching pattern, erectness of leaves, increase in 25 fertilization efficiency, enhanced seed dry matter accumulation rate, modification of seed development, enhanced seed filling or by increasing the content of oil, starch or protein in the seeds would have many applications in agricultural and non-agricultural uses such as in the biotechnological production of pharmaceuticals, antibodies or vaccines. 30 Vegetable or seed oils are the major source of energy and nutrition in human and animal diet. They are also used for the production of industrial products, such as paints, inks and lubricants. In addition, plant oils represent renewable sources of long-chain WO 2013/128448 PCT/IL2013/050172 2 hydrocarbons which can be used as fuel. Since the currently used fossil fuels are finite resources and are gradually being depleted, fast growing biomass crops may be used as alternative fuels or for energy feedstocks and may reduce the dependence on fossil energy supplies. However, the major bottleneck for increasing consumption of plant 5 oils as bio-fuel is the oil price, which is still higher than fossil fuel. In addition, the production rate of plant oil is limited by the availability of agricultural land and water. Thus, increasing plant oil yields from the same growing area can effectively overcome the shortage in production space and can decrease vegetable oil prices at the same time. Studies aiming at increasing plant oil yields focus on the identification of genes 10 involved in oil metabolism as well as in genes capable of increasing plant and seed yields in transgenic plants. Genes known to be involved in increasing plant oil yields include those participating in fatty acid synthesis or sequestering such as desaturase [e.g., DELTA6, DELTA12 or acyl-ACP (Ssi2; Arabidopsis Information Resource (TAIR; Hypertext Transfer Protocol://World Wide Web (dot) arabidopsis (dot) org/), 15 TAIR No. AT2G43710)], OleosinA (TAIR No. AT3G01570) or FAD3 (TAIR No. AT2G29980), and various transcription factors and activators such as Lec [TAIR No. AT1G21970, Lotan et al. 1998. Cell. 26;93(7):1195-205], Lec2 [TAIR No. AT1G28300, Santos Mendoza et al. 2005, FEBS Lett. 579(21):4666-70], Fus3 (TAIR No. AT3G26790), ABI3 [TAIR No. AT3G24650, Lara et al. 2003. J Biol Chem. 20 278(23): 21003-11] and Wril [TAIR No. AT3G54320, Cernac and Benning, 2004. Plant J. 40(4): 575-85]. Genetic engineering efforts aiming at increasing oil content in plants (e.g., in seeds) include upregulating endoplasmic reticulum (FAD3) and plastidal (FAD7) fatty acid desaturases in potato (Zabrouskov V., et al., 2002; Physiol Plant. 116:172-185); 25 over-expressing the GmDof4 and GmDofl1 transcription factors (Wang HW et al., 2007; Plant J. 52:716-29); over-expressing a yeast glycerol-3-phosphate dehydrogenase under the control of a seed-specific promoter (Vigeolas H, et al. 2007, Plant Biotechnol J. 5:431-41; U.S. Pat. Appl. No. 20060168684); using Arabidopsis FAE1 and yeast SLC1-1 genes for improvements in erucic acid and oil content in rapeseed (Katavic V, 30 et al., 2000, Biochem Soc Trans. 28:935-7). Various patent applications disclose genes and proteins which can increase oil content in plants. These include for example, U.S. Pat. Appl. No. 20080076179 (lipid WO 2013/128448 PCT/IL2013/050172 3 metabolism protein); U.S. Pat. Apple. No. 20060206961 (the Ypr140w polypeptide); U.S. Pat. Apple. No. 20060174373 [triacylglycerols synthesis enhancing protein (TEP)]; U.S. Pat. Apple. Nos. 20070169219, 20070006345, 20070006346 and 20060195943 (disclose transgenic plants with improved nitrogen use efficiency which can be used for 5 the conversion into fuel or chemical feedstocks); W02008/122980 (polynucleotides for increasing oil content, growth rate, biomass, yield and/or vigor of a plant). A common approach to promote plant growth has been, and continues to be, the use of natural as well as synthetic nutrients (fertilizers). Thus, fertilizers are the fuel behind the "green revolution", directly responsible for the exceptional increase in crop 10 yields during the last 40 years, and are considered the number one overhead expense in agriculture. For example, inorganic nitrogenous fertilizers such as ammonium nitrate, potassium nitrate, or urea, typically accounts for 40 % of the costs associated with crops such as corn and wheat. Of the three macronutrients provided as main fertilizers [Nitrogen (N), Phosphate (P) and Potassium (K)], nitrogen is often the rate-limiting 15 element in plant growth and all field crops have a fundamental dependence on inorganic nitrogenous fertilizer. Nitrogen is responsible for biosynthesis of amino and nucleic acids, prosthetic groups, plant hormones, plant chemical defenses, etc. and usually needs to be replenished every year, particularly for cereals, which comprise more than half of the cultivated areas worldwide. Thus, nitrogen is translocated to the shoot, where 20 it is stored in the leaves and stalk during the rapid step of plant development and up until flowering. In corn for example, plants accumulate the bulk of their organic nitrogen during the period of grain germination, and until flowering. Once fertilization of the plant has occurred, grains begin to form and become the main sink of plant nitrogen. The stored nitrogen can be then redistributed from the leaves and stalk that 25 served as storage compartments until grain formation. Since fertilizer is rapidly depleted from most soil types, it must be supplied to growing crops two or three times during the growing season. In addition, the low nitrogen use efficiency (NUE) of the main crops (e.g., in the range of only 30-70 %) negatively affects the input expenses for the farmer, due to the excess fertilizer applied. 30 Moreover, the over and inefficient use of fertilizers are major factors responsible for environmental problems such as eutrophication of groundwater, lakes, rivers and seas, nitrate pollution in drinking water which can cause methemoglobinemia, phosphate WO 2013/128448 PCT/IL2013/050172 4 pollution, atmospheric pollution and the like. However, in spite of the negative impact of fertilizers on the environment, and the limits on fertilizer use, which have been legislated in several countries, the use of fertilizers is expected to increase in order to support food and fiber production for rapid population growth on limited land 5 resources. For example, it has been estimated that by 2050, more than 150 million tons of nitrogenous fertilizer will be used worldwide annually. Increased use efficiency of nitrogen by plants should enable crops to be cultivated with lower fertilizer input, or alternatively to be cultivated on soils of poorer quality and would therefore have significant economic impact in both developed and 10 developing agricultural systems. Genetic improvement of fertilizer use efficiency (FUE) in plants can be generated either via traditional breeding or via genetic engineering. Attempts to generate plants with increased FUE have been described in U.S. Pat. Appl. No. 20020046419 to Choo, et al.; U.S. Pat. Appl. No. 20050108791 to Edgerton 15 et al.; U.S. Pat. Appl. No. 20060179511 to Chomet et al.; Good, A, et al. 2007 (Engineering nitrogen use efficiency with alanine aminotransferase. Canadian Journal of Botany 85: 252-262); and Good AG et al. 2004 (Trends Plant Sci. 9:597-605). Yanagisawa et al. (Proc. Natl. Acad. Sci. U.S.A. 2004 101:7833-8) describe Dof 1 transgenic plants which exhibit improved growth under low-nitrogen conditions. 20 U.S. Pat. No. 6,084,153 to Good et al. discloses the use of a stress responsive promoter to control the expression of Alanine Amine Transferase (AlaAT) and transgenic canola plants with improved drought and nitrogen deficiency tolerance when compared to control plants. Abiotic stress (ABS; also referred to as "environmental stress") conditions such 25 as salinity, drought, flood, suboptimal temperature and toxic chemical pollution, cause substantial damage to agricultural plants. Most plants have evolved strategies to protect themselves against these conditions. However, if the severity and duration of the stress conditions are too great, the effects on plant development, growth and yield of most crop plants are profound. Furthermore, most of the crop plants are highly susceptible to 30 abiotic stress and thus necessitate optimal growth conditions for commercial crop yields. Continuous exposure to stress causes major alterations in the plant metabolism which ultimately leads to cell death and consequently yield losses.
WO 2013/128448 PCT/IL2013/050172 5 Drought is a gradual phenomenon, which involves periods of abnormally dry weather that persists long enough to produce serious hydrologic imbalances such as crop damage, water supply shortage and increased susceptibility to various diseases. In severe cases, drought can last many years and results in devastating effects on 5 agriculture and water supplies. Furthermore, drought is associated with increase susceptibility to various diseases. For most crop plants, the land regions of the world are too arid. In addition, overuse of available water results in increased loss of agriculturally-usable land (desertification), and increase of salt accumulation in soils adds to the loss of available 10 water in soils. Salinity, high salt levels, affects one in five hectares of irrigated land. None of the top five food crops, i.e., wheat, corn, rice, potatoes, and soybean, can tolerate excessive salt. Detrimental effects of salt on plants result from both water deficit, which leads to osmotic stress (similar to drought stress), and the effect of excess sodium 15 ions on critical biochemical processes. As with freezing and drought, high salt causes water deficit; and the presence of high salt makes it difficult for plant roots to extract water from their environment. Soil salinity is thus one of the more important variables that determine whether a plant may thrive. In many parts of the world, sizable land areas are uncultivable due to naturally high soil salinity. Thus, salination of soils that 20 are used for agricultural production is a significant and increasing problem in regions that rely heavily on agriculture, and is worsen by over-utilization, over-fertilization and water shortage, typically caused by climatic change and the demands of increasing population. Salt tolerance is of particular importance early in a plant's lifecycle, since evaporation from the soil surface causes upward water movement, and salt accumulates 25 in the upper soil layer where the seeds are placed. On the other hand, germination normally takes place at a salt concentration which is higher than the mean salt level in the whole soil profile. Salt and drought stress signal transduction consist of ionic and osmotic homeostasis signaling pathways. The ionic aspect of salt stress is signaled via the SOS 30 pathway where a calcium-responsive SOS3-SOS2 protein kinase complex controls the expression and activity of ion transporters such as SOS1. The osmotic component of WO 2013/128448 PCT/IL2013/050172 6 salt stress involves complex plant reactions that overlap with drought and/or cold stress responses. Suboptimal temperatures affect plant growth and development through the whole plant life cycle. Thus, low temperatures reduce germination rate and high 5 temperatures result in leaf necrosis. In addition, mature plants that are exposed to excess of heat may experience heat shock, which may arise in various organs, including leaves and particularly fruit, when transpiration is insufficient to overcome heat stress. Heat also damages cellular structures, including organelles and cytoskeleton, and impairs membrane function. Heat shock may produce a decrease in overall protein synthesis, 10 accompanied by expression of heat shock proteins, e.g., chaperones, which are involved in refolding proteins denatured by heat. High-temperature damage to pollen almost always occurs in conjunction with drought stress, and rarely occurs under well-watered conditions. Combined stress can alter plant metabolism in novel ways. Excessive chilling conditions, e.g., low, but above freezing, temperatures affect crops of tropical 15 origins, such as soybean, rice, maize, and cotton. Typical chilling damage includes wilting, necrosis, chlorosis or leakage of ions from cell membranes. The underlying mechanisms of chilling sensitivity are not completely understood yet, but probably involve the level of membrane saturation and other physiological deficiencies. Excessive light conditions, which occur under clear atmospheric conditions subsequent 20 to cold late summer/autumn nights, can lead to photoinhibition of photosynthesis (disruption of photosynthesis). In addition, chilling may lead to yield losses and lower product quality through the delayed ripening of maize. Common aspects of drought, cold and salt stress response [Reviewed in Xiong and Zhu (2002) Plant Cell Environ. 25: 131-139] include: (a) transient changes in the 25 cytoplasmic calcium levels early in the signaling event; (b) signal transduction via mitogen-activated and/or calcium dependent protein kinases (CDPKs) and protein phosphatases; (c) increases in abscisic acid levels in response to stress triggering a subset of responses; (d) inositol phosphates as signal molecules (at least for a subset of the stress responsive transcriptional changes; (e) activation of phospholipases which in 30 turn generates a diverse array of second messenger molecules, some of which might regulate the activity of stress responsive kinases; (f) induction of late embryogenesis abundant (LEA) type genes including the CRT/DRE responsive COR/RD genes; (g) WO 2013/128448 PCT/IL2013/050172 7 increased levels of antioxidants and compatible osmolytes such as proline and soluble sugars; and (h) accumulation of reactive oxygen species such as superoxide, hydrogen peroxide, and hydroxyl radicals. Abscisic acid biosynthesis is regulated by osmotic stress at multiple steps. Both ABA-dependent and -independent osmotic stress 5 signaling first modify constitutively expressed transcription factors, leading to the expression of early response transcriptional activators, which then activate downstream stress tolerance effector genes. Several genes which increase tolerance to cold or salt stress can also improve drought stress protection, these include for example, the transcription factor 10 AtCBF/DREB1, OsCDPK7 (Saijo et al. 2000, Plant J. 23: 319-327) or AVP1 (a vacuolar pyrophosphatase-proton pump, Gaxiola et al. 2001, Proc. Natl. Acad. Sci. USA 98: 11444-11449). Studies have shown that plant adaptations to adverse environmental conditions are complex genetic traits with polygenic nature. Conventional means for crop and 15 horticultural improvements utilize selective breeding techniques to identify plants having desirable characteristics. However, selective breeding is tedious, time consuming and has an unpredictable outcome. Furthermore, limited germplasm resources for yield improvement and incompatibility in crosses between distantly related plant species represent significant problems encountered in conventional 20 breeding. Advances in genetic engineering have allowed mankind to modify the germplasm of plants by expression of genes-of-interest in plants. Such a technology has the capacity to generate crops or plants with improved economic, agronomic or horticultural traits. Genetic engineering efforts, aimed at conferring abiotic stress tolerance to 25 transgenic crops, have been described in various publications [Apse and Blumwald (Curr Opin Biotechnol. 13:146-150, 2002), Quesada et al. (Plant Physiol. 130:951-963, 2002), Holmstram et al. (Nature 379: 683-684, 1996), Xu et al. (Plant Physiol 110: 249 257, 1996), Pilon-Smits and Ebskamp (Plant Physiol 107: 125-130, 1995) and Tarczynski et al. (Science 259: 508-510, 1993)]. 30 Various patents and patent applications disclose genes and proteins which can be used for increasing tolerance of plants to abiotic stresses. These include for example, U.S. Pat. Nos. 5,296,462 and 5,356,816 (for increasing tolerance to cold stress); U.S.
WO 2013/128448 PCT/IL2013/050172 8 Pat. No. 6,670,528 (for increasing ABST); U.S. Pat. No. 6,720,477 (for increasing ABST); U.S. Application Ser. Nos. 09/938842 and 10/342224 (for increasing ABST); U.S. Application Ser. No. 10/231035 (for increasing ABST); W02004/104162 (for increasing ABST and biomass); W02007/020638 (for increasing ABST, biomass, vigor 5 and/or yield); W02007/049275 (for increasing ABST, biomass, vigor and/or yield); W02010/076756 (for increasing ABST, biomass and/or yield);. W02009/083958 (for increasing water use efficiency, fertilizer use efficiency, biotic/abiotic stress tolerance, yield and/or biomass); W02010/020941 (for increasing nitrogen use efficiency, abiotic stress tolerance, yield and/or biomass); W02009/141824 (for increasing plant utility); 10 W02010/049897 (for increasing plant yield). Nutrient deficiencies cause adaptations of the root architecture, particularly notably for example is the root proliferation within nutrient rich patches to increase nutrient uptake. Nutrient deficiencies cause also the activation of plant metabolic pathways which maximize the absorption, assimilation and distribution processes such 15 as by activating architectural changes. Engineering the expression of the triggered genes may cause the plant to exhibit the architectural changes and enhanced metabolism also under other conditions. In addition, it is widely known that the plants usually respond to water deficiency by creating a deeper root system that allows access to moisture located in 20 deeper soil layers. Triggering this effect will allow the plants to access nutrients and water located in deeper soil horizons particularly those readily dissolved in water like nitrates. Cotton and cotton by-products provide raw materials that are used to produce a wealth of consumer-based products in addition to textiles including cotton foodstuffs, 25 livestock feed, fertilizer and paper. The production, marketing, consumption and trade of cotton-based products generate an excess of $100 billion annually in the U.S. alone, making cotton the number one value-added crop. Even though 90 % of cotton's value as a crop resides in the fiber (lint), yield and fiber quality has declined due to general erosion in genetic diversity of cotton varieties, 30 and an increased vulnerability of the crop to environmental conditions. There are many varieties of cotton plant, from which cotton fibers with a range of characteristics can be obtained and used for various applications. Cotton fibers may WO 2013/128448 PCT/IL2013/050172 9 be characterized according to a variety of properties, some of which are considered highly desirable within the textile industry for the production of increasingly high quality products and optimal exploitation of modem spinning technologies. Commercially desirable properties include length, length uniformity, fineness, maturity 5 ratio, decreased fuzz fiber production, micronaire, bundle strength, and single fiber strength. Much effort has been put into the improvement of the characteristics of cotton fibers mainly focusing on fiber length and fiber fineness. In particular, there is a great demand for cotton fibers of specific lengths. A cotton fiber is composed of a single cell that has differentiated from an 10 epidermal cell of the seed coat, developing through four stages, i.e., initiation, elongation, secondary cell wall thickening and maturation stages. More specifically, the elongation of a cotton fiber commences in the epidermal cell of the ovule immediately following flowering, after which the cotton fiber rapidly elongates for approximately 21 days. Fiber elongation is then terminated, and a secondary cell wall is formed and 15 grown through maturation to become a mature cotton fiber. Several candidate genes which are associated with the elongation, formation, quality and yield of cotton fibers were disclosed in various patent applications such as U.S. Pat. No. 5,880,100 and U.S. patent applications Ser. Nos. 08/580,545, 08/867,484 and 09/262,653 (describing genes involved in cotton fiber elongation stage); 20 W00245485 (improving fiber quality by modulating sucrose synthase); U.S. Pat. No. 6,472,588 and WO0117333 (increasing fiber quality by transformation with a DNA encoding sucrose phosphate synthase); W09508914 (using a fiber-specific promoter and a coding sequence encoding cotton peroxidase); W09626639 (using an ovary specific promoter sequence to express plant growth modifying hormones in cotton 25 ovule tissue, for altering fiber quality characteristics such as fiber dimension and strength); U.S. Pat. No. 5,981,834, U.S. Pat. No. 5,597,718, U.S. Pat. No. 5,620,882, U.S. Pat. No. 5,521,708 and U.S. Pat. No. 5,495,070 (coding sequences to alter the fiber characteristics of transgenic fiber producing plants); U.S. patent applications U.S. 2002049999 and U.S. 2003074697 (expressing a gene coding for endoxyloglucan 30 transferase, catalase or peroxidase for improving cotton fiber characteristics); WO 01/40250 (improving cotton fiber quality by modulating transcription factor gene expression); WO 96/40924 (a cotton fiber transcriptional initiation regulatory region WO 2013/128448 PCT/IL2013/050172 10 associated which is expressed in cotton fiber); EP0834566 (a gene which controls the fiber formation mechanism in cotton plant); W02005/121364 (improving cotton fiber quality by modulating gene expression); W02008/075364 (improving fiber quality, yield/biomass/vigor and/or abiotic stress tolerance of plants). 5 WO publication No. 2004/104162 discloses methods of increasing abiotic stress tolerance and/or biomass in plants and plants generated thereby. WO publication No. 2004/111183 discloses nucleotide sequences for regulating gene expression in plant trichomes and constructs and methods utilizing same. WO publication No. 2004/081173 discloses novel plant derived regulatory 10 sequences and constructs and methods of using such sequences for directing expression of exogenous polynucleotide sequences in plants. WO publication No. 2005/121364 discloses polynucleotides and polypeptides involved in plant fiber development and methods of using same for improving fiber quality, yield and/or biomass of a fiber producing plant. 15 WO publication No. 2007/049275 discloses isolated polypeptides, polynucleotides encoding same, transgenic plants expressing same and methods of using same for increasing fertilizer use efficiency, plant abiotic stress tolerance and biomass. WO publication No. 2007/020638 discloses methods of increasing abiotic stress 20 tolerance and/or biomass in plants and plants generated thereby. WO publication No. 2008/122980 discloses genes constructs and methods for increasing oil content, growth rate and biomass of plants. WO publication No. 2008/075364 discloses polynucleotides involved in plant fiber development and methods of using same. 25 WO publication No. 2009/083958 discloses methods of increasing water use efficiency, fertilizer use efficiency, biotic/abiotic stress tolerance, yield and biomass in plant and plants generated thereby. WO publication No. 2009/141824 discloses isolated polynucleotides and methods using same for increasing plant utility. 30 WO publication No. 2009/013750 discloses genes, constructs and methods of increasing abiotic stress tolerance, biomass and/or yield in plants generated thereby.
WO 2013/128448 PCT/IL2013/050172 11 WO publication No. 2010/020941 discloses methods of increasing nitrogen use efficiency, abiotic stress tolerance, yield and biomass in plants and plants generated thereby. WO publication No. 2010/076756 discloses isolated polynucleotides for 5 increasing abiotic stress tolerance, yield, biomass, growth rate, vigor, oil content, fiber yield, fiber quality, and/or nitrogen use efficiency of a plant. W02010/100595 publication discloses isolated polynucleotides and polypeptides, and methods of using same for increasing plant yield and/or agricultural characteristics. 10 WO publication No. 2010/049897 discloses isolated polynucleotides and polypeptides and methods of using same for increasing plant yield, biomass, growth rate, vigor, oil content, abiotic stress tolerance of plants and nitrogen use efficiency. W02010/143138 publication discloses isolated polynucleotides and polypeptides, and methods of using same for increasing nitrogen use efficiency, 15 fertilizer use efficiency, yield, growth rate, vigor, biomass, oil content, abiotic stress tolerance and/or water use efficiency WO publication No. 2011/080674 discloses isolated polynucleotides and polypeptides and methods of using same for increasing plant yield, biomass, growth rate, vigor, oil content, abiotic stress tolerance of plants and nitrogen use efficiency. 20 W02011/015985 publication discloses polynucleotides and polypeptides for increasing desirable plant qualities. SUMMARY OF THE INVENTION According to an aspect of some embodiments of the present invention there is 25 provided a method of increasing yield, growth rate, biomass, vigor, oil content, seed yield, fiber yield, fiber quality, nitrogen use efficiency, and/or abiotic stress of a plant, comprising expressing within the plant an exogenous polynucleotide comprising a nucleic acid sequence encoding a polypeptide at least 80 % homologous (e.g., identical) to SEQ ID NO: 362-601, 2429-4085 or 4086, thereby increasing the yield, growth rate, 30 biomass, vigor, oil content, seed yield, fiber yield, fiber quality, nitrogen use efficiency, and/or abiotic stress of the plant.
WO 2013/128448 PCT/IL2013/050172 12 According to an aspect of some embodiments of the present invention there is provided a method of increasing yield, growth rate, biomass, vigor, oil content, seed yield, fiber yield, fiber quality, nitrogen use efficiency, and/or abiotic stress of a plant, comprising expressing within the plant an exogenous polynucleotide comprising a 5 nucleic acid sequence encoding a polypeptide selected from the group consisting of SEQ ID NOs: 362-601, 2429-4085 and 4086, thereby increasing the yield, growth rate, biomass, vigor, oil content, seed yield, fiber yield, fiber quality, nitrogen use efficiency, and/or abiotic stress of the plant. According to an aspect of some embodiments of the present invention there is 10 provided a method of producing a crop comprising growing a crop of a plant expressing an exogenous polynucleotide comprising a nucleic acid sequence encoding a polypeptide at least 80 % homologous (e.g., identical) to the amino acid sequence selected from the group consisting of SEQ ID NOs: 362-601, 2429-4085 and 4086, wherein the plant is derived from a plant selected for increased yield, increased growth 15 rate, increased biomass, increased vigor, increased oil content, increased seed yield, increased fiber yield, increased fiber quality, increased nitrogen use efficiency, and/or increased abiotic stress tolerance as compared to a control plant, thereby producing the crop. According to an aspect of some embodiments of the present invention there is 20 provided a method of increasing yield, growth rate, biomass, vigor, oil content, seed yield, fiber yield, fiber quality, nitrogen use efficiency, and/or abiotic stress of a plant, comprising expressing within the plant an exogenous polynucleotide comprising a nucleic acid sequence at least 80 % identical to SEQ ID NO: 1-361, 602-2427 or 2428, thereby increasing the yield, growth rate, biomass, vigor, oil content, seed yield, fiber 25 yield, fiber quality, nitrogen use efficiency, and/or abiotic stress of the plant. According to an aspect of some embodiments of the present invention there is provided a method of increasing yield, growth rate, biomass, vigor, oil content, seed yield, fiber yield, fiber quality, nitrogen use efficiency, and/or abiotic stress of a plant, comprising expressing within the plant an exogenous polynucleotide comprising the 30 nucleic acid sequence selected from the group consisting of SEQ ID NOs:1-361, 602 2427 and 2428, thereby increasing the yield, growth rate, biomass, vigor, oil content, WO 2013/128448 PCT/IL2013/050172 13 seed yield, fiber yield, fiber quality, nitrogen use efficiency, and/or abiotic stress of the plant. According to an aspect of some embodiments of the present invention there is provided a method of producing a crop comprising growing a crop of a plant expressing 5 an exogenous polynucleotide which comprises a nucleic acid sequence which is at least 80 % identical to the nucleic acid sequence selected from the group consisting of SEQ ID NOs:1-361, 602-2427 and 2428, wherein the plant is derived from a plant selected for increased yield, increased growth rate, increased biomass, increased vigor, increased oil content, increased seed yield, increased fiber yield, increased fiber quality, increased 10 nitrogen use efficiency, and/or increased abiotic stress tolerance as compared to a control plant, thereby producing the crop According to an aspect of some embodiments of the present invention there is provided an isolated polynucleotide comprising a nucleic acid sequence encoding a polypeptide which comprises an amino acid sequence at least 80 % homologous (e.g., 15 identical) to the amino acid sequence set forth in SEQ ID NO: 362-601, 2429-4085 or 4086, wherein the amino acid sequence is capable of increasing yield, growth rate, biomass, vigor, oil content, seed yield, fiber yield, fiber quality, nitrogen use efficiency, and/or abiotic stress of a plant. According to an aspect of some embodiments of the present invention there is 20 provided an isolated polynucleotide comprising a nucleic acid sequence encoding a polypeptide which comprises the amino acid sequence selected from the group consisting of SEQ ID NOs: 362-601, 2429-4085 and 4086. According to an aspect of some embodiments of the present invention there is provided an isolated polynucleotide comprising a nucleic acid sequence at least 80 % 25 identical to SEQ ID NO: 1-361, 602-2427 or 2428, wherein the nucleic acid sequence is capable of increasing yield, growth rate, biomass, vigor, oil content, seed yield, fiber yield, fiber quality, nitrogen use efficiency, and/or abiotic stress of a plant. According to an aspect of some embodiments of the present invention there is provided an isolated polynucleotide comprising the nucleic acid sequence selected from 30 the group consisting of SEQ ID NOs: 1-361, 602-2427 and 2428. According to an aspect of some embodiments of the present invention there is provided a nucleic acid construct comprising the isolated polynucleotide of some WO 2013/128448 PCT/IL2013/050172 14 embodiments of the invention, and a promoter for directing transcription of the nucleic acid sequence in a host cell. According to an aspect of some embodiments of the present invention there is provided an isolated polypeptide comprising an amino acid sequence at least 80% 5 homologous (e.g., identical) to SEQ ID NO: 362-601, 2429-4085 or 4086, wherein the amino acid sequence is capable of increasing yield, growth rate, biomass, vigor, oil content, seed yield, fiber yield, fiber quality, nitrogen use efficiency, and/or abiotic stress of a plant. According to an aspect of some embodiments of the present invention there is 10 provided an isolated polypeptide comprising the amino acid sequence selected from the group consisting of SEQ ID NOs: 362-601, 2429-4085 and 4086. According to an aspect of some embodiments of the present invention there is provided a plant cell exogenously expressing the polynucleotide of some embodiments of the invention, or the nucleic acid construct of some embodiments of the invention. 15 According to an aspect of some embodiments of the present invention there is provided a plant cell exogenously expressing the polypeptide of some embodiments of the invention. According to some embodiments of the invention, the nucleic acid sequence encodes an amino acid sequence selected from the group consisting of SEQ ID NOs: 20 362-601, 2429-4085 and 4086. According to some embodiments of the invention, the nucleic acid sequence is selected from the group consisting of SEQ ID NOs: 1-361, 602-2427 and 2428. According to some embodiments of the invention, the polynucleotide consists of the nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1-361, 25 602-2427 and 2428. According to some embodiments of the invention, the nucleic acid sequence encodes the amino acid sequence selected from the group consisting of SEQ ID NOs: 362-601, 2429-4085 and 4086. According to some embodiments of the invention, the plant cell forms part of a 30 plant. According to some embodiments of the invention, the method further comprising growing the plant expressing the exogenous polynucleotide under the abiotic stress.
WO 2013/128448 PCT/IL2013/050172 15 According to some embodiments of the invention, the abiotic stress is selected from the group consisting of salinity, drought, osmotic stress, water deprivation, flood, etiolation, low temperature, high temperature, heavy metal toxicity, anaerobiosis, nutrient deficiency, nutrient excess, atmospheric pollution and UV irradiation. 5 According to some embodiments of the invention, the yield comprises seed yield or oil yield. According to an aspect of some embodiments of the present invention there is provided a transgenic plant comprising the nucleic acid construct of some embodiments of the invention or the plant cell of some embodiments of the invention. 10 According to some embodiments of the invention, the method further comprising growing the plant expressing the exogenous polynucleotide under nitrogen-limiting conditions. According to some embodiments of the invention, the promoter is heterologous to the isolated polynucleotide and/or to the host cell. 15 According to an aspect of some embodiments of the present invention there is provided a method of growing a crop, the method comprising seeding seeds and/or planting plantlets of a plant transformed with the isolated polynucleotide of some embodiments of the invention, or the nucleic acid construct of some embodiments of the invention, wherein the plant is derived from plants selected for at least one trait selected 20 from the group consisting of: increased nitrogen use efficiency, increased abiotic stress tolerance, increased biomass, increased growth rate, increased vigor, increased yield, increased fiber yield or quality, and increased oil content as compared to a non transformed plant, thereby growing the crop. According to some embodiments of the invention, the non-transformed plant is a 25 wild type plant of identical genetic background. According to some embodiments of the invention, the non-transformed plant is a wild type plant of the same species. According to some embodiments of the invention, the non-transformed plant is grown under identical growth conditions. 30 Unless otherwise defined, all technical and/or scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which WO 2013/128448 PCT/IL2013/050172 16 the invention pertains. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of embodiments of the invention, exemplary methods and/or materials are described below. In case of conflict, the patent specification, including definitions, will control. In addition, the materials, methods, and 5 examples are illustrative only and are not intended to be necessarily limiting. BRIEF DESCRIPTION OF THE DRAWINGS Some embodiments of the invention are herein described, by way of example only, with reference to the accompanying drawings. With specific reference now to the 10 drawings in detail, it is stressed that the particulars shown are by way of example and for purposes of illustrative discussion of embodiments of the invention. In this regard, the description taken with the drawings makes apparent to those skilled in the art how embodiments of the invention may be practiced. In the drawings: 15 FIG. 1 is a schematic illustration of the modified pGI binary plasmid containing the new At6669 promoter (SEQ ID NO: 4111) and the GUSintron (pQYN 6669) used for expressing the isolated polynucleotide sequences of the invention. RB - T-DNA right border; LB - T-DNA left border; MCS - Multiple cloning sites; RE - any restriction enzyme; NOS pro = nopaline synthase promoter; NPT-II = neomycin 20 phosphotransferase gene; NOS ter nopaline synthase terminator; Poly-A signal (polyadenylation signal); GUSintron - the GUS reporter gene (coding sequence and intron). The isolated polynucleotide sequences of the invention were cloned into the vector while replacing the GUSintron reporter gene. FIG. 2 is a schematic illustration of the modified pGI binary plasmid containing 25 the new At6669 promoter (SEQ ID NO: 4111) (pQFN or pQFNc) used for expressing the isolated polynucleotide sequences of the invention. RB - T-DNA right border; LB T-DNA left border; MCS - Multiple cloning site; RE - any restriction enzyme; NOS pro = nopaline synthase promoter; NPT-II = neomycin phosphotransferase gene; NOS ter = nopaline synthase terminator; Poly-A signal (polyadenylation signal); The isolated 30 polynucleotide sequences of the invention were cloned into the MCS of the vector. FIGs. 3A-F are images depicting visualization of root development of transgenic plants exogenously expressing the polynucleotide of some embodiments of the WO 2013/128448 PCT/IL2013/050172 17 invention when grown in transparent agar plates under normal (Figures 3A-B), osmotic stress (15 % PEG; Figures 3C-D) or nitrogen-limiting (Figures 3E-F) conditions. The different transgenes were grown in transparent agar plates for 17 days (7 days nursery and 10 days after transplanting). The plates were photographed every 3-4 days starting 5 at day 1 after transplanting. Figure 3A - An image of a photograph of plants taken following 10 after transplanting days on agar plates when grown under normal (standard) conditions. Figure 3B - An image of root analysis of the plants shown in Figure 3A in which the lengths of the roots measured are represented by arrows. Figure 3C - An image of a photograph of plants taken following 10 days after transplanting on 10 agar plates, grown under high osmotic (PEG 15 %) conditions. Figure 3D - An image of root analysis of the plants shown in Figure 3C in which the lengths of the roots measured are represented by arrows. Figure 3E - An image of a photograph of plants taken following 10 days after transplanting on agar plates, grown under low nitrogen conditions. Figure 3F - An image of root analysis of the plants shown in Figure 3E in 15 which the lengths of the roots measured are represented by arrows. FIG. 4 is a schematic illustration of the modified pGI binary plasmid containing the Root Promoter (pQNa RP) used for expressing the isolated polynucleotide sequences of the invention. RB - T-DNA right border; LB - T-DNA left border; NOS pro nopaline synthase promoter; NPT-II = neomycin phosphotransferase gene; NOS 20 ter nopaline synthase terminator; Poly-A signal (polyadenylation signal); the isolated polynucleotide sequences according to some embodiments of the invention were cloned into the MCS (Multiple cloning site) of the vector. FIG. 5 is a schematic illustration of the pQYN plasmid. FIG. 6 is a schematic illustration of the pQFN plasmid. 25 FIG. 7 is a schematic illustration of the pQFYN plasmid. FIG. 8 is a schematic illustration of the modified pGI binary plasmid (pQXNc) used for expressing the isolated polynucleotide sequences of some embodiments of the invention. RB - T-DNA right border; LB - T-DNA left border; NOS pro = nopaline synthase promoter; NPT-II = neomycin phosphotransferase gene; NOS ter = nopaline 30 synthase terminator; RE = any restriction enzyme; Poly-A signal (polyadenylation signal); 35S - the 35S promoter (pqfnc; SEQ ID NO: 4107). The isolated WO 2013/128448 PCT/IL2013/050172 18 polynucleotide sequences of some embodiments of the invention were cloned into the MCS (Multiple cloning site) of the vector. DESCRIPTION OF SPECIFIC EMBODIMENTS OF THE INVENTION 5 The present invention, in some embodiments thereof, relates to isolated polynucleotides and polypeptides, nucleic acid constructs encoding same, cells expressing same, transgenic plants expressing same and methods of using same for increasing yield, biomass, growth rate, vigor, oil content, fiber yield, fiber quality, nitrogen use efficiency and/or abiotic stress tolerance of a plant. 10 Before explaining at least one embodiment of the invention in detail, it is to be understood that the invention is not necessarily limited in its application to the details set forth in the following description or exemplified by the Examples. The invention is capable of other embodiments or of being practiced or carried out in various ways. The present inventors have identified novel polypeptides and polynucleotides 15 which can be used to generate nucleic acid constructs, transgenic plants and to increase yield, growth rate, vigor, biomass, oil content, fiber yield, fiber quality, fiber length, nitrogen use efficiency, fertilizer use efficiency, abiotic stress tolerance and/or water use efficiency of a plant. Thus, as shown in the Examples section which follows, the present inventors 20 have utilized bioinformatics tools to identify polynucleotides which enhance yield (e.g., seed yield, oil yield, oil content), growth rate, biomass, vigor and/or abiotic stress tolerance of a plant. Genes which affect the trait-of-interest were identified based on expression profiles of genes of several Arabidopsis, tomato, B. Juncea, Soghum, Soybean, Brachypodium and cotton ecotypes, varieties and accessions in various tissues 25 and under various growth conditions, homology with genes known to affect the trait-of interest and using digital expression profile in specific tissues and conditions (Tables 1 53, Examples 1-12). Homologous (e.g., orthologous) polypeptides and polynucleotides having the same function were also identified (Table 54, Example 13). Transgenic plants over-expressing the identified polynucleotides were found to exhibit increased 30 seed yield, oil yield, biomass, vigor, photosynthetic area, dry matter, harvest index, growth rate, rosette area, oil percentage in seed and weight of 1000 seeds (Tables 56-69; Examples 15-17). Altogether, these results suggest the use of the novel polynucleotides WO 2013/128448 PCT/IL2013/050172 19 and polypeptides of the invention for increasing yield (including oil yield, seed yield and oil content), growth rate, biomass, vigor, fiber yield and/or quality, nitrogen use efficiency and/or abiotic stress tolerance of a plant. Thus, according to an aspect of some embodiments of the invention, there is 5 provided method of increasing yield, oil content, growth rate, biomass, vigor, fiber yield, fiber quality, fertilizer use efficiency (e.g., nitrogen use efficiency) and/or abiotic stress tolerance of a plant, comprising expressing within the plant an exogenous polynucleotide comprising a nucleic acid sequence encoding a polypeptide at least about 80 %, at least about 81 %, at least about 82 %, at least about 83 %, at least about 10 84 %, at least about 85 %, at least about 86 %, at least about 87 %, at least about 88 %, at least about 89 %, at least about 90 %, at least about 91 %, at least about 92 %, at least about 93 %, at least about 94 %, at least about 95 %, at least about 96 %, at least about 97 %, at least about 98 %, at least about 99 %, or more say 100 % homologous to the amino acid sequence selected from the group consisting of SEQ ID NOs: 362-601, 15 2429-4085 and 4086, thereby increasing the yield, oil content, growth rate, biomass, vigor, fiber yield, fiber quality, fertilizer use efficiency (e.g., nitrogen use efficiency) and/or abiotic stress tolerance of the plant. As used herein the phrase "plant yield" refers to the amount (e.g., as determined by weight or size) or quantity (numbers) of tissues or organs produced per plant or per 20 growing season. Hence increased yield could affect the economic benefit one can obtain from the plant in a certain growing area and/or growing time. It should be noted that a plant yield can be affected by various parameters including, but not limited to, plant biomass; plant vigor; growth rate; seed yield; seed or grain quantity; seed or grain quality; oil yield; content of oil, starch and/or protein in 25 harvested organs (e.g., seeds or vegetative parts of the plant); number of flowers (florets) per panicle (expressed as a ratio of number of filled seeds over number of primary panicles); harvest index; number of plants grown per area; number and size of harvested organs per plant and per area; number of plants per growing area (density); number of harvested organs in field; total leaf area; carbon assimilation and carbon 30 partitioning (the distribution/allocation of carbon within the plant); resistance to shade; number of harvestable organs (e.g. seeds), seeds per pod, weight per seed; and modified WO 2013/128448 PCT/IL2013/050172 20 architecture [such as increase stalk diameter, thickness or improvement of physical properties (e.g. elasticity)]. As used herein the phrase "seed yield" refers to the number or weight of the seeds per plant, seeds per pod, or per growing area or to the weight of a single seed, or 5 to the oil extracted per seed. Hence seed yield can be affected by seed dimensions (e.g., length, width, perimeter, area and/or volume), number of (filled) seeds and seed filling rate and by seed oil content. Hence increase seed yield per plant could affect the economic benefit one can obtain from the plant in a certain growing area and/or growing time; and increase seed yield per growing area could be achieved by increasing 10 seed yield per plant, and/or by increasing number of plants grown on the same given area. The term "seed" (also referred to as "grain" or "kernel") as used herein refers to a small embryonic plant enclosed in a covering called the seed coat (usually with some stored food), the product of the ripened ovule of gymnosperm and angiosperm plants 15 which occurs after fertilization and some growth within the mother plant. The phrase "oil content" as used herein refers to the amount of lipids in a given plant organ, either the seeds (seed oil content) or the vegetative portion of the plant (vegetative oil content) and is typically expressed as percentage of dry weight (10 % humidity of seeds) or wet weight (for vegetative portion). 20 It should be noted that oil content is affected by intrinsic oil production of a tissue (e.g., seed, vegetative portion), as well as the mass or size of the oil-producing tissue per plant or per growth period. In one embodiment, increase in oil content of the plant can be achieved by increasing the size/mass of a plant's tissue(s) which comprise oil per growth period. 25 Thus, increased oil content of a plant can be achieved by increasing the yield, growth rate, biomass and vigor of the plant. As used herein the phrase "plant biomass" refers to the amount (e.g., measured in grams of air-dry tissue) of a tissue produced from the plant in a growing season, which could also determine or affect the plant yield or the yield per growing area. An 30 increase in plant biomass can be in the whole plant or in parts thereof such as aboveground (harvestable) parts, vegetative biomass, roots and seeds.
WO 2013/128448 PCT/IL2013/050172 21 As used herein the phrase "growth rate" refers to the increase in plant organ/tissue size per time (can be measured in cm 2 per day). As used herein the phrase "plant vigor" refers to the amount (measured by weight) of tissue produced by the plant in a given time. Hence increased vigor could 5 determine or affect the plant yield or the yield per growing time or growing area. In addition, early vigor (seed and/or seedling) results in improved field stand. Improving early vigor is an important objective of modern rice breeding programs in both temperate and tropical rice cultivars. Long roots are important for proper soil anchorage in water-seeded rice. Where rice is sown directly into flooded 10 fields, and where plants must emerge rapidly through water, longer shoots are associated with vigor. Where drill-seeding is practiced, longer mesocotyls and coleoptiles are important for good seedling emergence. The ability to engineer early vigor into plants would be of great importance in agriculture. For example, poor early vigor has been a limitation to the introduction of maize (Zea mays L.) hybrids based on Corn Belt 15 germplasm in the European Atlantic. It should be noted that a plant yield can be determined under stress (e.g., abiotic stress, nitrogen-limiting conditions) and/or non-stress (normal) conditions. As used herein, the phrase "non-stress conditions" refers to the growth conditions (e.g., water, temperature, light-dark cycles, humidity, salt concentration, 20 fertilizer concentration in soil, nutrient supply such as nitrogen, phosphorous and/or potassium), that do not significantly go beyond the everyday climatic and other abiotic conditions that plants may encounter, and which allow optimal growth, metabolism, reproduction and/or viability of a plant at any stage in its life cycle (e.g., in a crop plant from seed to a mature plant and back to seed again). Persons skilled in the art are aware 25 of normal soil conditions and climatic conditions for a given plant in a given geographic location. It should be noted that while the non-stress conditions may include some mild variations from the optimal conditions (which vary from one type/species of a plant to another), such variations do not cause the plant to cease growing without the capacity to resume growth. 30 The phrase "abiotic stress" as used herein refers to any adverse effect on metabolism, growth, reproduction and/or viability of a plant. Accordingly, abiotic stress can be induced by suboptimal environmental growth conditions such as, for WO 2013/128448 PCT/IL2013/050172 22 example, salinity, water deprivation, flooding, freezing, low or high temperature, heavy metal toxicity, anaerobiosis, nutrient deficiency, atmospheric pollution or UV irradiation. The implications of abiotic stress are discussed in the Background section. The phrase "abiotic stress tolerance" as used herein refers to the ability of a 5 plant to endure an abiotic stress without suffering a substantial alteration in metabolism, growth, productivity and/or viability. Plants are subject to a range of environmental challenges. Several of these, including salt stress, general osmotic stress, drought stress and freezing stress, have the ability to impact whole plant and cellular water availability. Not surprisingly, then, 10 plant responses to this collection of stresses are related. Zhu (2002) Ann. Rev. Plant Biol. 53: 247-273 et al. note that "most studies on water stress signaling have focused on salt stress primarily because plant responses to salt and drought are closely related and the mechanisms overlap". Many examples of similar responses and pathways to this set of stresses have been documented. For example, the CBF transcription factors have 15 been shown to condition resistance to salt, freezing and drought (Kasuga et al. (1999) Nature Biotech. 17: 287-291). The Arabidopsis rd29B gene is induced in response to both salt and dehydration stress, a process that is mediated largely through an ABA signal transduction process (Uno et al. (2000) Proc. Natl. Acad. Sci. USA 97: 11632 11637), resulting in altered activity of transcription factors that bind to an upstream 20 element within the rd29B promoter. In Mesembryanthemum crystallinum (ice plant), Patharker and Cushman have shown that a calcium-dependent protein kinase (McCDPK1) is induced by exposure to both drought and salt stresses (Patharker and Cushman (2000) Plant J. 24: 679-691). The stress-induced kinase was also shown to phosphorylate a transcription factor, presumably altering its activity, although transcript 25 levels of the target transcription factor are not altered in response to salt or drought stress. Similarly, Saijo et al. demonstrated that a rice salt/drought-induced calmodulin dependent protein kinase (OsCDPK7) conferred increased salt and drought tolerance to rice when overexpressed (Saijo et al. (2000) Plant J. 23: 319-327). Exposure to dehydration invokes similar survival strategies in plants as does 30 freezing stress (see, for example, Yelenosky (1989) Plant Physiol 89: 444-451) and drought stress induces freezing tolerance (see, for example, Siminovitch et al. (1982) Plant Physiol 69: 250-255; and Guy et al. (1992) Planta 188: 265-270). In addition to WO 2013/128448 PCT/IL2013/050172 23 the induction of cold-acclimation proteins, strategies that allow plants to survive in low water conditions may include, for example, reduced surface area, or surface oil or wax production. In another example increased solute content of the plant prevents evaporation and water loss due to heat, drought, salinity, osmoticum, and the like 5 therefore providing a better plant tolerance to the above stresses. It will be appreciated that some pathways involved in resistance to one stress (as described above), will also be involved in resistance to other stresses, regulated by the same or homologous genes. Of course, the overall resistance pathways are related, not identical, and therefore not all genes controlling resistance to one stress will control 10 resistance to the other stresses. Nonetheless, if a gene conditions resistance to one of these stresses, it would be apparent to one skilled in the art to test for resistance to these related stresses. Methods of assessing stress resistance are further provided in the Examples section which follows. As used herein the phrase "water use efficiency (WUE)" refers to the level of 15 organic matter produced per unit of water consumed by the plant, i.e., the dry weight of a plant in relation to the plant's water use, e.g., the biomass produced per unit transpiration. As used herein the phrase "fertilizer use efficiency" refers to the metabolic process(es) which lead to an increase in the plant's yield, biomass, vigor, and growth 20 rate per fertilizer unit applied. The metabolic process can be the uptake, spread, absorbent, accumulation, relocation (within the plant) and use of one or more of the minerals and organic moieties absorbed by the plant, such as nitrogen, phosphates and/or potassium. As used herein the phrase "fertilizer-limiting conditions" refers to growth 25 conditions which include a level (e.g., concentration) of a fertilizer applied which is below the level needed for normal plant metabolism, growth, reproduction and/or viability. As used herein the phrase "nitrogen use efficiency (NUE)" refers to the metabolic process(es) which lead to an increase in the plant's yield, biomass, vigor, and 30 growth rate per nitrogen unit applied. The metabolic process can be the uptake, spread, absorbent, accumulation, relocation (within the plant) and use of nitrogen absorbed by the plant.
WO 2013/128448 PCT/IL2013/050172 24 As used herein the phrase "nitrogen-limiting conditions" refers to growth conditions which include a level (e.g., concentration) of nitrogen (e.g., ammonium or nitrate) applied which is below the level needed for normal plant metabolism, growth, reproduction and/or viability. 5 Improved plant NUE and FUE is translated in the field into either harvesting similar quantities of yield, while implementing less fertilizers, or increased yields gained by implementing the same levels of fertilizers. Thus, improved NUE or FUE has a direct effect on plant yield in the field. Thus, the polynucleotides and polypeptides of some embodiments of the invention positively affect plant yield, seed yield, and plant 10 biomass. In addition, the benefit of improved plant NUE will certainly improve crop quality and biochemical constituents of the seed such as protein yield and oil yield. It should be noted that improved ABST will confer plants with improved vigor also under non-stress conditions, resulting in crops having improved biomass and/or yield e.g., elongated fibers for the cotton industry, higher oil content. 15 The term "fiber" is usually inclusive of thick-walled conducting cells such as vessels and tracheids and to fibrillar aggregates of many individual fiber cells. Hence, the term "fiber" refers to (a) thick-walled conducting and non-conducting cells of the xylem; (b) fibers of extraxylary origin, including those from phloem, bark, ground tissue, and epidermis; and (c) fibers from stems, leaves, roots, seeds, and flowers or 20 inflorescences (such as those of Sorghum vulgare used in the manufacture of brushes and brooms). Example of fiber producing plants, include, but are not limited to, agricultural crops such as cotton, silk cotton tree (Kapok, Ceiba pentandra), desert willow, creosote bush, winterfat, balsa, kenaf, roselle, jute, sisal abaca, flax, corn, sugar cane, hemp, 25 ramie, kapok, coir, bamboo, spanish moss and Agave spp. (e.g. sisal). As used herein the phrase "fiber quality" refers to at least one fiber parameter which is agriculturally desired, or required in the fiber industry (further described hereinbelow). Examples of such parameters, include but are not limited to, fiber length, fiber strength, fiber fitness, fiber weight per unit length, maturity ratio and uniformity 30 (further described hereinbelow.
WO 2013/128448 PCT/IL2013/050172 25 Cotton fiber (lint) quality is typically measured according to fiber length, strength and fineness. Accordingly, the lint quality is considered higher when the fiber is longer, stronger and finer. As used herein the phrase "fiber yield" refers to the amount or quantity of fibers 5 produced from the fiber producing plant. As used herein the term "increasing" refers to at least about 2 %, at least about 3 %, at least about 4 %, at least about 5 %, at least about 10 %, at least about 15 %, at least about 20 %, at least about 30 %, at least about 40 %, at least about 50 %, at least about 60 %, at least about 70 %, at least about 80 %, increase in yield, oil content, 10 growth rate, biomass, vigor, fiber yield, fiber quality, fertilizer use efficiency (e.g., nitrogen use efficiency) and/or abiotic stress tolerance of a plant as compared to a native plant or a wild type plant [i.e., a plant not modified with the biomolecules (polynucleotide or polypeptides) of the invention, e.g., a non-transformed plant of the same species which is grown under the same (e.g., identical) growth conditions]. 15 The phrase "expressing within the plant an exogenous polynucleotide" as used herein refers to upregulating the expression level of an exogenous polynucleotide within the plant by introducing the exogenous polynucleotide into a plant cell or plant and expressing by recombinant means, as further described herein below. As used herein "expressing" refers to expression at the mRNA and optionally 20 polypeptide level. As used herein, the phrase "exogenous polynucleotide" refers to a heterologous nucleic acid sequence which may not be naturally expressed within the plant (e.g., a nucleic acid sequence from a different species) or which overexpression in the plant is desired. The exogenous polynucleotide may be introduced into the plant in a stable or 25 transient manner, so as to produce a ribonucleic acid (RNA) molecule and/or a polypeptide molecule. It should be noted that the exogenous polynucleotide may comprise a nucleic acid sequence which is identical or partially homologous to an endogenous nucleic acid sequence of the plant. The term "endogenous" as used herein refers to any polynucleotide or 30 polypeptide which is present and/or naturally expressed within a plant or a cell thereof. According to some embodiments of the invention, the exogenous polynucleotide of the invention comprises a nucleic acid sequence encoding a polypeptide having an WO 2013/128448 PCT/IL2013/050172 26 amino acid sequence at least about 80 %, at least about 81 %, at least about 82 %, at least about 83 %, at least about 84 %, at least about 85 %, at least about 86 %, at least about 87 %, at least about 88 %, at least about 89 %, at least about 90 %, at least about 91 %, at least about 92 %, at least about 93 %, at least about 94 %, at least about 95 %, 5 at least about 96 %, at least about 97 %, at least about 98 %, at least about 99 %, or more say 100 % homologous to the amino acid sequence selected from the group consisting of SEQ ID NOs: 362-601, 2429-4085 and 4086. Homologous sequences include both orthologous and paralogous sequences. The term "paralogous" relates to gene-duplications within the genome of a species 10 leading to paralogous genes. The term "orthologous" relates to homologous genes in different organisms due to ancestral relationship. One option to identify orthologues in monocot plant species is by performing a reciprocal blast search. This may be done by a first blast involving blasting the sequence-of-interest against any sequence database, such as the publicly available NCBI 15 database which may be found at: Hypertext Transfer Protocol://World Wide Web (dot) ncbi (dot) nlm (dot) nih (dot) gov. If orthologues in rice were sought, the sequence-of interest would be blasted against, for example, the 28,469 full-length cDNA clones from Oryza sativa Nipponbare available at NCBI. The blast results may be filtered. The full-length sequences of either the filtered results or the non-filtered results are then 20 blasted back (second blast) against the sequences of the organism from which the sequence-of-interest is derived. The results of the first and second blasts are then compared. An orthologue is identified when the sequence resulting in the highest score (best hit) in the first blast identifies in the second blast the query sequence (the original sequence-of-interest) as the best hit. Using the same rational a paralogue (homolog to a 25 gene in the same organism) is found. In case of large sequence families, the ClustalW program may be used [Hypertext Transfer Protocol://World Wide Web (dot) ebi (dot) ac (dot) uk/Tools/clustalw2/index (dot) html], followed by a neighbor-joining tree (Hypertext Transfer Protocol://en (dot) wikipedia (dot) org/wiki/Neighbor-joining) which helps visualizing the clustering. 30 Homology (e.g., percent homology, identity + similarity) can be determined using any homology comparison software computing a pairwise sequence alignment.
WO 2013/128448 PCT/IL2013/050172 27 Identity (e.g., percent homology) can be determined using any homology comparison software, including for example, the BlastN software of the National Center of Biotechnology Information (NCBI) such as by using default parameters. According to some embodiments of the invention, the identity is a global 5 identity, i.e., an identity over the entire amino acid or nucleic acid sequences of the invention and not over portions thereof. According to some embodiments of the invention, the term "homology" or "homologous" refers to identity of two or more nucleic acid sequences; or identity of two or more amino acid sequences; or the identity of an amino acid sequence to one or 10 more nucleic acid sequence. According to some embodiments of the invention, the homology is a global homology, i.e., an homology over the entire amino acid or nucleic acid sequences of the invention and not over portions thereof. The degree of homology or identity between two or more sequences can be 15 determined using various known sequence comparison tools. Following is a non limiting description of such tools which can be used along with some embodiments of the invention. Pairwise global alignment was defined by S. B. Needleman and C. D. Wunsch, "A general method applicable to the search of similarities in the amino acid sequence of 20 two proteins" Journal of Molecular Biology, 1970, pages 443-53, volume 48). For example, when starting from a polypeptide sequence and comparing to other polypeptide sequences, the EMBOSS-6.0.1 Needleman-Wunsch algorithm (available from hup:/etmcan be used to find the optimum alignment (including gaps) of two sequences along their 25 entire length - a "Global alignment". Default parameters for Needleman-Wunsch algorithm (EMBOSS-6.0.1) include: gapopen=10; gapextend=0.5; datafile= EBLOSUM62; brief=YES. According to some embodiments of the invention, the parameters used with the EMBOSS-6.0.1 tool (for protein-protein comparison) include: gapopen=8; 30 gapextend=2; datafile= EBLOSUM62; brief=YES. According to some embodiments of the invention, the threshold used to determine homology using the EMBOSS-6.0.1 Needleman-Wunsch algorithm is 80%, WO 2013/128448 PCT/IL2013/050172 28 81%, 82 %, 83 %, 84 %, 85 %, 86 %, 87 %, 88 %, 89 %, 90 %, 91 %, 92 %, 93 %, 94 %, 95 %, 96 %, 97 %, 98 %, 99 %, or 100 %. When starting from a polypeptide sequence and comparing to polynucleotide sequences, the OneModel FramePlus algorithm [Halperin, E., Faigler, S. and Gill-More, 5 R. (1999) - FramePlus: aligning DNA to protein sequences. Bioinformatics, 15, 867 873) (available from http://www(dot)biocceleration(dot)com/Products(dot)html] can be used with following default parameters: model=frame+_p2n.model mode=local. According to some embodiments of the invention, the parameters used with the OneModel FramePlus algorithm are model=frame+_p2n.model, mode=qglobal. 10 According to some embodiments of the invention, the threshold used to determine homology using the OneModel FramePlus algorithm is 80%, 81%, 82 %, 83 %, 84 %, 85 %, 86 %, 87 %, 88 %, 89 %, 90 %, 91 %, 92 %, 93 %, 94 %, 95 %, 96 %, 97 %, 98 %, 99 %, or 100 %. When starting with a polynucleotide sequence and comparing to other 15 polynucleotide sequences the EMBOSS-6.0.1 Needleman-Wunsch algorithm (available from http://emboss (dot) sourceforge(dot)net/apps/cvs/emboss/apps/needle(dot)html) can be used with the following default parameters: (EMBOSS-6.0.1) gapopen=10; gapextend=0.5; datafile= EDNAFULL; brief=YES. According to some embodiments of the invention, the parameters used with the 20 EMBOSS-6.0.1 Needleman-Wunsch algorithm are gapopen=10; gapextend=0.2; datafile= EDNAFULL; brief=YES. According to some embodiments of the invention, the threshold used to determine homology using the EMBOSS-6.0.1 Needleman-Wunsch algorithm for comparison of polynucleotides with polynucleotides is 80%, 81%, 82 %, 83 %, 84 %, 25 85 %, 86 %, 87 %, 88 %, 89 %, 90 %, 91 %, 92 %, 93 %, 94 %, 95 %, 96 %, 97 %, 98 %, 99 %, or 100 %. According to some embodiment, determination of the degree of homology further requires employing the Smith-Waterman algorithm (for protein-protein comparison or nucleotide-nucleotide comparison). 30 Default parameters for GenCore 6.0 Smith-Waterman algorithm include: model =sw.model. According to some embodiments of the invention, the threshold used to WO 2013/128448 PCT/IL2013/050172 29 determine homology using the Smith-Waterman algorithm is 80%, 81%, 82 %, 83 %, 84 %, 85 %, 86 %, 87 %, 88 %, 89 %, 90 %, 91 %, 92 %, 93 %, 94 %, 95 %, 96 %, 97 %, 98 %, 99 %, or 100 %. According to some embodiments of the invention, the global homology is 5 performed on sequences which are pre-selected by local homology to the polypeptide or polynucleotide of interest (e.g., 60% identity over 60% of the sequence length), prior to performing the global homology to the polypeptide or polynucleotide of interest (e.g., 80% global homology on the entire sequence). For example, homologous sequences are selected using the BLAST software with the Blastp and tBlastn algorithms as filters for 10 the first stage, and the needle (EMBOSS package) or Frame+ algorithm alignment for the second stage. Local identity (Blast alignments) is defined with a very permissive cutoff - 60% Identity on a span of 60% of the sequences lengths because it is used only as a filter for the global alignment stage. In this specific embodiment (when the local identity is used), the default filtering of the Blast package is not utilized (by setting the 15 parameter "-F F"). In the second stage, homologs are defined based on a global identity of at least 80% to the core gene polypeptide sequence. According to some embodiments of the invention, two distinct forms for finding the optimal global alignment for protein or nucleotide sequences are used: 20 1. Between two proteins (following the blastp filter): EMBOSS-6.0.1 Needleman-Wunsch algorithm with the following modified parameters: gapopen=8 gapextend=2. The rest of the parameters are unchanged from the default options listed here: Standard (Mandatory) qualifiers: 25 [-asequence] sequence Sequence filename and optional format, or reference (input USA) [-bsequence] seqall Sequence(s) filename and optional format, or reference (input USA) -gapopen float [10.0 for any sequence]. The gap open penalty is the score 30 taken away when a gap is created. The best value depends on the choice of comparison matrix. The default value assumes you are using the EBLOSUM62 matrix for protein WO 2013/128448 PCT/IL2013/050172 30 sequences, and the EDNAFULL matrix for nucleotide sequences. (Floating point number from 1.0 to 100.0) -gapextend float [0.5 for any sequence]. The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap. This is how long gaps 5 are penalized. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps. You can get this result by setting the gap open penalty to zero (or very low) and using the gap extension penalty to control gap scoring. 10 (Floating point number from 0.0 to 10.0) [-outfile] align [*.needle] Output alignment file name Additional (Optional) qualifiers: -datafile matrixf [EBLOSUM62 for protein, EDNAFULL for DNA]. This is the scoring matrix file used when comparing sequences. By default it is the file 15 'EBLOSUM62' (for proteins) or the file 'EDNAFULL' (for nucleic sequences). These files are found in the 'data' directory of the EMBOSS installation. Advanced (Unprompted) qualifiers: -[no]brief boolean [Y] Brief identity and similarity Associated qualifiers: 20 "-asequence" associated qualifiers -sbegin1 integer Start of the sequence to be used -sendl integer End of the sequence to be used -sreversel boolean Reverse (if DNA) -saskI boolean Ask for begin/end/reverse 25 -snucleotidel boolean Sequence is nucleotide -sproteinI boolean Sequence is protein -slowerl boolean Make lower case -supperl boolean Make upper case -sformatl string Input sequence format 30 -sdbnamel string Database name -sidl string Entryname -ufo 1 string UFO features WO 2013/128448 PCT/IL2013/050172 31 -fformatl string Features format -fopenfile 1 string Features file name "-bsequence" associated qualifiers -sbegin2 integer Start of each sequence to be used 5 -send2 integer End of each sequence to be used -sreverse2 boolean Reverse (if DNA) -sask2 boolean Ask for begin/end/reverse -snucleotide2 boolean Sequence is nucleotide -sprotein2 boolean Sequence is protein 10 -slower2 boolean Make lower case -supper2 boolean Make upper case -sformat2 string Input sequence format -sdbname2 string Database name -sid2 string Entryname 15 -ufo2 string UFO features -fformat2 string Features format -fopenfile2 string Features file name "-outfile" associated qualifiers -aformat3 string Alignment format 20 -aextension3 string File name extension -adirectory3 string Output directory -aname3 string Base file name -awidth3 integer Alignment width -aaccshow3 boolean Show accession number in the header 25 -adesshow3 boolean Show description in the header -ausashow3 boolean Show the full USA in the alignment -aglobal3 boolean Show the full sequence in alignment General qualifiers: -auto boolean Turn off prompts 30 -stdout boolean Write first file to standard output -filter boolean Read first file from standard input, write first file to standard output WO 2013/128448 PCT/IL2013/050172 32 -options boolean Prompt for standard and additional values -debug boolean Write debug output to program.dbg -verbose boolean Report some/full command line options -help boolean Report command line options. More information on 5 associated and general qualifiers can be found with -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report dying program messages 10 2. Between a protein sequence and a nucleotide sequence (following the tblastn filter): GenCore 6.0 OneModel application utilizing the Frame+ algorithm with the following parameters: model=frame+_p2n.model mode=qglobal q=protein.sequence -db= nucleotide.sequence. The rest of the parameters are unchanged from the default options: 15 Usage: om -model=<modelfname> [-q=]query [-db=]database [options] -model=<modelfname> Specifies the model that you want to run. All models supplied by Compugen are located in the directory $CGNROOT/models/. Valid command line parameters: 20 -dev=<devname> Selects the device to be used by the application. Valid devices are: bic - Bioccelerator (valid for SW, XSW, FRAME_N2P, and FRAME_P2N models). xlg - BioXL/G (valid for all models except XSW). 25 xlp - BioXL/P (valid for SW, FRAME+_N2P, and FRAME_P2N models). xlh - BioXL/H (valid for SW, FRAME+_N2P, and FRAME_P2N models). soft - Software device (for all models). 30 -q=<query> Defines the query set. The query can be a sequence file or a database reference. You can specify a query by its name or by accession number. The format is detected automatically. However, you may specify a format using the -qfmt parameter.
WO 2013/128448 PCT/IL2013/050172 33 If you do not specify a query, the program prompts for one. If the query set is a database reference, an output file is produced for each sequence in the query. -db=<database name> Chooses the database set. The database set can be a sequence file or a database reference. The database format is detected automatically. However, 5 you may specify a format using -dfmt parameter. -qacc Add this parameter to the command line if you specify query using accession numbers. -dacc Add this parameter to the command line if you specify a database using accession numbers. 10 -dfmt/-qfmt=<formattype> Chooses the database/query format type. Possible formats are: fasta - fasta with seq type auto-detected. fastap - fasta protein seq. fastan - fasta nucleic seq. 15 gcg - gcg format, type is auto-detected. gcg9seq - gcg9 format, type is auto-detected. gcg9seqp - gcg9 format protein seq. gcg9seqn - gcg9 format nucleic seq. nbrf - nbrf seq, type is auto-detected. 20 nbrfp - nbrf protein seq. nbrfn - nbrf nucleic seq. embl - embl and swissprot format. genbank - genbank format (nucleic). blast - blast format. 25 nbrf_gcg - nbrf-gcg seq, type is auto-detected. nbrf_gcgp - nbrf-gcg protein seq. nbrf_gcgn - nbrf-gcg nucleic seq. raw - raw ascii sequence, type is auto-detected. rawp - raw ascii protein sequence. 30 rawn - raw ascii nucleic sequence. pir - pir codata format, type is auto-detected. profile - gcg profile (valid only for -qfmt WO 2013/128448 PCT/IL2013/050172 34 in SW, XSW, FRAMEP2N, and FRAME+_P2N). -out=<outfname> The name of the output file. -suffix=<name> The output file name suffix. -gapop=<n> Gap open penalty. This parameter is not valid for FRAME+. For 5 FrameSearch the default is 12.0. For other searches the default is 10.0. -gapext=<n> Gap extend penalty. This parameter is not valid for FRAME+. For FrameSearch the default is 4.0. For other models: the default for protein searches is 0.05, and the default for nucleic searches is 1.0. -qgapop=<n> The penalty for opening a gap in the query sequence. The default is 10 10.0. Valid for XSW. -qgapext=<n> The penalty for extending a gap in the query sequence. The default is 0.05. Valid for XSW. -start=<n> The position in the query sequence to begin the search. -end=<n> The position in the query sequence to stop the search. 15 -qtrans Performs a translated search, relevant for a nucleic query against a protein database. The nucleic query is translated to six reading frames and a result is given for each frame. Valid for SW and XSW. -dtrans Performs a translated search, relevant for a protein query against a DNA 20 database. Each database entry is translated to six reading frames and a result is given for each frame. Valid for SW and XSW. Note: "-qtrans" and "-dtrans" options are mutually exclusive. -matrix=<matrixfile> Specifies the comparison matrix to be used in the search. The 25 matrix must be in the BLAST format. If the matrix file is not located in $CGNROOT/tables/matrix, specify the full path as the value of the -matrix parameter. -trans=<transtabname> Translation table. The default location for the table is $CGNROOT/tables/trans. -onestrand Restricts the search to just the top strand of the query/database nucleic 30 sequence. -list=<n> The maximum size of the output hit list. The default is 50.
WO 2013/128448 PCT/IL2013/050172 35 -docalign=<n> The number of documentation lines preceding each alignment. The default is 10. -thrscore=<scorename> The score that places limits on the display of results. Scores that are smaller than -thr_min value or larger than -thrmax value are not shown. Valid 5 options are: quality. zscore. escore. -thrmax=<n> The score upper threshold. Results that are larger than -thrmax value are not shown. 10 -thrmin=<n> The score lower threshold. Results that are lower than -thr_min value are not shown. -align=<n> The number of alignments reported in the output file. -noalign Do not display alignment. Note: "-align" and "-noalign" parameters are mutually exclusive. 15 -outfmt=<format_name> Specifies the output format type. The default format is PFS. Possible values are: PFS - PFS text format FASTA - FASTA text format BLAST - BLAST text format 20 -nonorm Do not perform score normalization. -norm=<normname> Specifies the normalization method. Valid options are: log - logarithm normalization. std - standard normalization. stat - Pearson statistical method. 25 Note: "-nonorm" and "-norm" parameters cannot be used together. Note: Parameters -xgapop, -xgapext, -fgapop, -fgapext, -ygapop, -ygapext, -delop, and -delext apply only to FRAME+. -xgapop=<n> The penalty for opening a gap when inserting a codon (triplet). The default is 12.0. 30 -xgapext=<n> The penalty for extending a gap when inserting a codon (triplet). The default is 4.0.
WO 2013/128448 PCT/IL2013/050172 36 -ygapop=<n> The penalty for opening a gap when deleting an amino acid. The default is 12.0. -ygapext=<n> The penalty for extending a gap when deleting an amino acid. The default is 4.0. 5 -fgapop=<n> The penalty for opening a gap when inserting a DNA base. The default is 6.0. -fgapext=<n> The penalty for extending a gap when inserting a DNA base. The default is 7.0. -delop=<n> The penalty for opening a gap when deleting a DNA base. The default is 10 6.0. -delext=<n> The penalty for extending a gap when deleting a DNA base. The default is 7.0. -silent No screen output is produced. -host=<hostname> The name of the host on which the server runs. By default, the 15 application uses the host specified in the file $CGNROOT/cgnhosts. -wait Do not go to the background when the device is busy. This option is not relevant for the Parseq or Soft pseudo device. -batch Run the job in the background. When this option is specified, the file "$CGNROOT/defaults/batch.defaults" is used for choosing the batch command. If this 20 file does not exist, the command "at now" is used to run the job. Note:"-batch" and "-wait" parameters are mutually exclusive. -version Prints the software version number. -help Displays this help message. To get more specific help type: "om -model=<modelfname> -help". 25 According to some embodiments the homology is a local homology or a local identity. Local alignments tools include, but are not limited to the BlastP, BlastN, BlastX or TBLASTN software of the National Center of Biotechnology Information (NCBI), FASTA, and the Smith-Waterman algorithm. 30 A tblastn search allows the comparison between a protein sequence to the six frame translations of a nucleotide database. It can be a very productive way of finding homologous protein coding regions in unannotated nucleotide sequences such as WO 2013/128448 PCT/IL2013/050172 37 expressed sequence tags (ESTs) and draft genome records (HTG), located in the BLAST databases est and htgs, respectively. Default parameters for blastp include: Max target sequences: 100; Expected threshold: e-5; Word size: 3; Max matches in a query range: 0; Scoring parameters: 5 Matrix - BLOSUM62; filters and masking: Filter - low complexity regions. Local alignments tools, which can be used include, but are not limited to, the tBLASTX algorithm, which compares the six-frame conceptual translation products of a nucleotide query sequence (both strands) against a protein sequence database. Default parameters include: Max target sequences: 100; Expected threshold: 10; Word size: 3; 10 Max matches in a query range: 0; Scoring parameters: Matrix - BLOSUM62; filters and masking: Filter - low complexity regions. According to some embodiments of the invention, the exogenous polynucleotide of the invention encodes a polypeptide having an amino acid sequence at least about 80 %, at least about 81 %, at least about 82 %, at least about 83 %, at least about 84 %, at 15 least about 85 %, at least about 86 %, at least about 87 %, at least about 88 %, at least about 89 %, at least about 90 %, at least about 91 %, at least about 92 %, at least about 93 %, at least about 94 %, at least about 95 %, at least about 96 %, at least about 97 %, at least about 98 %, at least about 99 %, or more say 100 % identical to the amino acid sequence selected from the group consisting of SEQ ID NOs:362-601, 2429-4085 and 20 4086. According to some embodiments of the invention, the method of increasing yield, oil content, growth rate, biomass, vigor, fiber yield, fiber quality, fertilizer use efficiency (e.g., nitrogen use efficiency) and/or abiotic stress tolerance of a plant, is effected by expressing within the plant an exogenous polynucleotide comprising a 25 nucleic acid sequence encoding a polypeptide at least at least about 80 %, at least about 81 %, at least about 82 %, at least about 83 %, at least about 84 %, at least about 85 %, at least about 86 %, at least about 87 %, at least about 88 %, at least about 89 %, at least about 90 %, at least about 91 %, at least about 92 %, at least about 93 %, at least about 94 %, at least about 95 %, at least about 96 %, at least about 97 %, at least about 98 %, 30 at least about 99 %, or more say 100 % identical to the amino acid sequence selected from the group consisting of SEQ ID NOs:362-601, 2429-4085 and 4086, thereby increasing the yield, oil content, growth rate, biomass, vigor, fiber yield, fiber quality, WO 2013/128448 PCT/IL2013/050172 38 fertilizer use efficiency (e.g., nitrogen use efficiency) and/or abiotic stress tolerance of the plant. According to some embodiments of the invention, the exogenous polynucleotide encodes a polypeptide consisting of the amino acid sequence set forth by SEQ ID 5 NO:362-601, 2429-4085 or 4086. According to an aspect of some embodiments of the invention, the method of increasing yield, oil content, growth rate, biomass, vigor, fiber yield, fiber quality, fertilizer use efficiency (e.g., nitrogen use efficiency) and/or abiotic stress tolerance of a plant, is effected by expressing within the plant an exogenous polynucleotide 10 comprising a nucleic acid sequence encoding a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NOs:362-601, 2429-4085 and 4086, thereby increasing the yield, oil content, growth rate, biomass, vigor, fiber yield, fiber quality, fertilizer use efficiency (e.g., nitrogen use efficiency) and/or abiotic stress tolerance of the plant. 15 According to an aspect of some embodiments of the invention, there is provided a method of increasing yield, oil content, growth rate, biomass, vigor, fiber yield, fiber quality, fertilizer use efficiency (e.g., nitrogen use efficiency) and/or abiotic stress tolerance of a plant, comprising expressing within the plant an exogenous polynucleotide comprising a nucleic acid sequence encoding a polypeptide selected from 20 the group consisting of SEQ ID NOs: 362-601, 2429-4085 and 4086, thereby increasing the yield, oil content, growth rate, biomass, vigor, fiber yield, fiber quality, fertilizer use efficiency (e.g., nitrogen use efficiency) and/or abiotic stress tolerance of the plant. According to some embodiments of the invention, the exogenous polynucleotide encodes a polypeptide consisting of the amino acid sequence set forth by SEQ ID NO: 25 362-601, 2429-4085 or 4086. According to some embodiments of the invention the exogenous polynucleotide comprises a nucleic acid sequence which is at least about 80 %, at least about 81 %, at least about 82 %, at least about 83 %, at least about 84 %, at least about 85 %, at least about 86 %, at least about 87 %, at least about 88 %, at least about 89 %, at least about 30 90 %, at least about 91 %, at least about 92 %, at least about 93 %, at least about 93 %, at least about 94 %, at least about 95 %, at least about 96 %, at least about 97 %, at least WO 2013/128448 PCT/IL2013/050172 39 about 98 %, at least about 99 %, e.g., 100 % identical to the nucleic acid sequence selected from the group consisting of SEQ ID NOs:1-361, 602-2427 and 2428. According to an aspect of some embodiments of the invention, there is provided a method of increasing yield, oil content, growth rate, biomass, vigor, fiber yield, fiber 5 quality, fertilizer use efficiency (e.g., nitrogen use efficiency) and/or abiotic stress tolerance of a plant, comprising expressing within the plant an exogenous polynucleotide comprising a nucleic acid sequence at least about 80 %, at least about 81 %, at least about 82 %, at least about 83 %, at least about 84 %, at least about 85 %, at least about 86 %, at least about 87 %, at least about 88 %, at least about 89 %, at least 10 about 90 %, at least about 91 %, at least about 92 %, at least about 93 %, at least about 93 %, at least about 94 %, at least about 95 %, at least about 96 %, at least about 97 %, at least about 98 %, at least about 99 %, e.g., 100 % identical to the nucleic acid sequence selected from the group consisting of SEQ ID NOs:1-361, 602-2427 and 2428, thereby increasing the yield, oil content, growth rate, biomass, vigor, fiber yield, fiber 15 quality, fertilizer use efficiency (e.g., nitrogen use efficiency) and/or abiotic stress tolerance of the plant. According to some embodiments of the invention the exogenous polynucleotide is at least about 80 %, at least about 81 %, at least about 82 %, at least about 83 %, at least about 84 %, at least about 85 %, at least about 86 %, at least about 87 %, at least 20 about 88 %, at least about 89 %, at least about 90 %, at least about 91 %, at least about 92 %, at least about 93 %, at least about 93 %, at least about 94 %, at least about 95 %, at least about 96 %, at least about 97 %, at least about 98 %, at least about 99 %, e.g., 100 % identical to the polynucleotide selected from the group consisting of SEQ ID NOs:1-361, 602-2427 and 2428. 25 According to some embodiments of the invention the exogenous polynucleotide is set forth by SEQ ID NO:1-361, 602-2427 or 2428. As used herein the term "polynucleotide" refers to a single or double stranded nucleic acid sequence which is isolated and provided in the form of an RNA sequence, a complementary polynucleotide sequence (cDNA), a genomic polynucleotide sequence 30 and/or a composite polynucleotide sequences (e.g., a combination of the above). The term "isolated" refers to at least partially separated from the natural environment e.g., from a plant cell.
WO 2013/128448 PCT/IL2013/050172 40 As used herein the phrase "complementary polynucleotide sequence" refers to a sequence, which results from reverse transcription of messenger RNA using a reverse transcriptase or any other RNA dependent DNA polymerase. Such a sequence can be subsequently amplified in vivo or in vitro using a DNA dependent DNA polymerase. 5 As used herein the phrase "genomic polynucleotide sequence" refers to a sequence derived (isolated) from a chromosome and thus it represents a contiguous portion of a chromosome. As used herein the phrase "composite polynucleotide sequence" refers to a sequence, which is at least partially complementary and at least partially genomic. A 10 composite sequence can include some exonal sequences required to encode the polypeptide of the present invention, as well as some intronic sequences interposing therebetween. The intronic sequences can be of any source, including of other genes, and typically will include conserved splicing signal sequences. Such intronic sequences may further include cis acting expression regulatory elements. 15 Nucleic acid sequences encoding the polypeptides of the present invention may be optimized for expression. Examples of such sequence modifications include, but are not limited to, an altered G/C content to more closely approach that typically found in the plant species of interest, and the removal of codons atypically found in the plant species commonly referred to as codon optimization. 20 The phrase "codon optimization" refers to the selection of appropriate DNA nucleotides for use within a structural gene or fragment thereof that approaches codon usage within the plant of interest. Therefore, an optimized gene or nucleic acid sequence refers to a gene in which the nucleotide sequence of a native or naturally occurring gene has been modified in order to utilize statistically-preferred or 25 statistically-favored codons within the plant. The nucleotide sequence typically is examined at the DNA level and the coding region optimized for expression in the plant species determined using any suitable procedure, for example as described in Sardana et al. (1996, Plant Cell Reports 15:677-681). In this method, the standard deviation of codon usage, a measure of codon usage bias, may be calculated by first finding the 30 squared proportional deviation of usage of each codon of the native gene relative to that of highly expressed plant genes, followed by a calculation of the average squared deviation. The formula used is: 1 SDCU = n = 1 N [ ( Xn - Yn ) / Yn ] 2 / N, where Xn WO 2013/128448 PCT/IL2013/050172 41 refers to the frequency of usage of codon n in highly expressed plant genes, where Yn to the frequency of usage of codon n in the gene of interest and N refers to the total number of codons in the gene of interest. A Table of codon usage from highly expressed genes of dicotyledonous plants is compiled using the data of Murray et al. 5 (1989, Nuc Acids Res. 17:477-498). One method of optimizing the nucleic acid sequence in accordance with the preferred codon usage for a particular plant cell type is based on the direct use, without performing any extra statistical calculations, of codon optimization Tables such as those provided on-line at the Codon Usage Database through the NIAS (National Institute of 10 Agrobiological Sciences) DNA bank in Japan (Hypertext Transfer Protocol://World Wide Web (dot) kazusa (dot) or (dot) jp/codon/). The Codon Usage Database contains codon usage tables for a number of different species, with each codon usage Table having been statistically determined based on the data present in Genbank. By using the above Tables to determine the most preferred or most favored 15 codons for each amino acid in a particular species (for example, rice), a naturally occurring nucleotide sequence encoding a protein of interest can be codon optimized for that particular plant species. This is effected by replacing codons that may have a low statistical incidence in the particular species genome with corresponding codons, in regard to an amino acid, that are statistically more favored. However, one or more less 20 favored codons may be selected to delete existing restriction sites, to create new ones at potentially useful junctions (5' and 3' ends to add signal peptide or termination cassettes, internal sites that might be used to cut and splice segments together to produce a correct full-length sequence), or to eliminate nucleotide sequences that may negatively effect mRNA stability or expression. 25 The naturally-occurring encoding nucleotide sequence may already, in advance of any modification, contain a number of codons that correspond to a statistically favored codon in a particular plant species. Therefore, codon optimization of the native nucleotide sequence may comprise determining which codons, within the native nucleotide sequence, are not statistically-favored with regards to a particular plant, and 30 modifying these codons in accordance with a codon usage table of the particular plant to produce a codon optimized derivative. A modified nucleotide sequence may be fully or partially optimized for plant codon usage provided that the protein encoded by the WO 2013/128448 PCT/IL2013/050172 42 modified nucleotide sequence is produced at a level higher than the protein encoded by the corresponding naturally occurring or native gene. Construction of synthetic genes by altering the codon usage is described in for example PCT Patent Application 93/07278. 5 According to some embodiments of the invention, the exogenous polynucleotide is a non-coding RNA. As used herein the phrase 'non-coding RNA" refers to an RNA molecule which does not encode an amino acid sequence (a polypeptide). Examples of such non-coding RNA molecules include, but are not limited to, an antisense RNA, a pre-miRNA 10 (precursor of a microRNA), or a precursor of a Piwi-interacting RNA (piRNA). A non-limiting example of a non-coding RNA polynucleotide is provided in SEQ ID NO: 731. Thus, the invention encompasses nucleic acid sequences described hereinabove; fragments thereof, sequences hybridizable therewith, sequences homologous thereto, 15 sequences encoding similar polypeptides with different codon usage, altered sequences characterized by mutations, such as deletion, insertion or substitution of one or more nucleotides, either naturally occurring or man induced, either randomly or in a targeted fashion. The invention provides an isolated polynucleotide comprising a nucleic acid 20 sequence at least about 80 %, at least about 81 %, at least about 82 %, at least about 83 %, at least about 84 %, at least about 85 %, at least about 86 %, at least about 87 %, at least about 88 %, at least about 89 %, at least about 90 %, at least about 91 %, at least about 92 %, at least about 93 %, at least about 93 %, at least about 94 %, at least about 95 %, at least about 96 %, at least about 97 %, at least about 98 %, at least about 99 %, 25 e.g., 100 % identical to the polynucleotide selected from the group consisting of SEQ ID NOs:1-361, 602-2427 and 2428. According to some embodiments of the invention the nucleic acid sequence is capable of increasing yield, oil content, growth rate, biomass, vigor, fiber yield, fiber quality, fertilizer use efficiency (e.g., nitrogen use efficiency) and/or abiotic stress 30 tolerance of a plant.
WO 2013/128448 PCT/IL2013/050172 43 According to some embodiments of the invention the isolated polynucleotide comprising the nucleic acid sequence selected from the group consisting of SEQ ID NOs:1-361, 602-2427 and 2428. According to some embodiments of the invention the isolated polynucleotide is 5 set forth by SEQ ID NO: 1-361, 602-2427 or 2428. The invention provides an isolated polynucleotide comprising a nucleic acid sequence encoding a polypeptide which comprises an amino acid sequence at least about 80 %, at least about 81 %, at least about 82 %, at least about 83 %, at least about 84 %, at least about 85 %, at least about 86 %, at least about 87 %, at least about 88 %, 10 at least about 89 %, at least about 90 %, at least about 91 %, at least about 92 %, at least about 93 %, at least about 93 %, at least about 94 %, at least about 95 %, at least about 96 %, at least about 97 %, at least about 98 %, at least about 99 %, or more say 100 % homologous to the amino acid sequence selected from the group consisting of SEQ ID NO: 362-601, 2429-4085 or 4086. 15 According to some embodiments of the invention the amino acid sequence is capable of increasing yield, oil content, growth rate, biomass, vigor, fiber yield, fiber quality, fertilizer use efficiency (e.g., nitrogen use efficiency) and/or abiotic stress tolerance of a plant. The invention provides an isolated polynucleotide comprising a nucleic acid 20 sequence encoding a polypeptide which comprises the amino acid sequence selected from the group consisting of SEQ ID NOs:362-601, 2429-4085 and 4086. According to an aspect of some embodiments of the invention, there is provided a nucleic acid construct comprising the isolated polynucleotide of the invention, and a promoter for directing transcription of the nucleic acid sequence in a host cell. 25 The invention provides an isolated polypeptide comprising an amino acid sequence at least about 80 %, at least about 81 %, at least about 82 %, at least about 83 %, at least about 84 %, at least about 85 %, at least about 86 %, at least about 87 %, at least about 88 %, at least about 89 %, at least about 90 %, at least about 91 %, at least about 92 %, at least about 93 %, at least about 93 %, at least about 94 %, at least about 30 95 %, at least about 96 %, at least about 97 %, at least about 98 %, at least about 99 %, or more say 100 % homologous to an amino acid sequence selected from the group consisting of SEQ ID NO: 362-601, 2429-4085 or 4086.
WO 2013/128448 PCT/IL2013/050172 44 According to some embodiments of the invention, the polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NOs:362-601, 2429-4085 and 4086. According to some embodiments of the invention, the polypeptide is set forth by 5 SEQ ID NO: 362-601, 2429-4085 or 4086. The invention also encompasses fragments of the above described polypeptides and polypeptides having mutations, such as deletions, insertions or substitutions of one or more amino acids, either naturally occurring or man induced, either randomly or in a targeted fashion. 10 The term "'plant" as used herein encompasses whole plants, ancestors and progeny of the plants and plant parts, including seeds, shoots, stems, roots (including tubers), and plant cells, tissues and organs. The plant may be in any form including suspension cultures, embryos, meristematic regions, callus tissue, leaves, gametophytes, sporophytes, pollen, and microspores. Plants that are particularly useful in the methods 15 of the invention include all plants which belong to the superfamily Viridiplantae, in particular monocotyledonous and dicotyledonous plants including a fodder or forage legume, ornamental plant, food crop, tree, or shrub selected from the list comprising Acacia spp., Acer spp., Actinidia spp., Aesculus spp., Agathis australis, Albizia amara, Alsophila tricolor, Andropogon spp., Arachis spp, Areca catechu, Astelia fragrans, 20 Astragalus cicer, Baikiaea plurijuga, Betula spp., Brassica spp., Bruguiera gymnorrhiza, Burkea africana, Butea frondosa, Cadaba farinosa, Calliandra spp, Camellia sinensis, Canna indica, Capsicum spp., Cassia spp., Centroema pubescens, Chacoomeles spp., Cinnamomum cassia, Coffea arabica, Colophospermum mopane, Coronillia varia, Cotoneaster serotina, Crataegus spp., Cucumis spp., Cupressus spp., Cyathea dealbata, 25 Cydonia oblonga, Cryptomeria japonica, Cymbopogon spp., Cynthea dealbata, Cydonia oblonga, Dalbergia monetaria, Davallia divaricata, Desmodium spp., Dicksonia squarosa, Dibeteropogon amplectens, Dioclea spp, Dolichos spp., Dorycnium rectum, Echinochloa pyramidalis, Ehraffia spp., Eleusine coracana, Eragrestis spp., Erythrina spp., Eucalypfus spp., Euclea schimperi, Eulalia vi/losa, Pagopyrum spp., Feijoa 30 sellowlana, Fragaria spp., Flemingia spp, Freycinetia banksli, Geranium thunbergii, GinAgo biloba, Glycine javanica, Gliricidia spp, Gossypium hirsutum, Grevillea spp., Guibourtia coleosperma, Hedysarum spp., Hemaffhia altissima, Heteropogon contoffus, WO 2013/128448 PCT/IL2013/050172 45 Hordeum vulgare, Hyparrhenia rufa, Hypericum erectum, Hypeffhelia dissolute, Indigo incamata, Iris spp., Leptarrhena pyrolifolia, Lespediza spp., Lettuca spp., Leucaena leucocephala, Loudetia simplex, Lotonus bainesli, Lotus spp., Macrotyloma axillare, Malus spp., Manihot esculenta, Medicago saliva, Metasequoia glyptostroboides, Musa 5 sapientum, Nicotianum spp., Onobrychis spp., Ornithopus spp., Oryza spp., Peltophorum africanum, Pennisetum spp., Persea gratissima, Petunia spp., Phaseolus spp., Phoenix canariensis, Phormium cookianum, Photinia spp., Picea glauca, Pinus spp., Pisum sativam, Podocarpus totara, Pogonarthria fleckii, Pogonaffhria squarrosa, Populus spp., Prosopis cineraria, Pseudotsuga menziesii, Pterolobium stellatum, Pyrus 10 communis, Quercus spp., Rhaphiolepsis umbellata, Rhopalostylis sapida, Rhus natalensis, Ribes grossularia, Ribes spp., Robinia pseudoacacia, Rosa spp., Rubus spp., Salix spp., Schyzachyrium sanguineum, Sciadopitys vefficillata, Sequoia sempervirens, Sequoiadendron giganteum, Sorghum bicolor, Spinacia spp., Sporobolus fimbriatus, Stiburus alopecuroides, Stylosanthos humilis, Tadehagi spp, Taxodium distichum, 15 Themeda triandra, Trifolium spp., Triticum spp., Tsuga heterophylla, Vaccinium spp., Vicia spp., Vitis vinifera, Watsonia pyramidata, Zantedeschia aethiopica, Zea mays, amaranth, artichoke, asparagus, broccoli, Brussels sprouts, cabbage, canola, carrot, cauliflower, celery, collard greens, flax, kale, lentil, oilseed rape, okra, onion, potato, rice, soybean, straw, sugar beet, sugar cane, sunflower, tomato, squash tea, maize, 20 wheat, barely, rye, oat, peanut, pea, lentil and alfalfa, cotton, rapeseed, canola, pepper, sunflower, tobacco, eggplant, eucalyptus, a tree, an ornamental plant, a perennial grass and a forage crop. Alternatively algae and other non-Viridiplantae can be used for the methods of the present invention. According to some embodiments of the invention, the plant used by the method 25 of the invention is a crop plant such as rice, maize, wheat, barley, peanut, potato, sesame, olive tree, palm oil, banana, soybean, sunflower, canola, sugarcane, alfalfa, millet, leguminosae (bean, pea), flax, lupinus, rapeseed, tobacco, poplar and cotton. According to some embodiments of the invention the plant is a dicotyledonous plant. 30 According to some embodiments of the invention the plant is a monocotyledonous plant.
WO 2013/128448 PCT/IL2013/050172 46 According to some embodiments of the invention, there is provided a plant cell exogenously expressing the polynucleotide of some embodiments of the invention, the nucleic acid construct of some embodiments of the invention and/or the polypeptide of some embodiments of the invention. 5 According to some embodiments of the invention, expressing the exogenous polynucleotide of the invention within the plant is effected by transforming one or more cells of the plant with the exogenous polynucleotide, followed by generating a mature plant from the transformed cells and cultivating the mature plant under conditions suitable for expressing the exogenous polynucleotide within the mature plant. 10 According to some embodiments of the invention, the transformation is effected by introducing to the plant cell a nucleic acid construct which includes the exogenous polynucleotide of some embodiments of the invention and at least one promoter for directing transcription of the exogenous polynucleotide in a host cell (a plant cell). Further details of suitable transformation approaches are provided hereinbelow. 15 As mentioned, the nucleic acid construct according to some embodiments of the invention comprises a promoter sequence and the isolated polynucleotide of the invention. According to some embodiments of the invention, the isolated polynucleotide is operably linked to the promoter sequence. 20 A coding nucleic acid sequence is "operably linked" to a regulatory sequence (e.g., promoter) if the regulatory sequence is capable of exerting a regulatory effect on the coding sequence linked thereto. As used herein, the term "promoter" refers to a region of DNA which lies upstream of the transcriptional initiation site of a gene to which RNA polymerase binds 25 to initiate transcription of RNA. The promoter controls where (e.g., which portion of a plant) and/or when (e.g., at which stage or condition in the lifetime of an organism) the gene is expressed. According to some embodiments of the invention, the promoter is heterologous to the isolated polynucleotide and/or to the host cell. 30 As used herein the phrase "heterologous promoter" refers to a promoter from a different species or from the same species but from a different gene locus as of the isolated polynucleotide sequence.
WO 2013/128448 PCT/IL2013/050172 47 Any suitable promoter sequence can be used by the nucleic acid construct of the present invention. Preferably the promoter is a constitutive promoter, a tissue-specific, or an abiotic stress-inducible promoter. According to some embodiments of the invention, the promoter is a plant 5 promoter, which is suitable for expression of the exogenous polynucleotide in a plant cell. Suitable promoters for expression in wheat include, but are not limited to, Wheat SPA promoter (SEQ ID NO: 4087; Albanietal, Plant Cell, 9: 171- 184, 1997, which is fully incorporated herein by reference), wheat LMW (SEQ ID NO: 4088 (longer LMW 10 promoter), and SEQ ID NO: 4089 (LMW promoter) and HMW glutenin-1 (SEQ ID NO: 4090 (Wheat HMW glutenin-1 longer promoter); and SEQ ID NO: 4091 (Wheat HMW glutenin-1 Promoter); Thomas and Flavell, The Plant Cell 2:1171-1180; Furtado et al., 2009 Plant Biotechnology Journal 7:240-253, each of which is fully incorporated herein by reference), wheat alpha, beta and gamma gliadins [e.g., SEQ ID NO: 4092 15 (wheat alpha gliadin, B genome, promoter); SEQ ID NO: 4093 (wheat gamma gliadin promoter); EMBO 3:1409-15, 1984, which is fully incorporated herein by reference], wheat TdPR60 [SEQ ID NO: 4094 (wheat TdPR60 longer promoter) or SEQ ID NO: 4095 (wheat TdPR60 promoter); Kovalchuk et al., Plant Mol Biol 71:81-98, 2009, which is fully incorporated herein by reference], maize Ub 1 Promoter [cultivar Nongda 20 105 (SEQ ID NO: 4096); GenBank: DQ141598.1; Taylor et al., Plant Cell Rep 1993 12: 491-495, which is fully incorporated herein by reference; and cultivar B73 (SEQ ID NO: 4097); Christensen, AH, et al. Plant Mol. Biol. 18 (4), 675-689 (1992), which is fully incorporated herein by reference]; rice actin 1 (SEQ ID NO: 4098; Mc Elroy et al. 1990, The Plant Cell, Vol. 2, 163-17 1, which is fully incorporated herein by reference), 25 rice GOS2 [SEQ ID NO: 4099 (rice GOS2 longer promoter) and SEQ ID NO: 4100 (rice GOS2 Promoter); De Pater et al. Plant J. 1992; 2: 837-44, which is fully incorporated herein by reference], arabidopsis Phol [SEQ ID NO: 4101 (arabidopsis Phol Promoter); Hamburger et al., Plant Cell. 2002; 14: 889-902, which is fully incorporated herein by reference], ExpansinB promoters, e.g., rice ExpB5 [SEQ ID NO: 30 4102 (rice ExpB5 longer promoter) and SEQ ID NO: 4103 (rice ExpB5 promoter)] and Barley ExpB1 [SEQ ID NO: 4104 (barley ExpB1 Promoter), Won et al. Mol Cells. 2010; 30:369-76, which is fully incorporated herein by reference], barley SS2 (sucrose WO 2013/128448 PCT/IL2013/050172 48 synthase 2) [(SEQ ID NO: 4105), Guerin and Carbonero, Plant Physiology May 1997 vol. 114 no. 1 55-62, which is fully incorporated herein by reference], and rice PG5a [SEQ ID NO:4106, US 7,700,835, Nakase et al., Plant Mol Biol. 32:621-30, 1996, each of which is fully incorporated herein by reference]. 5 Suitable constitutive promoters include, for example, CaMV 35S promoter [SEQ ID NO: 4107 (CaMV 35S (QFNC) Promoter); SEQ ID NO: 4108 (PJJ 35S from Brachypodium); SEQ ID NO: 4109 (CaMV 35S (OLD) Promoter) (Odell et al., Nature 313:810-812, 1985)], Arabidopsis At6669 promoter (SEQ ID NO: 4110 (Arabidopsis At6669 (OLD) Promoter); see PCT Publication No. W004081173A2 or the new 10 At6669 promoter (SEQ ID NO: 4111 (Arabidopsis At6669 (NEW) Promoter)); maize UbI Promoter [cultivar Nongda 105 (SEQ ID NO:4096); GenBank: DQ141598.1; Taylor et al., Plant Cell Rep 1993 12: 491-495, which is fully incorporated herein by reference; and cultivar B73 (SEQ ID NO:4097); Christensen, AH, et al. Plant Mol. Biol. 18 (4), 675-689 (1992), which is fully incorporated herein by reference]; rice actin 1 15 (SEQ ID NO: 4098, McElroy et al., Plant Cell 2:163-171, 1990); pEMU (Last et al., Theor. Appl. Genet. 81:581-588, 1991); CaMV 19S (Nilsson et al., Physiol. Plant 100:456-462, 1997); rice GOS2 [SEQ ID NO: 4099 (rice GOS2 longer Promoter) and SEQ ID NO: 4100 (rice GOS2 Promoter), de Pater et al, Plant J Nov;2(6):837-44, 1992]; RBCS promoter (SEQ ID NO:4112); Rice cyclophilin (Bucholz et al, Plant Mol 20 Biol. 25(5):837-43, 1994); Maize H3 histone (Lepetit et al, Mol. Gen. Genet. 231: 276 285, 1992); Actin 2 (An et al, Plant J. 10(1);107-121, 1996) and Synthetic Super MAS (Ni et al., The Plant Journal 7: 661-76, 1995). Other constitutive promoters include those in U.S. Pat. Nos. 5,659,026, 5,608,149; 5.608,144; 5,604,121; 5.569,597: 5.466,785; 5,399,680; 5,268,463; and 5,608,142. 25 Suitable tissue-specific promoters include, but not limited to, leaf-specific promoters [e.g., AT5G06690 (Thioredoxin) (high expression, SEQ ID NO: 4113), AT5G61520 (AtSTP3) (low expression, SEQ ID NO: 4114) described in Buttner et al 2000 Plant, Cell and Environment 23, 175-184, or the promoters described in Yamamoto et al., Plant J. 12:255-265, 1997; Kwon et al., Plant Physiol. 105:357-67, 30 1994; Yamamoto et al., Plant Cell Physiol. 35:773-778, 1994; Gotor et al., Plant J. 3:509-18, 1993; Orozco et al., Plant Mol. Biol. 23:1129-1138, 1993; and Matsuoka et al., Proc. Natl. Acad. Sci. USA 90:9586-9590, 1993; as well as Arabidopsis STP3 WO 2013/128448 PCT/IL2013/050172 49 (AT5G61520) promoter (Buttner et al., Plant, Cell and Environment 23:175-184, 2000)], seed-preferred promoters [e.g., Napin (originated from Brassica napus which is characterized by a seed specific promoter activity; Stuitje A. R. et. al. Plant Biotechnology Journal 1 (4): 301-309; SEQ ID NO: 4115 (Brassica napus NAPIN 5 Promoter) from seed specific genes (Simon, et al., Plant Mol. Biol. 5. 191, 1985; Scofield, et al., J. Biol. Chem. 262: 12202, 1987; Baszczynski, et al., Plant Mol. Biol. 14: 633, 1990), rice PG5a (SEQ ID NO: 4106; US 7,700,835), early seed development Arabidopsis BAN (AT1G61720) (SEQ ID NO: 4116, US 2009/0031450 Al), late seed development Arabidopsis ABI3 (AT3G24650) (SEQ ID NO: 4117 (Arabidopsis ABI3 10 (AT3G24650) longer Promoter) or 4118 (Arabidopsis ABI3 (AT3G24650) Promoter)) (Ng et al., Plant Molecular Biology 54: 25-38, 2004), Brazil Nut albumin (Pearson' et al., Plant Mol. Biol. 18: 235- 245, 1992), legumin (Ellis, et al. Plant Mol. Biol. 10: 203 214, 1988), Glutelin (rice) (Takaiwa, et al., Mol. Gen. Genet. 208: 15-22, 1986; Takaiwa, et al., FEBS Letts. 221: 43-47, 1987), Zein (Matzke et al Plant Mol Biol, 15 143).323-32 1990), napA (Stalberg, et al, Planta 199: 515-519, 1996), Wheat SPA (SEQ ID NO: 4087; Albanietal, Plant Cell, 9: 171- 184, 1997), sunflower oleosin (Cummins, et al., Plant Mol. Biol. 19: 873- 876, 1992)], endosperm specific promoters [e.g., wheat LMW (SEQ ID NO: 4088 (Wheat LMW Longer Promoter), and SEQ ID NO: 4089 (Wheat LMW Promoter) and HMW glutenin-1 [(SEQ ID NO: 4090 (Wheat HMW 20 glutenin-1 longer Promoter)); and SEQ ID NO: 4091 (Wheat HMW glutenin-1 Promoter), Thomas and Flavell, The Plant Cell 2:1171-1180, 1990; Mol Gen Genet 216:81-90, 1989; NAR 17:461-2), wheat alpha, beta and gamma gliadins (SEQ ID NO: 4092 (wheat alpha gliadin (B genome) promoter); SEQ ID NO: 4093 (wheat gamma gliadin promoter); EMBO 3:1409-15, 1984), Barley ltrl promoter, barley Bi, C, D 25 hordein (Theor Appl Gen 98:1253-62, 1999; Plant J 4:343-55, 1993; Mol Gen Genet 250:750- 60, 1996), Barley DOF (Mena et al, The Plant Journal, 116(1): 53- 62, 1998), Biz2 (EP99106056.7), Barley SS2 (SEQ ID NO: 4105 (Barley SS2 Promoter); Guerin and Carbonero Plant Physiology 114: 1 55-62, 1997), wheat Tarp60 (Kovalchuk et al., Plant Mol Biol 71:81-98, 2009), barley D-hordein (D-Hor) and B-hordein (B-Hor) 30 (Agnelo Furtado, Robert J. Henry and Alessandro Pellegrineschi (2009)], Synthetic promoter (Vicente-Carbajosa et al., Plant J. 13: 629-640, 1998), rice prolamin NRP33, rice -globulin Glb-1 (Wu et al, Plant Cell Physiology 39(8) 885- 889, 1998), rice alpha- WO 2013/128448 PCT/IL2013/050172 50 globulin REB/OHP-1 (Nakase et al. Plant Mol. Biol. 33: 513-S22, 1997), rice ADP glucose PP (Trans Res 6:157-68, 1997), maize ESR gene family (Plant J 12:235-46, 1997), sorgum gamma- kafirin (PMB 32:1029-35, 1996)], embryo specific promoters [e.g., rice OSHI (Sato et al, Proc. Natl. Acad. Sci. USA, 93: 8117-8122), KNOX 5 (Postma-Haarsma ef al, Plant Mol. Biol. 39:257-71, 1999), rice oleosin (Wu et at, J. Biochem., 123:386, 1998)], and flower-specific promoters [e.g., AtPRP4, chalene synthase (chsA) (Van der Meer, et al., Plant Mol. Biol. 15, 95-109, 1990), LAT52 (Twell et al Mol. Gen Genet. 217:240-245; 1989), Arabidopsis apetala- 3 (Tilly et al., Development. 125:1647-57, 1998), Arabidopsis APETALA 1 (AT1G69120, API) 10 (SEQ ID NO: 4119 (Arabidopsis (AT1G69120) APETALA 1)) (Hempel et al., Development 124:3845-3853, 1997)], and root promoters [e.g., the ROOTP promoter [SEQ ID NO: 4120]; rice ExpB5 (SEQ ID NO:4103 (rice ExpB5 Promoter); or SEQ ID NO: 4102 (rice ExpB5 longer Promoter)) and barley ExpB1 promoters (SEQ ID NO:4104) (Won et al. Mol. Cells 30: 369-376, 2010); arabidopsis ATTPS-CIN 15 (AT3G25820) promoter (SEQ ID NO: 4121; Chen et al., Plant Phys 135:1956-66, 2004); arabidopsis Phol promoter (SEQ ID NO: 4101, Hamburger et al., Plant Cell. 14: 889-902, 2002), which is also slightly induced by stress]. Suitable abiotic stress-inducible promoters include, but not limited to, salt inducible promoters such as RD29A (Yamaguchi-Shinozalei et al., Mol. Gen. Genet. 20 236:331-340, 1993); drought-inducible promoters such as maize rabl7 gene promoter (Pla et. al., Plant Mol. Biol. 21:259-266, 1993), maize rab28 gene promoter (Busk et. al., Plant J. 11:1285-1295, 1997) and maize Ivr2 gene promoter (Pelleschi et. al., Plant Mol. Biol. 39:373-380, 1999); heat-inducible promoters such as heat tomato hsp80 promoter from tomato (U.S. Pat. No. 5,187,267). 25 The nucleic acid construct of some embodiments of the invention can further include an appropriate selectable marker and/or an origin of replication. According to some embodiments of the invention, the nucleic acid construct utilized is a shuttle vector, which can propagate both in E. coli (wherein the construct comprises an appropriate selectable marker and origin of replication) and be compatible with 30 propagation in cells. The construct according to the present invention can be, for example, a plasmid, a bacmid, a phagemid, a cosmid, a phage, a virus or an artificial chromosome.
WO 2013/128448 PCT/IL2013/050172 51 The nucleic acid construct of some embodiments of the invention can be utilized to stably or transiently transform plant cells. In stable transformation, the exogenous polynucleotide is integrated into the plant genome and as such it represents a stable and inherited trait. In transient transformation, the exogenous polynucleotide is expressed 5 by the cell transformed but it is not integrated into the genome and as such it represents a transient trait. There are various methods of introducing foreign genes into both monocotyledonous and dicotyledonous plants (Potrykus, I., Annu. Rev. Plant. Physiol., Plant. Mol. Biol. (1991) 42:205-225; Shimamoto et al., Nature (1989) 338:274-276). 10 The principle methods of causing stable integration of exogenous DNA into plant genomic DNA include two main approaches: (i) Agrobacterium-mediated gene transfer: Klee et al. (1987) Annu. Rev. Plant Physiol. 38:467-486; Klee and Rogers in Cell Culture and Somatic Cell Genetics of Plants, Vol. 6, Molecular Biology of Plant Nuclear Genes, eds. Schell, J., and Vasil, 15 L. K., Academic Publishers, San Diego, Calif. (1989) p. 2-25; Gatenby, in Plant Biotechnology, eds. Kung, S. and Amtzen, C. J., Butterworth Publishers, Boston, Mass. (1989) p. 93-112. (ii) Direct DNA uptake: Paszkowski et al., in Cell Culture and Somatic Cell Genetics of Plants, Vol. 6, Molecular Biology of Plant Nuclear Genes eds. Schell, J., 20 and Vasil, L. K., Academic Publishers, San Diego, Calif. (1989) p. 52-68; including methods for direct uptake of DNA into protoplasts, Toriyama, K. et al. (1988) Bio/Technology 6:1072-1074. DNA uptake induced by brief electric shock of plant cells: Zhang et al. Plant Cell Rep. (1988) 7:379-384. Fromm et al. Nature (1986) 319:791-793. DNA injection into plant cells or tissues by particle bombardment, Klein 25 et al. Bio/Technology (1988) 6:559-563; McCabe et al. Bio/Technology (1988) 6:923 926; Sanford, Physiol. Plant. (1990) 79:206-209; by the use of micropipette systems: Neuhaus et al., Theor. Appl. Genet. (1987) 75:30-36; Neuhaus and Spangenberg, Physiol. Plant. (1990) 79:213-217; glass fibers or silicon carbide whisker transformation of cell cultures, embryos or callus tissue, U.S. Pat. No. 5,464,765 or by the direct 30 incubation of DNA with germinating pollen, DeWet et al. in Experimental Manipulation of Ovule Tissue, eds. Chapman, G. P. and Mantell, S. H. and Daniels, WO 2013/128448 PCT/IL2013/050172 52 W. Longman, London, (1985) p. 197-209; and Ohta, Proc. Natl. Acad. Sci. USA (1986) 83:715-719. The Agrobacterium system includes the use of plasmid vectors that contain defined DNA segments that integrate into the plant genomic DNA. Methods of 5 inoculation of the plant tissue vary depending upon the plant species and the Agrobacterium delivery system. A widely used approach is the leaf disc procedure which can be performed with any tissue explant that provides a good source for initiation of whole plant differentiation. See, e.g., Horsch et al. in Plant Molecular Biology Manual A5, Kluwer Academic Publishers, Dordrecht (1988) p. 1-9. A 10 supplementary approach employs the Agrobacterium delivery system in combination with vacuum infiltration. The Agrobacterium system is especially viable in the creation of transgenic dicotyledonous plants. There are various methods of direct DNA transfer into plant cells. In electroporation, the protoplasts are briefly exposed to a strong electric field. In 15 microinjection, the DNA is mechanically injected directly into the cells using very small micropipettes. In microparticle bombardment, the DNA is adsorbed on microprojectiles such as magnesium sulfate crystals or tungsten particles, and the microprojectiles are physically accelerated into cells or plant tissues. Following stable transformation plant propagation is exercised. The most 20 common method of plant propagation is by seed. Regeneration by seed propagation, however, has the deficiency that due to heterozygosity there is a lack of uniformity in the crop, since seeds are produced by plants according to the genetic variances governed by Mendelian rules. Basically, each seed is genetically different and each will grow with its own specific traits. Therefore, it is preferred that the transformed plant be 25 produced such that the regenerated plant has the identical traits and characteristics of the parent transgenic plant. Therefore, it is preferred that the transformed plant be regenerated by micropropagation which provides a rapid, consistent reproduction of the transformed plants. Micropropagation is a process of growing new generation plants from a single 30 piece of tissue that has been excised from a selected parent plant or cultivar. This process permits the mass reproduction of plants having the preferred tissue expressing the fusion protein. The new generation plants which are produced are genetically WO 2013/128448 PCT/IL2013/050172 53 identical to, and have all of the characteristics of, the original plant. Micropropagation allows mass production of quality plant material in a short period of time and offers a rapid multiplication of selected cultivars in the preservation of the characteristics of the original transgenic or transformed plant. The advantages of cloning plants are the speed 5 of plant multiplication and the quality and uniformity of plants produced. Micropropagation is a multi-stage procedure that requires alteration of culture medium or growth conditions between stages. Thus, the micropropagation process involves four basic stages: Stage one, initial tissue culturing; stage two, tissue culture multiplication; stage three, differentiation and plant formation; and stage four, 10 greenhouse culturing and hardening. During stage one, initial tissue culturing, the tissue culture is established and certified contaminant-free. During stage two, the initial tissue culture is multiplied until a sufficient number of tissue samples are produced to meet production goals. During stage three, the tissue samples grown in stage two are divided and grown into individual plantlets. At stage four, the transformed plantlets are 15 transferred to a greenhouse for hardening where the plants' tolerance to light is gradually increased so that it can be grown in the natural environment. According to some embodiments of the invention, the transgenic plants are generated by transient transformation of leaf cells, meristematic cells or the whole plant. Transient transformation can be effected by any of the direct DNA transfer 20 methods described above or by viral infection using modified plant viruses. Viruses that have been shown to be useful for the transformation of plant hosts include CaMV, Tobacco mosaic virus (TMV), brome mosaic virus (BMV) and Bean Common Mosaic Virus (BV or BCMV). Transformation of plants using plant viruses is described in U.S. Pat. No. 4,855,237 (bean golden mosaic virus; BGV), EP-A 67,553 25 (TMV), Japanese Published Application No. 63-14693 (TMV), EPA 194,809 (BV), EPA 278,667 (BV); and Gluzman, Y. et al., Communications in Molecular Biology: Viral Vectors, Cold Spring Harbor Laboratory, New York, pp. 172-189 (1988). Pseudovirus particles for use in expressing foreign DNA in many hosts, including plants are described in WO 87/06261. 30 According to some embodiments of the invention, the virus used for transient transformations is avirulent and thus is incapable of causing severe symptoms such as reduced growth rate, mosaic, ring spots, leaf roll, yellowing, streaking, pox formation, WO 2013/128448 PCT/IL2013/050172 54 tumor formation and pitting. A suitable avirulent virus may be a naturally occurring avirulent virus or an artificially attenuated virus. Virus attenuation may be effected by using methods well known in the art including, but not limited to, sub-lethal heating, chemical treatment or by directed mutagenesis techniques such as described, for 5 example, by Kurihara and Watanabe (Molecular Plant Pathology 4:259-269, 2003), Gal-on et al. (1992), Atreya et al. (1992) and Huet et al. (1994). Suitable virus strains can be obtained from available sources such as, for example, the American Type culture Collection (ATCC) or by isolation from infected plants. Isolation of viruses from infected plant tissues can be effected by techniques 10 well known in the art such as described, for example by Foster and Tatlor, Eds. "Plant Virology Protocols: From Virus Isolation to Transgenic Resistance (Methods in Molecular Biology (Humana Pr), Vol 81)", Humana Press, 1998. Briefly, tissues of an infected plant believed to contain a high concentration of a suitable virus, preferably young leaves and flower petals, are ground in a buffer solution (e.g., phosphate buffer 15 solution) to produce a virus infected sap which can be used in subsequent inoculations. Construction of plant RNA viruses for the introduction and expression of non viral exogenous polynucleotide sequences in plants is demonstrated by the above references as well as by Dawson, W. 0. et al., Virology (1989) 172:285-292; Takamatsu et al. EMBO J. (1987) 6:307-311; French et al. Science (1986) 231:1294 20 1297; Takamatsu et al. FEBS Letters (1990) 269:73-76; and U.S. Pat. No. 5,316,931. When the virus is a DNA virus, suitable modifications can be made to the virus itself. Alternatively, the virus can first be cloned into a bacterial plasmid for ease of constructing the desired viral vector with the foreign DNA. The virus can then be excised from the plasmid. If the virus is a DNA virus, a bacterial origin of replication 25 can be attached to the viral DNA, which is then replicated by the bacteria. Transcription and translation of this DNA will produce the coat protein which will encapsidate the viral DNA. If the virus is an RNA virus, the virus is generally cloned as a cDNA and inserted into a plasmid. The plasmid is then used to make all of the constructions. The RNA virus is then produced by transcribing the viral sequence of 30 the plasmid and translation of the viral genes to produce the coat protein(s) which encapsidate the viral RNA.
WO 2013/128448 PCT/IL2013/050172 55 In one embodiment, a plant viral polynucleotide is provided in which the native coat protein coding sequence has been deleted from a viral polynucleotide, a non-native plant viral coat protein coding sequence and a non-native promoter, preferably the subgenomic promoter of the non-native coat protein coding sequence, capable of 5 expression in the plant host, packaging of the recombinant plant viral polynucleotide, and ensuring a systemic infection of the host by the recombinant plant viral polynucleotide, has been inserted. Alternatively, the coat protein gene may be inactivated by insertion of the non-native polynucleotide sequence within it, such that a protein is produced. The recombinant plant viral polynucleotide may contain one or 10 more additional non-native subgenomic promoters. Each non-native subgenomic promoter is capable of transcribing or expressing adjacent genes or polynucleotide sequences in the plant host and incapable of recombination with each other and with native subgenomic promoters. Non-native (foreign) polynucleotide sequences may be inserted adjacent the native plant viral subgenomic promoter or the native and a non 15 native plant viral subgenomic promoters if more than one polynucleotide sequence is included. The non-native polynucleotide sequences are transcribed or expressed in the host plant under control of the subgenomic promoter to produce the desired products. In a second embodiment, a recombinant plant viral polynucleotide is provided as in the first embodiment except that the native coat protein coding sequence is placed 20 adjacent one of the non-native coat protein subgenomic promoters instead of a non native coat protein coding sequence. In a third embodiment, a recombinant plant viral polynucleotide is provided in which the native coat protein gene is adjacent its subgenomic promoter and one or more non-native subgenomic promoters have been inserted into the viral polynucleotide. The 25 inserted non-native subgenomic promoters are capable of transcribing or expressing adjacent genes in a plant host and are incapable of recombination with each other and with native subgenomic promoters. Non-native polynucleotide sequences may be inserted adjacent the non-native subgenomic plant viral promoters such that the sequences are transcribed or expressed in the host plant under control of the 30 subgenomic promoters to produce the desired product.
WO 2013/128448 PCT/IL2013/050172 56 In a fourth embodiment, a recombinant plant viral polynucleotide is provided as in the third embodiment except that the native coat protein coding sequence is replaced by a non-native coat protein coding sequence. The viral vectors are encapsidated by the coat proteins encoded by the 5 recombinant plant viral polynucleotide to produce a recombinant plant virus. The recombinant plant viral polynucleotide or recombinant plant virus is used to infect appropriate host plants. The recombinant plant viral polynucleotide is capable of replication in the host, systemic spread in the host, and transcription or expression of foreign gene(s) (exogenous polynucleotide) in the host to produce the desired protein. 10 Techniques for inoculation of viruses to plants may be found in Foster and Taylor, eds. "Plant Virology Protocols: From Virus Isolation to Transgenic Resistance (Methods in Molecular Biology (Humana Pr), Vol 81)", Humana Press, 1998; Maramorosh and Koprowski, eds. "Methods in Virology" 7 vols, Academic Press, New York 1967-1984; Hill, S.A. "Methods in Plant Virology", Blackwell, Oxford, 1984; 15 Walkey, D.G.A. "Applied Plant Virology", Wiley, New York, 1985; and Kado and Agrawa, eds. "Principles and Techniques in Plant Virology", Van Nostrand-Reinhold, New York. In addition to the above, the polynucleotide of the present invention can also be introduced into a chloroplast genome thereby enabling chloroplast expression. 20 A technique for introducing exogenous polynucleotide sequences to the genome of the chloroplasts is known. This technique involves the following procedures. First, plant cells are chemically treated so as to reduce the number of chloroplasts per cell to about one. Then, the exogenous polynucleotide is introduced via particle bombardment into the cells with the aim of introducing at least one exogenous polynucleotide 25 molecule into the chloroplasts. The exogenous polynucleotides selected such that it is integratable into the chloroplast's genome via homologous recombination which is readily effected by enzymes inherent to the chloroplast. To this end, the exogenous polynucleotide includes, in addition to a gene of interest, at least one polynucleotide stretch which is derived from the chloroplast's genome. In addition, the exogenous 30 polynucleotide includes a selectable marker, which serves by sequential selection procedures to ascertain that all or substantially all of the copies of the chloroplast genomes following such selection will include the exogenous polynucleotide. Further WO 2013/128448 PCT/IL2013/050172 57 details relating to this technique are found in U.S. Pat. Nos. 4,945,050; and 5,693,507 which are incorporated herein by reference. A polypeptide can thus be produced by the protein expression system of the chloroplast and become integrated into the chloroplast's inner membrane. 5 Since processes which increase yield, growth rate, biomass, vigor, oil content, seed yield, fiber yield, fiber quality, nitrogen use efficiency, and/or abiotic stress of a plant can involve multiple genes acting additively or in synergy (see, for example, in Quesda et al., Plant Physiol. 130:951-063, 2002), the present invention also envisages expressing a plurality of exogenous polynucleotides in a single host plant to thereby 10 achieve superior effect on oil content, yield, growth rate, biomass, vigor and/or abiotic stress tolerance. Expressing a plurality of exogenous polynucleotides in a single host plant can be effected by co-introducing multiple nucleic acid constructs, each including a different exogenous polynucleotide, into a single plant cell. The transformed cell can then be 15 regenerated into a mature plant using the methods described hereinabove. Alternatively, expressing a plurality of exogenous polynucleotides in a single host plant can be effected by co-introducing into a single plant-cell a single nucleic-acid construct including a plurality of different exogenous polynucleotides. Such a construct can be designed with a single promoter sequence which can transcribe a polycistronic 20 messenger RNA including all the different exogenous polynucleotide sequences. To enable co-translation of the different polypeptides encoded by the polycistronic messenger RNA, the polynucleotide sequences can be inter-linked via an internal ribosome entry site (IRES) sequence which facilitates translation of polynucleotide sequences positioned downstream of the IRES sequence. In this case, a transcribed 25 polycistronic RNA molecule encoding the different polypeptides described above will be translated from both the capped 5' end and the two internal IRES sequences of the polycistronic RNA molecule to thereby produce in the cell all different polypeptides. Alternatively, the construct can include several promoter sequences each linked to a different exogenous polynucleotide sequence. 30 The plant cell transformed with the construct including a plurality of different exogenous polynucleotides, can be regenerated into a mature plant, using the methods described hereinabove.
WO 2013/128448 PCT/IL2013/050172 58 Alternatively, expressing a plurality of exogenous polynucleotides in a single host plant can be effected by introducing different nucleic acid constructs, including different exogenous polynucleotides, into a plurality of plants. The regenerated transformed plants can then be cross-bred and resultant progeny selected for superior 5 abiotic stress tolerance, water use efficiency, fertilizer use efficiency, growth, biomass, yield and/or vigor traits, using conventional plant breeding techniques. According to some embodiments of the invention, the method further comprising growing the plant expressing the exogenous polynucleotide under the abiotic stress. 10 Non-limiting examples of abiotic stress conditions include, salinity, osmotic stress, drought, water deprivation, excess of water (e.g., flood, waterlogging), etiolation, low temperature (e.g., cold stress), high temperature, heavy metal toxicity, anaerobiosis, nutrient deficiency, nutrient excess, atmospheric pollution and UV irradiation. According to some embodiments of the invention, the method further 15 comprising growing the plant expressing the exogenous polynucleotide under fertilizer limiting conditions (e.g., nitrogen-limiting conditions). Non-limiting examples include growing the plant on soils with low nitrogen content (40-50% Nitrogen of the content present under normal or optimal conditions), or even under sever nitrogen deficiency (0-10% Nitrogen of the content present under normal or optimal conditions). 20 Thus, the invention encompasses plants exogenously expressing the polynucleotide(s), the nucleic acid constructs and/or polypeptide(s) of the invention. Once expressed within the plant cell or the entire plant, the level of the polypeptide encoded by the exogenous polynucleotide can be determined by methods well known in the art such as, activity assays, Western blots using antibodies capable of 25 specifically binding the polypeptide, Enzyme-Linked Immuno Sorbent Assay (ELISA), radio-immuno-assays (RIA), immunohistochemistry, immunocytochemistry, immunofluorescence and the like. Methods of determining the level in the plant of the RNA transcribed from the exogenous polynucleotide are well known in the art and include, for example, Northern 30 blot analysis, reverse transcription polymerase chain reaction (RT-PCR) analysis (including quantitative, semi-quantitative or real-time RT-PCR) and RNA-in situ hybridization.
WO 2013/128448 PCT/IL2013/050172 59 The sequence information and annotations uncovered by the present teachings can be harnessed in favor of classical breeding. Thus, sub-sequence data of those polynucleotides described above, can be used as markers for marker assisted selection (MAS), in which a marker is used for indirect selection of a genetic determinant or 5 determinants of a trait of interest (e.g., biomass, growth rate, oil content, yield, abiotic stress tolerance, water use efficiency, nitrogen use efficiency and/or fertilizer use efficiency). Nucleic acid data of the present teachings (DNA or RNA sequence) may contain or be linked to polymorphic sites or genetic markers on the genome such as restriction fragment length polymorphism (RFLP), microsatellites and single nucleotide 10 polymorphism (SNP), DNA fingerprinting (DFP), amplified fragment length polymorphism (AFLP), expression level polymorphism, polymorphism of the encoded polypeptide and any other polymorphism at the DNA or RNA sequence. Examples of marker assisted selections include, but are not limited to, selection for a morphological trait (e.g., a gene that affects form, coloration, male sterility or 15 resistance such as the presence or absence of awn, leaf sheath coloration, height, grain color, aroma of rice); selection for a biochemical trait (e.g., a gene that encodes a protein that can be extracted and observed; for example, isozymes and storage proteins); selection for a biological trait (e.g., pathogen races or insect biotypes based on host pathogen or host parasite interaction can be used as a marker since the genetic 20 constitution of an organism can affect its susceptibility to pathogens or parasites). The polynucleotides and polypeptides described hereinabove can be used in a wide range of economical plants, in a safe and cost effective manner. Plant lines exogenously expressing the polynucleotide or the polypeptide of the invention are screened to identify those that show the greatest increase of the desired 25 plant trait. Thus, according to an additional embodiment of the present invention, there is provided a method of evaluating a trait of a plant, the method comprising: (a) expressing in a plant or a portion thereof the nucleic acid construct of some embodiments of the invention; and (b) evaluating a trait of a plant as compared to a wild 30 type plant of the same type (e.g., a plant not transformed with the claimed biomolecules); thereby evaluating the trait of the plant. According to an aspect of some embodiments of the invention there is provided WO 2013/128448 PCT/IL2013/050172 60 a method of producing a crop comprising growing a crop of a plant expressing an exogenous polynucleotide comprising a nucleic acid sequence encoding a polypeptide at least about 80 %, at least about 81 %, at least about 82 %, at least about 83 %, at least about 84 %, at least about 85 %, at least about 86 %, at least about 87 %, at least about 5 88 %, at least about 89 %, at least about 90 %, at least about 91 %, at least about 92 %, at least about 93 %, at least about 94 %, at least about 95 %, at least about 96 %, at least about 97 %, at least about 98 %, at least about 99 %, or more say 100 % homologous (e.g., identical) to the amino acid sequence selected from the group consisting of SEQ ID NOs: 362-601, 2429-4085 and 4086, wherein the plant is derived from a plant 10 selected for increased yield, increased growth rate, increased biomass, increased vigor, increased fiber yield, increased fiber quality, increased fertilizer use efficiency (e.g., nitrogen use efficiency), increased oil content, and/or increased abiotic stress tolerance as compared to a control plant, thereby producing the crop. According to an aspect of some embodiments of the invention there is provided 15 a method of producing a crop comprising growing a crop of a plant expressing an exogenous polynucleotide which comprises a nucleic acid sequence which is at least about 80 %, at least about 81 %, at least about 82 %, at least about 83 %, at least about 84 %, at least about 85 %, at least about 86 %, at least about 87 %, at least about 88 %, at least about 89 %, at least about 90 %, at least about 91 %, at least about 92 %, at least 20 about 93 %, at least about 93 %, at least about 94 %, at least about 95 %, at least about 96 %, at least about 97 %, at least about 98 %, at least about 99 %, e.g., 100 % identical to the nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1-36 1, 602-2427 and 2428 wherein the plant is derived from a plant selected for increased yield, increased growth rate, increased biomass, increased vigor, increased fiber yield, 25 increased fiber quality, increased fertilizer use efficiency (e.g., nitrogen use efficiency), increased oil content, and/or increased abiotic stress tolerance as compared to a control plant, thereby producing the crop. According to an aspect of some embodiments of the invention there is provided a method of growing a crop comprising seeding seeds and/or planting plantlets of a plant 30 transformed with the exogenous polynucleotide of the invention, e.g., the polynucleotide which encodes the polypeptide of some embodiments of the invention, wherein the plant is derived from plants selected for at least one trait selected from the group consisting of: WO 2013/128448 PCT/IL2013/050172 61 increased yield, increased fiber yield or quality, increased oil content, increased biomass, increased growth rate, increased vigor, abiotic stress tolerance, and/or increased nitrogen use efficiency, as compared to a non-transformed plant. According to some embodiments of the invention the method of growing a crop 5 comprising seeding seeds and/or planting plantlets of a plant transformed with an exogenous polynucleotide comprising a nucleic acid sequence encoding a polypeptide at least about 80 %, at least about 81 %, at least about 82 %, at least about 83 %, at least about 84 %, at least about 85 %, at least about 86 %, at least about 87 %, at least about 88 %, at least about 89 %, at least about 90 %, at least about 91 %, at least about 92 %, 10 at least about 93 %, at least about 93 %, at least about 94 %, at least about 95 %, at least about 96 %, at least about 97 %, at least about 98 %, at least about 99 %, e.g., 100 % identical to SEQ ID NO: 362-601, 2429-4085 or 4086, wherein the plant is derived from plants selected for at least one trait selected from the group consisting of increased yield, increased fiber yield or quality, increased biomass, increased oil content, increased 15 growth rate, increased vigor, abiotic stress tolerance, and/or increased nitrogen use efficiency as compared to a non-transformed plant, thereby growing the crop. According to some embodiments of the invention the method of growing a crop comprising seeding seeds and/or planting plantlets of a plant transformed with an exogenous polynucleotide comprising the nucleic acid sequence at least about 80 %, at 20 least about 81 %, at least about 82 %, at least about 83 %, at least about 84 %, at least about 85 %, at least about 86 %, at least about 87 %, at least about 88 %, at least about 89 %, at least about 90 %, at least about 91 %, at least about 92 %, at least about 93 %, at least about 93 %, at least about 94 %, at least about 95 %, at least about 96 %, at least about 97 %, at least about 98 %, at least about 99 %, e.g., 100 % identical to SEQ ID 25 NO: 1-361, 602-2427 or 2428, wherein the plant is derived from plants selected for at least one trait selected from the group consisting of increased yield, increased fiber yield or quality, increased biomass, increased growth rate, increased vigor, increased oil content, increased abiotic stress tolerance, and/or increased nitrogen use efficiency as compared to a non-transformed plant, thereby growing the crop. 30 The effect of the transgene (the exogenous polynucleotide encoding the polypeptide) on abiotic stress tolerance can be determined using known methods such as detailed below and in the Examples section which follows.
WO 2013/128448 PCT/IL2013/050172 62 Abiotic stress tolerance - Transformed (i.e., expressing the transgene) and non transformed (wild type) plants are exposed to an abiotic stress condition, such as water deprivation, suboptimal temperature (low temperature, high temperature), nutrient deficiency, nutrient excess, a salt stress condition, osmotic stress, heavy metal toxicity, 5 anaerobiosis, atmospheric pollution and UV irradiation. Salinity tolerance assay - Transgenic plants with tolerance to high salt concentrations are expected to exhibit better germination, seedling vigor or growth in high salt. Salt stress can be effected in many ways such as, for example, by irrigating the plants with a hyperosmotic solution, by cultivating the plants hydroponically in a 10 hyperosmotic growth solution (e.g., Hoagland solution), or by culturing the plants in a hyperosmotic growth medium [e.g., 50 % Murashige-Skoog medium (MS medium)]. Since different plants vary considerably in their tolerance to salinity, the salt concentration in the irrigation water, growth solution, or growth medium can be adjusted according to the specific characteristics of the specific plant cultivar or variety, 15 so as to inflict a mild or moderate effect on the physiology and/or morphology of the plants (for guidelines as to appropriate concentration see, Bernstein and Kafkafi, Root Growth Under Salinity Stress In: Plant Roots, The Hidden Half 3rd ed. Waisel Y, Eshel A and Kafkafi U. (editors) Marcel Dekker Inc., New York, 2002, and reference therein). For example, a salinity tolerance test can be performed by irrigating plants at 20 different developmental stages with increasing concentrations of sodium chloride (for example 50 mM, 100 mM, 200 mM, 400 mM NaCl) applied from the bottom and from above to ensure even dispersal of salt. Following exposure to the stress condition the plants are frequently monitored until substantial physiological and/or morphological effects appear in wild type plants. Thus, the external phenotypic appearance, degree of 25 wilting and overall success to reach maturity and yield progeny are compared between control and transgenic plants. Quantitative parameters of tolerance measured include, but are not limited to, the average wet and dry weight, growth rate, leaf size, leaf coverage (overall leaf area), the weight of the seeds yielded, the average seed size and the number of seeds produced 30 per plant. Transformed plants not exhibiting substantial physiological and/or morphological effects, or exhibiting higher biomass than wild-type plants, are identified as abiotic stress tolerant plants.
WO 2013/128448 PCT/IL2013/050172 63 Osmotic tolerance test - Osmotic stress assays (including sodium chloride and mannitol assays) are conducted to determine if an osmotic stress phenotype was sodium chloride-specific or if it was a general osmotic stress related phenotype. Plants which are tolerant to osmotic stress may have more tolerance to drought and/or freezing. For 5 salt and osmotic stress germination experiments, the medium is supplemented for example with 50 mM, 100 mM, 200 mM NaCl or 100 mM, 200 mM NaCl, 400 mM mannitol. Drought tolerance assay/Osmoticum assay - Tolerance to drought is performed to identify the genes conferring better plant survival after acute water deprivation. To 10 analyze whether the transgenic plants are more tolerant to drought, an osmotic stress produced by the non-ionic osmolyte sorbitol in the medium can be performed. Control and transgenic plants are germinated and grown in plant-agar plates for 4 days, after which they are transferred to plates containing 500 mM sorbitol. The treatment causes growth retardation, then both control and transgenic plants are compared, by measuring 15 plant weight (wet and dry), yield, and by growth rates measured as time to flowering. Conversely, soil-based drought screens are performed with plants overexpressing the polynucleotides detailed above. Seeds from control Arabidopsis plants, or other transgenic plants overexpressing the polypeptide of the invention are germinated and transferred to pots. Drought stress is obtained after irrigation is ceased 20 accompanied by placing the pots on absorbent paper to enhance the soil-drying rate. Transgenic and control plants are compared to each other when the majority of the control plants develop severe wilting. Plants are re-watered after obtaining a significant fraction of the control plants displaying a severe wilting. Plants are ranked comparing to controls for each of two criteria: tolerance to the drought conditions and recovery 25 (survival) following re-watering. Cold stress tolerance - To analyze cold stress, mature (25 day old) plants are transferred to 4 'C chambers for 1 or 2 weeks, with constitutive light. Later on plants are moved back to greenhouse. Two weeks later damages from chilling period, resulting in growth retardation and other phenotypes, are compared between both 30 control and transgenic plants, by measuring plant weight (wet and dry), and by comparing growth rates measured as time to flowering, plant size, yield, and the like.
WO 2013/128448 PCT/IL2013/050172 64 Heat stress tolerance - Heat stress tolerance is achieved by exposing the plants to temperatures above 34 'C for a certain period. Plant tolerance is examined after transferring the plants back to 22 'C for recovery and evaluation after 5 days relative to internal controls (non-transgenic plants) or plants not exposed to neither cold or heat 5 stress. Water use efficiency - can be determined as the biomass produced per unit transpiration. To analyze WUE, leaf relative water content can be measured in control and transgenic plants. Fresh weight (FW) is immediately recorded; then leaves are soaked for 8 hours in distilled water at room temperature in the dark, and the turgid 10 weight (TW) is recorded. Total dry weight (DW) is recorded after drying the leaves at 60 'C to a constant weight. Relative water content (RWC) is calculated according to the following Formula I: Formula I RWC = [(FW - DW) / (TW - DW)] x 100 15 Fertilizer use efficiency - To analyze whether the transgenic plants are more responsive to fertilizers, plants are grown in agar plates or pots with a limited amount of fertilizer, as described, for example, in Yanagisawa et al (Proc Natl Acad Sci U S A. 2004; 101:7833-8). The plants are analyzed for their overall size, time to flowering, yield, protein content of shoot and/or grain. The parameters checked are the overall size 20 of the mature plant, its wet and dry weight, the weight of the seeds yielded, the average seed size and the number of seeds produced per plant. Other parameters that may be tested are: the chlorophyll content of leaves (as nitrogen plant status and the degree of leaf verdure is highly correlated), amino acid and the total protein content of the seeds or other plant parts such as leaves or shoots, oil content, etc. Similarly, instead of 25 providing nitrogen at limiting amounts, phosphate or potassium can be added at increasing concentrations. Again, the same parameters measured are the same as listed above. In this way, nitrogen use efficiency (NUE), phosphate use efficiency (PUE) and potassium use efficiency (KUE) are assessed, checking the ability of the transgenic plants to thrive under nutrient restraining conditions. 30 Nitrogen use efficiency - To analyze whether the transgenic plants (e.g., Arabidopsis plants) are more responsive to nitrogen, plant are grown in 0.75-3 mM (nitrogen deficient conditions) or 6-10 mM (optimal nitrogen concentration). Plants are WO 2013/128448 PCT/IL2013/050172 65 allowed to grow for additional 25 days or until seed production. The plants are then analyzed for their overall size, time to flowering, yield, protein content of shoot and/or grain/ seed production. The parameters checked can be the overall size of the plant, wet and dry weight, the weight of the seeds yielded, the average seed size and the number of 5 seeds produced per plant. Other parameters that may be tested are: the chlorophyll content of leaves (as nitrogen plant status and the degree of leaf greenness is highly correlated), amino acid and the total protein content of the seeds or other plant parts such as leaves or shoots and oil content. Transformed plants not exhibiting substantial physiological and/or morphological effects, or exhibiting higher measured parameters 10 levels than wild-type plants, are identified as nitrogen use efficient plants. Nitrogen Use efficiency assay using plantlets - The assay is done according to Yanagisawa-S. et al. with minor modifications ("Metabolic engineering with DofI transcription factor in plants: Improved nitrogen assimilation and growth under low nitrogen conditions" Proc. Natl. Acad. Sci. USA 101, 7833-7838). Briefly, transgenic 15 plants which are grown for 7-10 days in 0.5 x MS [Murashige-Skoog] supplemented with a selection agent are transferred to two nitrogen-limiting conditions: MS media in which the combined nitrogen concentration (NH 4
NO
3 and KNO 3 ) was 0.75 mM (nitrogen deficient conditions) or 6-15 mM (optimal nitrogen concentration). Plants are allowed to grow for additional 30-40 days and then photographed, individually removed 20 from the Agar (the shoot without the roots) and immediately weighed (fresh weight) for later statistical analysis. Constructs for which only TI seeds are available are sown on selective media and at least 20 seedlings (each one representing an independent transformation event) are carefully transferred to the nitrogen-limiting media. For constructs for which T2 seeds are available, different transformation events are 25 analyzed. Usually, 20 randomly selected plants from each event are transferred to the nitrogen-limiting media allowed to grow for 3-4 additional weeks and individually weighed at the end of that period. Transgenic plants are compared to control plants grown in parallel under the same conditions. Mock- transgenic plants expressing the uidA reporter gene (GUS) under the same promoter or transgenic plants carrying the 30 same promoter but lacking a reporter gene are used as control. Nitrogen determination - The procedure for N (nitrogen) concentration determination in the structural parts of the plants involves the potassium persulfate WO 2013/128448 PCT/IL2013/050172 66 digestion method to convert organic N to NO3- (Purcell and King 1996 Argon. J. 88:111-113, the modified Cd- mediated reduction of NO3- to N0 2 (Vodovotz 1996 Biotechniques 20:390-394) and the measurement of nitrite by the Griess assay (Vodovotz 1996, supra). The absorbance values are measured at 550 nm against a 5 standard curve of NaNO 2 . The procedure is described in details in Samonte et al. 2006 Agron. J. 98:168-176. Germination tests - Germination tests compare the percentage of seeds from transgenic plants that could complete the germination process to the percentage of seeds from control plants that are treated in the same manner. Normal conditions are 10 considered for example, incubations at 22 'C under 22-hour light 2-hour dark daily cycles. Evaluation of germination and seedling vigor is conducted between 4 and 14 days after planting. The basal media is 50 % MS medium (Murashige and Skoog, 1962 Plant Physiology 15, 473-497). Germination is checked also at unfavorable conditions such as cold (incubating 15 at temperatures lower than 10 'C instead of 22 C) or using seed inhibition solutions that contain high concentrations of an osmolyte such as sorbitol (at concentrations of 50 mM, 100 mM, 200 mM, 300 mM, 500 mM, and up to 1000 mM) or applying increasing concentrations of salt (of 50 mM, 100 mM, 200 mM, 300 mM, 500 mM NaCl). The effect of the transgene on plant's vigor, growth rate, biomass, yield and/or 20 oil content can be determined using known methods. Plant vigor - The plant vigor can be calculated by the increase in growth parameters such as leaf area, fiber length, rosette diameter, plant fresh weight and the like per time. Growth rate - The growth rate can be measured using digital analysis of 25 growing plants. For example, images of plants growing in greenhouse on plot basis can be captured every 3 days and the rosette area can be calculated by digital analysis. Rosette area growth is calculated using the difference of rosette area between days of sampling divided by the difference in days between samples. Evaluation of growth rate can be done by measuring plant biomass produced, 30 rosette area, leaf size or root length per time (can be measured in cm 2 per day of leaf area). Relative growth area can be calculated using Formula II.
WO 2013/128448 PCT/IL2013/050172 67 Formula II: Growth rate area = Regression coefficient of area along time course. Thus, the growth rate area is in units of 1/day and length growth rate is in units of 1/day. 5 Seed yield - Evaluation of the seed yield per plant can be done by measuring the amount (weight or size) or quantity (i.e., number) of dry seeds produced and harvested from 8-16 plants and divided by the number of plants. For example, the total seeds from 8-16 plants can be collected, weighted using e.g., an analytical balance and the total weight can be divided by the number of plants. 10 Seed yield per growing area can be calculated in the same manner while taking into account the growing area given to a single plant. Increase seed yield per growing area could be achieved by increasing seed yield per plant, and/or by increasing number of plants capable of growing in a given area. In addition, seed yield can be determined via the weight of 1000 seeds. The 15 weight of 1000 seeds can be determined as follows: seeds are scattered on a glass tray and a picture is taken. Each sample is weighted and then using the digital analysis, the number of seeds in each sample is calculated. The 1000 seeds weight can be calculated using formula III: Formula III: 20 1000 Seed Weight = number of seed in sample/ sample weight X 1000 The Harvest Index can be calculated using Formula IV Formula IV: Harvest Index = Average seed yield per plant/ Average dry weight Grain protein concentration - Grain protein content (g grain protein m- 2 ) is 25 estimated as the product of the mass of grain N (g grain N m-2) multiplied by the N/protein conversion ratio of k-5.13 (Mosse 1990, supra). The grain protein concentration is estimated as the ratio of grain protein content per unit mass of the grain (g grain protein kg- 1 grain). Fiber length - Fiber length can be measured using fibrograph. The fibrograph 30 system was used to compute length in terms of "Upper Half Mean" length. The upper half mean (UHM) is the average length of longer half of the fiber distribution. The fibrograph measures length in span lengths at a given percentage point (Hypertext WO 2013/128448 PCT/IL2013/050172 68 Transfer Protocol://World Wide Web (dot) cottoninc (dot) com/ClassificationofCotton/ Pg=4#Length). According to some embodiments of the invention, increased yield of corn may be manifested as one or more of the following: increase in the number of plants per 5 growing area, increase in the number of ears per plant, increase in the number of rows per ear, number of kernels per ear row, kernel weight, thousand kernel weight (1000 weight), ear length/diameter, increase oil content per kernel and increase starch content per kernel. As mentioned, the increase of plant yield can be determined by various 10 parameters. For example, increased yield of rice may be manifested by an increase in one or more of the following: number of plants per growing area, number of panicles per plant, number of spikelets per panicle, number of flowers per panicle, increase in the seed filling rate, increase in thousand kernel weight (1000-weight), increase oil content per seed, increase starch content per seed, among others. An increase in yield may also 15 result in modified architecture, or may occur because of modified architecture. Similarly, increased yield of soybean may be manifested by an increase in one or more of the following: number of plants per growing area, number of pods per plant, number of seeds per pod, increase in the seed filling rate, increase in thousand seed weight (1000-weight), reduce pod shattering, increase oil content per seed, increase 20 protein content per seed, among others. An increase in yield may also result in modified architecture, or may occur because of modified architecture. Increased yield of canola may be manifested by an increase in one or more of the following: number of plants per growing area, number of pods per plant, number of seeds per pod, increase in the seed filling rate, increase in thousand seed weight (1000 25 weight), reduce pod shattering, increase oil content per seed, among others. An increase in yield may also result in modified architecture, or may occur because of modified architecture. Increased yield of cotton may be manifested by an increase in one or more of the following: number of plants per growing area, number of bolls per plant, number of 30 seeds per boll, increase in the seed filling rate, increase in thousand seed weight (1000 weight), increase oil content per seed, improve fiber length, fiber strength, among WO 2013/128448 PCT/IL2013/050172 69 others. An increase in yield may also result in modified architecture, or may occur because of modified architecture. Oil content - The oil content of a plant can be determined by extraction of the oil from the seed or the vegetative portion of the plant. Briefly, lipids (oil) can be removed 5 from the plant (e.g., seed) by grinding the plant tissue in the presence of specific solvents (e.g., hexane or petroleum ether) and extracting the oil in a continuous extractor. Indirect oil content analysis can be carried out using various known methods such as Nuclear Magnetic Resonance (NMR) Spectroscopy, which measures the resonance energy absorbed by hydrogen atoms in the liquid state of the sample [See for 10 example, Conway TF. and Earle FR., 1963, Journal of the American Oil Chemists' Society; Springer Berlin / Heidelberg, ISSN: 0003-021X (Print) 1558-9331 (Online)]; the Near Infrared (NI) Spectroscopy, which utilizes the absorption of near infrared energy (1100-2500 nm) by the sample; and a method described in WO/2001/023884, which is based on extracting oil a solvent, evaporating the solvent in a gas stream which 15 forms oil particles, and directing a light into the gas stream and oil particles which forms a detectable reflected light. Thus, the present invention is of high agricultural value for promoting the yield of commercially desired crops (e.g., biomass of vegetative organ such as poplar wood, or reproductive organ such as number of seeds or seed biomass). 20 Any of the transgenic plants described hereinabove or parts thereof may be processed to produce a feed, meal, protein or oil preparation, such as for ruminant animals. The transgenic plants described hereinabove, which exhibit an increased oil content can be used to produce plant oil (by extracting the oil from the plant). 25 The plant oil (including the seed oil and/or the vegetative portion oil) produced according to the method of the invention may be combined with a variety of other ingredients. The specific ingredients included in a product are determined according to the intended use. Exemplary products include animal feed, raw material for chemical modification, biodegradable plastic, blended food product, edible oil, biofuel, cooking 30 oil, lubricant, biodiesel, snack food, cosmetics, and fermentation process raw material. Exemplary products to be incorporated to the plant oil include animal feeds, human food products such as extruded snack foods, breads, as a food binding agent, WO 2013/128448 PCT/IL2013/050172 70 aquaculture feeds, fermentable mixtures, food supplements, sport drinks, nutritional food bars, multi-vitamin supplements, diet drinks, and cereal foods. According to some embodiments of the invention, the oil comprises a seed oil. According to some embodiments of the invention, the oil comprises a vegetative 5 portion oil (oil of the vegetative portion of the plant). According to some embodiments of the invention, the plant cell forms a part of a plant. According to another embodiment of the present invention, there is provided a food or feed comprising the plants or a portion thereof of the present invention. 10 As used herein the term "about" refers to ± 10 %. The terms "comprises", "comprising", "includes", "including", "having" and their conjugates mean "including but not limited to". The term "consisting of' means "including and limited to". The term "consisting essentially of" means that the composition, method or 15 structure may include additional ingredients, steps and/or parts, but only if the additional ingredients, steps and/or parts do not materially alter the basic and novel characteristics of the claimed composition, method or structure. As used herein, the singular form "a", "an" and "the" include plural references unless the context clearly dictates otherwise. For example, the term "a compound" or "at 20 least one compound" may include a plurality of compounds, including mixtures thereof. Throughout this application, various embodiments of this invention may be presented in a range format. It should be understood that the description in range format is merely for convenience and brevity and should not be construed as an inflexible limitation on the scope of the invention. Accordingly, the description of a range should 25 be considered to have specifically disclosed all the possible subranges as well as individual numerical values within that range. For example, description of a range such as from 1 to 6 should be considered to have specifically disclosed subranges such as from I to 3, from I to 4, from I to 5, from 2 to 4, from 2 to 6, from 3 to 6 etc., as well as individual numbers within that range, for example, 1, 2, 3, 4, 5, and 6. This applies 30 regardless of the breadth of the range. Whenever a numerical range is indicated herein, it is meant to include any cited numeral (fractional or integral) within the indicated range. The phrases "ranging/ranges WO 2013/128448 PCT/IL2013/050172 71 between" a first indicate number and a second indicate number and "ranging/ranges from" a first indicate number "to" a second indicate number are used herein interchangeably and are meant to include the first and second indicated numbers and all the fractional and integral numerals therebetween. 5 As used herein the term "method" refers to manners, means, techniques and procedures for accomplishing a given task including, but not limited to, those manners, means, techniques and procedures either known to, or readily developed from known manners, means, techniques and procedures by practitioners of the chemical, pharmacological, biological, biochemical and medical arts. 10 It is appreciated that certain features of the invention, which are, for clarity, described in the context of separate embodiments, may also be provided in combination in a single embodiment. Conversely, various features of the invention, which are, for brevity, described in the context of a single embodiment, may also be provided 15 separately or in any suitable subcombination or as suitable in any other described embodiment of the invention. Certain features described in the context of various embodiments are not to be considered essential features of those embodiments, unless the embodiment is inoperative without those elements. Various embodiments and aspects of the present invention as delineated 20 hereinabove and as claimed in the claims section below find experimental support in the following examples. EXAMPLES Reference is now made to the following examples, which together with the 25 above descriptions illustrate some embodiments of the invention in a non limiting fashion. Generally, the nomenclature used herein and the laboratory procedures utilized in the present invention include molecular, biochemical, microbiological and recombinant DNA techniques. Such techniques are thoroughly explained in the 30 literature. See, for example, "Molecular Cloning: A laboratory Manual" Sambrook et al., (1989); "Current Protocols in Molecular Biology" Volumes I-III Ausubel, R. M., ed. (1994); Ausubel et al., "Current Protocols in Molecular Biology", John Wiley and Sons, WO 2013/128448 PCT/IL2013/050172 72 Baltimore, Maryland (1989); Perbal, "A Practical Guide to Molecular Cloning", John Wiley & Sons, New York (1988); Watson et al., "Recombinant DNA", Scientific American Books, New York; Birren et al. (eds) "Genome Analysis: A Laboratory Manual Series", Vols. 1-4, Cold Spring Harbor Laboratory Press, New York (1998); 5 methodologies as set forth in U.S. Pat. Nos. 4,666,828; 4,683,202; 4,801,531; 5,192,659 and 5,272,057; "Cell Biology: A Laboratory Handbook", Volumes I-III Cellis, J. E., ed. (1994); "Current Protocols in Immunology" Volumes I-III Coligan J. E., ed. (1994); Stites et al. (eds), "Basic and Clinical Immunology" (8th Edition), Appleton & Lange, Norwalk, CT (1994); Mishell and Shiigi (eds), "Selected Methods in Cellular 10 Immunology", W. H. Freeman and Co., New York (1980); available immunoassays are extensively described in the patent and scientific literature, see, for example, U.S. Pat. Nos. 3,791,932; 3,839,153; 3,850,752; 3,850,578; 3,853,987; 3,867,517; 3,879,262; 3,901,654; 3,935,074; 3,984,533; 3,996,345; 4,034,074; 4,098,876; 4,879,219; 5,011,771 and 5,281,521; "Oligonucleotide Synthesis" Gait, M. J., ed. (1984); "Nucleic 15 Acid Hybridization" Hames, B. D., and Higgins S. J., eds. (1985); "Transcription and Translation" Hames, B. D., and Higgins S. J., Eds. (1984); "Animal Cell Culture" Freshney, R. I., ed. (1986); "Immobilized Cells and Enzymes" IRL Press, (1986); "A Practical Guide to Molecular Cloning" Perbal, B., (1984) and "Methods in Enzymology" Vol. 1-317, Academic Press; "PCR Protocols: A Guide To Methods And 20 Applications", Academic Press, San Diego, CA (1990); Marshak et al., "Strategies for Protein Purification and Characterization - A Laboratory Course Manual" CSHL Press (1996); all of which are incorporated by reference as if fully set forth herein. Other general references are provided throughout this document. The procedures therein are believed to be well known in the art and are provided for the convenience of the reader. 25 All the information contained therein is incorporated herein by reference. GENERAL EXPERIMENTAL AND BIOINFORMATICS METHODS RNA extraction - Tissues growing at various growth conditions (as described below) were sampled and RNA was extracted using TRIzol Reagent from Invitrogen 30 [Hypertext Transfer Protocol://World Wide Web (dot) invitrogen (dot) com/content (dot)cfm pageid=469]. Approximately 30-50 mg of tissue was taken from samples. The weighed tissues were ground using pestle and mortar in liquid nitrogen and resuspended WO 2013/128448 PCT/IL2013/050172 73 in 500 pl of TRIzol Reagent. To the homogenized lysate, 100 tl of chloroform was added followed by precipitation using isopropanol and two washes with 75 % ethanol. The RNA was eluted in 30 tl of RNase-free water. RNA samples were cleaned up using Qiagen's RNeasy minikit clean-up protocol as per the manufacturer's protocol 5 (QIAGEN Inc, CA USA). For convenience, each micro-array expression information tissue type has received an expression Set ID. Correlation analysis - was performed for selected genes according to some embodiments of the invention, in which the characterized parameters (measured parameters according to the correlation IDs) were used as "x axis" for correlation with 10 the tissue transcriptome which was used as the "Y axis". For each gene and measured parameter a correlation coefficient "R" was calculated (using Pearson correlation) along with a p-value for the significance of the correlation. When the correlation coefficient (R) between the levels of a gene's expression in a certain tissue and a phenotypic performance across ecotypes/variety/hybrid is high in absolute value (between 0.5-1), 15 there is an association between the gene (specifically the expression level of this gene) the phenotypic characteristic (e.g., improved nitrogen use efficiency, abiotic stress tolerance, yield, growth rate and the like). EXAMPLE 1 20 IDENTIFICATION OF GENES AND PREDICTED ROLE USING BIOINFORMATICS TOOLS The present inventors have identified polynucleotides which can increase plant yield, seed yield, oil yield, oil content, biomass, growth rate, fiber yield and/or quality, abiotic stress tolerance, nitrogen use efficiency and/or vigor of a plant, as follows. 25 The nucleotide sequence datasets used here were from publicly available databases or from sequences obtained using the Solexa technology (e.g. Barley and Sorghum). Sequence data from 100 different plant species was introduced into a single, comprehensive database. Other information on gene expression, protein annotation, enzymes and pathways were also incorporated. Major databases used include: 30 Genomes Arabidopsis genome [TAIR genome version 8 (Hypertext Transfer Protocol://World Wide Web (dot) arabidopsis (dot) org/)]; WO 2013/128448 PCT/IL2013/050172 74 Rice genome [build 6.0 (Hypertext Transfer Protocol:!! http://rice (dot) plantbiology(dot)msu(dot)edu/index.shtml]; Poplar [Populus trichocarpa release 1.1 from JGI (assembly release v1.0) (Hypertext Transfer Protocol://World Wide Web (dot) genome (dot) jgi-psf (dot) org/)]; 5 Brachypodium [JGI 4x assembly, Hypertext Transfer Protocol://World Wide Web (dot) brachypodium (dot) org)]; Soybean [DOE-JGI SCP, version Glymal (Hypertext Transfer Protocol://World Wide Web (dot) phytozome (dot) net/)]; Grape [French-Italian Public Consortium for Grapevine Genome 10 Characterization grapevine genome (Hypertext Transfer Protocol:// World Wide Web (dot) genoscope (dot) cns (dot) fr /)]; Castobean [TIGR/J Craig Venter Institute 4x assembly [(Hypertext Transfer Protocol://msc (dot) jcvi (dot) org/r communis]; Sorghum [DOE-JGI SCP, version Sbil [Hypertext Transfer Protocol://World 15 Wide Web (dot) phytozome (dot) net/)]; Partially assembled genome of Maize [Hypertext Transfer Protocol://maizesequence (dot) org/]; Expressed EST and mRNA sequences were extracted from the following databases: 20 EST and RNA sequences from NCBI (Hypertext Transfer Protocol://World Wide Web (dot) ncbi (dot) nlm (dot) nih (dot) gov/dbEST/); RefSeq (Hypertext Transfer Protocol://World Wide Web (dot) ncbi (dot) nlm (dot) nih (dot) gov/RefSeq/); TAIR (Hypertext Transfer Protocol://World Wide Web (dot) arabidopsis (dot) 25 org/); Protein and pathway databases Uniprot [Hypertext Transfer Protocol://World Wide Web (dot) uniprot (dot) org/]. AraCyc [Hypertext Transfer Protocol://World Wide Web (dot) arabidopsis (dot) 30 org/biocyc/index (dot) jsp]. ENZYME [Hypertext Transfer Protocol://expasy (dot) org/enzyme/].
WO 2013/128448 PCT/IL2013/050172 75 Microarray datasets were downloaded from: GEO (Hypertext Transfer Protocol://World Wide Web.ncbi.nlm.nih.gov/geo/) TAIR (Hypertext Transfer Protocol://World Wide Web. arabidopsis. org/). Proprietary microarray data (See W02008/122980) and Examples 2-9 below. 5 QTL and SNPs information Gramene [Hypertext Transfer Protocol://World Wide Web (dot) gramene (dot) org/qtl/]. Panzea [Hypertext Transfer Protocol://World Wide Web (dot) panzea (dot) org/index (dot) html]. 10 Database Assembly - was performed to build a wide, rich, reliable annotated and easy to analyze database comprised of publicly available genomic mRNA, ESTs DNA sequences, data from various crops as well as gene expression, protein annotation and pathway data QTLs, and other relevant information. Database assembly is comprised of a toolbox of gene refining, structuring, 15 annotation and analysis tools enabling to construct a tailored database for each gene discovery project. Gene refining and structuring tools enable to reliably detect splice variants and antisense transcripts, generating understanding of various potential phenotypic outcomes of a single gene. The capabilities of the "LEADS" platform of Compugen LTD for analyzing human genome have been confirmed and accepted by the 20 scientific community [see e.g., "Widespread Antisense Transcription", Yelin, et al. (2003) Nature Biotechnology 21, 379-85; "Splicing of Alu Sequences", Lev-Maor, et al. (2003) Science 300 (5623), 1288-91; "Computational analysis of alternative splicing using EST tissue information", Xie H et al. Genomics 2002], and have been proven most efficient in plant genomics as well. 25 EST clustering and gene assembly - For gene clustering and assembly of organisms with available genome sequence data (arabidopsis, rice, castorbean, grape, brachypodium, poplar, soybean, sorghum) the genomic LEADS version (GANG) was employed. This tool allows most accurate clustering of ESTs and mRNA sequences on genome, and predicts gene structure as well as alternative splicing events and anti-sense 30 transcription. For organisms with no available full genome sequence data, "expressed LEADS" clustering software was applied.
WO 2013/128448 PCT/IL2013/050172 76 Gene annotation - Predicted genes and proteins were annotated as follows: Blast search [Hypertext Transfer Protocol://blast (dot) ncbi (dot) nlm (dot) nih (dot) gov /Blast (dot) cgi] against all plant UniProt [Hypertext Transfer Protocol://World Wide Web (dot) uniprot (dot) org/] sequences was performed. Open 5 reading frames of each putative transcript were analyzed and longest ORF with higher number of homologues was selected as predicted protein of the transcript. The predicted proteins were analyzed by InterPro [Hypertext Transfer Protocol://World Wide Web (dot) ebi (dot) ac (dot) uk/interpro/]. Blast against proteins from AraCyc and ENZYME databases was used to map 10 the predicted transcripts to AraCyc pathways. Predicted proteins from different species were compared using blast algorithm [Hypertext Transfer Protocol://World Wide Web (dot) ncbi (dot) nlm (dot) nih (dot) gov /Blast (dot) cgi] to validate the accuracy of the predicted protein sequence, and for efficient detection of orthologs. 15 Gene expression profiling - Several data sources were exploited for gene expression profiling which combined microarray data and digital expression profile (see below). According to gene expression profile, a correlation analysis was performed to identify genes which are co-regulated under different developmental stages and environmental conditions and which are associated with different phenotypes. 20 Publicly available microarray datasets were downloaded from TAIR and NCBI GEO sites, renormalized, and integrated into the database. Expression profiling is one of the most important resource data for identifying genes important for yield, biomass, growth rate, vigor, oil content, abiotic stress tolerance of plants and nitrogen use efficieny. 25 A digital expression profile summary was compiled for each cluster according to all keywords included in the sequence records comprising the cluster. Digital expression, also known as electronic Northern Blot, is a tool that displays virtual expression profile based on the EST sequences forming the gene cluster. The tool provides the expression profile of a cluster in terms of plant anatomy (e.g., the 30 tissue/organ in which the gene is expressed), developmental stage (e.g., the developmental stages at which a gene can be found/expressed) and profile of treatment (provides the physiological conditions under which a gene is expressed such as drought, WO 2013/128448 PCT/IL2013/050172 77 cold, pathogen infection, etc). Given a random distribution of ESTs in the different clusters, the digital expression provides a probability value that describes the probability of a cluster having a total of N ESTs to contain X ESTs from a certain collection of libraries. For the probability calculations, the following is taken into consideration: a) 5 the number of ESTs in the cluster, b) the number of ESTs of the implicated and related libraries, c) the overall number of ESTs available representing the species. Thereby clusters with low probability values are highly enriched with ESTs from the group of libraries of interest indicating a specialized expression. Recently, the accuracy of this system was demonstrated by Portnoy et al., 2009 10 (Analysis Of The Melon Fruit Transcriptome Based On 454 Pyrosequencing) in: Plant & Animal Genomes XVII Conference, San Diego, CA. Transcriptomic analysis, based on relative EST abundance in data was performed by 454 pyrosequencing of cDNA representing mRNA of the melon fruit. Fourteen double strand cDNA samples obtained from two genotypes, two fruit tissues (flesh and rind) and four developmental stages 15 were sequenced. GS FLX pyrosequencing (Roche/454 Life Sciences) of non normalized and purified cDNA samples yielded 1,150,657 expressed sequence tags that assembled into 67,477 unigenes (32,357 singletons and 35,120 contigs). Analysis of the data obtained against the Cucurbit Genomics Database [Hypertext Transfer Protocol://World Wide Web (dot) icugi (dot) org/] confirmed the accuracy of the 20 sequencing and assembly. Expression patterns of selected genes fitted well their qRT PCR data. EXAMPLE 2 PRODUCTION OF ARABIDOPSIS TRANSCRIPTOME AND HIGH 25 THROUGHPUT CORRELATION ANALYSIS OF YIELD, BIOMASS AND/OR VIGOR RELATED PARAMETERS USING 44KARABIDOPSIS FULL GENOME OLIGONUCLEOTIDE MICRO-ARRAY To produce a high throughput correlation analysis, the present inventors utilized an Arabidopsis thaliana oligonucleotide micro-array, produced by Agilent Technologies 30 [Hypertext Transfer Protocol://World Wide Web (dot) chem. (dot) agilent (dot) com/Scripts/PDS (dot) asp lPage=50879]. The array oligonucleotide represents about 40,000 A. thaliana genes and transcripts designed based on data from the TIGR ATHI WO 2013/128448 PCT/IL2013/050172 78 v.5 database and Arabidopsis MPSS (University of Delaware) databases. To define correlations between the levels of RNA expression and yield, biomass components or vigor related parameters, various plant characteristics of 15 different Arabidopsis ecotypes were analyzed. Among them, nine ecotypes encompassing the observed 5 variance were selected for RNA expression analysis. The correlation between the RNA levels and the characterized parameters was analyzed using Pearson correlation test [Hypertext Transfer Protocol://World Wide Web (dot) davidmlane (dot) com/hyperstat/A34739 (dot) html]. Experimental procedures 10 Analyzed Arabidopsis tissues - Five tissues at different developmental stages including root, leaf, flower at anthesis, seed at 5 days after flowering (DAF) and seed at 12 DAF, representing different plant characteristics, were sampled and RNA was extracted as described hereinabove under "GENERAL EXPERIMENTAL AND BIOINFORMATICS METHODS". For convenience, each micro-array expression 15 information tissue type has received a Set ID as summarized in Table 1 below. Table 1 Tissues used for Arabidopsis transcriptome expression sets Expression Set Set ID Leaf 1 Root 2 Seed 5DAF 3 Flower at anthesis 4 Seed 12DAF 5 20 Table 1: Provided are the identification (ID) digits of each of the Arabidopsis expression sets (1-5). DAF = days after flowering. Yield components and vigor related parameters assessment - Eight out of the nine Arabidopsis ecotypes were used in each of 5 repetitive blocks (named A, B, C, D 25 and E), each containing 20 plants per plot. The plants were grown in a greenhouse at controlled conditions in 22'C, and the N:P:K fertilizer (20:20:20; weight ratios) [nitrogen (N), phosphorus (P) and potassium (K)] was added. During this time data was collected, documented and analyzed. Additional data was collected through the seedling stage of plants grown in a tissue culture in vertical grown transparent agar 30 plates. Most of chosen parameters were analyzed by digital imaging.
WO 2013/128448 PCT/IL2013/050172 79 Digital imaging in Tissue culture - A laboratory image acquisition system was used for capturing images of plantlets sawn in square agar plates. The image acquisition system consists of a digital reflex camera (Canon EOS 300D) attached to a 55 mm focal length lens (Canon EF-S series), mounted on a reproduction device (Kaiser RS), which 5 included 4 light units (4x150 Watts light bulb) and located in a darkroom. Digital imaging in Greenhouse - The image capturing process was repeated every 3-4 days starting at day 7 till day 30. The same camera attached to a 24 mm focal length lens (Canon EF series), placed in a custom made iron mount, was used for capturing images of larger plants sawn in white tubs in an environmental controlled 10 greenhouse. The white tubs were square shape with measurements of 36 x 26.2 cm and 7.5 cm deep. During the capture process, the tubs were placed beneath the iron mount, while avoiding direct sun light and casting of shadows. This process was repeated every 3-4 days for up to 30 days. An image analysis system was used, which consists of a personal desktop 15 computer (Intel P4 3.0 GHz processor) and a public domain program - ImageJ 1.37, Java based image processing program, which was developed at the U.S National Institutes of Health and is freely available on the internet at Hypertext Transfer Protocol://rsbweb (dot) nih (dot) gov/. Images were captured in resolution of 6 Mega Pixels (3072 x 2048 pixels) and stored in a low compression JPEG (Joint Photographic 20 Experts Group standard) format. Next, analyzed data was saved to text files and processed using the JMP statistical analysis software (SAS institute). Leaf analysis - Using the digital analysis leaves data was calculated, including leaf number, area, perimeter, length and width. On day 30, 3-4 representative plants were chosen from each plot of blocks A, B and C. The plants were dissected, each leaf 25 was separated and was introduced between two glass trays, a photo of each plant was taken and the various parameters (such as leaf total area, laminar length etc.) were calculated from the images. The blade circularity was calculated as laminar width divided by laminar length. Root analysis - During 17 days, the different ecotypes were grown in 30 transparent agar plates. The plates were photographed every 3 days starting at day 7 in the photography room and the roots development was documented (see examples in Figures 3A-F). The growth rate of roots was calculated according to Formula V.
WO 2013/128448 PCT/IL2013/050172 80 Formula V: Growth rate of root coverage = Regression coefficient of root coverage along time course. Vegetative growth rate analysis - was calculated according to Formula VI. The 5 analysis was ended with the appearance of overlapping plants. Formula VI Vegetative growth rate area = Regression coefficient of vegetative area along time course. For comparison between ecotypes the calculated rate was normalized using plant 10 developmental stage as represented by the number of true leaves. In cases where plants with 8 leaves had been sampled twice (for example at day 10 and day 13), only the largest sample was chosen and added to the Anova comparison. Seeds in siliques analysis - On day 70, 15-17 siliques were collected from each plot in blocks D and E. The chosen siliques were light brown color but still intact. The 15 siliques were opened in the photography room and the seeds were scatter on a glass tray, a high resolution digital picture was taken for each plot. Using the images the number of seeds per silique was determined. Seeds average weight - At the end of the experiment all seeds from plots of blocks A-C were collected. An average weight of 0.02 grams was measured from each 20 sample, the seeds were scattered on a glass tray and a picture was taken. Using the digital analysis, the number of seeds in each sample was calculated. Oil percentage in seeds - At the end of the experiment all seeds from plots of blocks A-C were collected. Columbia seeds from 3 plots were mixed grounded and then mounted onto the extraction chamber. 210 ml of n-Hexane (Cat No. 080951 Biolab 25 Ltd.) were used as the solvent. The extraction was performed for 30 hours at medium heat 50'C. Once the extraction has ended the n-Hexane was evaporated using the evaporator at 35'C and vacuum conditions. The process was repeated twice. The information gained from the Soxhlet extractor (Soxhlet, F. Die gewichtsanalytische Bestimmung des Milchfettes, Polytechnisches J. (Dingler's) 1879, 232, 461) was used to 30 create a calibration curve for the Low Resonance NMR. The content of oil of all seed samples was determined using the Low Resonance NMR (MARAN Ultra- Oxford Instrument) and its MultiQuant sowftware package.
WO 2013/128448 PCT/IL2013/050172 81 Silique length analysis - On day 50 from sowing, 30 siliques from different plants in each plot were sampled in block A. The chosen siliques were green-yellow in color and were collected from the bottom parts of a grown plant's stem. A digital photograph was taken to determine silique's length. 5 Dry weight and seed yield - On day 80 from sowing, the plants from blocks A-C were harvested and left to dry at 30'C in a drying chamber. The biomass and seed weight of each plot was separated, measured and divided by the number of plants. Dry weight = total weight of the vegetative portion above ground (excluding roots) after drying at 30'C in a drying chamber; Seed yield per plant = total seed weight per plant 10 (gr). Oil yield - The oil yield was calculated using Formula VII. Formula VII: Seed Oil yield = Seed yield per plant (gr.) * Oil % in seed. Harvest Index (seed) - The harvest index was calculated using Formula IV 15 (described above): Harvest Index = Average seed yield per plant/ Average dry weight. Experimental Results Nine different Arabidopsis ecotypes were grown and characterized for 18 parameters (named as vectors). 20 Table 2 Arabidopsis correlated parameters (vectors) Correlated parameter with Correlation ID Seeds per silique (number) 1 Harvest Index (value) 2 seed yield per plant (gr) 3 Dry matter per plant (gr) 4 Total Leaf Area per plant (cm 2 ) 5 Oil % per seed (percent) 6 Oil yield per plant (mg) 7 relative root growth (cm/day) 8 root length day 7 (cm) 9 root length day 13 (cm) 10 fresh weight (gr) 11 seed weight (gr) 12 Vegetative growth rate (cm 2 /day) 13 Lamina length (cm) 14 Lamina width(cm) 15 Leaf width/length (ratio) 16 Blade circularity 17 WO 2013/128448 PCT/IL2013/050172 82 Correlated parameter with Correlation ID Silique length (cm) 18 Table 2.Provided are the Arabidopsis correlated parameters (correlation ID Nos. 1-18). Abbreviations: Cm = centimeter(s); gr = gram(s); mg = milligram(s). The characterized values are summarized in Table 3 below. 5 Table 3 Measured parameters in Arabidopsis ecotypes Trait Line-i Line-2 Line-3 Line-4 Line-5 Line-6 Line-7 Line-8 Line-9 1 45.44 53.47 58.47 35.27 48.56 37.00 39.38 40.53 25.53 2 0.53 0.35 0.56 0.33 0.37 0.32 0.45 0.51 0.41 3 0.34 0.44 0.59 0.42 0.61 0.43 0.36 0.62 0.55 4 0.64 1.27 1.05 1.28 1.69 1.34 0.81 1.21 1.35 5 46.86 109.89 58.36 56.80 114.66 110.82 88.49 121.79 93.04 6 34.42 31.19 38.05 27.76 35.49 32.91 31.56 30.79 34.02 7 118.63 138.73 224.06 116.26 218.27 142.11 114.15 190.06 187.62 8 0.63 0.66 1.18 1.09 0.91 0.77 0.61 0.70 0.78 9 0.94 1.76 0.70 0.73 0.99 1.16 1.28 1.41 1.25 10 4.42 8.53 5.62 4.83 5.96 6.37 5.65 7.06 7.04 11 1.51 3.61 1.94 2.08 3.56 4.34 3.47 3.48 3.71 12 0.02 0.02 0.03 0.03 0.02 0.03 0.02 0.02 0.02 13 0.31 0.38 0.48 0.47 0.43 0.64 0.43 0.38 0.47 14 2.77 3.54 3.27 3.78 3.69 4.60 3.88 3.72 4.15 15 1.38 1.70 1.46 1.37 1.83 1.65 1.51 1.82 1.67 16 0.35 0.29 0.32 0.26 0.36 0.27 0.30 0.34 0.31 17 0.51 0.48 0.45 0.37 0.50 0.38 0.39 0.49 0.41 18 1.06 1.26 1.31 1.47 1.24 1.09 1.18 1.18 1.00 Table 3. Provided are the values of each of the parameters measured in Arabidopsis 10 ecotypes: 3 = Seed yield per plant (gram); 7= oil yield per plant (mg); 6 = oil % per seed; 12 = 1000 seed weight (gr); 4 = dry matter per plant (gr); 2 = harvest index; 5 = total leaf area per plant (cm); 1 = seeds per silique; 18 = Silique length (cm); 13 = Vegetative growth rate (cm 2 /day) until 8 true leaves; 8 = relative root growth (cm/day) (day 13); 9 = Root length day 7 (cm); 10 = Root length day 13 (cm); 11 = fresh weight per plant (gr.) at bolting stage; 14. = 15 Lamina length (cm); 15 = Lamina width (cm); 16 = Leaf width/length; 17 = Blade circularity. Table 4 Correlation between the expression level of selected genes of some embodiments of the 20 invention in various tissues and the phenotypic performance under normal conditions across Arabidopsis accessions Gene Set Corr. Gene Set Corr. Name R P value ID Set Name R P value ID Set ID ID LYD521 0.85 1.65E-02 2 3 LYD521 0.81 2.73E-02 2 6 LYD521 0.89 6.63E-03 2 7 LYD521 0.84 1.88E-02 2 8 LYD522 0.76 2.72E-02 5 5 LYD522 0.75 3.22E-02 5 14 LYD522 0.83 1.02E-02 5 11 LYD522 0.71 5.02E-02 5 13 LYD524 0.70 5.28E-02 3 3 LYD525 0.84 8.98E-03 1 18 WO 2013/128448 PCT/IL2013/050172 83 GeeSt Corr. GeeStCorr. GNe R P value St Set Gene R P value St Set ID ID LYD525 0.86 6.06E-03 5 2 LYD526 0.72 4.42E-02 3 3 LYD526 0.76 2.90E-02 3 8 LYD526 0.71 5.06E-02 5 3 LYD526 0.74 3.61E-02 5 7 LYD526 0.75 3.09E-02 5 8 LYD527 0.75 5.37E-02 2 16 LYD527 0.73 3.81E-02 5 1 LYD527 0.72 4.43E-02 5 8 LYD528 0.70 7.84E-02 2 15 LYD528 0.76 4.65E-02 2 5 LYD529 0.80 1.69E-02 1 16 LYD529 0.76 4.77E-02 2 2 LYD529 0.77 2.48E-02 3 15 LYD529 0.71 4.92E-02 3 5 LYD529 0.78 2.21E-02 3 3 LYD529 0.71 5.06E-02 5 2 LYD529 0.74 3.74E-02 4 2 LYD530 0.71 4.99E-02 1 10 LYD530 0.72 6.54E-02 2 1 LYD530 0.78 3.97E-02 2 18 LYD530 0.84 1.92E-02 2 8 LYD530 0.75 3.35E-02 3 1 LYD530 0.73 3.78E-02 5 1 LYD530 0.88 3.71E-03 4 1 LYD531 0.70 7.71E-02 2 9 LYD531 0.72 4.55E-02 5 6 LYD531 0.70 5.19E-02 5 7 LYD533 0.77 4.43E-02 2 17 LYD533 0.73 4.13E-02 5 15 LYD533 0.74 3.63E-02 4 1 LYD533 0.80 1.66E-02 4 17 LYD534 0.78 2.38E-02 1 10 LYD534 0.87 1.01E-02 2 3 LYD534 0.85 1.47E-02 2 7 LYD534 0.70 7.86E-02 2 8 LYD534 0.74 3.65E-02 3 15 LYD534 0.77 2.53E-02 3 3 LYD534 0.74 3.49E-02 3 7 LYD534 0.74 3.65E-02 5 18 LYD534 0.71 4.97E-02 5 8 LYD535 0.82 1.33E-02 1 1 LYD535 0.85 7.25E-03 3 8 LYD535 0.89 3.39E-03 5 14 LYD535 0.72 4.50E-02 5 13 LYD536 0.74 3.58E-02 3 6 LYD536 0.74 3.70E-02 5 8 LYD536 0.85 7.90E-03 4 8 Table 4. Provided are the corelations (R) between the expression levels of yield improving genes and their homologues in tissues [leaf, flower, seed and root; Expression sets (Exp)] and the phenotypic performance in various yield, biomass, growth rate and/or vigor components [Correlation vector (corr.)] under stress conditions or normal conditions across 5 Arabidopsis accessions. P = p value. EXAMPLE 3 PRODUCTION OF ARABIDOPSIS TRANSCRIPTOME AND HIGH THROUGHPUT CORRELATION ANALYSIS OF NORMAL AND NITROGEN LIMITING CONDITIONS USING 44K ARABIDOPSIS OLIGONUCLEOTIDE 10 MICRO-ARRAY In order to produce a high throughput correlation analysis, the present inventors utilized an Arabidopsis oligonucleotide micro-array, produced by Agilent Technologies [Hypertext Transfer Protocol://World Wide Web (dot) chem (dot) agilent (dot) com/Scripts/PDS (dot) asp lPage=50879]. The array oligonucleotide represents about 15 44,000 Arabidopsis genes and transcripts. To define correlations between the levels of RNA expression with NUE, yield components or vigor related parameters various plant WO 2013/128448 PCT/IL2013/050172 84 characteristics of 14 different Arabidopsis ecotypes were analyzed. Among them, ten ecotypes encompassing the observed variance were selected for RNA expression analysis. The correlation between the RNA levels and the characterized parameters was analyzed using Pearson correlation test [Hypertext Transfer Protocol://World Wide Web 5 (dot) davidmlane (dot) com/hyperstat/A34739 (dot) html]. Experimental procedures Two tissues of plants [leaves and stems] growing at two different nitrogen fertilization levels (1.5 mM Nitrogen or 6 mM Nitrogen) were sampled and RNA was extracted as described hereinabove under "GENERAL EXPERIMENTAL AND 10 BIOINFORMATICS METHODS". For convenience, each micro-array expression information tissue type has received a Set ID as summarized in Table 5 below. Table 5 Tissues used for Arabidopsis transcriptome expression sets Expression Set Set ID Leaves at 1.5 mM Nitrogen fertilization 1 Stems at 6 mM Nitrogen fertilization 2 Leaves at 6 mM Nitrogen fertilization 3 Stems at 1.5 mM Nitrogen fertilization 4 15 Table 5: Provided are the identification (ID) digits of each of the Arabidopsis expression sets. Assessment of Arabidopsis yield components and vigor related parameters under different nitrogen fertilization levels - 10 Arabidopsis accessions in 2 repetitive 20 plots each containing 8 plants per plot were grown at greenhouse. The growing protocol used was as follows: surface sterilized seeds were sown in Eppendorf tubes containing 0.5 x Murashige-Skoog basal salt medium and grown at 23'C under 12-hour light and 12-hour dark daily cycles for 10 days. Then, seedlings of similar size were carefully transferred to pots filled with a mix of perlite and peat in a 1:1 ratio. Constant nitrogen 25 limiting conditions were achieved by irrigating the plants with a solution containing 1.5 mM inorganic nitrogen in the form of KNO 3 , supplemented with 2 mM CaCl 2 , 1.25 mM
KH
2
PO
4 , 1.50 mM MgSO 4 , 5 mM KCl, 0.01 mM H 3 B0 3 and microelements, while normal irrigation conditions (Normal Nitrogen conditions) was achieved by applying a solution of 6 mM inorganic nitrogen also in the form of KNO 3 , supplemented with 2 30 mM CaCl 2 , 1.25 mM KH 2
PO
4 , 1.50 mM MgSO 4 , 0.01 mM H 3 B0 3 and microelements. To follow plant growth, trays were photographed the day nitrogen limiting conditions WO 2013/128448 PCT/IL2013/050172 85 were initiated and subsequently every 3 days for about 15 additional days. Rosette plant area was then determined from the digital pictures. ImageJ software was used for quantifying the plant size from the digital pictures [Hypertext Transfer Protocol://rsb (dot) info (dot) nih (dot) gov/ij/] utilizing proprietary scripts designed to analyze the size 5 of rosette area from individual plants as a function of time. The image analysis system included a personal desktop computer (Intel P4 3.0 GHz processor) and a public domain program - ImageJ 1.37 (Java based image processing program, which was developed at the U.S. National Institutes of Health and freely available on the internet [Hypertext Transfer Protocol://rsbweb (dot) nih (dot) gov/]. Next, analyzed data was saved to text 10 files and processed using the JMP statistical analysis software (SAS institute). Data parameters collected are summarized in Table 6, herein below. Table 6 Arabidopsis correlated parameters (vectors) 15 Correlated parameter with Correlation ID N 6 mlM; Seed Yield [gr./plant] 1 N 6 mM; Harvest Index 2 N 6 mM; 1000 Seeds weight [gr.] 3 N 6 mM; seed yield/ rosette area day at day 10 [gr./cm 2 ] 4 N 6 mM; seed yield/leaf blade area [gr./cm 2 ] 5 N 1.5 mM; Rosette Area at day 8 [cm 2 ] 6 N 1.5 mM; Rosette Area at day 10 [cm 2 ] 7 N 1.5 mM; Leaf Number at day 10 8 N 1.5 mM; Leaf Blade Area at day 10 [cm 2 ] 9 N 1.5 mM; RGR of Rosette Area at day 3 [cm 2 /day] 10 N 1.5 mM; t50 Flowering [day] 11 N 1.5 mM; Dry Weight [gr./plant] 12 N 1.5 mM; Seed Yield [gr./plant] 13 N 1.5 mM; Harvest Index 14 N 1.5 mM; 1000 Seeds weight [gr.] 15 N 1.5 mM; seed yield/ rosette area at day 10 [gr./cm 2 ] 16 N 1.5 mM; seed yield/leaf blade area [gr./cm 2 ] 17 N 1.5 mM; % Seed yield reduction compared to N 6 mM 18 N 1.5 mM; % Biomass reduction compared to N 6 mM 19 N 6 mM; Rosette Area at day 8 [cm 2 ] 20 N 6 mM; Rosette Area at day 10 [cm 2 ] 21 N 6 mM; Leaf Number at day 10 22 N 6 mM; Leaf Blade Area at day 10 23 N 6 mM; RGR of Rosette Area at day 3 [cm 2 /gr.] 24 N 6 mM; t50 Flowering [day] 25 N 6 mM; Dry Weight [gr./plant] 26 N 6 mM; N level /DW (SPAD unit/gr. plant) 27 WO 2013/128448 PCT/IL2013/050172 86 Correlated parameter with Correlation ID N 6 mM; DW/ N level [gr./ SPAD unit] 28 N 6 mM; N level / FW 29 N 6 mM; Seed yield/N unit [gr./ SPAD unit] 30 N 1.5 mM; N level /FW [SPAD unit/gr.] 31 N 1.5 mM; N level /DW [SPAD unit/gr.] 32 N 1.5 mM; DW/ N level [gr/ SPAD unit] 33 N 1.5 mM; seed yield/ N level [gr/ SPAD unit] 34 Table 6. Provided are the Arabidopsis correlated parameters (vectors). "N" = Nitrogen at the noted concentrations; "gr." = grams; "SPAD" = chlorophyll levels; "t50" = time where 50% of plants flowered; "gr./ SPAD unit" = plant biomass expressed in grams per unit of nitrogen in plant measured by SPAD. "DW" = Plant Dry Weight; "FW" = Plant Fresh weight; 5 "N level /DW" = plant Nitrogen level measured in SPAD unit per plant biomass [gr.]; "DW/ N level" = plant biomass per plant [gr.]/SPAD unit; Rosette Area (measured using digital analysis); Plot Coverage at the indicated day [%](calculated by the dividing the total plant area with the total plot area); Leaf Blade Area at the indicated day [cm 2 ] (measured using digital analysis); RGR (relative growth rate) of Rosette Area at the indicated day [cm 2 /day]; t50 10 Flowering [day[ (the day in which 50% of plant flower); seed yield/ rosette area at day 10 [gr/cm 2 ] (calculated); seed yield/leaf blade [gr/cm 2 ] (calculated); seed yield/ N level [gr/ SPAD unit] (calculated). Assessment of NUE, yield components and vigor-related parameters - Ten 15 Arabidopsis ecotypes were grown in trays, each containing 8 plants per plot, in a greenhouse with controlled temperature conditions for about 12 weeks. Plants were irrigated with different nitrogen concentration as described above depending on the treatment applied. During this time, data was collected documented and analyzed. Most of chosen parameters were analyzed by digital imaging. 20 Digital imaging - Greenhouse assay An image acquisition system, which consists of a digital reflex camera (Canon EOS 400D) attached with a 55 mm focal length lens (Canon EF-S series) placed in a custom made Aluminum mount, was used for capturing images of plants planted in containers within an environmental controlled greenhouse. The image capturing process 25 is repeated every 2-3 days starting at day 9-12 till day 16-19 (respectively) from transplanting. The image processing system which was used is described in Example 4 above. Images were captured in resolution of 10 Mega Pixels (3888x2592 pixels) and stored in a low compression JPEG (Joint Photographic Experts Group standard) format. Next, 30 image processing output data was saved to text files and analyzed using the JMP statistical analysis software (SAS institute).
WO 2013/128448 PCT/IL2013/050172 87 Leaf analysis - Using the digital analysis leaves data was calculated, including leaf number, leaf blade area, plot coverage, Rosette diameter and Rosette area. Relative growth rate area: The relative growth rate area of the rosette and the leaves was calculated according to Formulas VIII and IX, respectively. 5 Formula VIII: Growth rate of rosette area = Regression coefficient of rosette area along time course. Formula IX Growth rate of plant leaf number = Regression coefficient of plant leaf number 10 along time course. Seed yield and 1000 seeds weight - At the end of the experiment all seeds from all plots were collected and weighed in order to measure seed yield per plant in terms of total seed weight per plant (gr.). For the calculation of 1000 seed weight, an average weight of 0.02 grams was measured from each sample, the seeds were scattered on a 15 glass tray and a picture was taken. Using the digital analysis, the number of seeds in each sample was calculated. Dry weight and seed yield - At the end of the experiment, plant were harvested and left to dry at 30'C in a drying chamber. The biomass was separated from the seeds, weighed and divided by the number of plants. Dry weight = total weight of the 20 vegetative portion above ground (excluding roots) after drying at 30'C in a drying chamber. Harvest Index (seed) - The harvest index was calculated using Formula IV as described above [Harvest Index = Average seed yield per plant/ Average dry weight]. Tso days to flowering - Each of the repeats was monitored for flowering date. 25 Days of flowering was calculated from sowing date till 50 % of the plots flowered. Plant nitrogen level - The chlorophyll content of leaves is a good indicator of the nitrogen plant status since the degree of leaf greenness is highly correlated to this parameter. Chlorophyll content was determined using a Minolta SPAD 502 chlorophyll meter and measurement was performed at time of flowering. SPAD meter readings 30 were done on young fully developed leaf. Three measurements per leaf were taken per plot. Based on this measurement, parameters such as the ratio between seed yield per nitrogen unit [seed yield/N level = seed yield per plant [gr.]/SPAD unit], plant DW per WO 2013/128448 PCT/IL2013/050172 88 nitrogen unit [DW/ N level= plant biomass per plant [gr.]/SPAD unit], and nitrogen level per gram of biomass [N level/DW= SPAD unit/ plant biomass per plant (gr.)] were calculated. Percent of seed yield reduction- measures the amount of seeds obtained in 5 plants when grown under nitrogen-limiting conditions compared to seed yield produced at normal nitrogen levels expressed in percentages (%). Experimental Results 10 different Arabidopsis accessions (ecotypes) were grown and characterized for 37 parameters as described above. The average for each of the measured parameters was 10 calculated using the JMP software (Table 7 below). Subsequent correlation analysis between the various transcriptome sets (Table 5) and the average parameters were conducted. Table 7 Measured parameters in Arabidopsis accessions 15 Ecotypel Line-i Line- Line-3 Line-4 Line- Line-6 Line- Line- Line-9 Line Treatment 2 5 7 8 10 1 0.12 0.17 0.11 0.08 0.12 0.14 0.11 0.14 0.09 0.07 2 0.28 0.31 0.28 0.16 0.21 0.28 0.17 0.21 0.17 0.14 3 0.01 0.02 0.02 0.01 0.02 0.02 0.01 0.02 0.02 0.02 4 0.08 0.11 0.04 0.03 0.06 0.06 0.06 0.05 0.06 0.03 5 0.34 0.53 0.21 0.18 0.28 0.28 0.25 0.27 0.24 0.16 6 0.76 0.71 1.06 1.16 1.00 0.91 0.94 1.12 0.64 1.00 7 1.43 1.33 1.77 1.97 1.83 1.82 1.64 2.00 1.15 1.75 8 6.88 7.31 7.31 7.88 7.75 7.63 7.19 8.63 5.93 7.94 9 0.33 0.27 0.37 0.39 0.37 0.39 0.35 0.38 0.31 0.37 10 0.63 0.79 0.50 0.49 0.72 0.83 0.65 0.67 0.64 0.61 11 15.97 20.97 14.84 24.71 23.70 18.06 19.49 23.57 21.89 23.57 12 0.16 0.12 0.08 0.11 0.12 0.13 0.11 0.15 0.17 0.18 13 0.03 0.03 0.02 0.01 0.01 0.03 0.02 0.01 0.01 0.01 14 0.19 0.20 0.29 0.08 0.07 0.24 0.18 0.08 0.08 0.03 15 0.02 0.02 0.02 0.01 0.02 0.01 0.01 0.02 0.02 0.02 16 0.02 0.02 0.01 0.01 0.00 0.02 0.01 0.01 0.01 0.00 17 0.09 0.09 0.06 0.03 0.02 0.08 0.06 0.03 0.04 0.01 18 72.56 84.70 78.78 88.00 92.62 76.71 81.94 91.30 85.76 91.82 19 60.75 76.71 78.56 78.14 78.64 73.19 83.07 77.19 70.12 62.97 20 0.76 0.86 1.48 1.28 1.10 1.24 1.09 1.41 0.89 1.22 21 1.41 1.57 2.67 2.42 2.14 2.47 1.97 2.72 1.64 2.21 22 6.25 7.31 8.06 8.75 8.75 8.38 7.13 9.44 6.31 8.06 23 0.34 0.31 0.52 0.45 0.43 0.50 0.43 0.51 0.41 0.43 24 0.69 1.02 0.61 0.60 0.65 0.68 0.58 0.61 0.52 0.48 25 16.37 20.50 14.63 24.00 23.60 15.03 19.75 22.89 18.80 23.38 26 0.42 0.53 0.38 0.52 0.58 0.50 0.63 0.65 0.57 0.50 WO 2013/128448 PCT/IL2013/050172 89 Ecotypel Line-i Line- Line-3 Line-4 Line- Line-6 Line- Line- Line-9 Line Treatment 2 5 7 8 10 27 22.49 28.27 33.32 39.00 17.64 28 0.02 0.02 0.02 0.01 0.03 29 53.71 54.62 66.48 68.05 35.55 30 0.00 0.00 0.01 0.00 0.00 31 45.59 42.11 53.11 67.00 28.15 32 167.30 241.06 194.98 169.34 157.82 33 0.01 0.00 0.01 0.01 0.01 34 0.00 0.00 0.00 0.00 0.00 Table 7. Provided are the measured parameters under various treatments in various ecotypes (Arabidopsis accessions). Table 8 5 Correlation between the expression level of selected genes of some embodiments of the invention in various tissues and the phenotypic performance under normal or abiotic stress conditions across Arabidopsis accessions Gene R P value Exp. Corr. Gene R P value Exp. Corr. Name set Set ID Name set Set ID LYD522 0.72 2.88E-02 2 22 LYD522 0.77 1.50E-02 2 21 LYD522 0.74 2.24E-02 2 7 LYD522 0.70 3.46E-02 2 23 LYD522 0.77 8.54E-03 3 1 LYD524 0.77 9.08E-03 1 2 LYD524 0.74 2.21E-02 2 2 LYD524 0.87 1.19E-03 4 2 LYD524 0.85 2.01E-03 4 1 LYD525 0.80 5.42E-03 1 22 LYD525 0.73 1.60E-02 1 20 LYD525 0.85 1.68E-03 1 6 LYD525 0.75 1.28E-02 1 21 LYD525 0.83 3.18E-03 1 7 LYD525 0.70 3.49E-02 2 3 LYD526 0.75 1.28E-02 1 20 LYD526 0.73 1.70E-02 1 9 LYD526 0.73 1.58E-02 1 23 LYD527 0.71 2.24E-02 1 2 LYD527 0.78 8.40E-03 1 14 LYD527 0.72 1.87E-02 4 14 LYD529 0.72 2.OOE-02 3 19 LYD531 0.72 1.84E-02 1 11 LYD531 0.76 1.16E-02 1 25 LYD531 0.86 1.51E-03 1 18 LYD533 0.77 8.61E-03 1 11 LYD533 0.88 8.25E-04 1 25 LYD533 0.80 5.35E-03 1 18 LYD535 0.72 1.93E-02 3 8 LYD536 0.74 1.46E-02 1 2 LYD536 0.73 1.75E-02 1 16 LYD536 0.88 7.61E-04 1 4 LYD536 0.76 1.04E-02 1 17 LYD536 0.86 1.36E-03 1 5 LYD536 0.82 4.02E-03 1 24 1 1 Table 8. Provided are the correlations (R) between the expression levels of yield 10 improving genes and their homologues in tissues [Leaves or stems; Expression sets (Exp)] and the phenotypic performance in various yield, biomass, growth rate and/or vigor components [Correlation vector (corr.)] under stress conditions or normal conditions across Arabidopsis accessions. P = p value.
WO 2013/128448 PCT/IL2013/050172 90 EXAMPLE 4 PRODUCTION OF TOMATO TRANSCRIPTOME AND HIGH THROUGHPUT CORRELATION ANALYSIS USING 44K TOMATO OLIGONUCLEO TIDE MICRO-ARRAY 5 In order to produce a high throughput correlation analysis between NUE related phenotypes and gene expression, the present inventors utilized a Tomato oligonucleotide micro-array, produced by Agilent Technologies [Hypertext Transfer Protocol://World Wide Web (dot) chem. (dot) agilent (dot) com/Scripts/PDS (dot) asp lPage=50879]. The array oligonucleotide represents about 44,000 Tomato genes 10 and transcripts. In order to define correlations between the levels of RNA expression with NUE, ABST, yield components or vigor related parameters various plant characteristics of 18 different Tomato varieties were analyzed. Among them, 10 varieties encompassing the observed variance were selected for RNA expression analysis. The correlation between the RNA levels and the characterized parameters was 15 analyzed using Pearson correlation test [Hypertext Transfer Protocol://World Wide Web (dot) davidmlane (dot) com/hyperstat/A34739 (dot) html]. Correlation of Tomato varieties across ecotypes grown under low Nitrogen, drought and regular growth conditions Experimental procedures: 20 10 Tomato varieties were grown in 3 repetitive blocks, each containing 6 plants per plot were grown at net house. Briefly, the growing protocol was as follows: 1. Regular growth conditions: Tomato varieties were grown under normal conditions (4-6 Liters/m 2 of water per day and fertilized with NPK as recommended in protocols for commercial tomato production). 25 2. Low Nitrogen fertilization conditions: Tomato varieties were grown under normal conditions (4-6 Liters/m 2 per day and fertilized with NPK as recommended in protocols for commercial tomato production) until flower stage. At this time, Nitrogen fertilization was stopped. 3. Drought stress: Tomato variety was grown under normal conditions (4-6 30 Liters/m 2 per day) until flower stage. At this time, irrigation was reduced to 50 % compared to normal conditions. Plants were phenotyped on a daily basis following the standard descriptor of tomato (Table 10). Harvest was conducted while 50 % of the WO 2013/128448 PCT/IL2013/050172 91 fruits were red (mature). Plants were separated to the vegetative part and fruits, of them, 2 nodes were analyzed for additional inflorescent parameters such as size, number of flowers, and inflorescent weight. Fresh weight of all vegetative material was measured. Fruits were separated to colors (red vs. green) and in accordance with the fruit size 5 (small, medium and large). Next, analyzed data was saved to text files and processed using the JMP statistical analysis software (SAS institute). Data parameters collected are summarized in Tables 11-13, herein below. Analyzed Tomato tissues - Two tissues at different developmental stages [flower and leaf], representing different plant characteristics, were sampled and RNA 10 was extracted as described above. For convenience, each micro-array expression information tissue type has received a Set ID as summarized in Table 9 below. Table 9 Tomato transcriptome expression sets 15 Expression Set Set ID Leaf at reproductive stage under Low N conditions 1+10 Flower under normal conditions 5+2 Leaf at reproductive stage under normal conditions 8+3 Flower under drought conditions 9+7 Leaf at reproductive stage under drought conditions 11+4 Flower under Low N conditions 12+6 Table 9: Provided are the identification (ID) digits of each of the tomato expression sets. Table 10 provides the tomato correlated parameters (Vectors). The average for each of the measured parameter was calculated using the JMP software and values are 20 summarized in Tables 11-13 below. Subsequent correlation analysis was conducted. Results were integrated to the database. Table 10 Tomato correlated parameters (vectors) 25 Correlated parameter with Correlation ID NUE [yield (gr)/SPAD] (Normal) 1 NUpE [biomass (gr)/SPAD] (Normal) 2 HI [yield/yield + biomass] (Normal) (ratio) 3 NUE2 [total biomass (gr)/SPAD] (Normal) 4 Total Leaf Area [cm 2 ] (Normal) 5 Leaflet Length [cm] (Normal) 6 Leaflet Width (Normal) (cm) 7 100 weight green fruit (Normal) (gr) 8 WO 2013/128448 PCT/IL2013/050172 92 Correlated parameter with Correlation ID 100 weight red fruit (Normal) (gr) 9 SLA [leaf area/plant biomass] (Normal) (cm 2 /gr) 10 Yield/total leaf area (Normal) (gr/cm 2 ) 11 Yield/SLA (Normal) gr 2 / cm 2 12 Fruit Yield/Plant (Low N) (gr) 13 FW/Plant (Low N) (gr) 14 Average red fruit weight (Low N) (gr) 15 Fruit yield (Low N)/Fruit yield (Normal) (ratio) 16 FW (Low N)/ FW (Normal) (ratio) 17 SPAD (Low N) (number) 18 RWC (Low N) (percentage) 19 SPAD 100% RWC (NUE) (number) 20 SPAD (Low N)/ SPAD (Normal) (ratio) 21 SPAD 100% RWC (Low N)/ SPAD 100% RWC (Normal) (ratio) 22 RWC (Low N)/ RWC (Normal) (ratio) 23 Number of flowers ((Low N) (number) 24 Weight clusters (flowers) (Low N) (gr) 25 Number of Flowers (Low N)/ Number of Flowers (Normal) 26 (ratio) Cluster Weight (Low N)/ Cluster Weight (Normal) (ratio) 27 RWC Drought (percentage) 28 RWC Drought/ RWC Normal (ratio) 29 Number of flowers (Drought) (number) 30 Weight flower clusters (Drought) (gr) 31 Number of Flower Drought/Normal (number) 32 Number of Flower Drought/ Number of Flower Drought (Low N) 33 (ratio) flower cluster weight (Drought)/ flower cluster weight (Normal) 34 (ratio) flower cluster weight Drought/ flower cluster weight (Low N) 35 (ratio) Fruit Yield/Plant (Drought) (gr) 36 FW/Plant (Drought) (gr) 37 Average red fruit weight Drought (gr) 38 Fruit Yield (Drought)/ Fruit Yield (Normal) (ratio) 39 Fruit (Drought)/ Fruit (Low N) (ratio) 40 FW (drought)/ FW Normal (ratio) 41 red fruit weight (Drought)/ red fruit weight (Normal) (ratio) 42 Fruit yield /Plant (Normal) (gr) 43 FW/Plant (Normal) (gr) 44 average red fruit weight (Normal) (gr) 45 SPAD (Normal) (number) 46 RWC (Normal) (percentage) 47 SPAD 100% RWC (Normal) (number) 48 Number of flowers (Normal) (number) 49 Weight Flower clusters (Normal) (gr) 50 Total Leaf Area [cm 2 ]) (Drought) 51 Leaflet Length [cm]) (Drought) 52 Leaflet Width [cm] (Drought) 53 100 weight green fruit (Drought) (gr) 54 WO 2013/128448 PCT/IL2013/050172 93 Correlated parameter with Correlation ID 100 weight red fruit (Drought) (gr) 55 NUE [yield (gr)/SPAD] (Low N) 56 NUpE [biomass (gr)/SPAD] (Low N) 57 HI [yield/yield + biomass] (Low N) (ratio) 58 NUE2 [total biomass (gr)/SPAD] (Low N) 59 Total Leaf Area [cm 2 ] (Low N) 60 Leaflet Length [cm] (Low N) 61 Leaflet Width (Low N) (cm) 62 100 weight green fruit (Low N) (gr) 63 SLA [leaf area/plant biomass] (Low N) (cm 2 /gr) 64 Yield/total leaf area (Low N) (gr/cm 2 ) 65 Yield/SLA (Low N) (gr 2 / cm 2 ) 66 100 weight red fruit (Low N) (gr) 67 Table 10. Provided are the tomato correlated parameters. "gr." = grams; "FW" = fresh weight; "NUE" = nitrogen use efficiency; "RWC" = relative water content; "NUpE" = nitrogen uptake efficiency; "SPAD" = chlorophyll levels (number); "HI" = harvest index (vegetative weight divided on yield); "SLA" = specific leaf area (leaf area divided by leaf dry weight), 5 Treatment in the parenthesis. Fruit Weight (grams) - At the end of the experiment [when 50 % of the fruits were ripe (red)] all fruits from plots within blocks A-C were collected. The total fruits were counted and weighted. The average fruits weight was calculated by dividing the 10 total fruit weight by the number of fruits. Plant vegetative Weight (grams) - At the end of the experiment [when 50 % of the fruit were ripe (red)] all plants from plots within blocks A-C were collected. Fresh weight was measured (grams). Inflorescence Weight (grams) - At the end of the experiment [when 50 % of the 15 fruits were ripe (red)] two Inflorescence from plots within blocks A-C were collected. The Inflorescence weight (gr.) and number of flowers per inflorescence were counted. SPAD - Chlorophyll content was determined using a Minolta SPAD 502 chlorophyll meter and measurement was performed at time of flowering. SPAD meter readings were done on young fully developed leaf. Three measurements per leaf were 20 taken per plot. Water use efficiency (WUE) - can be determined as the biomass produced per unit transpiration. To analyze WUE, leaf relative water content was measured in control and transgenic plants. Fresh weight (FW) was immediately recorded; then leaves were soaked for 8 hours in distilled water at room temperature in the dark, and 25 the turgid weight (TW) was recorded. Total dry weight (DW) was recorded after drying WO 2013/128448 PCT/IL2013/050172 94 the leaves at 60'C to a constant weight. Relative water content (RWC) was calculated according to the following Formula I [(FW - DW/TW - DW) x 100] as described above. Plants that maintain high relative water content (RWC) compared to control lines were considered more tolerant to drought than those exhibiting reduced relative 5 water content Experimental Results Table 11 Measured parameters in Tomato accessions (lines 1-6) Ecotype/Treatment Line-i Line-2 Line-3 Line-4 Line-5 Line-6 1 0.02 0.01 0.01 0.00 0.01 0.01 2 0.03 0.09 0.05 0.02 0.05 0.05 3 0.35 0.10 0.14 0.12 0.18 0.19 4 0.05 0.09 0.06 0.02 0.06 0.06 5 426.10 582.38 291.40 593.58 6 6.34 7.99 5.59 7.70 7 3.69 4.77 3.43 4.56 8 0.56 3.05 0.24 2.58 9 0.82 2.46 0.50 2.76 10 140.99 689.67 130.22 299.12 11 0.00 0.00 0.00 0.00 12 0.00 0.00 0.00 0.00 13 0.41 0.66 0.48 0.46 1.35 0.35 14 4.04 1.21 2.25 2.54 1.85 3.06 15 0.02 0.19 0.01 0.01 0.10 0.00 16 0.49 1.93 0.97 3.80 2.78 0.78 17 2.65 0.38 0.74 3.01 0.83 1.54 18 38.40 39.40 47.50 37.00 44.60 41.70 19 74.07 99.08 69.49 63.24 77.36 77.91 20 28.47 39.04 33.01 23.42 34.53 32.51 21 0.77 1.06 0.85 0.80 0.93 0.96 22 0.79 1.37 0.92 0.75 1.31 0.97 23 1.02 1.30 1.08 0.94 1.41 1.00 24 19.00 5.33 9.00 13.00 10.67 16.67 25 0.53 0.37 0.31 0.35 0.47 0.25 26 3.35 0.28 1.42 1.70 1.10 2.00 27 0.46 1.07 0.44 0.01 1.08 0.02 28 72.12 74.51 65.33 72.22 66.13 68.33 29 0.99 0.97 1.02 1.08 1.21 0.88 30 16.67 6.50 15.67 20.33 11.67 25.33 31 0.37 0.41 0.33 0.29 0.55 0.31 32 2.94 0.34 2.47 2.65 1.21 3.04 33 0.88 1.22 1.74 1.56 1.09 1.52 34 0.32 1.19 0.47 0.01 1.25 0.03 35 0.69 1.11 1.06 0.82 1.16 1.25 36 0.47 0.48 0.63 0.35 2.04 0.25 37 2.62 1.09 1.85 2.22 2.63 2.71 WO 2013/128448 PCT/IL2013/050172 95 Ecotype/Treatment Line-i Line-2 Line-3 Line-4 Line-5 Line-6 38 0.01 0.19 0.21 0.00 0.10 0.00 39 0.57 1.41 1.27 2.88 4.20 0.55 40 1.15 0.73 1.32 0.76 1.51 0.71 41 1.72 0.34 0.61 2.63 1.18 1.36 42 0.19 24.37 25.38 0.02 20.26 0.04 43 0.83 0.34 0.49 0.12 0.49 0.45 44 1.53 3.17 3.02 0.84 2.24 1.98 45 0.05 0.01 0.01 0.29 0.01 0.05 46 49.70 37.20 55.80 46.40 48.20 43.40 47 72.83 76.47 64.29 67.07 54.79 77.61 48 36.17 28.45 35.89 31.09 26.38 33.68 49 5.67 19.33 6.33 7.67 9.67 8.33 50 1.17 0.34 0.69 56.35 0.44 11.31 51 ND ND ND ND ND ND 52 ND ND ND ND ND ND 53 ND ND ND ND ND ND 54 ND ND ND ND ND ND 55 ND ND ND ND ND ND 56 0.01 0.02 0.01 0.02 0.04 0.01 57 0.14 0.03 0.07 0.11 0.05 0.09 58 0.09 0.35 0.18 0.15 0.42 0.10 59 0.16 0.05 0.08 0.13 0.09 0.11 60 565.93 384.77 294.83 378.00 476.39 197.08 61 6.40 5.92 3.69 5.43 6.95 3.73 62 3.47 1.97 1.79 2.55 3.52 1.73 63 0.87 3.66 0.57 0.37 3.40 0.68 64 140.04 317.12 131.29 148.82 257.51 64.34 65 0.00 0.00 0.00 0.00 0.00 0.00 66 0.00 0.00 0.00 0.00 0.01 0.01 67 1.06 6.87 0.65 0.53 7.17 0.44 Table 11. Provided are the values of each of the parameters (as described above) measured in tomato accessions (Seed ID) under all growth conditions. Growth conditions are specified in the experimental procedure section. 5 Table 12 Measured parameters in Tomato accessions (lines 7-12) Ecotype/Treatment Line-7 Line-8 Line-9 Line-10 Line-i1 Line-12 1 0.01 0.01 0.00 0.01 0.02 0.00 2 0.02 0.04 0.05 0.05 0.05 0.08 3 0.38 0.17 0.06 0.10 0.27 0.05 4 0.03 0.05 0.06 0.06 0.06 0.08 5 947.59 233.35 340.73 339.11 190.14 421.79 6 7.85 6.22 6.16 5.65 4.39 4.44 7 4.44 3.15 3.37 3.13 2.40 2.02 8 6.32 5.75 0.38 0.30 1.95 2.53 9 5.32 5.24 0.61 0.66 2.70 0.70 10 1117.74 111.77 106.29 123.14 104.99 111.88 WO 2013/128448 PCT/IL2013/050172 96 Ecotype/Treatment Line-7 Line-8 Line-9 Line-10 Line-i1 Line-12 11 0.00 0.00 0.00 0.00 0.00 0.00 12 0.00 0.00 0.00 0.00 0.01 0.00 13 0.01 0.51 0.44 0.47 1.59 0.39 14 3.13 2.54 1.84 1.52 1.91 1.86 15 0.01 0.01 0.01 0.01 0.02 0.01 16 0.02 1.16 2.07 1.51 2.41 2.06 17 3.70 1.22 0.58 0.55 1.06 0.49 18 34.40 50.00 44.70 53.70 35.70 58.80 19 80.49 67.40 67.16 66.07 69.57 69.30 20 27.66 33.68 30.04 35.50 24.81 40.77 21 0.80 0.94 0.76 1.05 0.89 1.24 22 1.11 0.95 0.79 0.92 0.94 1.36 23 1.38 1.01 1.04 0.88 1.05 1.10 24 6.00 16.00 15.00 6.00 17.00 13.00 25 0.29 0.47 0.40 0.30 0.82 0.40 26 1.20 1.92 1.50 0.86 1.89 1.63 27 0.37 0.81 0.55 0.36 0.95 0.80 28 78.13 18.46 73.21 62.50 67.21 75.76 29 1.34 0.28 1.13 0.83 1.01 1.20 30 29.73 17.33 14.67 29.67 15.00 10.33 31 0.45 0.56 0.30 0.31 0.31 0.31 32 5.95 2.08 1.47 4.24 1.67 1.29 33 4.96 1.08 0.98 4.94 0.88 0.79 34 0.56 0.96 0.42 0.38 0.36 0.62 35 1.52 1.19 0.76 1.04 0.38 0.78 36 0.05 0.45 0.29 1.02 0.60 0.49 37 3.41 2.11 1.95 1.76 1.72 1.92 38 0.03 0.01 0.01 0.00 0.01 0.01 39 0.09 1.03 1.39 3.28 0.91 2.62 40 5.06 0.89 0.67 2.17 0.38 1.27 41 4.02 1.01 0.61 0.64 0.95 0.51 42 0.15 0.02 0.86 0.74 0.09 1.72 43 0.53 0.44 0.21 0.31 0.66 0.19 44 0.85 2.09 3.21 2.75 1.81 3.77 45 0.23 0.29 0.01 0.01 0.06 0.01 46 42.90 53.30 58.50 51.10 40.00 47.60 47 58.18 66.51 64.71 75.25 66.23 63.21 48 24.98 35.47 37.87 38.43 26.49 30.07 49 5.00 8.33 10.00 7.00 9.00 8.00 50 0.79 0.58 0.73 0.83 0.86 0.50 51 ND ND ND ND ND 337.63 52 ND ND ND ND ND 5.15 53 ND ND ND ND ND 2.55 54 ND ND ND ND ND 0.80 55 ND ND ND ND ND 0.89 56 0.00 0.02 0.01 0.01 0.06 0.01 57 0.11 0.08 0.06 0.04 0.08 0.05 58 0.00 0.17 0.19 0.24 0.45 0.17 59 0.11 0.09 0.08 0.06 0.14 0.06 60 453.24 625.51 748.01 453.96 164.85 338.30 WO 2013/128448 PCT/IL2013/050172 97 Ecotype/Treatment Line-7 Line-8 Line-9 Line-10 Line-i1 Line-12 61 4.39 6.72 6.66 4.39 3.90 5.29 62 1.87 3.54 3.28 2.52 2.61 2.61 63 0.45 0.47 0.54 0.39 0.97 0.91 64 144.60 246.05 405.55 299.32 86.19 182.32 65 0.00 0.00 0.00 0.00 0.01 0.00 66 0.00 0.00 0.00 0.00 0.02 0.00 67 1 0.55 0.75 0.58 1.27 1.34 Table 12. Provided are the values of each of the parameters (as described above) measured in tomato accessions (Seed ID) under all growth conditions. Growth conditions are specified in the experimental procedure section. 5 Table 13 Measured parameters in Tomato accessions (lines 13-18) Ecotype/Treatment Line-13 Line-14 Line-15 Line-16 Line-17 Line-18 1 0.01 0.01 0.01 0.01 0.01 0.00 2 0.03 0.04 0.05 0.03 0.07 0.04 3 0.31 0.12 0.14 0.17 0.09 0.11 4 0.05 0.05 0.06 0.04 0.08 0.04 5 581.33 807.51 784.06 351.80 255.78 1078.10 6 6.77 7.42 6.71 5.87 4.16 10.29 7 3.80 3.74 2.98 3.22 2.09 5.91 8 1.42 2.03 1.39 2.27 0.45 0.42 9 2.64 4.67 2.17 0.49 0.34 0.75 10 307.95 419.37 365.81 212.93 84.94 469.87 11 0.00 0.00 0.00 0.00 0.00 0.00 12 0.00 0.00 0.00 0.00 0.00 0.00 13 0.32 0.45 0.14 0.40 1.44 0.50 14 2.47 2.62 1.08 1.17 0.92 1.09 15 0.01 0.05 0.36 0.04 0.63 16 0.38 1.64 0.41 1.21 4.59 1.70 17 1.31 1.36 0.51 0.71 0.31 0.47 18 47.50 45.20 39.00 45.00 65.30 51.90 19 100.00 57.66 90.79 68.00 59.65 72.17 20 47.47 26.06 35.38 30.60 38.97 37.46 21 0.82 0.94 0.89 0.83 1.57 0.88 22 1.44 1.50 1.05 0.56 1.48 0.84 23 1.76 1.60 1.17 0.68 0.94 0.96 24 8.67 9.33 12.67 6.67 9.33 8.00 25 0.35 0.43 0.35 0.45 0.28 0.47 26 1.63 1.17 1.65 0.74 0.88 0.89 27 0.34 0.61 0.94 0.68 0.40 1.44 28 62.82 70.69 55.75 75.22 63.68 62.31 29 1.11 1.97 0.72 0.75 1.01 0.83 30 18.33 12.00 20.33 12.67 12.67 11.33 31 8.36 0.29 0.34 0.44 0.27 0.43 32 3.44 1.50 2.65 1.41 1.19 1.26 33 2.12 1.29 1.61 1.90 1.36 1.42 34 8.20 0.41 0.91 0.67 0.38 1.31 35 24.12 0.67 0.97 0.99 0.95 0.91 WO 2013/128448 PCT/IL2013/050172 98 Ecotype/Treatment Line-13 Line-14 Line-15 Line-16 Line-17 Line-18 36 0.27 0.68 0.14 0.53 0.55 0.41 37 2.21 3.73 0.75 1.76 0.63 1.11 38 0.00 0.01 0.30 0.14 0.04 0.09 39 0.32 2.48 0.41 1.62 1.76 1.42 40 0.84 1.51 0.98 1.34 0.38 0.84 41 1.17 1.94 0.35 1.06 0.21 0.48 42 0.17 0.02 10.50 27.89 11.79 9.98 43 0.85 0.27 0.35 0.33 0.31 0.29 44 1.89 1.93 2.14 1.65 3.01 2.29 45 0.03 0.26 0.03 0.00 0.00 0.01 46 57.90 48.30 43.60 54.50 41.60 59.10 47 56.77 35.96 77.62 100.00 63.16 75.13 48 32.89 17.35 33.82 54.47 26.25 44.43 49 5.33 8.00 7.67 9.00 10.67 9.00 50 1.02 0.70 0.38 0.66 0.70 0.33 51 130.78 557.93 176.67 791.86 517.05 832.27 52 3.38 7.14 5.48 8.62 6.35 6.77 53 2.04 4.17 3.09 4.69 3.87 2.91 54 0.28 0.38 0.63 2.86 1.16 4.40 55 0.35 0.63 2.27 7.40 2.94 11.60 56 0.01 0.02 0.00 0.01 0.04 0.01 57 0.05 0.10 0.03 0.04 0.02 0.03 58 0.12 0.15 0.12 0.25 0.61 0.31 59 0.06 0.12 0.03 0.05 0.06 0.04 60 396.00 236.15 174.58 441.78 489.18 707.80 61 6.32 5.11 4.72 6.83 7.10 8.21 62 3.58 2.56 2.48 3.43 3.30 3.69 63 0.36 0.35 0.57 4.38 2.02 8.13 64 160.18 90.10 160.99 379.03 531.08 650.68 65 0.00 0.00 0.00 0.00 0.00 0.00 66 0.00 0.00 0.00 0.00 0.00 0.00 67 0.52 0.57 0.94 6.17 3.67 11.33 Table 13: Provided are the values of each of the parameters (as described above) measured in tomato accessions (Seed ID) under all growth conditions. Growth conditions are specified in the experimental procedure section. 5 Table 14 Correlation between the expression level of selected genes of some embodiments of the invention in various tissues and the phenotypic performance under normal and stress conditions across tomato ecotypes Gene Exp. Corr. Gene Exp Corr. R P value XJ* Set Gen Px vorr. Name set Se Name R P value set Set ID ID LYD648 0.71 2.04E-02 1 20 LYD648 0.73 2.70E-02 2 1 LYD650 0.72 1.95E-02 5 45 LYD650 0.72 1.78E-02 9 37 LYD650 0.88 8.80E-04 9 41 LYD650 0.79 6.43E-03 11 41 LYD651 0.72 4.60E-02 2 10 LYD651 0.80 1.69E-02 2 5 LYD651 0.83 2.96E-03 8 43 LYD651 0.79 6.11E-03 11 35 WO 2013/128448 PCT/IL2013/050172 99 Gene Exp. Corr. Gene Exp Corr. Name R P value set Set Name R P value set Set ID ID LYD651 0.79 6.98E-03 11 31 LYD652 0.71 2.14E-02 1 27 LYD652 0.80 5.86E-03 10 61 LYD652 0.77 8.52E-03 10 64 LYD652 0.83 3.29E-03 10 63 LYD652 0.75 1.21E-02 10 67 LYD653 0.71 3.11E-02 2 2 LYD653 0.72 2.80E-02 3 2 LYD653 0.74 2.35E-02 3 4 LYD654 0.72 2.74E-02 3 2 LYD654 0.75 1.89E-02 3 4 LYD655 0.83 1.07E-02 2 9 LYD655 0.72 1.85E-02 12 19 LYD657 0.78 2.25E-02 2 12 LYD657 0.76 2.92E-02 2 11 LYD657 0.77 8.89E-03 5 47 LYD657 0.90 3.73E-04 5 48 LYD657 0.76 1.1OE-02 11 30 LYD657 0.77 9.90E-03 11 32 LYD658 0.79 1.94E-02 2 8 LYD658 0.73 1.62E-02 6 58 LYD658 0.75 1.27E-02 11 39 LYD658 0.82 3.75E-03 11 36 LYD659 0.85 1.72E-03 1 21 LYD659 0.80 8.96E-03 1 15 LYD659 0.88 4.08E-03 2 6 LYD659 0.89 3.26E-03 2 10 LYD659 0.95 2.50E-04 2 5 LYD659 0.85 7.44E-03 2 7 LYD659 0.75 1.18E-02 8 50 LYD659 0.77 9.47E-03 10 65 LYD659 0.73 1.67E-02 12 20 LYD659 0.73 1.63E-02 12 19 LYD660 0.81 8.70E-03 2 3 LYD660 0.74 2.21E-02 2 1 LYD660 0.80 5.64E-03 11 33 LYD660 0.72 2.01E-02 11 40 LYD662 0.93 9.15E-05 6 59 LYD662 0.86 1.49E-03 6 57 LYD662 0.74 1.45E-02 9 37 LYD662 0.81 4.76E-03 9 41 LYD662 0.86 1.51E-03 12 24 LYD662 0.75 1.31E-02 12 14 LYD662 0.75 1.30E-02 12 17 LYD662 0.82 3.37E-03 12 26 LYD663 0.72 1.82E-02 6 58 LYD663 0.75 1.22E-02 12 16 LYD663 0.82 3.57E-03 12 21 LYD663 0.88 1.57E-03 12 15 LYD663 0.86 1.37E-03 12 18 LYD664 0.71 4.97E-02 2 5 LYD664 0.88 7.76E-04 5 50 LYD664 0.80 5.82E-03 5 45 LYD664 0.89 4.84E-04 11 33 LYD664 0.89 4.73E-04 11 30 LYD664 0.83 2.93E-03 11 32 LYD665 0.71 2.24E-02 1 21 LYD665 0.91 2.59E-04 8 50 LYD666 0.89 6.17E-04 6 56 LYD666 0.87 1.00E-03 6 65 LYD666 0.75 1.31E-02 10 60 LYD666 0.83 2.68E-03 10 64 LYD666 0.84 2.39E-03 12 13 LYD666 0.73 2.69E-02 12 15 LYD667 0.78 7.42E-03 12 20 LYD667 0.71 2.13E-02 12 23 LYD667 0.77 9.13E-03 12 19 LYD668 0.79 1.12E-02 2 3 LYD668 0.75 1.95E-02 2 1 LYD669 0.89 5.38E-04 6 59 LYD669 0.86 1.55E-03 6 57 LYD669 0.93 7.72E-05 12 24 LYD669 0.82 3.72E-03 12 14 LYD669 0.81 4.92E-03 12 17 LYD669 0.94 5.22E-05 12 26 LYD669 0.77 9.06E-03 12 18 LYD670 0.79 6.65E-03 1 20 LYD670 0.77 8.66E-03 1 22 LYD670 0.88 4.33E-03 2 12 LYD670 0.76 1.79E-02 2 3 LYD670 0.88 1.57E-03 2 1 LYD670 0.78 2.37E-02 2 11 LYD670 0.73 2.59E-02 3 3 LYD670 0.88 1.58E-03 3 1 LYD672 0.71 2.05E-02 8 43 LYD672 0.83 3.24E-03 11 35 LYD672 0.74 1.36E-02 11 34 LYD672 0.82 3.71E-03 11 31 LYD673 0.94 4.23E-04 2 6 LYD673 0.90 2.12E-03 2 10 LYD673 0.95 3.89E-04 2 5 LYD673 0.95 3.25E-04 2 7 LYD673 0.73 1.70E-02 10 63 LYD673 0.70 2.34E-02 12 19 LYD674 0.72 4.59E-02 2 5 LYD674 0.73 1.68E-02 11 36 WO 2013/128448 PCT/IL2013/050172 100 Gene Exp. Corr. Gene Exp Corr. Name R P value set Set Name R P value set Set ID ID LYD675 0.79 2.OOE-02 2 6 LYD675 0.84 9.67E-03 2 10 LYD675 0.88 4.05E-03 2 5 LYD675 0.72 4.37E-02 2 7 LYD675 0.91 2.96E-04 11 35 LYD675 0.84 2.25E-03 11 34 LYD675 0.90 4.48E-04 11 31 LYD676 0.73 1.55E-02 8 43 LYD676 0.78 8.05E-03 11 35 LYD676 0.77 9.17E-03 11 31 LYD677 0.75 1.91E-02 2 3 LYD677 0.77 2.50E-02 2 10 LYD677 0.73 4.09E-02 2 5 LYD678 0.78 8.42E-03 8 49 LYD678 0.72 1.99E-02 11 42 LYD678 0.87 1.12E-03 11 38 LYD679 0.77 8.47E-03 1 19 LYD679 0.78 2.22E-02 2 6 LYD679 0.83 1.17E-02 2 10 LYD679 0.85 7.58E-03 2 5 LYD679 0.75 3.29E-02 2 7 LYD679 0.84 4.95E-03 3 3 LYD679 0.72 2.97E-02 3 1 LYD679 0.72 1.99E-02 5 43 LYD679 0.81 4.78E-03 9 35 LYD679 0.81 4.89E-03 9 34 LYD679 0.81 4.67E-03 9 31 LYD679 0.71 3.31E-02 12 15 LYD679 0.84 2.28E-03 12 22 LYD680 0.73 1.71E-02 1 27 LYD680 0.72 4.47E-02 2 7 LYD680 0.71 2.19E-02 8 46 LYD680 0.80 5.67E-03 10 63 LYD680 0.74 1.48E-02 10 67 LYD681 0.82 1.26E-02 2 9 LYD681 0.83 5.53E-03 3 1 LYD681 0.71 2.17E-02 8 48 LYD681 0.73 1.71E-02 9 37 LYD682 0.75 1.96E-02 2 4 LYD682 0.73 2.54E-02 3 3 LYD682 0.70 2.29E-02 6 58 LYD682 0.72 2.OOE-02 12 16 LYD682 0.76 1.07E-02 12 21 LYD682 0.80 8.91E-03 12 15 LYD682 0.72 1.94E-02 11 42 LYD683 0.71 2.22E-02 10 59 LYD684 0.70 2.33E-02 9 32 LYD685 0.71 2.1OE-02 5 43 LYD685 0.93 1.00E-04 5 45 LYD685 0.75 1.20E-02 8 43 LYD685 0.74 1.52E-02 9 41 LYD685 0.89 6.58E-04 11 35 LYD685 0.83 3.23E-03 11 34 LYD685 0.88 6.67E-04 11 31 LYD686 0.79 6.31E-03 9 35 LYD686 0.72 1.86E-02 9 34 LYD686 0.78 8.07E-03 9 31 LYD690 0.85 7.24E-03 2 12 LYD690 0.77 2.66E-02 2 11 LYD690 0.75 1.25E-02 11 35 LYD690 0.75 1.20E-02 11 34 LYD690 0.75 1.31E-02 11 31 Table 14. Provided are the correlations (R) between the expression levels yield improving genes and their homologs in various tissues [Expression (Exp) sets] and the phenotypic performance [yield, biomass, growth rate and/or vigor components (Correlation vector (Corr))] under normal conditions across tomato ecotypes. P = p value. 5 EXAMPLE 5 PRODUCTION OF TOMATO TRANSCRIPTOME AND HIGH THROUGHPUT CORRELATION ANALYSIS USING 44K TOMATO OLIGONUCLEO TIDE MICRO-ARRAY 10 In order to produce a high throughput correlation analysis, the present inventors utilized a Tomato oligonucleotide micro-array, produced by Agilent Technologies [Hypertext Transfer Protocol://World Wide Web (dot) chem. (dot) agilent (dot) WO 2013/128448 PCT/IL2013/050172 101 com/Scripts/PDS (dot) asp lPage=50879]. The array oligonucleotide represents about 44,000 Tomato genes and transcripts. In order to define correlations between the levels of RNA expression with ABST, yield components or vigor related parameters various plant characteristics of 18 different Tomato varieties were analyzed. Among them, 10 5 varieties encompassing the observed variance were selected for RNA expression analysis. The correlation between the RNA levels and the characterized parameters was analyzed using Pearson correlation test. I. Correlation of Tomato varieties across ecotype grown under 50 % irrigation conditions 10 Experimental procedures Growth procedure - Tomato variety was grown under normal conditions (4-6 Liters/m 2 per day) until flower stage. At this time, irrigation was reduced to 50 % compared to normal conditions. RNA extraction - Two tissues at different developmental stages [flower and 15 leaf], representing different plant characteristics, were sampled and RNA was extracted as described above. Fruit Yield (grams) - At the end of the experiment [when 50 % of the fruit were ripe (red)] all fruits from plots within blocks A-C were collected. The total fruits were counted and weighted. The average fruits weight was calculated by dividing the total 20 fruit weight by the number of fruits. Yield/SLA and Yield/total leaf area - Fruit yield divided by the specific leaf area or the total leaf area gives a measurement of the balance between reproductive and vegetative processes. Plant Fresh Weight (grams) - At the end of the experiment [when 50 % of the 25 fruit were ripe (red)] all plants from plots within blocks A-C were collected. Fresh weight was measured (grams). Inflorescence Weight (grams) - At the end of the experiment [when 50 % of the fruits were ripe (red)] two inflorescence from plots within blocks A-C were collected. The inflorescence weight (gr.) and number of flowers per inflorescence were counted. 30 SPAD - Chlorophyll content was determined using a Minolta SPAD 502 chlorophyll meter and measurement was performed at time of flowering. SPAD meter WO 2013/128448 PCT/IL2013/050172 102 readings were done on young fully developed leaf. Three measurements per leaf were taken per plot. Water use efficiency (WUE) - can be determined as the biomass produced per unit transpiration. To analyze WUE, leaf relative water content was measured in control 5 and transgenic plants. Fresh weight (FW) was immediately recorded; then leaves were soaked for 8 hours in distilled water at room temperature in the dark, and the turgid weight (TW) was recorded. Total dry weight (DW) was recorded after drying the leaves at 60'C to a constant weight. Relative water content (RWC) was calculated according to the following Formula I [(FW - DW/TW - DW) x 100] as described above. 10 Plants that maintain high relative water content (RWC) compared to control lines were considered more tolerant to drought than those exhibiting reduced relative water content Table 15 Tissues used for tomato transcriptome expression sets 15 Expression Set Set ID Root grown under normal growth conditions 1+7 Root grown under NUE growth conditions 2+4 Leaf grown under normal growth conditions 3+5 Leaf grown under NUE growth conditions 6+8 Table 15: Provided are the identification (ID) digits of each of the tomato expression sets. Tomato yield components and vigor related parameters under 50 % water 20 irrigation assessment - 10 Tomato varieties in 3 repetitive blocks (named A, B, and C), each containing 6 plants per plot were grown at net house. Plants were phenotyped on a daily basis following the standard descriptor of tomato (Table 16, below). Harvest was conducted while 50 % of the fruits were red (mature). Plants were separated to the vegetative part and fruits, of them, 2 nodes were analyzed for additional inflorescent 25 parameters such as size, number of flowers, and inflorescent weight. Fresh weight of all vegetative material was measured. Fruits were separated to colors (red vs. green) and in accordance with the fruit size (small, medium and large). Next, analyzed data was saved to text files and processed using the JMP statistical analysis software (SAS institute). 30 Data parameters collected are summarized in Table 16, herein below.
WO 2013/128448 PCT/IL2013/050172 103 Table 16 Tomato correlated parameters (vectors) Correlated parameter with Correlation ID Shoot Biomass [DW] /SPAD (gr/SPAD) 1 Root Biomass [DW] /SPAD (gr/SPAD) 2 Total Biomass [Root + Shoot DW] /SPAD (gr/SPAD) 3 N level/Leaf [SPAD unit/leaf](SPAD/gr) 4 Shoot/Root (ratio) 5 Percent Shoot Biomass reduction compared to normal (%) 6 Percent Root Biomass reduction compared to normal (%) 7 Shoots NUE (gr) 8 Roots NUE (gr) 9 Total biomass NUE (gr) 10 Plant Height NUE (cm) 11 Plant Height Normal (cm) 12 SPAD NUE (number) 13 Leaf number NUE/Normal (ratio) 14 Plant Height NUE/Normal (ratio) 15 SPAD NUE/Normal (ratio) 16 leaf No. NUE (number) 17 leaf No. Normal (number) 18 Plant height Normal (cm) 19 SPAD Normal 20 Table 16: Provided are the tomato correlated parameters. "NUE" = nitrogen use 5 efficiency; "DW" = dry weight; "cm" = centimeter. Experimental Results RNA extraction - All 10 selected Tomato varieties were sampled per each treatment. Two tissues [leaves and flowers] growing at 50% irrigation or under normal 10 conditions were sampled and RNA was extracted using TRIzol Reagent from Invitrogen [Hypertext Transfer Protocol://World Wide Web (dot) invitrogen (dot) com/content (dot)cfm pageid=469]. Extraction of RNA from tissues was performed as described under "General Experimental And Bioinformatics Methods" above. 10 different Tomato varieties (accessions) were grown and characterized for 20 15 parameters as described above. The average for each of the measured parameter was calculated using the JMP software and values are summarized in Tables 17-18 below. Subsequent correlation analysis between expression of selected genes in various transcriptome expression sets and the measured parameters in tomato accessions (Tables 17-18) was conducted, and results were integrated to the database.
WO 2013/128448 PCT/IL2013/050172 104 Table 17 Measured parameters in Tomato accessions (line 1-6) Ecotype/Treatment Line-i Line-2 Line-3 Line-4 Line-5 Line-6 1 0.00 0.00 0.00 0.01 0.00 0.01 2 0.00 0.00 0.00 0.00 0.00 0.00 3 0.00 0.01 0.00 0.01 0.01 0.01 4 10.85 11.53 11.41 10.44 11.17 8.93 5 5.01 6.41 11.39 9.49 11.60 8.20 6 75.38 62.15 55.11 49.73 63.19 82.67 7 62.59 143.71 54.16 70.55 59.69 96.13 8 35.35 38.35 24.09 65.02 46.71 46.67 9 6.99 7.73 2.54 7.04 5.04 8.01 10 58.47 69.70 63.75 69.29 71.10 60.54 11 36.78 39.89 47.00 46.44 45.44 12 45.33 47.78 55.33 56.22 48.67 13 34.57 24.87 31.58 29.72 31.83 14 0.85 0.90 1.09 0.88 1.02 15 0.81 0.83 0.85 0.83 0.93 16 1.01 0.98 1.00 0.98 0.98 17 5.56 6.22 6.78 5.56 6.56 1 0.01 0.01 0.01 0.01 0.01 0.01 2 0.00 0.00 0.00 0.00 0.00 0.00 3 0.01 0.01 0.01 0.02 0.01 0.01 4 9.29 10.18 8.87 8.43 9.83 8.57 5 5.40 12.65 10.02 15.42 8.83 7.52 8 4.69 6.17 4.37 13.08 7.39 5.65 9 1.12 0.54 0.47 1.00 0.84 0.83 10 7.47 9.10 8.63 8.85 7.22 7.87 18 6.56 6.89 6.22 6.33 6.44 19 45.33 47.78 55.33 56.22 48.67 20 34.30 25.31 31.43 30.24 32.43 Table 17. Provided are the measured yield components and vigor related parameters 5 under normal or Nitrogen use efficiency parameters for the tomato accessions (Varieties) according to the Correlation ID numbers (described in Table 16 above) Table 18 Measured parameters in Tomato accessions (line 7-12) 10 Ecotype/Treatment Line-7 Line-8 Line-9 Line-10 Line-11 Line-12 1 0.01 0.01 0.01 0.01 0.0056 2 0.00 0.00 0.00 0.00 0.0015 3 0.01 0.01 0.01 0.01 0.007 4 7.93 7.99 10.30 8.59 14.491 5 10.38 10.52 8.24 7.97 3.9092 6 66.92 107.98 55.40 54.43 59.746 7 106.50 111.90 81.64 32.21 87.471 8 120.07 60.09 66.27 56.46 60.32 9 15.09 9.02 8.78 7.25 15.94 10 73.90 68.81 66.74 70.82 49.72 WO 2013/128448 PCT/IL2013/050172 105 Ecotype/Treatment Line-7 Line-8 Line-9 Line-10 Line-li Line-12 11 47.67 39.33 41.78 41.00 34.44 12 55.78 37.44 49.56 46.33 40.78 13 30.33 30.29 31.32 28.77 28.58 14 0.87 1.06 0.91 1.12 0.98 15 0.85 1.05 0.84 0.88 0.84 16 0.93 1.05 1.01 0.99 1.02 17 5.11 5.89 5.56 6.33 7.22 1 0.02 0.01 0.01 0.01 0.0094 2 0.00 0.00 0.00 0.00 0.0017 3 0.02 0.01 0.01 0.01 0.011 4 6.57 6.97 8.71 7.35 9.3699 5 12.61 7.99 14.31 4.80 6.2937 8 17.94 5.56 11.96 10.37 10.1 9 0.94 0.81 1.08 2.25 1.82 10 9.09 7.91 8.55 8.68 6.24 18 5.89 5.56 6.11 5.67 7.33 19 55.78 37.44 49.56 46.33 40.78 20 32.58 28.77 30.92 28.99 1 28.12 Table 18: Provided are the measured yield components and vigor related parameters under normal or Nitrogen use efficiency parameters for the tomato accessions (Varieties) according to the Correlation ID numbers (described in Table 16 above) Table 19 5 Correlation between the expression level of selected genes of some embodiments of the invention in various tissues and the phenotypic performance under normal or low nitrogen use conditions across tomato accessions GeeExp. Corr. GnEx.Corr. Ne R P value rSet Gene R P value r Set ID ID LYD648 0.73 2.42E 1 2 LYD648 0.72 2.90E-02 2 9 02 LYD648 0.71 3.18E- 2 2 LYD648 0.73 2.66E-02 4 9 02 LYD648 0.71 3.26E- 4 3 LYD648 0.72 2.88E-02 4 2 LYD648 0.73 2.69E- 7 2 LYD651 0.76 1.77E-02 6 7 02 LYD651 0.76 172E 8 7 LYD652 0.73 4.09E-02 3 18 02 LYD652 0.72 2.84E- 7 4 LYD653 0.76 2.70E-02 4 15 LYD653 0.79 1.22E 4 6 LYD654 0.81 8.61E-03 2 4 02 LYD654 0.78 1.31E- 4 4 LYD654 0.78 1.38E-02 6 7 LYD654 0.81 142E 7 18 LYD655 0.79 1.16E-02 2 8 02 LYD655 0.83 5.5- 2 9 LYD655 0.76 1.65E-02 2 3 03 WO 2013/128448 PCT/IL2013/050172 106 GeeExp. Corr. GnEx.Corr. GNe R P value Set Ne R P value et Set ID ID LYD655 0.75 194E- 2 1 LYD655 0.77 1.53E-02 2 2 0211 LYD655 0.79 1.14E 4 8 LYD655 0.83 5.95E-03 4 9 02 LYD655 0.76 1. 68E- 4 3 LYD655 0.75 1.96E-02 4 1 02 LYD655 0.76 1.66E 4 2 LYD657 0.91 1.90E-03 6 15 02 LYD657 0.88 1.67E 6 6 LYD658 0.73 2.67E-02 3 9 03 LYD658 0.73 2.48E 3 2 LYD659 0.89 1.15E-03 6 7 02 LYD660 0.81 1.44E- 4 17 LYD660 0.71 3.19E-02 6 2 02 LYD660 0.78 1.35E 6 7 LYD660 0.85 4.02E-03 7 4 02 LYD660 0.76 2.84E 7 18 LYD660 0.78 1.24E-02 8 7 02 LYD664 0.74 2.21E 6 7 LYD664 0.73 2.43E-02 8 7 02 LYD667 0.94 5.35E 4 15 LYD667 0.88 1.75E-03 4 6 04 LYD667 0.73 2.49E- 4 7 LYD667 0.81 1.41E-02 6 15 LYD667 0.89 1.39E 6 6 LYD668 0.74 2.32E-02 6 7 03 LYD669 0.92 1.38E 4 15 LYD669 0.89 3.23E-03 6 15 LYD669 0.94 1.50E 6 6 LYD670 0.75 3.38E-02 6 15 04 LYD670 0.74 2.35E 6 6 LYD672 0.74 2.26E-02 6 9 02 LYD672 0.71 3.33E 6 2 LYD672 0.79 1.17E-02 6 7 02 LYD673 0.74 3.51E- 4 12 LYD673 0.74 3.51E-02 7 19 02 LYD674 0.72 4.42E 6 17 LYD675 0.73 2.60E-02 6 9 02 LYD675 0.81 7.67E 6 7 LYD675 0.72 2.79E-02 8 9 03 LYD675 0.81 8.09E 8 7 LYD676 0.75 2.12E-02 6 7 03 LYD676 0.81 1.57E 7 18 LYD676 0.76 1.84E-02 8 7 02 LYD677 0.77 2.57E 3 19 LYD677 0.77 2.57E-02 6 12 02 -4. 30E LY68 0.72 02 4 16 LYD678 0.72 2.81E-02 4 6 WO 2013/128448 PCT/IL2013/050172 107 GeeExp. Corr. GnEx.Corr. GNe R P value .Set Gene R P value r Set ID ID LYD678 0.79 1*98E 6 15 LYD678 0.90 9.54E-04 6 6 02111 LYD680 0.71 5.02E 4 17 LYD682 0.74 3.43E-02 3 20 02 LYD683 0.70 3.48E 6 7 LYD684 0.85 3.56E-03 6 7 02 LYD690 0.70 3.56E 4 6 LYD690 0.83 1.16E-02 6 15 02 LYD690 0.93 3.18E 6 6 Table 19. Provided are the correlations (R) between the expression levels of yield improving genes and their homologues in tissues [Leaves or roots; Expression sets (Exp)] and the phenotypic performance in various yield, biomass, growth rate and/or vigor components [Correlation vector (corr.)] under stress conditions or normal conditions across tomato 5 accessions. P = p value. EXAMPLE 6 PRODUCTION OF B. JUNCEA TRANSCRIPTOME AND HIGH THROUGHPUT CORRELATION ANALYSIS WITH YIELD PARAMETRERS USING 60K B. 10 JUNCEA OLIGONUCLEOTIDE MICRO-ARRAYS In order to produce a high throughput correlation analysis, the present inventors utilized a B. juncea oligonucleotide micro-array, produced by Agilent Technologies [Hypertext Transfer Protocol://World Wide Web (dot) chem. (dot) agilent (dot) com/Scripts/PDS (dot) asp lPage=50879]. The array oligonucleotide represents about 15 60,000 B. juncea genes and transcripts. In order to define correlations between the levels of RNA expression with yield components or vigor related parameters, various plant characteristics of 11 different B. juncea varieties were analyzed and used for RNA expression analysis. The correlation between the RNA levels and the characterized parameters was analyzed using Pearson correlation test. 20 Correlation of B. juncea genes' expression levels with phenotypic characteristics across ecotype Experimental procedures Eleven B. juncea varieties were grown in three repetitive plots, in field. Briefly, the growing protocol was as follows: B. juncea seeds were sown in soil and grown 25 under normal condition till harvest. In order to define correlations between the levels of RNA expression with yield components or vigor related parameters, the eleven different B. juncea varieties were analyzed and used for gene expression analyses.
WO 2013/128448 PCT/IL2013/050172 108 Table 20 Tissues used for B, juncea transcriptome expression sets Expression Set Set ID Meristem at vegetative stage under normal growth conditions 1 Flower at flowering stage under normal growth conditions 2 Leaf at vegetative stage under normal growth conditions 3 Pod (R 1 -R3) under normal growth conditions 4 Pod (R4-R5) under normal growth conditions 5 Table 20: Provided are the identification (ID) digits of each of the B, juncea expression 5 sets. RNA extraction - All 11 selected B. juncea varieties were sample per each treatment. Plant tissues [leaf, Pod, Lateral meristem and flower] growing under normal conditions were sampled and RNA was extracted as described above. 10 The collected data parameters were as follows: Fresh weight (plot-harvest) [gr/plant] - total fresh weight per plot at harvest time normalized to the number of plants per plot. Seed Weight [milligrams /plant] - total seeds from each plot was extracted, weighted and normalized for plant number in each plot. 15 Harvest index - The harvest index was calculated: seed weight / fresh weight. Days till bolting /flowering - number of days till 50% bolting / flowering for each plot. SPAD - Chlorophyll content was determined using a Minolta SPAD 502 chlorophyll meter and measurement was performed at time of flowering. SPAD meter 20 readings were done on young fully developed leaf. Three measurements per leaf were taken for each plot. Main branch - average node length - total length / total number of nods on main branch. Lateral branch - average node length- total length / total number of nods on 25 lateral branch. Main branch - 20th length - the length of the pod on the 2 0 th node from the apex of main branch. Lateral branch - 20th length - the length of the pod on the 20th node from the apex of lateral branch.
WO 2013/128448 PCT/IL2013/050172 109 Main branch - 20th seed No. - number of seeds in the pod on the 2 0 th node from the apex of main branch. Lateral branch - 20th seed number - number of seeds in the pod on the 2 0 th node from the apex of lateral branch. 5 Number of lateral branches - total number of lateral branches, average of three plants per plot. Main branch height [cm] - total length of main branch. Min-lateral branch position - lowest node on the main branch that has developed lateral branch. 10 Max-lateral branch position [#node of main branch] - highest node on the main branch that has developed lateral branch. Max-number of nodes in lateral branch - the highest number of node that a lateral branch had per plant. Max length of lateral branch [cm] - the highest length of lateral branch per 15 plant. Max diameter of lateral branch [mm] - the highest base diameter that a lateral branch had per plant. Oil Content - Indirect oil content analysis was carried out using Nuclear Magnetic Resonance (NMR) Spectroscopy, which measures the resonance energy 20 absorbed by hydrogen atoms in the liquid state of the sample [See for example, Conway TF. and Earle FR., 1963, Journal of the American Oil Chemists' Society; Springer Berlin / Heidelberg, ISSN: 0003-021X (Print) 1558-9331 (Online)]; Fresh weight (single plant) (gr/plant) - average fresh weight of three plants per plot taken at the middle of the season. 25 Main branch base diameter [mm] - the based diameter of main branch, average of three plants per plot. 1000 Seeds [gr] - weight of 1000 seeds per plot. Experimental Results Eleven different B. juncea varieties (i.e., seed ID 646, 648, 650, 657, 661, 662, 30 663, 664, 669, 670, 671) were grown and characterized for 23 parameters as specified above. The average for each of the measured parameters was calculated using the JMP software and values are summarized in Tables 22-23 below. Subsequent correlation WO 2013/128448 PCT/IL2013/050172 110 analysis between the various transcriptome expression sets and the average parameters, was conducted. Results were then integrated to the database. Table 21 5 Correlated parameters in B. juncea accessions Correlated parameter with Correlation ID Days till bolting (days) 1 Fresh weight (plot-harvest) [gr/plant] 2 Seed weight per plant (gr) 3 Harvest index (ratio) 4 Days till flowering (days) 5 SPAD 6 Main branch - average node length (cm) 7 Lateral branch - average node length (cm) 8 Main branch - 20th length (cm) 9 Lateral branch - 20th length (cm) 10 Main branch - 20th seed number (number) 11 Lateral branch - 20th seed number (number) 12 Number of lateral branches (number) 13 Main branch height [cm] 14 Min-Lateral branch position ([#node of main branch) 15 Max-Lateral branch position [#node of main branch] 16 Max-Number of nodes in lateral branch (number) 17 Max-Length of lateral branch [cm] 18 Max-Diameter of lateral branch [nmm] 19 Oil content (mg) 20 Fresh weight (single plant) [gr/plant] 21 Main branch base diameter [nmm] 22 1000 Seeds [gr] 23 Table 21. Provided are the B. juncea correlated parameters. "gr." = grams; mm = millimeters; "cm" = centimeters; "mg" = milligrams; "SPAD" = chlorophyll levels; 10 Table 22 Measured parameters in B. juncea accessions (lines 1-6) Ecotype/Treatment Line-i Line-2 Line-3 Line-4 Line-5 Line-6 1 57.33 60.33 59.67 56.33 55.00 46.67 2 69.24 45.22 39.27 49.11 43.95 46.42 3 0.00 0.01 0.01 0.01 0.01 0.01 4 0.00 0.00 0.00 0.00 0.00 0.00 5 66.00 69.67 69.33 66.00 61.33 53.00 6 33.02 30.01 32.83 37.53 41.44 35.41 7 0.48 0.41 0.63 0.43 0.38 0.68 8 0.65 0.43 0.74 0.57 0.56 0.79 9 4.28 3.72 3.62 3.50 2.74 5.20 10 4.32 3.69 4.14 3.37 3.06 3.96 11 13.22 13.67 10.44 14.11 9.78 15.22 12 13.00 14.00 13.22 13.44 11.00 13.11 WO 2013/128448 PCT/IL2013/050172 111 Ecotype/Treatment Line-i Line-2 Line-3 Line-4 Line-5 Line-6 13 15.22 14.89 13.56 14.89 14.00 9.78 14 140.72 125.22 112.44 133.39 142.00 101.50 15 6.78 6.33 5.56 3.67 3.00 3.11 16 15.22 14.89 13.56 14.89 14.00 10.89 17 5.22 7.00 5.22 7.00 6.56 9.44 18 40.44 47.22 41.61 60.50 59.78 59.44 19 4.20 4.85 4.34 5.74 5.87 5.68 20 40.19 40.71 40.91 38.57 40.14 42.63 21 197.78 142.22 147.22 243.33 192.33 163.78 22 14.53 11.99 19.91 14.32 12.59 12.30 23 3.76 2.21 3.26 2.36 2.00 3.12 Table 22. Provided are the values of each of the parameters (as described above) measured in B. juncea accessions (Seed ID) under normal conditions. Table 23 Measured parameters in B. juncea accessions (lines 7-11) 5 Ecotype/Treatment Line-7 Line-8 Line-9 Line-10 Line-11 1 59.00 54.33 59.67 57.33 53.00 2 36.14 32.58 33.16 63.23 60.94 3 0.00 0.00 0.00 0.01 0.01 4 0.00 0.00 0.00 0.00 0.00 5 69.67 63.67 69.67 71.00 58.33 6 33.17 32.87 34.80 31.82 41.49 7 0.40 0.63 0.57 0.59 1.55 8 0.57 0.76 0.96 0.78 0.90 9 3.91 3.98 3.46 3.73 4.04 10 4.33 4.21 4.14 4.04 3.88 11 12.00 12.67 9.89 11.56 15.56 12 11.89 13.44 11.22 13.22 14.00 13 16.44 14.33 14.56 14.11 16.78 14 145.39 131.56 129.89 131.56 116.44 15 7.78 6.22 5.56 4.89 5.33 16 16.44 14.33 14.56 14.11 16.78 17 6.11 5.22 5.67 6.56 6.00 18 47.28 47.33 44.67 58.67 47.17 19 4.52 4.89 4.68 5.56 5.49 20 41.34 40.82 40.82 38.14 37.21 21 164.44 181.11 176.22 217.89 261.11 22 12.60 12.91 12.56 13.77 13.56 23 3.34 3.09 3.39 3.40 2.39 Table 23: Provided are the values of each of the parameters (as described above) measured in B. juncea accessions (Seed ID) under normal conditions.
WO 2013/128448 PCT/IL2013/050172 112 Table 24 Correlation between the expression level of selected genes of some embodiments of the invention in various tissues and the phenotypic performance under normal or normal conditions across B. Juncea accessions 5 GnEx.Corr. Gn x Corr. GNe R P value C r Set Gene R P value E Cp Set ID ID LYD537 0.76 7.70E-02 2 19 LYD537 0.84 3.50E-02 2 18 LYD537 0.73 9.84E-02 2 17 LYD537 0.73 9.68E-02 2 2 LYD537 0.72 1.95E-02 3 4 LYD538 0.77 7.11E-02 2 21 LYD538 0.90 1.59E-02 2 2 LYD538 0.72 1.09E-01 2 12 LYD538 0.70 2.40E-02 3 19 LYD538 0.82 4.06E-03 3 11 LYD538 0.72 2.OOE-02 3 3 LYD538 0.76 6.83E-03 5 7 LYD539 0.75 1.24E-02 3 4 LYD540 0.80 5.79E-02 2 21 LYD540 0.85 3.24E-02 2 3 LYD540 0.80 5.64E-02 2 7 LYD540 0.90 1.36E-02 2 2 LYD540 0.86 2.80E-02 2 12 LYD540 0.76 1.15E-02 3 4 LYD540 0.74 9.59E-03 5 17 Table 24. Provided are the correlations (R) between the expression levels of yield improving genes and their homologues in tissues [Leaves, meristem, flower and pods; Expression sets (Exp)] and the phenotypic performance in various yield, biomass, growth rate and/or vigor components [Correlation vector (corr.)] under stress conditions or normal 10 conditions across B, juncea accessions. P = p value. EXAMPLE 7 PRODUCTION OF B. JUNCEA TRANSCRIPTOME AND HIGH THROUGHPUT CORRELATION ANALYSIS WITH YIELD PARAMETERS OF JUNCEA GROWVN UNDER VARIOUS POPULATION DENSITIES USING 60K B. JUNCEA OLIGONUCLEOTIDE MICRO-ARRAYS In order to produce a high throughput correlation analysis, the present inventors 20 utilized a B. juncea oligonucleotide micro-array, produced by Agilent Technologies [Hypertext Transfer Protocol://World Wide Web (dot) chem. (dot) agilent (dot) com/Scripts/PDS (dot) asp lPage=50879]. The array oligonucleotide represents about 60,000 B. juncea genes and transcripts. In order to define correlations between the levels of RNA expression with yield components or vigor related parameters, various 25 plant characteristics of two different B. juncea varieties grown under seven different population densities were analyzed and used for RNA expression analysis. The correlation between the RNA levels and the characterized parameters was analyzed using Pearson correlation test. Correlation of B. juncea genes' expression levels with phenotypic 30 characteristics across seven population densities for two ecotypes Experimental procedures WO 2013/128448 PCT/IL2013/050172 113 Two B. juncea varieties were grown in a field under seven population densities (10, 60, 120, 160, 200, 250 and 300 plants per M 2 ) in two repetitive plots. Briefly, the growing protocol was as follows: B. juncea seeds were sown in soil and grown under normal condition till harvest. In order to define correlations between the levels of RNA 5 expression with yield components or vigor related parameters, the two different B. juncea varieties grown under various population densities were analyzed and used for gene expression analyses. The correlation between the RNA levels and the characterized parameters was analyzed using Pearson correlation test for each ecotype independently. 10 Table 25 Tissues used for B. juncea transcriptome expression sets Expression Set Set ID Meristem under normal growth conditions various population 1+2 densities Flower under normal growth conditions various population 3 densities Table 25: Provided are the identification (ID) digits of each of the B, juncea expression sets. 15 RNA extraction - the two B. juncea varieties grown under seven population densities were sample per each treatment. Plant tissues [Flower and Lateral meristem] growing under Normal conditions were sampled and RNA was extracted as described above. For convenience, each micro-array expression information tissue type has 20 received a Set ID. The collected data parameters were as follows: Fresh weight (plot-harvest) [gr/plant] - total fresh weight per plot at harvest time normalized to the number of plants per plot. Seed weight [gr/plant] - total seeds from each plot was extracted, weighted and 25 normalized for plant number in each plot. Harvest index - The harvest index was calculated: seed weight / fresh weight Days till bolting /flowering - number of days till 50% bolting / flowering for each plot. SPAD - Chlorophyll content was determined using a Minolta SPAD 502 30 chlorophyll meter and measurement was performed at time of flowering. SPAD meter WO 2013/128448 PCT/IL2013/050172 114 readings were done on young fully developed leaf. Three measurements per leaf were taken for each plot. Main branch - average node length - total length / total number of nods on main branch. 5 Lateral branch - average node length- total length / total number of nods on lateral branch. Main branch - 20th length - the length of the pod on the 2 0 th node from the apex of main branch. Lateral branch - 20th length - the length of the pod on the 20th node from the 10 apex of lateral branch. Main branch - 20th seed No. - number of seeds in the pod on the 2 0 th node from the apex of main branch. Lateral branch - 20th seed number - number of seeds in the pod on the 2 0 th node from the apex of lateral branch. 15 Number of lateral branches - total number of lateral branches, average of three plants per plot. Main branch height [cm] - total length of main branch. Min-Lateral branch position - lowest node on the main branch that has developed lateral branch. 20 Max-Lateral branch position [#node of main branch] - highest node on the main branch that has developed lateral branch. Max-number of nodes in lateral branch - the highest number of node that a lateral branch had per plant. Max-length of lateral branch [cm] - the highest length of lateral branch per 25 plant. Max diameter of lateral branch [mm] - the highest base diameter that a lateral branch had per plant. Oil content - Indirect oil content analysis was carried out using Nuclear Magnetic Resonance (NMR) Spectroscopy, which measures the resonance energy 30 absorbed by hydrogen atoms in the liquid state of the sample [See for example, Conway TF. and Earle FR., 1963, Journal of the American Oil Chemists' Society; Springer Berlin / Heidelberg, ISSN: 0003-021X (Print) 1558-9331 (Online)]; WO 2013/128448 PCT/IL2013/050172 115 Fresh weight (single plant) (gr/plant) - average fresh weight of three plants per plot taken at the middle of the season. Main branch base diameter [mm] - the based diameter of main branch, average of three plants per plot. 5 1000 Seeds [gr] - weight of 1000 seeds per plot. Main branch-total number of pods - total number of pods on the main branch, average of three plants per plot. Main branch-dist. 1-20 - the length between the youngest pod and pod number 20 on the main branch, average of three plants per plot. 10 Lateral branch-total number of pods - total number of pods on the lowest lateral branch, average of three plants per plot. Lateral branch-dis. 1-20 - the length between the youngest pod and pod number 20 on the lowest lateral branch, average of three plants per plot. Dry weight/plant - weight of total plants per plot at harvest after three days at 15 oven at 60 0 C normalized for the number of plants per plot. Total leaf area - Total leaf area per plot was calculated based on random three plants and normalized for number of plants per plot. Total Perim. - total perimeter of leaves, was calculated based on random three plants and normalized for number of plants per plot. 20 Experimental Results Two B. juncea varieties were grown under seven different population densities and characterized for 30. The average for each of the measured parameter was calculated using the JMP software and values are summarized in Tables 27-29 below. Subsequent correlation analysis between the expression of selected genes in various 25 transcriptome expression sets and the average parameters was conducted. Results were then integrated to the database. Table 26 Correlation parameters in B. juncea accessions 30 Correlated parameter with Correlation ID Main branch base diameter [mm] 1 Fresh Weight (single plant) [gr/plant] 2 Main branch height [cm] 3 Number of lateral branches (number) 4 Min-Lateral branch position (number of node on the main stem) 5 WO 2013/128448 PCT/IL2013/050172 116 Correlated parameter with Correlation ID Max-Lateral branch position (number of node on the main stem) 6 Max-Number of nodes in lateral branch (number) 7 Max-Length of lateral branch [cm] 8 Max-Diameter of lateral branch [mm] 9 Main branch-total number of pods (number) 10 Main branch-dist. 1-20 11 Main branch-20th length (cm) 12 Main branch-20th seed number (number) 13 Lateral branch-total number of pods (number) 14 Lateral branch-dist. 1-20 15 Lateral branch-20th length (cm) 16 Lateral branch-20th seed number (number) 17 Oil content (mg) 18 SPAD 19 days till bolting (days) 20 days till flowering (days) 21 Fresh weight (at harvest)/plant (gr/plant) 22 Dry weight/plant (gr/plant) 23 Seed weight/plant (gr/plant) 24 Fresh weight (harvest)/hectare (Kg/ hectare) 25 Dry weight/hectare (Kg/hectare) 26 Seed weight/hectare 27 100OSeeds [gr] 28 Total leaf area (cm) 29 Total perim. 30 Table 26. Provided are the B. juncea correlated parameters. "gr." = grams; mm = millimeters; "cm" = centimeters; "mg" = milligrams; "SPAD" = chlorophyll levels; "Kg." = kilograms; 5 Table 27 Measured parameters in B. juncea accessions at various population densities (line 1-6) Ecotype/Treatment Line-i Line-2 Line-3 Line-4 Line-5 Line-6 1 14.77 6.90 5.62 4.99 6.45 3.95 2 0.37 0.04 0.03 0.02 0.04 0.02 3 118.67 115.50 111.33 106.00 117.50 108.00 4 17.17 19.17 15.83 19.33 18.33 17.83 5 1.00 11.00 7.00 11.00 9.00 9.00 6 20.00 23.00 19.00 24.00 22.00 20.00 7 10.00 4.00 4.00 4.00 6.00 4.00 8 122.00 41.00 43.00 36.00 40.00 42.00 9 7.70 2.90 2.50 2.00 3.40 2.50 10 20.00 15.33 17.67 16.50 23.17 16.83 11 42.35 27.90 31.22 26.05 27.72 31.85 12 5.12 4.63 4.60 4.67 4.73 4.68 13 20.00 17.67 18.00 18.50 17.67 17.50 14 17.33 11.67 10.67 10.17 12.50 9.83 15 40.73 17.53 19.08 15.65 15.23 17.73 16 5.12 4.48 4.37 4.33 4.35 4.40 WO 2013/128448 PCT/IL2013/050172 117 Ecotype/Treatment Line-i Line-2 Line-3 Line-4 Line-5 Line-6 17 21.67 19.33 17.00 18.83 15.67 17.17 18 28.86 29.62 29.57 30.59 29.87 25.22 19 43.49 41.95 40.48 37.93 39.50 45.57 20 53.00 50.50 48.00 53.00 50.00 51.50 21 67.00 64.00 64.00 64.00 64.00 62.50 22 0.26 0.02 0.01 0.01 0.01 0.01 23 0.07 0.01 0.00 0.00 0.00 0.00 24 0.02 0.00 0.00 0.00 0.00 0.00 25 22434.19 22067.24 32929.29 18596.04 20654.32 24019.71 26 6109.02 9857.37 8940.70 4363.21 6702.22 6009.09 27 1797.45 2307.34 2552.84 1466.27 2100.38 1901.67 28 1.80 1.75 1.62 1.99 1.92 1.54 29 508.27 37.49 25.00 14.33 50.79 29.13 30 862.83 100.50 67.98 37.91 97.51 61.17 Table 27 Table 28 Measured parameters in B. juncea accessions at various population densities (line 7-12) Ecotype/Treatment Line-7 Line-8 Line-9 Line-10 Line-i1 Line-12 1 7.37 18.90 7.81 6.79 6.95 7.53333 2 0.07 0.34 0.04 0.03 0.025 0.02833 3 116.00 133.17 144.58 144.92 138.5 144.167 4 16.17 12.50 15.33 16.83 16.6667 16.6667 5 5.00 1.00 8.00 9.00 8 10 6 20.00 14.00 17.00 21.00 18 19 7 6.00 11.00 6.00 5.00 4 6 8 78.00 127.00 42.00 34.00 23 38 9 4.40 8.40 3.00 2.60 2.1 2.8 10 15.17 30.67 35.17 29.83 30.8333 29.3333 11 37.58 38.72 32.85 28.77 25.3 26.3833 12 5.10 4.67 3.85 4.43 4.11667 4.11667 13 17.67 14.33 10.33 13.83 10.3333 11 14 14.00 29.83 17.33 12.83 11.1667 13 15 28.25 33.42 14.27 9.83 8.6 10.9833 16 4.95 4.48 3.67 3.98 4.03333 3.96667 17 14.55 12.83 10.17 12.33 10.6667 9.83333 18 26.78 34.39 38.65 39.66 36.795 37.1 19 40.89 43.83 41.31 40.86 39.31 40.46 20 53.00 55.00 50.50 47.00 48 49 21 62.50 64.00 61.00 61.00 61 61 22 0.05 0.19 0.02 0.01 0.0098 0.00884 23 0.01 0.05 0.00 0.00 0.00377 0.00296 24 0.00 0.01 0.00 0.00 0.00084 0.00082 25 33376.44 16427.35 15747.62 18531.77 17182.5 16833.3 26 7906.66 3979.78 4609.25 5801.02 6581.38 5656.27 27 2247.01 1270.04 1560.53 1732.85 1472.18 1560.8 28 1.56 2.82 3.20 2.88 3.25697 3.27691 29 76.39 1338.58 76.82 34.46 28.2774 41.3294 WO 2013/128448 PCT/IL2013/050172 118 Ecotype/Treatment Line-7 Line-8 Line-9 Line-10 Line-i1 Line-12 30 219.14 1518.31 162.79 82.77 75.366 83.49 Table 28. Table 29 Measured parameters in B. juncea accessions at various population densities (line 13-14) Ecotype/Treatment Line-13 Line-14 1 5.44167 8.76667 2 0.02417 0.06583 3 135.75 157.333 4 15.5 12.8333 5 8 3 6 18 16 7 4 11 8 25 109 9 2.35 8 10 25.3333 33.8333 11 25.0667 45.25 12 4.23333 4.43333 13 10.6667 13.1667 14 9 18.5 15 6.35 21.5833 16 3.7 4.71667 17 9 11.1667 18 37.61 37.545 19 47.48 39.21 20 49 51.5 21 61 61 22 0.00839 0.03974 23 0.00253 0.01152 24 0.00073 0.0034 25 23055.7 20833.3 26 6882.52 6039.66 27 2005.71 1780.97 28 3.43024 2.77362 29 92.8963 218.155 30 143.902 328.97 Table 29: Provided are the values of each of the parameters (as described above) 5 measured in B. juncea (grown in seven population densities (Populat. Density) under normal conditions. Param. = parameter.
WO 2013/128448 PCT/IL2013/050172 119 Table 30 Correlation between the expression level of selected genes of some embodiments of the invention in various tissues and the phenotypic performance under normal conditions at different densities across B. Juncea accessions 5 Cor Gene R P value Exp. r. Gene R P value Exp. Corr. Name set Set Name set Set ID ID LYD537 0.90 6.06E-03 2 9 LYD537 0.89 6.54E-03 2 8 LYD537 0.94 1.69E-03 2 1 LYD537 0.88 9.11E-03 2 7 LYD537 0.89 7.83E-03 2 15 LYD537 0.76 4.62E-02 2 16 LYD537 0.99 4.02E-05 2 24 LYD537 0.97 2.88E-04 2 13 LYD537 0.98 1.22E-04 2 29 LYD537 0.75 5.44E-02 2 11 LYD537 0.98 8.94E-05 2 2 LYD537 0.83 2.18E-02 2 14 LYD537 0.99 4.94E-05 2 23 LYD537 0.97 2.91E-04 2 30 LYD537 0.88 8.80E-03 2 21 LYD537 0.98 5.98E-05 2 22 LYD537 0.82 2.42E-02 2 17 LYD538 0.82 2.28E-02 2 9 LYD538 0.81 2.80E-02 2 8 LYD538 0.89 7.67E-03 2 1 LYD538 0.82 2.47E-02 2 7 LYD538 0.81 2.78E-02 2 15 LYD538 0.94 1.52E-03 2 24 LYD538 0.95 1.10E-03 2 13 LYD538 0.94 1.59E-03 2 29 LYD538 0.94 1.59E-03 2 2 LYD538 0.73 6.OOE-02 2 14 LYD538 0.94 1.71E-03 2 23 LYD538 0.92 3.68E-03 2 30 LYD538 0.93 2.62E-03 2 21 LYD538 0.94 1.94E-03 2 22 LYD538 0.75 5.03E-02 2 17 LYD539 0.70 7.93E-02 2 9 LYD539 0.80 3.23E-02 2 8 LYD539 0.80 3.12E-02 2 15 LYD539 0.92 3.61E-03 2 16 LYD539 0.93 2.08E-03 2 12 LYD539 0.85 1.43E-02 2 11 LYD539 0.76 4.93E-02 2 14 LYD540 0.78 3.84E-02 2 6 LYD540 0.88 9.11E-03 2 5 1 1 1 Table 30. Provided are the coirelations (R) between the expression levels of yield improving genes and their homologues in tissues [meristem and flower; Expression sets (Exp)] and the phenotypic performance in various yield, biomass, growth rate and/or vigor components [Correlation vector (corr.)] under stress conditions or normal conditions across B, juncea 10 accessions. P = p value. EXAMPLE 8 15 PRODUCTION OF SORGHUM TRANSCRIPTOME AND HIGH THROUGHPUT CORRELATION ANALYSIS WITH ABST RELATED PARAMETERS USING 44K SORGHUM OLIGONUCLEOTIDE MICRO-ARRAYS In order to produce a high throughput correlation analysis between plant phenotype and gene expression level, the present inventors utilized a sorghum 20 oligonucleotide micro-array, produced by Agilent Technologies [Hypertext Transfer Protocol://World Wide Web (dot) chem. (dot) agilent (dot) com/Scripts/PDS (dot) asp lPage=50879]. The array oligonucleotide represents about 44,000 sorghum genes WO 2013/128448 PCT/IL2013/050172 120 and transcripts. In order to define correlations between the levels of RNA expression with ABST, yield and NUE components or vigor related parameters, various plant characteristics of 17 different sorghum hybrids were analyzed. Among them, 10 hybrids encompassing the observed variance were selected for RNA expression 5 analysis. The correlation between the RNA levels and the characterized parameters was analyzed using Pearson correlation test [Hypertext Transfer Protocol://World Wide Web (dot) davidmlane (dot) com/hyperstat/A34739 (dot) html]. Correlation of Sorghum varieties across ecotypes grown under regular growth conditions, severe drought conditions and low nitrogen conditions 10 Experimental procedures 17 Sorghum varieties were grown in 3 repetitive plots, in field. Briefly, the growing protocol was as follows: 1. Regular growth conditions: sorghum plants were grown in the field using commercial fertilization and irrigation protocols (370 liter per meter 2 , fertilization of 14 15 units of 21% urea per entire growth period). 2. Drought conditions: sorghum seeds were sown in soil and grown under normal condition until around 35 days from sowing, around stage V8 (eight green leaves are fully expanded, booting not started yet). At this point, irrigation was stopped, and severe drought stress was developed. 20 3. Low Nitrogen fertilization conditions: sorghum plants were fertilized with 50% less amount of nitrogen in the field than the amount of nitrogen applied in the regular growth treatment. All the fertilizer was applied before flowering. Analyzed Sorghum tissues - All 10 selected Sorghum hybrids were sample per each treatment. Tissues [Flag leaf, Flower meristem and Flower] from plants growing 25 under normal conditions, severe drought stress and low nitrogen conditions were sampled and RNA was extracted as described above. Each micro-array expression information tissue type has received a Set ID as summarized in Table 31 below. Table 31 30 Sorghum transcriptome expression sets Expression Set Set ID Flag leaf Normal 1 Flower meristem Normal 2 Flower Normal 3 WO 2013/128448 PCT/IL2013/050172 121 Expression Set Set ID Flag leaf Low Nitrogen 4 Flower meristem Low Nitrogen 5 Flower Low Nitrogen 6 Flag leaf Drought 7 Flower meristem Drought 8 Flower Drought 9 Table 31: Provided are the sorghum transcriptome expression sets 1, 2, 3 and 4. Flag leaf = the leaf below the flower; Flower meristem = Apical meristem following panicle initiation; Flower = the flower at the anthesis day. Expression sets 1, 2 and 3 are from plants grown under normal conditions. Expression sets 4-6 derived from plants grown under low 5 Nitrogen conditions. Expression sets 7-9 are from plants grown under drought conditions. The following parameters were collected using digital imaging system: At the end of the growing period the grains were separated from the Plant 'Head' and the following parameters were measured and collected: 10 Average Grain Area (cm 2 ) - A sample of -200 grains were weighted, photographed and images were processed using the below described image processing system. The grain area was measured from those images and was divided by the number of grains. (I) Upper and Lower Ratio Average of Grain Area, width, diameter and 15 perimeter - Grain projection of area, width, diameter and perimeter were extracted from the digital images using open source package imagej (nih). Seed data was analyzed in plot average levels as follows: Average of all seeds; Average of upper 20% fraction - contained upper 20% fraction of seeds; 20 Average of lower 20% fraction - contained lower 20% fraction of seeds; Further on, ratio between each fraction and the plot average was calculated for each of the data parameters. At the end of the growing period 5 'Heads' were, photographed and images were processed using the below described image processing system. 25 (II) Head Average Area (cm 2 ) - At the end of the growing period 5 'Heads' were, photographed and images were processed using the below described image processing system. The 'Head' area was measured from those images and was divided by the number of 'Heads'. (III) Head Average Length (cm) - At the end of the growing period 5 'Heads' 30 were, photographed and images were processed using the below described image WO 2013/128448 PCT/IL2013/050172 122 processing system. The 'Head' length (longest axis) was measured from those images and was divided by the number of 'Heads'. (IV) Head Average width (cm) - At the end of the growing period 5 'Heads' were, photographed and images were processed using the below described image 5 processing system. The 'Head' width was measured from those images and was divided by the number of 'Heads'. (V) Head Average width (cm) - At the end of the growing period 5 'Heads' were, photographed and images were processed using the below described image processing system. The 'Head' perimeter was measured from those images and was 10 divided by the number of 'Heads'. The image processing system was used, which consists of a personal desktop computer (Intel P4 3.0 GHz processor) and a public domain program - ImageJ 1.37, Java based image processing software, which was developed at the U.S. National Institutes of Health and is freely available on the internet at Hypertext Transfer 15 Protocol://rsbweb (dot) nih (dot) gov/. Images were captured in resolution of 10 Mega Pixels (3888x2592 pixels) and stored in a low compression JPEG (Joint Photographic Experts Group standard) format. Next, image processing output data for seed area and seed length was saved to text files and analyzed using the JMP statistical analysis software (SAS institute). 20 Additional parameters were collected either by sampling 5 plants per plot or by measuring the parameter across all the plants within the plot. Total Grain Weight/Head (gr.) (grain yield) - At the end of the experiment (plant 'Heads') heads from plots within blocks A-C were collected. 5 heads were separately threshed and grains were weighted, all additional heads were threshed 25 together and weighted as well. The average grain weight per head was calculated by dividing the total grain weight by number of total heads per plot (based on plot). In case of 5 heads, the total grains weight of 5 heads was divided by 5. FW Head/Plant gram - At the end of the experiment (when heads were harvested) total and 5 selected heads per plots within blocks A-C were collected 30 separately. The heads (total and 5) were weighted (gr.) separately and the average fresh weight per plant was calculated for total (FW Head/Plant gr. based on plot) and for 5 (FW Head/Plant gr. based on 5 plants).
WO 2013/128448 PCT/IL2013/050172 123 Plant height - Plants were characterized for height during growing period at 5 time points. In each measure, plants were measured for their height using a measuring tape. Height was measured from ground level to top of the longest leaf. SPAD - Chlorophyll content was determined using a Minolta SPAD 502 5 chlorophyll meter and measurement was performed 64 days post sowing. SPAD meter readings were done on young fully developed leaf. Three measurements per leaf were taken per plot. Vegetative fresh weight and Heads - At the end of the experiment (when Inflorescence were dry) all Inflorescence and vegetative material from plots within 10 blocks A-C were collected. The biomass and Heads weight of each plot was separated, measured and divided by the number of Heads. Plant biomass (Fresh weight)- At the end of the experiment (when Inflorescence were dry) the vegetative material from plots within blocks A-C were collected. The plants biomass without the Inflorescence were measured and divided by 15 the number of Plants. FW Heads/(FW Heads + FW Plants) - The total fresh weight of heads and their respective plant biomass were measured at the harvest day. The heads weight was divided by the sum of weights of heads and plants. Experimental Results 20 17 different sorghum varieties were grown and characterized for different parameters: The average for each of the measured parameter was calculated using the JMP software (Tables 33-34) and a subsequent correlation analysis between the various transcriptome expression sets (Table 31) and the average parameters (Tables 33-34), was conducted (Table 35). Results were then integrated to the database. 25 Table 32 Sorghum correlated parameters (vectors) Correlated parameter with Correlation ID Total grain weight /Head gr (based on plot), Normal 1 Total grain weight /Head gr (based on 5 heads), Normal 2 Head Average Area (cm 2 ), Normal 3 Head Average Perimeter (cm), Normal 4 Head Average Length (cm), Normal 5 Head Average Width (cm), Normal 6 Average Grain Area (cm 2 ), Normal 7 Upper Ratio Average Grain Area, Normal 8 WO 2013/128448 PCT/IL2013/050172 124 Correlated parameter with Correlation ID Lower Ratio Average Grain Area, Normal 9 Lower Ratio Average Grain Perimeter, Normal 10 Lower Ratio Average Grain Length, Normal 11 Lower Ratio Average Grain Width, Normal 12 Final Plant Height (cm), Normal 13 FW - Head/Plant gr (based on 5 plants), Normal 14 FW - Head/Plant gr (based on plot), Normal 15 FW/Plant gr (based on plot), Normal 16 Leaf SPAD 64 DPS (Days Post Sowing), Normal 17 FW Heads / (FW Heads + FW Plants) (all plot), Normal 18 [Plant biomass (FW)/SPAD 64 DPS],Normal 19 [Grain Yield + plant biomass/SPAD 64 DPS], Normal 20 [Grain yield /SPAD 64 DPS], Normal 21 Total grain weight /Head (based on plot) gr, Low N 22 Total grain weight /Head gr (based on 5 heads), Low N 23 Head Average Area (cm 2 ), Low N 24 Head Average Perimeter (cm), Low N 25 Head Average Length (cm), Low N 26 Head Average Width (cm), Low N 27 Average Grain Area (cm 2 ), Low N 28 Upper Ratio Average Grain Area, Low N 29 Lower Ratio Average Grain Area, Low N 30 Lower Ratio Average Grain Perimeter, Low N 31 Lower Ratio Average Grain Length, Low N 32 Lower Ratio Average Grain Width, Low N 33 Final Plant Height (cm), Low N 34 FW - Head/Plant gr (based on 5 plants), Low N 35 FW - Head/Plant gr (based on plot), Low N 36 FW/Plant gr (based on plot), Low N 37 Leaf SPAD 64 DPS (Days Post Sowing), Low N 38 FW Heads / (FW Heads+ FW Plants)(all plot), Low N 39 [Plant biomass (FW)/SPAD 64 DPS], Low N 40 [Grain Yield + plant biomass/SPAD 64 DPS], Low N 41 [Grain yield /SPAD 64 DPS], Low N 42 Total grain weight /Head gr (based on plot) Drought 43 Head Average Area (cm 2 ), Drought 44 Head Average Perimeter (cm), Drought 45 Head Average Length (cm), Drought 46 Head Average Width (cm), Drought 47 Average Grain Area (cm 2 ), Drought 48 Upper Ratio Average Grain Area, Drought 49 Final Plant Height (cm), Drought 50 FW - Head/Plant gr (based on plot), Drought 51 FW/Plant gr (based on plot), Drought 52 Leaf SPAD 64 DPS (Days Post Sowing), Drought 53 FW Heads / (FW Heads + FW Plants)(all plot), Drought 54 [Plant biomass (FW)/SPAD 64 DPS], Drought 55 Table 32. Provided are the Sorghum correlated parameters (vectors). "gr." = grams; "SPAD" = chlorophyll levels; "FW" = Plant Fresh weight; "normal" = standard growth conditions.
WO 2013/128448 PCT/IL2013/050172 125 Table 33 Measured parameters in Sorghum accessions Ecotypel Treatmen Line-i Line-2 Line-3 Line-4 Line-5 Line-6 Line- Line-8 Line-9 t 1 31.12 26.35 18.72 38.38 26.67 28.84 47.67 31.00 39.99 2 47.40 46.30 28.37 70.40 32.15 49.23 63.45 44.45 56.65 3 120.14 167.60 85.14 157.26 104.00 102.48 168.5 109.32 135.13 4 4 61.22 67.90 56.26 65.38 67.46 67.46 74.35 56.16 61.64 5 25.58 26.84 21.02 26.84 23.14 21.82 31.33 23.18 25.70 6 5.97 7.92 4.87 7.43 5.58 5.88 6.78 5.99 6.62 7 0.10 0.11 0.13 0.13 0.14 0.14 0.11 0.11 0.10 8 1.22 1.30 1.13 1.14 1.16 1.15 1.19 1.23 1.25 9 0.83 0.74 0.78 0.80 0.70 0.70 0.83 0.81 0.84 10 0.91 0.87 0.91 0.95 0.90 0.91 0.91 0.91 0.92 11 0.91 0.88 0.92 0.91 0.89 0.88 0.91 0.90 0.92 12 0.91 0.83 0.85 0.87 0.79 0.80 0.90 0.89 0.91 13 95.25 79.20 197.85 234.20 189.40 194.67 117.2 92.80 112.65 5 14 406.50 518.00 148.00 423.00 92.00 101.33 423.5 386.50 409.50 0 15 175.15 223.49 56.40 111.62 67.34 66.90 126.1 107.74 123.86 8 16 162.56 212.59 334.83 313.46 462.28 318.26 151.1 137.60 167.98 3 17 43.01 . 43.26 44.74 45.76 41.61 45.21 45.14 43.03 18 0.51 0.51 0.12 0.26 0.12 0.18 0.46 0.43 0.42 19 0.72 0.43 0.86 0.58 0.69 1.05 0.69 0.93 0.84 20 4.50 8.17 7.87 10.68 8.34 4.40 3.74 4.83 3.67 21 3.78 7.74 7.01 10.10 7.65 3.34 3.05 3.90 2.83 22 25.95 30.57 19.37 35.62 25.18 22.18 49.96 27.48 51.12 23 50.27 50.93 36.13 73.10 37.87 36.40 71.67 35.00 76.73 24 96.24 214.72 98.59 182.83 119.64 110.19 172.3 84.81 156.25 6 25 56.32 79.20 53.25 76.21 67.27 59.49 79.28 51.52 69.88 26 23.22 25.58 20.93 28.43 24.32 22.63 32.11 20.38 26.69 27 5.26 10.41 5.93 8.25 6.19 6.12 6.80 5.25 7.52 28 0.11 0.11 0.14 0.12 0.14 0.13 0.12 0.12 0.12 29 1.18 1.31 1.11 1.21 1.19 1.18 1.16 1.23 1.17 30 0.82 0.77 0.81 0.79 0.78 0.80 0.83 0.79 0.81 31 0.90 0.88 0.92 0.90 0.92 0.92 0.92 0.89 0.90 32 0.91 0.90 0.92 0.90 0.91 0.93 0.92 0.89 0.90 33 0.90 0.85 0.89 0.88 0.86 0.87 0.91 0.89 0.90 34 104.00 80.93 204.73 125.40 225.40 208.07 121.4 100.27 121.13 0 35 388.00 428.67 297.67 280.00 208.33 303.67 436.0 376.33 474.67 0 36 214.78 205.05 73.49 122.96 153.07 93.23 134.1 774 129.63 ____ ____ ____1 WO 2013/128448 PCT/IL2013/050172 126 Ecotypel Treatmen Line-i Line-2 Line-3 Line-4 Line-5 Line-6 Line- Line-8 Line-9 t 37 204.78 199.64 340.51 240.60 537.78 359.40 149.2 129.06 178.71 0 38 38.33 38.98 42.33 40.90 43.15 39.85 42.68 43.31 39.01 39 0.51 0.51 0.17 0.39 0.21 0.19 0.48 0.37 0.42 40 5.34 5.12 8.05 5.88 12.46 9.02 3.50 2.98 4.58 41 6.02 5.91 8.50 6.75 13.05 9.58 4.67 3.61 5.89 42 0.68 0.78 0.46 0.87 0.58 0.56 1.17 0.63 1.31 43 22.11 16.77 9.19 104.44 3.24 22.00 9.97 18.58 29.27 44 83.14 107.79 88.68 135.91 90.76 123.95 86.06 85.20 113.10 45 52.78 64.49 56.59 64.37 53.21 71.66 55.61 52.96 69.83 46 21.63 21.94 21.57 22.01 20.99 28.60 21.35 20.81 24.68 47 4.83 6.31 5.16 7.78 5.28 5.49 5.04 5.07 5.77 48 0.10 0.11 0.11 0.09 0.09 0.11 49 1.31 1.19 1.29 1.46 1.21 1.21 50 89.40 75.73 92.10 94.30 150.80 110.73 99.20 84.00 99.00 51 154.90 122.02 130.51 241.11 69.03 186.41 62.11 39.02 58.94 52 207.99 138.02 255.41 402.22 233.55 391.75 89.31 50.61 87.02 53 40.58 40.88 45.01 42.30 45.24 40.56 44.80 45.07 40.65 54 0.42 0.47 0.42 0.37 0.23 0.31 0.41 0.44 0.40 55 5.13 3.38 5.67 9.51 5.16 9.66 1.99 1.12 2.14 Table 33: Provided are the values of each of the parameters (as described above) measured in Sorghum accessions (ecotype) under normal, low nitrogen and drought conditions. Growth conditions are specified in the experimental procedure section. 5 Table 34 Additional measured parameters in Sorghum accessions Ecotypel Line- Line-1 Line-12 Line- Line- Line- Line- Line-17 Treatment 10 13 14 15 16 1 38.36 32.10 32.69 32.79 51.53 35.71 38.31 42.44 2 60.00 45.45 58.19 70.60 70.10 53.95 59.87 52.65 3 169.03 156.10 112.14 154.74 171.70 168.51 162.51 170.46 4 71.40 68.56 56.44 67.79 71.54 78.94 67.03 74.11 5 28.82 28.13 22.97 28.09 30.00 30.54 27.17 29.26 6 7.42 6.98 6.19 7.02 7.18 7.00 7.39 7.35 7 0.12 0.12 0.11 0.12 0.11 0.10 0.11 0.11 8 1.24 1.32 1.22 1.18 1.18 1.22 1.25 1.22 9 0.79 0.77 0.80 0.81 0.82 0.81 0.82 0.82 10 0.93 0.91 0.92 0.90 0.91 0.90 0.91 0.91 11 0.92 0.89 0.91 0.91 0.91 0.90 0.90 0.91 12 0.85 0.86 0.88 0.90 0.90 0.91 0.90 0.90 13 97.50 98.00 100.00 105.60 151.15 117.10 124.45 126.50 14 328.95 391.00 435.75 429.50 441.00 415.75 429.50 428.50 15 102.75 82.33 77.59 91.17 150.44 109.10 107.58 130.88 16 128.97 97.62 99.32 112.24 157.42 130.55 135.66 209.21 17 45.59 44.83 45.33 46.54 43.99 45.09 45.14 43.13 18 0.44 0.46 0.45 0.45 0.51 0.46 0.44 0.39 WO 2013/128448 PCT/IL2013/050172 127 Ecotypel Line- Line-1 Line-12 Line- Line- Line- Line- Line-17 Treatment 10 13 14 15 16 19 0.72 0.72 0.70 1.17 0.79 0.85 0.98 20 2.89 2.91 3.12 4.75 3.69 3.85 5.84 21 2.18 2.19 2.41 3.58 2.90 3.01 4.85 22 36.84 29.45 26.70 29.42 51.12 37.04 39.85 41.78 23 57.58 42.93 36.47 68.60 71.80 49.27 43.87 52.07 24 136.71 137.70 96.54 158.19 163.95 138.39 135.46 165.64 25 66.17 67.37 57.90 70.61 73.76 66.87 65.40 75.97 26 26.31 25.43 23.11 27.87 28.88 27.64 25.52 30.33 27 6.59 6.85 5.32 7.25 7.19 6.27 6.57 6.82 28 0.13 0.13 0.12 0.12 0.11 0.11 0.12 0.11 29 1.22 1.24 1.19 1.23 1.16 1.34 1.21 1.21 30 0.77 0.74 0.80 0.79 0.82 0.80 0.81 0.81 31 0.91 0.89 0.90 0.90 0.91 0.89 0.90 0.90 32 0.91 0.89 0.90 0.89 0.91 0.89 0.89 0.90 33 0.86 0.84 0.90 0.89 0.91 0.90 0.90 0.90 34 94.53 110.00 115.07 104.73 173.67 115.60 138.80 144.40 35 437.67 383.00 375.00 425.00 434.00 408.67 378.50 432.00 36 99.83 76.95 84.25 92.24 138.83 113.32 95.50 129.49 37 124.27 101.33 132.12 117.90 176.99 143.67 126.98 180.45 38 42.71 40.08 43.98 45.44 44.75 42.58 43.81 46.73 39 0.44 0.43 0.39 0.44 0.44 0.44 0.43 0.42 40 2.91 2.53 3.00 2.60 3.96 3.38 2.90 3.86 41 3.77 3.26 3.61 3.24 5.10 4.25 3.81 4.76 42 0.86 0.73 0.61 0.65 1.14 0.87 0.91 0.89 43 10.45 14.77 12.86 18.24 11.60 18.65 16.36 44 100.79 80.41 126.89 86.41 92.29 77.89 76.93 45 65.14 55.27 69.06 53.32 56.29 49.12 51.88 46 24.28 21.95 24.98 19.49 20.42 16.81 18.88 47 5.37 4.66 6.35 5.58 5.76 5.86 5.10 48 49 50 92.20 81.93 98.80 86.47 99.60 83.00 83.53 92.30 51 76.37 33.47 42.20 41.53 131.67 60.84 44.33 185.44 52 120.43 37.21 48.18 44.20 231.60 116.01 123.08 342.50 53 45.43 42.58 44.18 44.60 42.41 43.25 40.30 40.75 54 0.44 0.47 0.47 0.48 0.35 0.35 0.23 0.33 55 2.65 0.87 1.09 0.99 5.46 2.68 3.05 8.40 Table 34: Provided are the values of each of the parameters (as described above) measured in Sorghum accessions (ecotype) under normal, low nitrogen and drought conditions. Growth conditions are specified in the experimental procedure section.
WO 2013/128448 PCT/IL2013/050172 128 Table 35 Correlation between the expression level of selected genes of some embodiments of the invention in various tissues and the phenotypic performance under normal or abiotic stress conditions across Sorghum accessions 5 Gene Exp Corr. Gene Exp. Corr. Name R P value set Set Name R P value set Set ID ID LYD604 0.71 3.28E-02 1 20 LYD605 0.72 2.91E-02 1 21 LYD605 0.73 2.49E-02 1 20 LYD606 0.73 1.60E-02 3 13 LYD606 0.90 4.05E-04 3 1 LYD606 0.70 2.31E-02 3 9 LYD606 0.90 4.24E-04 8 53 LYD606 0.76 1.04E-02 6 30 LYD606 0.70 2.29E-02 6 33 LYD606 0.78 8.33E-03 6 32 LYD606 0.82 3.87E-03 6 31 LYD606 0.81 7.55E-03 1 21 LYD606 0.84 4.28E-03 1 20 LYD606 0.92 1.57E-04 9 50 LYD606 0.72 1.90E-02 7 51 LYD607 0.71 2.11E-02 2 13 LYD607 0.71 2.1OE-02 2 1 LYD607 0.82 3.42E-03 4 29 LYD607 0.86 1.33E-03 5 22 LYD607 0.85 1.86E-03 5 42 LYD607 0.80 5.95E-03 5 34 LYD608 0.88 9.15E-04 2 8 LYD608 0.82 4.05E-03 2 7 LYD608 0.86 1.29E-03 4 29 LYD608 0.71 2.22E-02 4 27 LYD608 0.77 8.57E-03 6 39 LYD608 0.75 1.30E-02 6 32 LYD608 0.72 1.77E-02 5 28 LYD608 0.80 9.74E-03 1 21 LYD608 0.83 5.67E-03 1 20 LYD609 0.76 1.04E-02 2 1 LYD609 0.79 6.60E-03 8 55 LYD609 0.71 2.15E-02 8 51 LYD609 0.80 5.47E-03 8 52 LYD609 0.74 1.46E-02 5 36 LYD609 0.74 1.38E-02 5 41 LYD609 0.76 1.04E-02 5 37 LYD610 0.89 6.35E-04 4 22 LYD610 0.78 7.43E-03 4 26 LYD610 0.83 2.67E-03 4 42 LYD610 0.71 2.21E-02 4 31 LYD610 0.81 4.83E-03 4 34 LYD610 0.78 1.41E-02 8 43 LYD610 0.77 1.61E-02 1 21 LYD610 0.78 7.89E-03 1 15 LYD610 0.77 1.48E-02 1 20 Table 35. Provided are the correlations (R) between the expression levels of yield improving genes and their homologues in tissues [Flag leaf, Flower meristem, stem and Flower; Expression sets (Exp)] and the phenotypic performance in various yield, biomass, growth rate and/or vigor components [Correlation vector (corr.)] under stress conditions (e.g., drought and 10 low nitrogen) or normal conditions across Sorghum accessions. P = p value. EXAMPLE 9 PRODUCTION OF SOYBEAN (GLYCINE MAX) TRANSCRIPTOME AND HIGH 15 THROUGHPUT CORRELATION ANALYSIS WITH YIELD PARAMETERS USING 44K B. SOYBEAN OLIGONUCLEOTIDE MICRO-ARRAYS In order to produce a high throughput correlation analysis, the present inventors utilized a Soybean oligonucleotide micro-array, produced by Agilent Technologies [Hypertext Transfer Protocol://World Wide Web (dot) chem. (dot) agilent (dot) 20 com/Scripts/PDS (dot) asp lPage=50879]. The array oligonucleotide represents about 42,000 Soybean genes and transcripts. In order to define correlations between the WO 2013/128448 PCT/IL2013/050172 129 levels of RNA expression with yield components or plant architecture related parameters or plant vigor related parameters, various plant characteristics of 29 different Glycine max varieties were analyzed and 12 varieties were further used for RNA expression analysis. The correlation between the RNA levels and the characterized 5 parameters was analyzed using Pearson correlation test. Correlation of Glycine max genes' expression levels with phenotypic characteristics across ecotype Experimental procedures 29 Soybean varieties were grown in three repetitive plots, in field. Briefly, the 10 growing protocol was as follows: Soybean seeds were sown in soil and grown under normal conditions until harvest. In order to define correlations between the levels of RNA expression with yield components or plant architecture related parameters or vigor related parameters, 12 different Soybean varieties (out of 29 varieties) were analyzed and used for gene expression analyses. Analysis was performed at two pre-determined 15 time periods: at pod set (when the soybean pods are formed) and at harvest time (when the soybean pods are ready for harvest, with mature seeds). Table 36 Soybean transcriptome expression sets Expression Set Set ID Apical meristem at vegetative stage under normal growth condition 1 Leaf at vegetative stage under normal growth condition 2 Leaf at flowering stage under normal growth condition 3 Leaf at pod setting stage under normal growth condition 4 Root at vegetative stage under normal growth condition 5 Root at flowering stage under normal growth condition 6 Root at pod setting stage under normal growth condition 7 Stem at vegetative stage under normal growth condition 8 Stem at pod setting stage under normal growth condition 9 Flower bud at flowering stage under normal growth condition 10 Pod (R3-R4) at pod setting stage under normal growth condition 11 20 Table 36. RNA extraction - All 12 selected Soybean varieties were sample per treatment. Plant tissues [leaf, root. Stem. Pod, apical meristem. Flower buds] growing under 25 normal conditions were sampled and RNA was extracted as described above. The collected data parameters were as follows: WO 2013/128448 PCT/IL2013/050172 130 Main branch base diameter [mm] at pod set - the diameter of the base of the main branch (based diameter) average of three plants per plot. Fresh weight [gr/plant] at pod set - total weight of the vegetative portion above ground (excluding roots) before drying at pod set, average of three plants per plot. 5 Dry weight [gr/plant] at pod set - total weight of the vegetative portion above ground (excluding roots) after drying at 70'C in oven for 48 hours at pod set, average of three plants per plot. Total number of nodes with pods on lateral branches [value/plant]- counting of nodes which contain pods in lateral branches at pod set, average of three plants per 10 plot. Number of lateral branches at pod set [value/plant] - counting number of lateral branches at pod set, average of three plants per plot. Total weight of lateral branches at pod set [gr/plant] - weight all lateral branches at pod set, average of three plants per plot. 15 Total weight of pods on main stem at pod set [gr/plant] - weight all pods on main stem at pod set, average of three plants per plot. Total number of nodes on main stem [value/plant] - count of number of nodes on main stem starting from first node above ground, average of three plants per plot. Total number of pods with 1 seed on lateral branches at pod set [value/plant] 20 count the number of pods containing 1 seed in all lateral branches at pod set, average of three plants per plot. Total number of pods with 2 seeds on lateral branches at pod set [value/plant] - count the number of pods containing 2 seeds in all lateral branches at pod set, average of three plants per plot. 25 Total number of pods with 3 seeds on lateral branches at pod set [value/plant] - count the number of pods containing 3 seeds in all lateral branches at pod set, average of three plants per plot. Total number of pods with 4 seeds on lateral branches at pod set [value/plant] - count the number of pods containing 4 seeds in all lateral branches at pod set, average 30 of three plants per plot.
WO 2013/128448 PCT/IL2013/050172 131 Total number of pods with 1 seed on main stem at pod set [value/plant] - count the number of pods containing 1 seed in main stem at pod set, average of three plants per plot. Total number of pods with 2 seeds on main stem at pod set [value/plant] 5 count the number of pods containing 2 seeds in main stem at pod set, average of three plants per plot. Total number of pods with 3 seeds on main stem at pod set [value/plant] count the number of pods containing 3 seeds in main stem at pod set, average of three plants per plot. 10 Total number of pods with 4 seeds on main stem at pod set [value/plant] count the number of pods containing 4 seeds in main stem at pod set, average of three plants per plot. Total number of seeds per plant at pod set [value/plant] - count number of seeds in lateral branches and main stem at pod set, average of three plants per plot. 15 Total number of seeds on lateral branches at pod set [value/plant] - count total number of seeds on lateral branches at pod set, average of three plants per plot. Total number of seeds on main stem at pod set [value/plant] - count total number of seeds on main stem at pod set, average of three plants per plot. Plant height at pod set [cm/plant] - total length from above ground till the tip of 20 the main stem at pod set, average of three plants per plot. Plant height at harvest [cm/plant] - total length from above ground till the tip of the main stem at harvest, average of three plants per plot. Total weight of pods on lateral branches at pod set [gr/plant] - weight of all pods on lateral branches at pod set, average of three plants per plot. 25 Ratio of the number of pods per node on main stem at pod set - calculated in Formula X, average of three plants per plot. Formula X: Total number of pods on main stem /Total number of nodes on main stem, average of three plants per plot. Ratio of total number of seeds in main stem to number of seeds on lateral 30 branches - calculated in formula XI, average of three plants per plot. Formula XI: Total number of seeds on main stem at pod set/ Total number of seeds on lateral branches at pod set.
WO 2013/128448 PCT/IL2013/050172 132 Total weight of pods per plant at pod set [gr/plant] - weight all pods on lateral branches and main stem at pod set, average of three plants per plot. Days till 50% flowering [days] - number of days till 50% flowering for each plot. 5 Days till 100%flowering [days] - number of days till 100% flowering for each plot. Maturity [days] - measure as 95% of the pods in a plot have ripened (turned 100% brown). Delayed leaf drop and green stems are not considered in assigning maturity. Tests are observed 3 days per week, every other day, for maturity. The 10 maturity date is the date that 95% of the pods have reached final color. Maturity is expressed in days after August 31 [according to the accepted definition of maturity in USA, Descriptor list for SOYBEAN, Hypertext Transfer Protocol://World Wide Web (dot) ars-grin (dot) gov/cgi-bin/npgs/html/desclist (dot) pl 51]. Seed quality [ranked 1-5] - measure at harvest, a visual estimate based on 15 several hundred seeds. Parameter is rated according to the following scores considering the amount and degree of wrinkling, defective coat (cracks), greenishness, and moldy or other pigment. Rating is 1-very good, 2-good, 3-fair, 4-poor, 5-very poor. Lodging [ranked 1-5] - is rated at maturity per plot according to the following scores: 1-most plants in a plot are erected, 2-All plants leaning slightly or a few plants 20 down, 3-all plants leaning moderately, or 25%-50% down, 4-all plants leaning considerably, or 50%-80% down, 5-most plants down. Note: intermediate score such as 1.5 are acceptable. Seed size [gr] - weight of 1000 seeds per plot normalized to 13 % moisture, measure at harvest. 25 Total weight of seeds per plant [gr/plant] - calculated at harvest (per 2 inner rows of a trimmed plot) as weight in grams of cleaned seeds adjusted to 13% moisture and divided by the total number of plants in two inner rows of a trimmed plot. Yield at harvest [bushels/hectare] - calculated at harvest (per 2 inner rows of a trimmed plot) as weight in grams of cleaned seeds, adjusted to 13% moisture, and then 30 expressed as bushels per acre.
WO 2013/128448 PCT/IL2013/050172 133 Average lateral branch seeds per pod [number] - Calculate Number of Seeds on lateral branches-at pod set and divide by the Number of Total number of pods with seeds on lateral branches-at pod set. Average main stem seeds per pod [number] - Calculate Total Number of Seeds 5 on main stem at pod set and divide by the Number of Total number of pods with seeds on main stem at pod setting. Main stem average internode length [cm] - Calculate Plant height at pod set and divide by the Total number of nodes on main stem at pod setting. Total Number of pods with seeds on main stem [number] - count all pods 10 containing seeds on the main stem at pod setting. Total Number of pods with seeds on lateral branches [number]- count all pods containing seeds on the lateral branches at pod setting. Total number of pods per plant at pod set [number]- count pods on main stem and lateral branches at pod setting. 15 Experimental Results Twelve different Soybean varieties were grown and characterized for 40 parameters as specified above. The average for each of the measured parameters was calculated using the JMP software and values are summarized in Tables 38-39 below. Subsequent correlation analysis between the various transcriptome expression sets and 20 the average parameters was conducted. Results were then integrated to the database (Table 40). Table 37 Soybean correlated parameters (vectors) 25 Correlated parameter with Correlation ID Base diameter at pod set (mm) 1 DW at pod set (gr) 2 fresh weight at pod set (gr) 3 Total number of nodes with pods on lateral branches (number) 4 Number of lateral branches (number) 5 Total weight of lateral branches at pod set (gr) 6 Total weight of pods on main stem at pod set (gr) 7 Total number of nodes on main stem (number) 8 Total no of pods with 1 seed on lateral branch (number) 9 Number of pods with 1 seed on main stem at pod set (number) 10 Total no of pods with 2 seed on lateral branch (number) 11 Number of pods with 2 seed on main stem (number) 12 Total no of pods with 3 seed on lateral branch (number) 13 WO 2013/128448 PCT/IL2013/050172 134 Correlated parameter with Correlation ID Number of pods with 3 seed on main stem (number) 14 Total no of pods with 4 seed on lateral branch (number) 15 Number of pods with 4 seed on main stem (number) 16 Total number of seeds per plant 17 Total Number of Seeds on lateral branches 18 Total Number of Seeds on main stem at pod set 19 Plant height at pod set (cm) 20 Total weight of pods on lateral branches (gr) 21 Ratio number of pods per node on main stem (ratio) 22 Ratio number of seeds per main stem to seeds per lateral branch 23 (ratio) Total weight of pods per plant (gr) 24 50 percent flowering (days) 25 Maturity (days) 26 100 percent flowering (days) 27 Plant height at harvest (cm) 28 Seed quality (score 1-5) 29 Total weight of seeds per plant (gr/plant) 30 Seed size (gr) 31 Lodging (score 1-5) 32 yield at harvest (bushel/hectare) 33 Average lateral branch seeds per pod (number) 34 Average main stem seeds per pod (number) 35 Total number of pods with seeds on main stem at pod set (number) 36 Number pods with seeds on lateral branches-at pod set (number) 37 Total number of pods per plant at pod set (number) 38 Main stem average internode length (cm/number) 39 Corrected Seed size (gr) 40 Table 37. Table 38 Measured parameters in Soybean varieties (lines 1-6) 5 Ecotype/Treatment Line-i Line-2 Line-3 Line-4 Line-5 Line-6 1 8.33 9.54 9.68 8.11 8.82 10.12 2 53.67 50.33 38.00 46.17 60.83 55.67 3 170.89 198.22 152.56 163.89 224.67 265.00 4 23.00 16.00 23.11 33.00 15.22 45.25 5 9.00 8.67 9.11 9.89 7.67 17.56 6 67.78 63.78 64.89 74.89 54.00 167.22 7 22.11 14.33 16.00 15.00 33.78 9.00 8 16.56 16.78 16.11 18.11 16.78 17.11 9 1.56 3.00 1.78 1.78 5.67 5.63 10 1.11 4.38 1.44 1.44 4.56 1.67 11 17.00 18.75 26.44 32.33 21.56 33.50 12 16.89 16.25 13.22 16.89 27.00 8.11 13 38.44 2.00 26.44 31.33 8.89 82.00 14 29.56 1.75 19.78 22.33 11.67 22.78 15 0.00 0.00 0.00 0.00 0.00 1.50 16 0.00 0.00 0.11 0.11 0.00 0.44 WO 2013/128448 PCT/IL2013/050172 135 Ecotype/Treatment Line-i Line-2 Line-3 Line-4 Line-5 Line-6 17 274.44 99.78 221.67 263.11 169.00 412.50 18 150.89 55.89 134.00 160.44 75.44 324.63 19 123.56 43.89 87.67 102.67 93.56 88.00 20 86.78 69.56 62.44 70.89 69.44 63.89 21 26.00 14.89 20.11 20.11 21.11 30.25 22 2.87 1.38 2.13 2.26 2.60 1.87 23 0.89 0.90 0.87 0.89 2.32 0.37 24 48.11 29.22 36.11 35.11 54.89 38.88 25 61.00 65.33 60.67 61.00 54.67 68.33 26 24.00 43.67 30.33 30.33 38.33 40.00 27 67.33 71.67 67.67 67.33 60.00 74.00 28 96.67 76.67 67.50 75.83 74.17 76.67 29 2.33 3.50 3.00 2.17 2.83 2.00 30 15.09 10.50 17.23 16.51 12.06 10.25 31 89.00 219.33 93.00 86.00 191.33 71.33 32 1.67 1.83 1.17 1.67 2.67 2.83 33 47.57 43.77 50.37 56.30 44.00 40.33 34 2.67 1.95 2.43 2.53 2.13 2.68 35 2.60 1.89 2.52 2.53 2.17 2.59 36 47.56 23.11 34.56 40.78 43.22 33.00 37 57.00 28.56 54.67 65.44 36.11 122.63 38 104.56 51.67 89.22 106.22 79.33 155.63 39 5.24 4.15 3.91 3.92 4.15 3.74 40 89.00 * 93.00 86.00 * 71.33 Table 38. Table 39 Measured parameters in Soybean varieties (lines 7-12) 5 Ecotype/Treatment Line-7 Line-8 Line-9 Line-10 Line-11 Line-12 1 8.46 8.09 8.26 7.73 8.16 7.89 2 48.00 52.00 44.17 52.67 56.00 47.50 3 160.67 196.33 155.33 178.11 204.44 164.22 4 8.25 25.44 21.88 16.33 22.56 24.22 5 11.67 12.11 8.00 9.11 6.78 10.00 6 45.44 83.22 64.33 52.00 76.89 67.00 7 9.03 16.00 15.89 14.56 30.44 18.00 8 18.78 18.89 16.78 21.11 19.33 20.78 9 2.88 3.00 1.25 2.67 1.78 3.00 10 4.00 4.33 2.11 1.89 3.44 1.22 11 8.50 22.78 21.75 10.67 23.78 25.67 12 21.33 17.67 20.33 16.11 28.11 16.56 13 9.00 42.11 32.75 25.67 45.00 44.33 14 11.11 28.22 24.11 36.44 39.67 32.33 15 0.00 0.33 0.00 1.11 0.00 0.00 16 0.00 0.56 0.00 3.89 0.00 0.00 17 136.00 302.78 260.50 264.44 363.00 318.67 18 46.88 176.22 143.00 105.44 184.33 187.33 19 80.00 126.56 115.11 159.00 178.67 131.33 20 89.78 82.11 70.56 101.67 79.56 67.22 WO 2013/128448 PCT/IL2013/050172 136 Ecotype/Treatment Line-7 Line-8 Line-9 Line-10 Line-li Line-12 21 4.13 20.11 17.00 9.22 28.11 22.56 22 1.98 2.71 2.78 2.75 3.70 2.84 23 3.90 0.78 1.18 1.98 1.03 0.83 24 14.25 36.11 32.75 23.78 58.56 40.56 25 66.50 65.67 62.33 67.67 61.67 64.33 26 41.00 38.33 31.00 39.00 27.33 32.67 27 73.00 72.33 68.67 73.67 68.00 70.67 28 101.67 98.33 75.83 116.67 76.67 71.67 29 3.50 2.50 2.17 2.33 2.17 2.17 30 7.30 11.38 15.68 10.83 12.98 15.16 31 88.00 75.00 80.67 75.67 76.33 77.33 32 2.67 2.50 1.83 3.50 3.33 1.50 33 34.23 44.27 53.67 42.47 43.60 52.20 34 2.12 2.58 2.58 2.67 2.62 2.58 35 2.22 2.49 2.47 2.71 2.51 2.61 36 36.44 50.78 43.63 58.33 71.22 50.11 37 20.38 68.22 55.75 40.11 70.56 73.00 38 61.00 119.00 103.25 98.44 141.78 123.11 39 4.80 4.36 4.20 4.82 4.12 3.83 40 88.00 75.00 80.67 75.67 76.33 77.33 Table 39. Table 40 Correlation between the expression level of selected genes of some embodiments of the 5 invention in various tissues and the phenotypic performance under normal conditions across soybean varieties Gene R P value Exp. Corr. Gene R P value Exp. Corr. Name set Set ID Name set Set ID LYD611 0.79 6.52E-03 7 3 LYD611 0.73 1.59E-02 7 1 LYD611 0.79 6.87E-03 5 3 LYD611 0.71 2.08E-02 5 2 LYD611 0.79 6.22E-03 5 32 LYD611 0.74 1.46E-02 5 15 LYD611 0.88 3.55E-03 9 16 LYD611 0.75 4.74E-03 1 3 LYD612 0.74 3.62E-02 9 30 LYD612 0.80 1.83E-02 9 33 LYD613 0.78 7.35E-03 8 13 LYD613 0.76 1.15E-02 8 18 LYD613 0.79 6.10E-03 8 5 LYD613 0.70 2.28E-02 8 17 LYD613 0.75 3.20E-02 9 8 LYD613 0.75 4.90E-03 10 23 LYD613 0.78 2.59E-03 10 9 LYD614 0.79 6.27E-03 7 30 LYD614 0.75 1.33E-02 7 33 LYD614 0.75 1.22E-02 5 8 LYD614 0.75 1.33E-02 8 13 LYD614 0.74 1.37E-02 8 18 LYD614 0.76 1.13E-02 8 5 LYD614 0.74 3.49E-02 9 30 LYD614 0.79 2.02E-02 9 33 LYD614 0.75 4.87E-03 1 20 LYD614 0.73 6.88E-03 10 6 LYD614 0.75 4.90E-03 10 4 LYD615 0.76 1.10E-02 7 20 LYD615 0.81 4.14E-03 7 28 LYD615 0.72 8.42E-03 11 29 LYD615 0.89 5.76E-04 5 14 LYD615 0.88 6.96E-04 5 19 LYD615 0.75 1.22E-02 5 22 LYD615 0.77 2.49E-02 9 5 LYD616 0.78 7.41E-03 8 3 LYD616 0.86 1.37E-03 8 15 LYD616 0.72 1.88E-02 8 6 LYD616 0.80 5.71E-03 8 9 LYD616 0.71 4.69E-02 9 30 LYD616 0.76 2.71E-02 9 33 LYD616 0.72 8.76E-03 4 7 WO 2013/128448 PCT/IL2013/050172 137 Gene R P value Exp. Corr. Gene R P value Exp. Corr. Name set Set ID Name set Set ID LYD616 0.75 4.86E-03 10 13 LYD616 0.72 8.10E-03 10 18 LYD616 0.77 3.73E-03 10 17 LYD617 0.70 2.31E-02 7 30 LYD617 0.71 1.01E-02 11 30 LYD617 0.75 5.35E-03 11 33 LYD617 0.71 2.21E-02 5 18 LYD617 0.81 4.31E-03 5 6 LYD617 0.80 5.72E-03 5 5 LYD617 0.79 6.36E-03 5 4 LYD617 0.80 5.60E-03 5 1 LYD617 0.72 4.53E-02 9 30 LYD617 0.73 3.94E-02 9 24 LYD617 0.72 4.48E-02 9 19 LYD617 0.78 2.12E-02 9 22 LYD617 0.76 2.82E-02 9 7 LYD617 0.72 7.75E-03 1 12 LYD617 0.79 2.14E-03 1 24 LYD617 0.79 2.28E-03 1 7 LYD617 0.72 8.95E-03 10 33 LYD618 0.82 3.46E-03 7 13 LYD618 0.87 1.13E-03 7 18 LYD618 0.83 2.69E-03 7 11 LYD618 0.87 1.23E-03 7 6 LYD618 0.88 8.01E-04 7 4 LYD618 0.88 1.76E-04 11 30 LYD618 0.84 6.36E-04 11 33 LYD618 0.77 8.80E-03 5 13 LYD618 0.76 1.12E-02 5 18 LYD618 0.74 1.50E-02 5 4 LYD618 0.73 1.75E-02 5 17 LYD618 0.71 2.16E-02 8 12 LYD618 0.78 7.21E-03 8 7 LYD618 0.72 4.22E-02 9 14 LYD618 0.71 4.93E-02 9 16 LYD618 0.91 1.47E-03 9 13 LYD618 0.88 4.13E-03 9 18 LYD618 0.73 3.99E-02 9 11 LYD618 0.80 1.61E-02 9 3 LYD618 0.98 3.10E-05 9 15 LYD618 0.95 3.66E-04 9 6 LYD618 0.92 1.24E-03 9 5 LYD618 0.88 3.76E-03 9 4 LYD618 0.92 1.31E-03 9 17 LYD618 0.89 2.69E-03 9 9 LYD618 0.75 7.41E-03 2 13 LYD619 0.75 1.28E-02 7 23 LYD619 0.72 1.83E-02 5 12 LYD619 0.71 2.13E-02 5 19 LYD619 0.76 1.O1E-02 5 22 LYD619 0.82 3.43E-03 8 15 LYD619 0.83 1.02E-02 9 7 LYD619 0.73 7.05E-03 4 14 LYD619 0.73 7.48E-03 4 13 LYD619 0.78 2.88E-03 4 17 LYD620 0.72 1.93E-02 7 8 LYD620 0.71 2.11E-02 7 20 LYD620 0.76 4.11E-03 11 8 LYD620 0.82 3.33E-03 5 29 LYD620 0.71 2.03E-02 5 19 LYD620 0.71 2.11E-02 8 18 LYD620 0.84 2.51E-03 8 3 LYD620 0.85 1.75E-03 8 15 LYD620 0.80 5.24E-03 8 6 LYD620 0.85 1.73E-03 8 5 LYD620 0.72 1.86E-02 8 4 LYD620 0.73 1.67E-02 8 1 LYD620 0.76 1.10E-02 8 9 LYD620 0.72 4.38E-02 9 8 LYD620 0.81 1.57E-02 9 10 LYD620 0.79 2.23E-03 1 3 LYD620 0.76 4.05E-03 1 9 LYD620 0.71 1.04E-02 10 33 LYD621 0.78 7.26E-03 5 14 LYD621 0.84 2.44E-03 5 19 LYD621 0.79 6.70E-03 5 22 LYD621 0.70 2.30E-02 8 13 LYD621 0.74 1.42E-02 8 18 LYD621 0.73 1.72E-02 8 3 LYD621 0.71 2.09E-02 8 15 LYD621 0.72 1.86E-02 8 6 LYD621 0.78 7.80E-03 8 4 LYD621 0.75 1.25E-02 8 9 LYD621 0.74 8.99E-03 2 22 LYD621 0.70 1.11E-02 4 14 LYD621 0.74 5.81E-03 4 33 LYD621 0.71 9.73E-03 4 22 LYD621 0.76 3.82E-03 1 22 LYD622 0.75 1.18E-02 7 33 LYD622 0.83 8.52E-04 11 30 LYD622 0.72 8.59E-03 11 33 LYD622 0.81 4.94E-03 5 23 LYD622 0.70 2.28E-02 8 14 LYD622 0.84 8.41E-03 9 12 LYD622 0.82 1.29E-02 9 3 LYD622 0.73 3.92E-02 9 7 WO 2013/128448 PCT/IL2013/050172 138 Gene R P value Exp. Corr. Gene R P value Exp. Corr. Name set Set ID Name set Set ID LYD622 0.90 2.38E-03 9 15 LYD622 0.90 2.49E-03 9 6 LYD622 0.77 2.48E-02 9 5 LYD622 0.81 1.58E-02 9 4 LYD622 0.85 8.19E-03 9 1 LYD622 0.81 1.38E-02 9 9 LYD623 0.72 8.09E-03 11 19 LYD623 0.74 5.57E-03 11 22 LYD623 0.79 7.12E-03 8 30 LYD623 0.80 5.75E-03 8 33 LYD623 0.81 1.39E-02 9 30 LYD623 0.74 3.69E-02 9 22 LYD624 0.84 2.21E-03 7 13 LYD624 0.86 1.25E-03 7 18 LYD624 0.74 1.47E-02 7 11 LYD624 0.85 1.85E-03 7 6 LYD624 0.85 1.98E-03 7 4 LYD624 0.83 2.84E-03 7 21 LYD624 0.80 5.49E-03 7 17 LYD624 0.75 1.18E-02 5 20 LYD624 0.72 1.80E-02 5 28 LYD624 0.73 1.59E-02 8 18 LYD624 0.76 1.05E-02 8 15 LYD624 0.86 1.55E-03 8 6 LYD624 0.84 2.38E-03 8 4 LYD624 0.81 1.40E-02 9 33 LYD625 0.72 1.82E-02 5 23 LYD625 0.78 2.12E-02 9 8 LYD625 0.72 4.46E-02 9 19 LYD625 0.85 7.44E-03 9 15 LYD625 0.77 2.61E-02 9 6 LYD625 0.80 1.81E-02 9 5 LYD625 0.81 1.52E-02 9 1 LYD625 0.73 4.02E-02 9 9 LYD625 0.74 5.84E-03 4 14 LYD625 0.71 9.18E-03 4 7 LYD626 0.75 3.26E-02 9 30 LYD626 0.73 7.55E-03 4 6 LYD626 0.72 7.75E-03 4 5 LYD627 0.74 3.61E-02 9 30 LYD627 0.72 8.06E-03 1 11 LYD627 0.74 5.63E-03 10 2 LYD627 0.82 9.94E-04 10 32 LYD629 0.74 1.51E-02 5 16 LYD629 0.73 1.62E-02 5 26 LYD629 0.73 1.74E-02 5 32 LYD629 0.77 9.29E-03 8 15 LYD629 0.71 2.17E-02 8 9 LYD629 0.76 2.78E-02 9 7 LYD629 0.70 1.11E-02 4 15 LYD629 0.73 6.53E-03 4 17 LYD630 0.72 1.99E-02 7 5 LYD630 0.83 2.92E-03 8 13 LYD630 0.84 2.26E-03 8 18 LYD630 0.82 3.48E-03 8 4 LYD630 0.72 1.81E-02 8 21 LYD630 0.84 2.26E-03 8 17 LYD631 0.76 1.O1E-02 5 30 LYD631 0.75 1.22E-02 5 19 LYD631 0.85 1.81E-03 5 22 LYD631 0.71 2.16E-02 8 9 LYD631 0.90 3.81E-04 8 31 LYD631 0.76 2.75E-02 9 23 LYD631 0.78 2.35E-02 9 31 LYD631 0.72 8.88E-03 4 15 LYD631 0.71 9.33E-03 1 7 LYD632 0.73 1.59E-02 7 30 LYD632 0.78 7.29E-03 7 33 LYD632 0.84 2.22E-03 5 15 LYD632 0.74 3.60E-02 9 33 LYD632 0.70 1.10E-02 1 16 LYD632 0.78 2.77E-03 1 20 LYD632 0.78 3.03E-03 1 28 LYD633 0.73 1.71E-02 5 11 LYD633 0.79 6.63E-03 5 3 LYD633 0.88 7.77E-04 5 9 LYD633 0.70 2.42E-02 8 3 LYD633 0.91 2.53E-04 8 15 LYD633 0.82 3.86E-03 8 6 LYD633 0.75 1.31E-02 8 5 LYD633 0.76 1.05E-02 8 4 LYD633 0.70 1.06E-02 1 16 LYD633 0.72 8.59E-03 1 15 LYD634 0.75 3.11E-02 9 8 LYD634 0.81 1.55E-03 1 8 LYD634 0.78 2.51E-03 1 20 LYD634 0.77 3.16E-03 10 14 LYD634 0.71 9.38E-03 10 19 LYD634 0.73 7.50E-03 10 17 LYD635 0.79 1.85E-02 9 14 LYD635 0.77 2.64E-02 9 8 LYD635 0.83 1.03E-02 9 19 LYD635 0.83 1.O1E-02 9 22 LYD635 0.76 4.03E-03 1 8 LYD635 0.73 6.59E-03 10 19 LYD635 0.77 3.53E-03 10 22 WO 2013/128448 PCT/IL2013/050172 139 Gene R P value Exp. Corr. Gene R P value Exp. Corr. Name set Set ID Name set Set ID LYD636 0.80 4.97E-03 8 14 LYD636 0.71 2.03E-02 8 13 LYD636 0.77 9.05E-03 8 17 LYD636 0.75 3.20E-02 9 14 LYD636 0.74 3.74E-02 9 22 LYD636 0.73 6.87E-03 1 14 LYD636 0.78 2.66E-03 10 14 LYD637 0.82 3.54E-03 8 1 LYD637 0.73 7.02E-03 10 31 LYD638 0.79 6.71E-03 7 11 LYD638 0.77 3.48E-03 11 30 LYD638 0.81 1.45E-03 11 33 LYD638 0.77 9.73E-03 8 13 LYD638 0.79 7.05E-03 8 18 LYD638 0.90 3.21E-04 8 15 LYD638 0.80 5.26E-03 8 6 LYD638 0.71 2.05E-02 8 5 LYD638 0.82 4.OOE-03 8 4 LYD638 0.73 1.63E-02 8 17 LYD639 0.70 5.11E-02 9 12 LYD639 0.78 2.37E-02 9 24 LYD639 0.96 2.19E-04 9 7 LYD639 0.87 2.55E-04 10 8 LYD641 0.82 3.64E-03 5 13 LYD641 0.78 7.22E-03 5 18 LYD641 0.75 1.19E-02 5 15 LYD641 0.75 1.32E-02 5 6 LYD641 0.73 1.76E-02 5 4 LYD641 0.75 1.21E-02 5 17 LYD641 0.77 2.46E-02 9 16 LYD641 0.84 8.62E-03 9 13 LYD641 0.82 1.27E-02 9 18 LYD641 0.71 4.90E-02 9 15 LYD641 0.77 2.67E-02 9 5 LYD641 0.76 2.91E-02 9 4 LYD641 0.78 2.19E-02 9 17 LYD641 0.79 3.48E-03 2 13 LYD641 0.70 1.56E-02 2 17 LYD642 0.77 9.07E-03 7 32 LYD642 0.84 2.18E-03 5 8 LYD642 0.71 2.22E-02 5 19 LYD642 0.72 8.83E-03 1 31 LYD643 0.85 1.79E-03 8 3 LYD643 0.85 2.02E-03 8 15 LYD643 0.80 5.19E-03 8 6 LYD643 0.72 1.94E-02 8 5 LYD643 0.71 2.06E-02 8 4 LYD643 0.76 9.96E-03 8 9 LYD643 0.78 2.77E-03 1 3 LYD643 0.77 3.63E-03 1 9 LYD643 0.75 4.85E-03 10 3 LYD643 0.74 6.03E-03 10 2 LYD644 0.76 1.07E-02 7 3 LYD644 0.85 1.83E-03 7 9 LYD644 0.80 5.37E-03 8 16 LYD644 0.72 1.79E-02 8 20 LYD644 0.84 2.37E-03 8 15 LYD644 0.75 1.31E-02 8 28 LYD644 0.74 3.71E-02 9 30 LYD644 0.84 9.39E-03 9 33 LYD644 0.74 6.07E-03 10 26 LYD644 0.72 8.41E-03 10 25 LYD645 0.85 7.94E-03 9 14 LYD645 0.80 1.60E-02 9 30 LYD645 0.84 9.84E-03 9 19 LYD645 0.89 3.41E-03 9 22 LYD645 0.70 1.54E-02 2 20 LYD646 0.84 5.76E-04 11 8 LYD646 0.76 3.03E-02 9 30 LYD646 0.76 2.86E-02 9 33 LYD646 0.70 1.05E-02 10 13 LYD646 0.73 7.14E-03 10 18 LYD646 0.71 1.02E-02 10 4 LYD646 0.74 6.41E-03 10 17 LYD647 0.73 3.98E-02 9 14 LYD647 0.81 1.50E-02 9 19 LYD647 0.83 1.06E-02 9 22 LYD647 0.76 2.93E-02 9 7 LYD647 0.73 7.06E-03 10 13 LYD647 0.74 6.23E-03 10 18 LYD647 0.70 1.07E-02 10 15 LYD647 0.80 1.69E-03 10 6 LYD623 0.77 9.13E-03 3 40 LYD627 0.70 2.28E-02 1 40 LYD637 0.85 7.18E-03 5 40 LYD637 0.78 1.39E-02 2 40 LYD637 0.76 1.02E-02 8 40 LYD639 0.76 2.80E-02 4 40 LYD646 0.72 4.52E-02 4 40 Table 40. Provided are the correlations (R) between the expression levels yield improving genes and their homologs in various tissues [Expression (Exp) sets] and the WO 2013/128448 PCT/IL2013/050172 140 phenotypic performance [yield, biomass, and plant architecture (Correlation vector (Corr))] under normal conditions across soybean varieties. P = p value. EXAMPLE 10 PRODUCTION OF BRACHYPODIUM TRANSCRIPTOME AND HIGH 5 THROUGHPUT CORRELATION ANALYSIS USING 60K BRACHYPODIUM OLIGONUCLEOTIDE MICRO-ARRAY In order to produce a high throughput correlation analysis comparing between plant phenotype and gene expression level, the present inventors utilized a brachypodium oligonucleotide micro-array, produced by Agilent Technologies 10 [Hypertext Transfer Protocol://World Wide Web (dot) chem. (dot) agilent (dot) com/Scripts/PDS (dot) asp lPage=50879]. The array oligonucleotide represents about 60K brachypodium genes and transcripts. In order to define correlations between the levels of RNA expression and yield or vigor related parameters, various plant characteristics of 24 different brachypodium accessions were analyzed. Among them, 15 22 accessions encompassing the observed variance were selected for RNA expression analysis and comparative genomic hybridization (CGH) analysis. The correlation between the RNA levels and the characterized parameters was analyzed using Pearson correlation test [Hypertext Transfer Protocol://World Wide Web (dot) davidmlane (dot) com/hyperstat/A34739 (dot) html]. 20 Additional correlation analysis was done by comparing plant phenotype and gene copy number. The correlation between the normalized copy number hybridization signal and the characterized parameters was analyzed using Pearson correlation test [Hypertext Transfer Protocol://World Wide Web (dot) davidmlane (dot) com/hyperstat/A34739 (dot) html]. 25 Experimental procedures Analyzed Brachypodium tissues - two tissues [leaf and spike] were sampled and RNA was extracted as described above. Each micro-array expression information tissue type has received a Set ID as summarized in Table 41 below.
WO 2013/128448 PCT/IL2013/050172 141 Table 41 Brachypodium transcriptome expression sets Expression Set Set ID Leaf at flowering stage under normal growth conditions 1+2 spike at flowering stage under normal growth conditions 3 Table 41. 5 Brachypodium yield components and vigor related parameters assessment 24 brachypodium accessions were grown in 4-6 repetitive plots (8 plant per plot), in a green house. The growing protocol was as follows: brachypodium seeds were sown in plots and grown under normal conditions. Plants were continuously phenotyped during 10 the growth period and at harvest (Table 43-48, below). The image analysis system included a personal desktop computer (Intel P4 3.0 GHz processor) and a public domain program - ImageJ 1.37 (Java based image processing program, which was developed at the U.S. National Institutes of Health and freely available on the internet [Hypertext Transfer Protocol://rsbweb (dot) nih (dot) gov/]. Next, analyzed data was saved to text 15 files and processed using the JMP statistical analysis software (SAS institute). At the end of the growing period the grains were separated from the spikes and the following parameters were measured using digital imaging system and collected: No. of tillering- all tillers were counted per plant at harvest (mean per plot). Head number - At the end of the experiment, heads were harvested from each 20 plot and were counted. Total Grains weight per plot (gr.) - At the end of the experiment (plant 'Heads') heads from plots were collected, the heads were threshed and grains were weighted. In addition, the average grain weight per head was calculated by dividing the total grain weight by number of total heads per plot (based on plot). 25 Highest number of spikelets - The highest spikelet number per head was calculated per plant (mean per plot). Mean number of spikelets - The mean spikelet number per head was calculated per plot. Plant height - Each of the plants was measured for its height using measuring 30 tape. Height was measured from ground level to spike base of the longest spike at harvest.
WO 2013/128448 PCT/IL2013/050172 142 Spikelets weight (gr.)- The biomass and spikes weight of each plot was separated, measured per plot. Average head weight - calculated by dividing spikelets weight with head number (gr.). 5 Harvest Index - The harvest index was calculated using Formula XII. Spikelets Index - The Spikelets index is calculated using Formula XIII. Formula XIII: Spikelets Index = Average Spikelets weight per plant/ (Average vegetative dry weight per plant plus Average Spikelets weight per plant). Percent Number of heads with spikelets - The number of heads with more than 10 one spikelet per plant were counted and the percent from all heads per plant was calculated. Total dry mater per plot - Calculated as Vegetative portion above ground plus all the spikelet dry weight per plot. 1000 grain weight - At the end of the experiment all grains from all plots were 15 collected and weighted and the weight of 1000 were calculated. The following parameters were collected using digital imaging system: At the end of the growing period the grains were separated from the spikes and the following parameters were measured and collected: (i) Average Grain Area (cm2) - A sample of -200 grains was weighted, 20 photographed and images were processed using the below described image processing system. The grain area was measured from those images and was divided by the number of grains. (ii) Average Grain Length, perimeter and width (cm) - A sample of -200 grains was weighted, photographed and images were processed using the below 25 described image processing system. The sum of grain lengths and width (longest axis) was measured from those images and was divided by the number of grains. The image processing system was used, which consists of a personal desktop computer (Intel P4 3.0 GHz processor) and a public domain program - ImageJ 1.37, Java based image processing software, which was developed at the U.S. National 30 Institutes of Health and is freely available on the internet at Hypertext Transfer Protocol://rsbweb (dot) nih (dot) gov/. Images were captured in resolution of 10 Mega Pixels (3888x2592 pixels) and stored in a low compression JPEG (Joint Photographic WO 2013/128448 PCT/IL2013/050172 143 Experts Group standard) format. Next, image processing output data for seed area and seed length was saved to text files and analyzed using the JMP statistical analysis software (SAS institute). Table 42 5 Brachypodium correlated parameters (vectors) Correlated parameter with Correlation ID % Number of heads with spikelets (number) 1+26 1000 grain weight (gr) 2+27 Average head weight (gr) 3+28 Grain area (cm 2 ) 4+29 Grain length (cm) 5+30 Grain Perimeter (cm2) 6+31 Grain width (cm) 7+32 Grains weight per plant (gr) 8+33 Grains weight per plot (gr) 9+34 Harvest index 10+35 Heads per plant (number) 11+36 Heads per plot (number) 12+37 Highest Number of spikelets per plot (number) 13+38 Mean Number of spikelets per plot (number) 14+39 Number of heads with spikelets per plant (number) 15+40 Plant height (cm) 16+41 Plant Vegetative DW (gr) 17+42 Plants number (number) 18+43 Spikelets DW per plant (gr) 19+44 Spikelets weight (gr) 20+45 Spikes index 21+46 Tillering (number) 22 Total dry mater per plant (gr) 23+47 Total dry mater per plot (gr) 24+48 Vegetative DW (gr) 25+49 Table 42. Provided are the Brachypodium correlated parameters. Experimental Results 10 24 different Brachypodium accessions were grown and characterized for different parameters as described above. The average for each of the measured parameters was calculated using the JMP software and values are summarized in Tables 43-48 below. Subsequent correlation analysis between the various transcriptome sets and the average parameters (Tables 43-48) was conducted. Follow, results were 15 integrated to the database.
WO 2013/128448 PCT/IL2013/050172 144 Table 43 Measured parameters of correlation IDs in Brachypodium accessions under normal conditions (lines 1-9) Ecotypel Treatment Line- Line- Line- Line- Line- Line Correlation Lie-i 2 3 Line-4 5 6 7 8 Line-9 ID 1 27.61 35.33 21.67 52.40 20.84 47.73 17.55 16.51 5.42 2 3.75 3.78 3.35 3.70 3.90 4.87 4.82 4.76 5.54 3 0.06 0.04 0.05 0.09 0.04 0.09 0.06 0.06 0.04 4 0.10 0.10 0.09 0.09 0.09 0.11 0.10 0.11 0.11 5 0.73 0.72 0.72 0.75 0.72 0.87 0.79 0.79 0.83 6 1.67 1.62 1.62 1.65 1.60 1.90 1.80 1.82 1.82 7 0.18 0.17 0.17 0.15 0.15 0.16 0.17 0.18 0.16 8 0.14 0.06 0.08 0.35 0.27 0.44 0.32 0.07 0.14 9 1.05 0.44 0.61 2.58 2.03 3.40 2.58 0.39 1.11 10 0.13 0.14 0.15 0.21 0.17 0.18 0.15 0.11 0.20 11 16.29 7.08 6.59 16.11 21.40 17.05 25.88 8.02 10.48 12 121.75 56.60 52.75 123.50 156.8 135.0 207.0 48.60 82.40 13 3.00 2.60 3.00 2.83 2.33 4.50 2.60 2.00 2.00 14 2.10 2.10 1.72 2.17 1.85 2.85 1.93 1.56 1.38 15 5.27 2.50 2.06 9.44 5.02 7.72 4.90 1.87 0.71 16 31.65 23.44 22.75 45.35 29.41 46.74 38.39 29.15 34.36 17 0.42 0.12 0.13 0.82 0.67 1.05 0.87 0.31 0.32 18 7.50 8.00 8.00 7.50 7.33 7.88 8.00 6.40 7.80 19 0.96 0.31 0.33 1.46 0.96 1.42 1.56 0.45 0.44 20 7.18 2.50 2.68 11.31 7.16 11.05 12.44 2.66 3.45 21 0.71 0.72 0.73 0.68 0.60 0.57 0.65 0.60 0.58 22 16.84 7.20 7.00 16.99 23.61 18.25 27.20 8.60 10.67 23 1.38 0.43 0.47 2.28 1.63 2.47 2.43 0.76 0.76 24 10.26 3.45 3.74 17.78 12.29 19.27 19.40 4.47 6.00 25 3.08 0.95 1.06 6.47 5.13 8.23 6.96 1.81 2.55 5 Table 43. Correlation IDs refer to those described in Table 42 above [Brachypodium correlated parameters (vectors)]. Table 44 Measured parameters of correlation IDs in Brachypodium accessions under normal 10 conditions (lines 10-18) Ecotypel Line- Line- Line- Line- Line- Line- Line- Line- Line-18 Treatment 10 11 12 13 14 15 16 17 1 15.42 14.00 6.40 4.51 15.52 20.34 8.11 53.21 55.41 2 4.98 4.88 4.83 5.54 4.73 5.24 4.96 4.00 3.84 3 0.06 0.07 0.05 0.04 0.05 0.05 0.06 0.10 0.08 4 0.11 0.09 0.10 0.11 0.10 0.12 0.10 0.10 0.10 5 0.82 0.74 0.78 0.90 0.75 0.86 0.74 0.84 0.75 6 1.83 1.69 1.74 1.93 1.69 1.91 1.71 1.81 1.68 7 0.17 0.16 0.17 0.16 0.17 0.19 0.17 0.15 0.17 8 0.14 0.26 0.14 0.11 0.39 0.14 0.13 0.37 0.08 WO 2013/128448 PCT/IL2013/050172 145 Ecotypel Line- Line- Line- Line- Line- Line- Line- Line- Line-18 Treatment 10 11 12 13 14 15 16 17 9 1.07 1.96 1.09 0.84 3.07 1.09 1.07 2.99 0.50 10 0.16 0.20 0.14 0.26 0.22 0.09 0.18 0.09 0.07 11 9.09 11.63 14.13 5.88 23.75 16.06 9.74 22.19 11.89 12 70.13 83.40 0.3 47.00 185.50 125. 80.75 177.50 81.50 3 13 2.25 2.20 1.83 2.00 2.50 2.40 2.00 3.50 3.50 14 1.65 1.69 1.43 1.25 1.76 1.83 1.42 2.71 2.41 15 1.94 2.08 1.08 0.35 4.98 3.70 0.89 12.58 7.59 16 28.65 31.95 28.88 24.74 37.30 45.09 22.39 55.04 31.40 17 0.32 0.38 0.39 0.13 0.87 0.69 0.34 1.72 0.44 18 7.75 7.20 7.83 8.00 7.75 8.00 8.25 8.00 6.50 19 0.56 0.88 0.67 0.26 1.14 0.83 0.59 2.27 0.92 20 4.29 6.42 5.29 2.04 8.89 6.65 4.92 18.15 6.25 21 0.66 0.71 0.64 0.66 0.59 0.54 0.68 0.56 0.69 22 9.38 11.97 14.58 6.35 25.50 16.56 10.53 27.15 12.38 23 0.88 1.25 1.06 0.38 2.01 1.53 0.93 3.99 1.36 24 6.78 9.12 8.34 3.04 15.79 12.20 7.76 31.94 9.21 25 2.48 2.69 3.05 1.00 6.89 5.55 2.84 13.80 2.96 Table 44. Correlation IDs refer to those described in Table 42 above [Brachypodium correlated parameters (vectors)]. 5 Table 45 Measured parameters of correlation IDs in Brachypodium accessions under normal conditions (lines 19-22) Ecotype/Treatment Line-19 Line-20 Line-21 Line-22 1 47.81 42.81 59.01 34.92 2 4.26 5.99 3.76 4.34 3 0.08 0.08 0.09 0.06 4 0.09 0.12 0.09 0.09 5 0.80 0.84 0.76 0.74 6 1.75 1.87 1.68 1.66 7 0.14 0.18 0.15 0.16 8 0.49 0.31 0.30 0.20 9 3.52 2.41 1.92 1.47 10 0.16 0.18 0.09 0.11 11 24.32 13.25 25.54 19.22 12 172.80 98.60 177.00 143.17 13 3.80 2.80 3.17 2.83 14 2.61 2.12 2.79 2.15 15 12.13 6.35 15.36 7.15 16 45.34 40.20 58.82 39.18 17 1.32 0.48 1.73 0.63 18 7.00 7.60 6.83 7.33 19 1.91 1.09 2.25 1.26 20 13.49 8.35 15.55 9.42 21 0.59 0.70 0.57 0.66 22 26.30 13.56 29.09 20.79 WO 2013/128448 PCT/IL2013/050172 146 Ecotype/Treatment Line-19 Line-20 Line-21 Line-22 23 3.23 1.57 3.98 1.89 24 22.78 12.04 27.67 14.14 25 9.28 3.70 12.12 4.72 Table 45. Correlation IDs refer to those described in Table 51 above [Brachypodium correlated parameters (vectors)]. Table 46 5 Measured parameters of correlation IDs in Brachypodium accessions under normal conditions (lines 23-30) Ecotypel Line-23 Line- Line-25 Line-26 Line- Line- Line- Line Treatment 24 27 28 29 30 26 27.61 35.33 21.67 14.00 5.42 15.42 6.40 4.51 27 3.75 3.78 3.35 4.88 5.54 4.98 4.83 5.54 28 0.06 0.04 0.05 0.07 0.04 0.06 0.05 0.04 29 0.10 0.10 0.09 0.09 0.11 0.11 0.10 0.11 30 0.73 0.72 0.72 0.74 0.83 0.82 0.78 0.90 31 1.67 1.62 1.62 1.69 1.82 1.83 1.74 1.93 32 0.18 0.17 0.17 0.16 0.16 0.17 0.17 0.16 33 0.14 0.06 0.08 0.26 0.14 0.14 0.14 0.11 34 1.05 0.44 0.61 1.96 1.11 1.07 1.09 0.84 35 0.13 0.14 0.15 0.20 0.20 0.16 0.14 0.26 36 16.29 7.08 6.59 11.63 10.48 9.09 14.13 5.88 37 121.75 56.60 52.75 83.40 82.40 70.13 110.33 47.00 38 3.00 2.60 3.00 2.20 2.00 2.25 1.83 2.00 39 2.10 2.10 1.72 1.69 1.38 1.65 1.43 1.25 40 5.27 2.50 2.06 2.08 0.71 1.94 1.08 0.35 41 31.65 23.44 22.75 31.95 34.36 28.65 28.88 24.74 42 0.42 0.12 0.13 0.38 0.32 0.32 0.39 0.13 43 7.50 8.00 8.00 7.20 7.80 7.75 7.83 8.00 44 0.96 0.31 0.33 0.88 0.44 0.56 0.67 0.26 45 7.18 2.50 2.68 6.42 3.45 4.29 5.29 2.04 46 0.71 0.72 0.73 0.71 0.58 0.66 0.64 0.66 22 16.84 7.20 7.00 11.97 10.67 9.38 14.58 6.35 47 1.38 0.43 0.47 1.25 0.76 0.88 1.06 0.38 48 10.26 3.45 3.74 9.12 6.00 6.78 8.34 3.04 49 3.08 0.95 1.06 2.69 2.55 2.48 3.05 1.00 Table 46. Correlation IDs refer to those described in Table 42 above [Brachypodium correlated parameters (vectors)]. 10 Table 47 Measured parameters of correlation IDs in Brachypodium accessions under normal conditions (lines 31-40) Ecotype/ Line- Line- Line Line Lin Line Line Lin Line- Line Treatmen 31 32 -33 -34 e-35 -36 -37 e-38 39 40 26 55.41 16.51 15.5 20.3 8.11 53.2 47.8 42.8 34.92 52.40 27 3.84 4.76 4.32 4 8.96 1 1 1 4.34 3.70 1 27 13.84 14.76 14.73 15.24 14.96 14.00 14.26 15.99 1 4.34 13.70_ WO 2013/128448 PCT/IL2013/050172 147 28 0.08 0.06 0.05 0.05 0.06 0.10 0.08 0.08 0.06 0.09 29 0.10 0.11 0.10 0.12 0.10 0.10 0.09 0.12 0.09 0.09 30 0.75 0.79 0.75 0.86 0.74 0.84 0.80 0.84 0.74 0.75 31 1.68 1.82 1.69 1.91 1.71 1.81 1.75 1.87 1.66 1.65 32 0.17 0.18 0.17 0.19 0.17 0.15 0.14 0.18 0.16 0.15 33 0.08 0.07 0.39 0.14 0.13 0.37 0.49 0.31 0.20 0.35 34 0.50 0.39 3.07 1.09 1.07 2.99 3.52 2.41 1.47 2.58 35 0.07 0.11 0.22 0.09 0.18 0.09 0.16 0.18 0.11 0.21 36 11.89 8.02 23.7 16.0 22.1 24.3 13.2 19.22 16.11 5 6 9 2 5 37 81.50 48.60 185. 125. 80.7 177. 172. 98.6 143.17 123.5 50 00 5 50 80 38 3.50 2.00 2.50 2.40 2.00 3.50 3.80 2.80 2.83 2.83 39 2.41 1.56 1.76 1.83 1.42 2.71 2.61 2.12 2.15 2.17 40 7.59 1.87 4.98 3.70 0.89 12.5 12.1 6.35 7.15 9.44 8 3 41 31.40 29.15 37.3 45.0 22.3 55.0 45.3 40.2 39.18 45.35 0 9 9 4 4 0 42 0.44 0.31 0.87 0.69 0.34 1.72 1.32 0.48 0.63 0.82 43 6.50 6.40 7.75 8.00 8.25 8.00 7.00 7.60 7.33 7.50 44 0.92 0.45 1.14 0.83 0.59 2.27 1.91 1.09 1.26 1.46 45 6.25 2.66 8.89 6.65 4.92 18.1 13.4 8.35 9.42 11.31 5 9 46 0.69 0.60 0.59 0.54 0.68 0.56 0.59 0.70 0.66 0.68 22 12.38 8.60 25.5 16.5 10.5 27.1 26.3 13.5 20.79 16.99 0 6 3 5 0 6 47 1.36 0.76 2.01 1.53 0.93 3.99 3.23 1.57 1.89 2.28 48 9.21 4.47 15.7 12.2 7.76 31.9 22.7 12.0 14.14 17.78 9 0 7.6 4 8 4 49 2.96 1.81 6.89 5.55 2.84 13.8 9.28 3.70 4.72 6.47 Table 47. Coirelation IDs refer to those described in Table 42 above [Brachypodium correlated parameters (vectors)]. 5 Table 48 Measured parameters of correlation IDs in Brachypodium accessions under normal conditions (lines 41-44) Ecotype/Treatment Line-41 Line-42 Line-43 Line-44 26 20.84 17.55 47.73 59.01 27 3.90 4.82 4.87 3.76 28 0.04 0.06 0.09 0.09 29 0.09 0.10 0.11 0.09 30 0.72 0.79 0.87 0.76 31 1.60 1.80 1.90 1.68 32 0.15 0.17 0.16 0.15 33 0.27 0.32 0.44 0.30 34 2.03 2.58 3.40 1.92 35 0.17 0.15 0.18 0.09 36 21.40 25.88 17.05 25.54 37 156.83 207.00 135.00 177.00 WO 2013/128448 PCT/IL2013/050172 148 Ecotype/Treatment Line-41 Line-42 Line-43 Line-44 38 2.33 2.60 4.50 3.17 39 1.85 1.93 2.85 2.79 40 5.02 4.90 7.72 15.36 41 29.41 38.39 46.74 58.82 42 0.67 0.87 1.05 1.73 43 7.33 8.00 7.88 6.83 44 0.96 1.56 1.42 2.25 45 7.16 12.44 11.05 15.55 46 0.60 0.65 0.57 0.57 22 23.61 27.20 18.25 29.09 47 1.63 2.43 2.47 3.98 48 12.29 19.40 19.27 27.67 49 5.13 6.96 8.23 12.12 Table 48. Correlation IDs refer to those described in Table 42 above [Brachypodium correlated parameters (vectors)]. Table 49 5 Correlation between the expression level of selected genes of some embodiments of the invention in various tissues and the phenotypic performance under normal conditions across brachypodium varieties GeeEp Corr GnEx.Corr GNe R P value set 'Set Ge R P value ep Set ID ID LYD542 0.80 3.32E-03 2 46 LYD543 0.75 1.17E-02 3 30 LYD543 0.75 1.22E-02 3 31 LYD544 0.72 8.85E-03 1 8 LYD544 0.73 7.10E-03 1 9 LYD544 0.71 1.39E-02 2 29 LYD545 0.82 1.84E-03 2 37 LYD545 0.86 7.41E-04 2 22 LYD545 0.79 3.49E-03 2 48 LYD545 0.80 3.10E-03 2 44 LYD545 0.80 3.05E-03 2 49 LYD545 0.82 1.88E-03 2 42 LYD545 0.79 4.13E-03 2 40 LYD545 0.78 4.87E-03 2 45 LYD545 0.83 1.68E-03 2 36 LYD545 0.82 2.17E-03 2 47 LYD546 0.70 1.06E-02 1 8 LYD546 0.78 2.93E-03 1 9 Table 49. Provided are the correlations (R) between the expression levels yield 10 improving genes and their homologs in various tissues [Expression (Exp) sets] and the phenotypic performance [yield, biomass, growth rate and/or vigor components (Correlation vector (Corr))] under normal conditions across brachypodium varieties. P = p value. 15 EXAMPLE 11 PLANT FIBER DEVELOPMENT IN COTTON PRODUCTION OF COTTON TRANSCRIPTOME AND HIGH THROUGHPUT CORRELATION ANALYSIS USING COTTON OLIGONUCLEOTIDE MICROARRAY 20 In order to conduct high throughput gene expression correlation analysis, the present inventors used cotton oligonucleotide microarray, designed and produced by WO 2013/128448 PCT/IL2013/050172 149 "Comparative Evolutionary Genomics of Cotton" [Hypertext Transfer Protocol (http)://cottonevolution (dot) info/). This Cotton Oligonucleotide Microarray is composed of 12,006 Integrated DNA Technologies (IDT) oligonucleotides derived from an assembly of more than 180,000 Gossypium ESTs sequenced from 30 cDNA 5 libraries. For additional details see PCT/IL2005/000627 and PCT/IL2007/001590 which are fully incorporated herein by reference. Table 50 Cotton transcriptome experimental sets 10 Expression Set Set ID Fiber 15 days after anthesis under normal growth conditions 1 Fiber 5 days after anthesis under normal growth conditions 2 Fiber 10 days after anthesis under normal growth conditions 3 Table 50. Provided are the cotton transcriptome expression sets. In order to define correlations between the levels of RNA expression and fiber length, fibers from 8 different cotton lines were analyzed. These fibers were selected 15 showing very good fiber quality and high lint index (Pima types, originating from other cotton species, namely G. barbadense), different levels of quality and lint indexes from various G. hirsutum lines: good quality and high lint index (Acala type), and poor quality and short lint index (Tamcot type, and old varieties). A summary of the fiber length of the different lines is provided in Table 51. 20 Experimental procedures RNA extraction - Fiber development stages, representing different fiber characteristics, at 5, 10 and 15 DPA were sampled and RNA was extracted as described above. Fiber length assessment - Fiber length of the selected cotton lines was 25 measured using fibrograph. The fibrograph system was used to compute length in terms of "Upper Half Mean" length. The upper half mean (UHM) is the average length of longer half of the fiber distribution. The fibrograph measures length in span lengths at a given percentage point World Wide Web (dot) cottoninc (dot) com/ClassificationofCotton/ Pg=4#Length].
WO 2013/128448 PCT/IL2013/050172 150 Experimental Results Eight different cotton lines were grown, and their fiber length was measured. The fibers UHM values are summarized in Table 51 herein below. The R square was calculated for each of the genes. 5 Table 51 Summary of the fiber length of the 8 different cotton lines Line- Line- Line- Line- Line- Line- Line- Line EcotypelTreatment 1 2 3 4 5 6 7 8 1 1.21 1.1 1.36 1.26 0.89 1.01 1.06 1.15 Table 51: Presented are the means 8 different cotton lines. 10 Table 52 Correlation between the expression level of selected genes of some embodiments of the invention in various tissues and the phenotypic performance under normal conditions across 15 cotton ecotypes Corr. Corr. Gene R P value Exp. Set Gene R P value Exp. Set Name set ID Name set ID LYD554 0.90 2.19E- 1 1 LYD555 0.73 3.82E- 1 1 03 11102 LYD555 0.85 1.50E- 3 1 LY55 085 02 ___ __ ___ Table 52. Provided are the correlations (R) between the expression levels yield improving genes and their homologs in various tissues [Expression (Exp) sets] and the phenotypic performance [yield, biomass, growth rate and/or vigor components (Correlation 20 vector (Corr))] under normal conditions across cotton ecotypes. P = p value. EXAMPLE 12 25 IDENTIFICATION OF GENES WHICH INCREASE YIELD, BIOMASS, GROWTH RATE, VIGOR, OIL CONTENT, ABIOTIC STRESS TOLERANCE OF PLANTS AND NITROGEN USE EFFICIENCY Based on the above described bioinformatics and experimental tools, the present inventors have identified 164 genes which have a major impact on yield, seed yield, oil 30 yield, biomass, growth rate, vigor, oil content, fiber yield, fiber quality, abiotic stress tolerance, and/or nitrogen use efficiency when expression thereof is increased in plants. The identified genes (including genes identified by bioinformatics tools and curated WO 2013/128448 PCT/IL2013/050172 151 sequences thereof), and polypeptide sequences encoded thereby are summarized in Table 53, hereinbelow. Table 53 5 Identified polynucleotides which affect plant yield, seed yield, oil yield, oil content, biomass, growth rate, vigor, fiber yield, fiber quality abiotic stress tolerance and/or nitrogen use efficiency of a plant Polyn. Polyp SEQ Gene Name Organism / Cluster tag SEQ ID ID NO: NO: LYD521 arabidopsisl lOvI AT 1 G08410 1 362 LYD522 arabidopsis|IOvlIAT1G19110 2 363 LYD524 arabidopsis|IOvlIAT2G20340 3 364 LYD525 arabidopsisl 1 OvI AT2G45030 4 365 LYD526 arabidopsis|IOvlIAT2G45730 5 366 LYD527 arabidopsis|IOvlIAT2G47920 6 367 LYD528 arabidopsis|IOvlIAT3G15650 7 368 LYD529 arabidopsis| 1OvI AT4G00500 8 369 LYD530 arabidopsis IOvI AT4G1 3110 9 370 LYD531 arabidopsis|IOvlIAT4G16146 10 371 LYD532 arabidopsis IOvI AT5GO2830 11 372 LYD533 arabidopsisl 1 OvI AT5G06700 12 373 LYD534 arabidopsis| 1OvI AT5G43150 13 374 LYD535 arabidopsisl 1 OvI AT5G46790 14 375 LYD536 arabidopsis| 1OvI AT5G65280 15 376 LYD537 bjunceal10v2IE6ANDIZ01AI14E 16 377 LYD538 bjunceal10v2IE6ANDIZ01AWH6F 17 378 LYD539 bjunceaI10v2|E6ANDIZ01BOPVK 18 379 LYD540 bjunceal10v2IE6ANDIZ01CQ2ZQ 19 380 LYD541 brapa11vIlBQ704427 20 381 LYD542 brachypodiuml09v 1 lDV480497 21 382 LYD543 brachypodiuml09vll GT759735 22 383 LYD544 brachypodium09vlIGT835824 23 384 LYD545 brachypodiumI09vlIGT841411 24 385 LYD546 brachypodiuml09v ISRR031797S0017542 25 386 LYD547 canolal0vlICD822163 26 387 LYD548 canolal0vlICX192172 27 388 LYD549 canolal0vlIlEE556201 28 389 LYD550 canolaIlvlIDY020414 29 390 LYD551 canolallvllEE429972 30 391 LYD552 canolallvllEE440823 31 392 LYD553 canolallvllEE481252 32 393 LYD554 cottonI10v2IDN804535 33 394 LYD555 cotton|I1vlIC0098912 34 395 LYD556 lotusl09vllAW719664 35 396 LYD558 medicagolO9vlILLAW329230 36 397 LYD559 medicagol11vlIAI083094 37 398 LYD560 medicagol11vlIAI974457 38 399 WO 2013/128448 PCT/IL2013/050172 152 Gene Name Organism / Cluster tag SPElyn I NO NO: LYD561 medicagol11vlIAJ388759 39 400 LYD562 medicagol11vlIAL368425 40 401 LYD563 medicagolI11vIAL370319 41 402 LYD564 medicagolI11vIAL372358 42 403 LYD565 medicagolI11vIAL383170 43 404 LYD566 medicagolI11vIAL384827 44 405 LYD567 medicagol11vlIAW125911 45 406 LYD568 medicagol11vlIAW126198 46 407 LYD570 medicagolI11vIAW299069 47 408 LYD571 medicagolI11vIAW299099 48 409 LYD572 medicagol11vlIAW683620 49 410 LYD573 medicagol11vlIAW684312 50 411 LYD574 medicagol11vlIAW686798 51 412 LYD575 medicagol11vlIAW688064 52 413 LYD576 medicagol11vlIAW688428 53 414 LYD577 medicagolI11vIAW690765 54 415 LYD578 medicagol11vlIAW691134 55 416 LYD579 medicagolI11vIAW695894 56 417 LYD580 medicagol11vlIAW775280 57 418 LYD581 medicagol11vlIAW980738 58 419 LYD583 medicagol11vlIBE204527 59 420 LYD584 medicagol11vlIBE325825 60 421 LYD585 medicagol11vlIBE942833 61 422 LYD586 medicagol11vlIBE998813 62 423 LYD587 medicagol11vlIBF005808 63 424 LYD588 medicagol11vlIBF640823 64 425 LYD589 medicagol11vlIBG644974 65 426 LYD590 medicagol11vlIBQ139188 66 427 LYD591 medicagol11vlIEV259134 67 428 LYD592 medicagollvllXM_003625686 68 429 LYD593 medicagol12vlIAL366306 69 430 LYD594 medicagol12vlIBF633538 70 431 LYD595 riceIgbl7010SOIG51360 71 432 LYD596 riceIgbl7010SOIG70930 72 433 LYD597 riceIgbl701OSO2G22020 73 434 LYD598 riceIgbl701OSO3G12840 74 435 LYD599 riceIgbl701OSO4G40100 75 436 LYD600 ricelgb 17010S06G01200 76 437 LYD601 riceIgbl701OSO6GO4250 77 438 LYD602 riceIgbl701OSO6G33810 78 439 LYD603 riceIgbl701OSO8G29170 79 440 LYD604 sorghum|09vlISBO1G049980 80 441 LYD605 sorghuml09v 1 lSB02G037340 81 442 LYD606 sorghuml09v 1 lSB03G025590 82 443 LYD607 sorghuml09v 1 lSB03G037600 83 444 LYD608 sorghuml09v 1 lSB06G006920 84 445 LYD609 sorghum|09v 1 ISB09GO25 850 85 446 LYD610 sorghum|IIvlISBO1G036260 86 447 WO 2013/128448 PCT/IL2013/050172 153 Gene Name Organism / Cluster tag SPElyn I NO NO: LYD611 soybean| 11vlIGLYMAO1G02290 87 448 LYD612 soybeanI11vIlGLYMA02G2070 88 449 LYD613 soybean| 11 v IGLYMA02GO4840 89 450 LYD614 soybean| 11 v IGLYMA02G42250 90 451 LYD615 soybeans |1vlIGLYMA03G27800 91 452 LYD616 soybeanI11vIlGLYMA03G36910 92 453 LYD617 soybean| 1vlIGLYMA03G37120 93 454 LYD618 soybean| 1vlIGLYMA03G41760 94 455 LYD619 soybean| 1vlIGLYMA04G38690 95 456 LYD620 soybean|IIvlIGLYMA05G0370 96 457 LYD621 soybean| 11 v IGLYMA05G34620 97 458 LYD622 soybean|IIvlIGLYMA06G3760 98 459 LYD623 soybean|IIvlIGLYMA06G5880 99 460 LYD624 soybean| 1vlIGLYMA06G1 1430 100 461 LYD625 soybean|IIvlIGLYMA07G27370 101 462 LYD626 soybean|IIvlIGLYMA08G14740 102 463 LYD627 soybean|IIvlIGLYMA08G39520 103 464 LYD628 soybean| 1vlIGLYMA09G27600 104 465 LYD629 soybean| 11 v IGLYMA09G30190 105 466 LYD630 soybean| 1vlIGLYMA09G35750 106 467 LYD631 soybean|IIvlIGLYMA09G36720 107 468 LYD632 soybean|IIvlIGLYMAOG40890 108 469 LYD633 soybean|IIvlIGLYMA12G2590 109 470 LYD633 soybean|IIvlIGLYMA12G2590 109 543 LYD634 soybeanIIvlIGLYMA12GO9830 110 471 LYD635 soybean| 1vlIGLYMA13GO4780 111 472 LYD636 soybeanIIvlIGLYMA13G18990 112 473 LYD637 soybeanIIvlIGLYMA13G22160 113 474 LYD638 soybeanIIvlIGLYMA13G41580 114 475 LYD639 soybean| 1vlIGLYMA14G32430 115 476 LYD640 soybean| 1vlIGLYMA14G35690 116 477 LYD641 soybean| 1vlIGLYMA15GO2690 117 478 LYD642 soybeanIIvlIGLYMA15G15380 118 479 LYD643 soybean| 1vlIGLYMA16GO3140 119 480 LYD644 soybean| 1vlIGLYMA17GO1400 120 481 LYD645 soybean| 1vlIGLYMA17GO2420 121 482 LYD646 soybean| 1vlIGLYMA17G10240 122 483 LYD647 soybean| 1vlIGLYMA18G15530 123 484 LYD648 tomatollOvlIAI780847 124 485 LYD650 tomatol11vilAF204783 125 486 LYD651 tomatollvlIlAF211784 126 487 LYD652 tomatollvlIAI771255 127 488 LYD653 tomatollvlIAI778101 128 489 LYD654 tomatollvlIAI782247 129 490 LYD655 tomatollvlIAI896168 130 491 LYD657 tomatollvlAWO30194 131 492 LYD658 tomatollvlAWO94631 132 493 LYD659 tomatollvllAW217526 133 494 WO 2013/128448 PCT/IL2013/050172 154 Gene Name Organism / Cluster tag SPElyn I NO NO: LYD660 tomatollvllAW616260 134 495 LYD661 tomatol11vllAW616620 135 496 LYD662 tomatol11vllAW618546 136 497 LYD663 tomatol11vIlAY376851 137 498 LYD664 tomatol11vilBE460507 138 499 LYD665 tomatollvllBF097728 139 500 LYD666 tomatoIl1vlIBG123259 140 501 LYD667 tomatol11v1lBG123287 141 502 LYD668 tomatoI11vIlBG125390 142 503 LYD669 tomatoI11vIlBG125858 143 504 LYD670 tomatol11v1lBG126384 144 505 LYD671 tomatoIl1vlIBG129734 145 506 LYD672 tomatoIl1vlIBG131939 146 507 LYD673 tomatoIl1vlIBG132287 147 508 LYD674 tomatoIl1vlIBG133722 148 509 LYD675 tomatoIl1vlIBG134175 149 510 LYD676 tomatoIl1vlIBG135207 150 511 LYD677 tomatoIl1vlIBG592613 151 512 LYD678 tomatoIl1vlIBG626546 152 513 LYD679 tomatoIl1vlIBG628242 153 514 LYD680 tomatoIl1vlIBG628985 154 515 LYD681 tomatoIl1vlIBG630045 155 516 LYD682 tomatoIl1vlIBG630298 156 517 LYD683 tomatoIl1vlIBG643762 157 518 LYD684 tomatoIl1vlIBG734982 158 519 LYD685 tomatollvllBI210592 159 520 LYD686 tomatollvllBI405665 160 521 LYD687 tomatollvlIBM066565 161 522 LYD688 tomatol11vilBM067954 162 523 LYD689 tomatoIl1vlIBQ512926 163 524 LYD690 tomatol11vilDV623174 164 525 LYD539_H11 arabidopsisIlOvlIAT2G35260 165 526 LYD532 arabidopsisIlOvilAT5GO2830 166 527 LYD535 arabidopsis|l1OviAT5G46790 167 375 LYD538 bjunceal10v2IE6ANDIZ01AWH6F 168 528 LYD539 bjuncea10v2IE6ANDIZ01BOPVK 169 529 LYD540 bjunceal10v2IE6ANDIZ01CQ2ZQ 170 530 LYD541 brapa11vilBQ704427 171 381 LYD544 brachypodium09vlIGT835824 172 531 LYD546 brachypodium09v ISRRO31797S0017542 173 532 LYD548 canolallOvlICX192172 174 533 LYD549 canolallOvllEE556201 175 534 LYD550 canolaIlvlIDY020414 176 535 LYD552 canolallvllEE440823 177 392 LYD553 canolallvllEE481252 178 536 LYD567 medicagollvlIAW125911 179 406 LYD581 medicagollvlIAW980738 180 419 LYD584 medicagol11vlIBE325825 181 537 WO 2013/128448 PCT/IL2013/050172 155 Gene Name Organism / Cluster tag SPElyn I NO NO: LYD587 medicagol11vlIBF005808 182 538 LYD589 medicagolI11v1BG644974 183 426 LYD591 medicagolI11vIEV259134 184 428 LYD592 medicagollvllXM_003625686 185 539 LYD595 ricelgbl7010S01G51360 186 432 LYD597 riceIgb17010SO2G22020 187 434 LYD600 riceIgb17010SO6GO1200 188 437 LYD604 sorghum|09vIlSBO1G049980 189 441 LYD606 sorghuml09v 1 lSB03G025590 190 443 LYD616 soybean|IIvlIGLYMA03G36910 191 453 LYD619 soybean| 1vlIGLYMA04G38690 192 540 LYD628 soybean| 11 vl lGLYMA09G27600 193 541 LYD632 soybean| 11 vl lGLYMA10G40890 194 542 LYD654 tomatollvlIAI782247 195 544 LYD663 tomatol11vilAY376851 196 498 LYD676 tomatol11vlIBG135207 197 545 LYD681 tomatoIl1vlIBG630045 198 516 LYD685 tomatollvllBI210592 199 520 LYD687 tomatollvlIBM066565 200 522 LYD690 tomatollvllDV623174 201 546 LYD521 arabidopsisl lOvi AT 1 G08410 202 362 LYD522 arabidopsis|IOvlIAT1G19110 203 363 LYD524 arabidopsis|IOvlIAT2G20340 204 364 LYD525 arabidopsisl 1 Ovi AT2G45030 205 365 LYD526 arabidopsisl 1 Ovi AT2G45730 206 366 LYD527 arabidopsis|IOvlIAT2G47920 207 547 LYD528 arabidopsis IOvi AT3G15650 208 368 LYD529 arabidopsisIOvlIAT4G0500 209 369 LYD530 arabidopsis|IOvlIAT4G13110 210 548 LYD531 arabidopsis|IOvlIAT4G16146 211 371 LYD532 arabidopsis IOvi AT5GO2830 212 549 LYD533 arabidopsisl 1 Ovi AT5G06700 213 373 LYD534 arabidopsis| 1Ovi AT5G43150 214 374 LYD535 arabidopsisl 1 Ovi AT5G46790 215 375 LYD536 arabidopsis IOvi AT5G65280 216 376 LYD537 bjunceal10v2IE6ANDIZ01AI14E 217 550 LYD538 bjunceal10v2IE6ANDIZ01AWH6F 218 378 LYD540 bjuncea10v2IE6ANDIZ01CQ2ZQ 219 551 LYD541 bjrapal1vlIBQ704427 220 381 LYD542 brachypodium09v 1 lDV480497 221 382 LYD543 brachypodiuml09vll GT759735 222 552 LYD545 brachypodiumI09vlIGT841411 223 385 LYD546 brachypodium09v ISRRO31797S0017542 224 386 LYD547 canolal1OvlICD822163 225 387 LYD548 canolal1OvlICX192172 226 553 LYD549 canolal1OvIlEE556201 227 554 LYD550 canolaIlIvIDY020414 228 555 LYD551 canolal11vllEE429972 229 391 WO 2013/128448 PCT/1L2013/050172 156 GeneNam Oranim IClutertagPolyn. Polyp SEQ Gen Nae rgaism/ luser agSEQ ID ID NO: NO: LYD552 canolalllvlEE44O823 230 392 LYD553 canolalllvlIEE48l252 231 556 LYD554 cottonI1Ov2IDN8O4535 232 557 LYD555 cottonl11v1C0098912 233 558 LYD556 1otus109v11IAW719664 234 396 LYD558 medicagoIO9v1 ILLAW329230 235 397 LYD559 medicagolIv IA1083094 236 559 LYD560 medicagolIv1 IA1974457 237 560 LYD561 medicagolIvl IAJ388759 238 400 LYD562 medicagolIv1 IAL368425 239 401 LYD563 medicagolIvI IAL370319 240 402 LYD564 medicagolIvI IAL372358 241 403 LYD565 medicagolIv1 IAL383170 242 404 LYD566 medicagolIv1 IAL384827 243 561 LYD567 medicagolIv IAW125911 244 406 LYD568 medicagolIIvI IAW126198 245 407 LYD570 medicagolIIv IAW299069 246 562 LYD571 medicagolIIv IAW299099 247 563 LYD572 medicagolIIv IAW683620 248 564 LYD573 medicagolIIv IAW684312 249 411 LYD574 medicagolIIvI IAW686798 250 412 LYD575 medicagolIIv IAW688064 251 565 LYD576 medicagolIIvI IAW688428 252 414 LYD577 medicagolIIvI IAW690765 253 566 LYD578 medicagolIIv IAW691134 254 567 LYD579 medicagolIIv IAW695894 255 568 LYD580 medicagolIIv IAW775280 256 569 LYD581 medicagolIIvI IAW980738 257 419 LYD583 medicagolIv IBE204527 258 570 LYD584 medicagolIvl IBE325825 259 421 LYD585 medicagolIvl IBE942833 260 422 LYD586 medicagolIvl IBE998813 261 423 LYD587 medicagolIvI IBF005808 262 571 LYD588 medicagolIv IBF640823 263 572 LYD589 medicagolIvl IBG644974 264 573 LYD591 medicagolIv IEV259134 265 574 LYD592 medicagolllvllXM_003625686 266 575 LYD593 medicagol 12v1 IAL366306 267 576 LYD594 medicagol 2vlIBF633538 268 577 LYD595 riceIgb710SOIlG51360 269 432 LYD596 riceIgbl17010SOIG70930 270 433 LYD597 riceIgb 170IOS02G22020 271 434 LYD598 riceIgbl1701OS03GIl2840 272 435 LYD599 riceIgbl17OIOSO4G4Ol100 273 436 LYD600 riceIgbl1701OS06GOl1200 274 437 LYD601 riceIgbl1701OS06GO4250 275 438 LYD602 riceIgb 170IOS06G338 10 276 439 LYD603 riceIgbl17OIOSO8G29l7O 277 440 WO 2013/128448 PCT/IL2013/050172 157 Gene Name Organism / Cluster tag SPElyn I NO NO: LYD604 sorghum|09vIlSBO1G049980 278 441 LYD605 sorghum|09vIlSB02GO37340 279 578 LYD606 sorghuml09v 1 lSB03G025590 280 443 LYD607 sorghuml09v 1 lSB03G037600 281 444 LYD608 sorghuml09v 1 lSB06G006920 282 445 LYD609 sorghum|09vIlSB09GO25850 283 446 LYD610 sorghum|IIvlISBO1G036260 284 447 LYD611 soybean| 11v IGLYMAO1G02290 285 448 LYD612 soybeanIIvlIGLYMA02GO2070 286 449 LYD613 soybean| 11 v IGLYMA02GO4840 287 450 LYD614 soybean| 1vlIGLYMA02G42250 288 451 LYD615 soybeanIIvlIGLYMA03G27800 289 452 LYD616 soybeanIIvlIGLYMA03G36910 290 453 LYD617 soybean| 1vlIGLYMA03G37120 291 454 LYD618 soybean| 1vlIGLYMA03G41760 292 579 LYD619 soybean| 1vlIGLYMA04G38690 293 580 LYD620 soybean| 1vlIGLYMA05G00370 294 457 LYD621 soybean| 1vlIGLYMA05G34620 295 458 LYD622 soybean|IIvlIGLYMA06G03760 296 459 LYD623 soybean| 1vlIGLYMA06G05880 297 460 LYD624 soybean|IIvlIGLYMA06G1 1430 298 461 LYD625 soybean| 1vlIGLYMA07G27370 299 462 LYD626 soybean| 11 vl lGLYMA08G14740 300 463 LYD627 soybean|IIvlIGLYMA08G39520 301 464 LYD628 soybean| 1vlIGLYMA09G27600 302 465 LYD629 soybean| 1vlIGLYMA09G30190 303 466 LYD630 soybean|IIvlIGLYMA09G35750 304 467 LYD631 soybean| 11 vl lGLYMA09G36720 305 468 LYD632 soybean| 1vlIGLYMA1OG40890 306 581 LYD633 soybeanIIvlIGLYMA12GO2590 307 470 LYD634 soybean| 1vlIGLYMA12GO9830 308 471 LYD635 soybean| 1vlIGLYMA13GO4780 309 472 LYD636 soybeanIIvlIGLYMA13G18990 310 473 LYD637 soybeanIIvlIGLYMA13G22160 311 582 LYD638 soybeanIIvlIGLYMA13G41580 312 475 LYD639 soybean| 1vlIGLYMA14G32430 313 476 LYD640 soybean| 1vlIGLYMA14G35690 314 477 LYD641 soybean| 1vlIGLYMA15GO2690 315 583 LYD642 soybeanIIvlIGLYMA15G15380 316 479 LYD643 soybean| 1vlIGLYMA16GO3140 317 480 LYD644 soybeanIIvlIGLYMA17GO1400 318 481 LYD645 soybean| 1vlIGLYMA17GO2420 319 482 LYD646 soybean| 1vlIGLYMA17G10240 320 584 LYD647 soybean| 1vlIGLYMA18G15530 321 484 LYD648 tomatollOvlIAI780847 322 485 LYD650 tomatollvllAF204783 323 585 LYD651 tomatollvlIlAF211784 324 586 LYD652 tomatollvlIAI771255 325 587 WO 2013/128448 PCT/IL2013/050172 158 Gene Name Organism / Cluster tag SEl nD I NO NO: LYD654 tomatollvlIAI782247 326 490 LYD655 tomatollvlIAI896168 327 491 LYD657 tomatollvllAW030194 328 492 LYD658 tomatollvllAW094631 329 493 LYD659 tomatollvllAW217526 330 494 LYD660 tomatollvllAW616260 331 588 LYD661 tomatollvllAW616620 332 496 LYD662 tomatollvllAW618546 333 497 LYD663 tomatol11vllAY376851 334 498 LYD664 tomatollvllBE460507 335 499 LYD665 tomatollvllBF097728 336 589 LYD666 tomatol11vllBG123259 337 590 LYD667 tomatollvllBG123287 338 591 LYD668 tomatollvllBG125390 339 592 LYD669 tomatollvllBG125858 340 504 LYD670 tomatollvllBG126384 341 505 LYD671 tomatol11vllBG129734 342 593 LYD672 tomatollvllBG131939 343 507 LYD673 tomatol11vllBG132287 344 594 LYD674 tomatol11vllBG133722 345 509 LYD675 tomatollvllBG134175 346 595 LYD676 tomatollvllBG135207 347 596 LYD677 tomatollvllBG592613 348 512 LYD678 tomatol11vllBG626546 349 513 LYD679 tomatollvllBG628242 350 597 LYD680 tomatollvllBG628985 351 598 LYD681 tomatollvllBG630045 352 516 LYD682 tomatollvllBG630298 353 517 LYD683 tomatollvllBG643762 354 599 LYD684 tomatollvllBG734982 355 519 LYD685 tomatollvllBI210592 356 600 LYD686 tomatollvllBI405665 357 521 LYD688 tomatoIllvlBM067954 358 601 LYD689 tomatol11vllBQ512926 359 524 LYD690 tomatollvllDV623174 360 525 LYD539_H11 arabidopsisIlOvlIAT2G35260 361 526 Table 53: Provided are the identified genes, their annotation (cluster tag), organism and polynucleotide and polypeptide sequence identifiers. "polyn." = polynucleotide; "polyp." = polypeptide.
WO 2013/128448 PCT/IL2013/050172 159 EXAMPLE 13 IDENTIFICATION OF HOMOLOGOUS SEQUENCES THAT INCREASE SEED YIELD, OIL YIELD, GROWTH RATE, OIL CONTENT, FIBER YIELD, FIBER QUALITY, BIOMASS, VIGOR, ABST AND/OR NUE OF A PLANT 5 The concepts of orthology and paralogy have recently been applied to functional characterizations and classifications on the scale of whole-genome comparisons. Orthologs and paralogs constitute two major types of homologs: The first evolved from a common ancestor by specialization, and the latter are related by duplication events. It is assumed that paralogs arising from ancient duplication events are likely to have 10 diverged in function while true orthologs are more likely to retain identical function over evolutionary time. To identify putative orthologs of the genes affecting plant yield, oil yield, oil content, seed yield, growth rate, vigor, biomass, abiotic stress tolerance and/or nitrogen use efficiency, all sequences were aligned using the BLAST (Basic Local Alignment 15 Search Tool). Sequences sufficiently similar were tentatively grouped. These putative orthologs were further organized under a Phylogram - a branching diagram (tree) assumed to be a representation of the evolutionary relationships among the biological taxa. Putative ortholog groups were analyzed as to their agreement with the phylogram and in cases of disagreements these ortholog groups were broken accordingly. 20 Expression data was analyzed and the EST libraries were classified using a fixed vocabulary of custom terms such as developmental stages (e.g., genes showing similar expression profile through development with up regulation at specific stage, such as at the seed filling stage) and/or plant organ (e.g., genes showing similar expression profile across their organs with up regulation at specific organs such as seed). The annotations 25 from all the ESTs clustered to a gene were analyzed statistically by comparing their frequency in the cluster versus their abundance in the database, allowing the construction of a numeric and graphic expression profile of that gene, which is termed "digital expression". The rationale of using these two complementary methods with methods of phenotypic association studies of QTLs, SNPs and phenotype expression 30 correlation is based on the assumption that true orthologs are likely to retain identical function over evolutionary time. These methods provide different sets of indications on WO 2013/128448 PCT/IL2013/050172 160 function similarities between two homologous genes, similarities in the sequence level identical amino acids in the protein domains and similarity in expression profiles. The search and identification of homologous genes involves the screening of sequence information available, for example, in public databases such as the DNA 5 Database of Japan (DDBJ), Genbank, and the European Molecular Biology Laboratory Nucleic Acid Sequence Database (EMBL) or versions thereof or the MIPS database. A number of different search algorithms have been developed, including but not limited to the suite of programs referred to as BLAST programs. There are five implementations of BLAST, three designed for nucleotide sequence queries (BLASTN, BLASTX, and 10 TBLASTX) and two designed for protein sequence queries (BLASTP and TBLASTN) (Coulson, Trends in Biotechnology: 76-80, 1994; Birren et al., Genome Analysis, I: 543, 1997). Such methods involve alignment and comparison of sequences. The BLAST algorithm calculates percent sequence identity and performs a statistical analysis of the similarity between the two sequences. The software for performing 15 BLAST analysis is publicly available through the National Centre for Biotechnology Information. Other such software or algorithms are GAP, BESTFIT, FASTA and TFASTA. GAP uses the algorithm of Needleman and Wunsch (J. Mol. Biol. 48: 443 453, 1970) to find the alignment of two complete sequences that maximizes the number of matches and minimizes the number of gaps. 20 The homologous genes may belong to the same gene family. The analysis of a gene family may be carried out using sequence similarity analysis. To perform this analysis one may use standard programs for multiple alignments e.g. Clustal W. A neighbour-joining tree of the proteins homologous to the genes in this invention may be used to provide an overview of structural and ancestral relationships. Sequence identity 25 may be calculated using an alignment program as described above. It is expected that other plants will carry a similar functional gene (ortholog) or a family of similar genes and those genes will provide the same preferred phenotype as the genes presented here. Advantageously, these family members may be useful in the methods of the invention. Example of other plants are included here but not limited to, barley (Hordeum vulgare), 30 Arabidopsis (Arabidopsis thaliana), maize (Zea mays), cotton (Gossypium), Oilseed rape (Brassica napus), Rice (Oryza sativa), Sugar cane (Saccharum officinarum), WO 2013/128448 PCT/IL2013/050172 161 Sorghum (Sorghum bicolor), Soybean (Glycine max), Sunflower (Helianthus annuus), Tomato (Lycopersicon esculentum), Wheat (Triticum aestivum). The above-mentioned analyses for sequence homology can be carried out on a full-length sequence, but may also be based on a comparison of certain regions such as 5 conserved domains. The identification of such domains, would also be well within the realm of the person skilled in the art and would involve, for example, a computer readable format of the nucleic acids of the present invention, the use of alignment software programs and the use of publicly available information on protein domains, conserved motifs and boxes. This information is available in the PRODOM (Hypertext 10 Transfer Protocol://World Wide Web (dot) biochem (dot) ucl (dot) ac (dot) uk/bsm/dbbrowser/protocol/prodomqry (dot) html), PIR (Hypertext Transfer Protocol://pir (dot) Georgetown (dot) edu/) or Pfam (Hypertext Transfer Protocol://World Wide Web (dot) sanger (dot) ac (dot) uk/Software/Pfam/) database. Sequence analysis programs designed for motif searching may be used for identification 15 of fragments, regions and conserved domains as mentioned above. Preferred computer programs include, but are not limited to, MEME, SIGNALSCAN, and GENESCAN. A person skilled in the art may use the homologous sequences provided herein to find similar sequences in other species and other organisms. Homologues of a protein encompass, peptides, oligopeptides, polypeptides, proteins and enzymes having amino 20 acid substitutions, deletions and/or insertions relative to the unmodified protein in question and having similar biological and functional activity as the unmodified protein from which they are derived. To produce such homologues, amino acids of the protein may be replaced by other amino acids having similar properties (conservative changes, such as similar hydrophobicity, hydrophilicity, antigenicity, propensity to form or break 25 a-helical structures or 3-sheet structures). Conservative substitution tables are well known in the art (see for example Creighton (1984) Proteins. W.H. Freeman and Company). Homologues of a nucleic acid encompass nucleic acids having nucleotide substitutions, deletions and/or insertions relative to the unmodified nucleic acid in question and having similar biological and functional activity as the unmodified nucleic 30 acid from which they are derived. Polynucleotides and polypeptides with significant homology to the identified genes described in Table 53 (Example 12 above) were identified from the databases WO 2013/128448 PCT/IL2013/050172 162 using BLAST software with the Blastp and tBlastn algorithms as filters for the first stage, and the needle (EMBOSS package) or Frame+ algorithm alignment for the second stage. Local identity (Blast alignments) was defined with a very permissive cutoff - 60% Identity on a span of 60% of the sequences lengths because it is used only 5 as a filter for the global alignment stage. The default filtering of the Blast package was not utilized (by setting the parameter "-F F"). In the second stage, homologs were defined based on a global identity of at least 80% to the core gene polypeptide sequence. Two distinct forms for finding the optimal global alignment for protein or nucleotide sequences were used in this 10 application: 1. Between two proteins (following the blastp filter): EMBOSS-6.0.1 Needleman-Wunsch algorithm with the following modified parameters: gapopen=8 gapextend=2. The rest of the parameters were unchanged from the default options described hereinabove. 15 2. Between a protein sequence and a nucleotide sequence (following the tblastn filter): GenCore 6.0 OneModel application utilizing the Frame+ algorithm with the following parameters: model=frame+_p2n.model mode=qglobal -q=protein. sequence -db= nucleotide.sequence. The rest of the parameters are unchanged from the default options 20 described hereinabove. The query polypeptide sequences were SEQ ID NOs: 362-601 (which are encoded by the polynucleotides SEQ ID NOs:1-361, shown in Table 53 above) and the identified orthologous and homologous sequences having at least 80% global sequence identity are provided in Table 54, below. These homologous genes are expected to 25 increase plant yield, seed yield, oil yield, oil content, growth rate, fiber yield, fiber quality, biomass, vigor, ABST and/or NUE of a plant.
WO 2013/128448 PCT/IL2013/050172 163 Table 54 Homologous polynucleotides and polypeptides which can increase plant yield, seed yield, oil yield, oil content, growth rate, fiber yield, fiber quality, biomass, vigor, ABST and/or NUE of a plant 5 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD521_11 arabidopsislyrata09vllJGIALOO 602 2429 362 95.9 globlastp 0805_P1 LYD521_H2 thellungiellaparvuluml1ivilBY 603 2430 362 89.2 globlastp 806918 LYD521_H3 thellungiellajhalophilum|l1vIlB 604 2431 362 88.3 globlastp Y806918 LYD521_H6 brapa|llvlICD813110 P1 605 2432 362 85.6 globlastp LYD521_H4 canolaIlvlEE468045_P1 606 2433 362 85.2 globlastp LYD521_H5 canolal11v1lES952287 1 607 2434 362 82.37 glotblastn LYD522_1 arabidopsislyrata09vllJGIALOO 608 2435 363 96.9 globlastp 2005_P1 LYD522_H2 thellungiellafhalophiluml lv lB 609 2436 363 92.1 globlastp Q079260 LYD522_H3 thellungiella-parvuluml 1vIBQ 610 2437 363 90.8 globlastp 079260 LYD522_H4 canola|11v1lFG573664 1 611 2438 363 89.27 glotblastn LYD522_H7 b rapa|11vlDY013296_P1 612 2439 363 89 globlastp LYD522 H8 b rapaIllvlIEE443767 P1 613 2440 363 88.4 globlastp LYD522_H5 canolaIllvlIES902667 1 614 2441 363 88.39 glotblastn LYD522_H6 canolaIllvlEE443767_P1 615 2442 363 87.6 globlastp LYD522 H9 b rapallvlIES270429 P1 616 2443 363 87.2 globlastp LYD524_1 arabidopsislyrata09vllJGIAL01 617 2444 364 97.1 globlastp 2501_P1 LYD524_H6 b-rapaI11vIE6ANDIZ01A63NK 618 2445 364 89.8 globlastp P1 LYD524_H2 thellungiellaflalophiluml1ivilE 619 2446 364 89.6 globlastp 11JGI1 1021169 LYD524_H3 thellungiellaflalophiluml IvilE 620 2447 364 87.8 globlastp 11JGI 1027144 LYD524_H7 b rapaIllvlICD822356_P1 621 2448 364 86.8 globlastp LYD524_H8 b rapallvlIES908014_P1 622 2449 364 85.7 globlastp LYD524_H4 radishIgb164IEV536118 623 2450 364 84.8 globlastp LYD524_H5 thellungiella-parvuluml IvIEP 624 2451 364 82.3 globlastp CRP013365 LYD524_H9 brapa|llvlISRR001111.64443_ 625 2452 364 81.8 globlastp P1 LYD525_H1 arabidopsislyrata09vllJGIAL01 626 2453 365 98.7 globlastp 5890_P1 LYD525_H2 arabidopsis|1vllAT1G45332_P 627 2454 365 98.7 globlastp WO 2013/128448 PCT/IL2013/050172 164 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD525_H3 thellungiella-halophilum| 11v llB 628 2455 365 95.5 globlastp Y819164 LYD525_H4 thellungiellapar vulum| I1vIlBY 629 2456 365 94.2 globlastp 819164 LYD525_H3 b rapa1vlIAT000510_P1 630 2457 365 92.7 globlastp 8 LYD525_H5 cacaol0vlIlCU478363 P1 631 2458 365 87.3 globlastp LYD525_H3 cotton|11v1lDT462624_P1 632 2459 365 86.3 globlastp 9 LYD525_H6 cotton|10v2|SRR032367S002387 633 2460 365 86.3 globlastp 2 LYD525_H4 gossypiumraimondil12vllDT46 634 2461 365 86.1 globlastp 0 2624_P1 LYD525_1H4 cotton|11v1lDT047985_P1 635 2462 365 86 globlastp 1 LYD525_H4 gossypiumraimondiil12vllES82 636 2463 365 86 globlastp 2 5881_P1 LYD525_H4 bean112vIlCB539945_P1 637 2464 365 85.3 globlastp 3 LYD525_H4 chickpeaI11vlIGR393166_P1 638 2465 365 84.8 globlastp 4 LYD525_H7 grape|11vllGSVIVT101818600 639 2466 365 84.5 globlastp LYD525_H4 beechl11vllSRR006294.21324_P 640 2467 365 84.4 globlastp LYD525_H8 cotton|10v2|SRR032367S000932 641 2468 365 84.2 globlastp 1 LYD525_H9 apple|11vlCN899815 P1 642 2469 365 84.1 globlastp LYD525_H1 clementine|llvlIDY261585_P1 643 2470 365 84 globlastp 0 LYD525_H1 orange|llvllDY261585_P1 644 2470 365 84 globlastp 1 LYD525_H1 cucumberI09vllDV631607_P1 645 2471 365 83.9 globlastp 2 LYD525_H1 amsoniaIvlISRR098688X1130 646 2472 365 83.66 glotblastn 3 63_T1 LYD525_1 poplarI0vlIlBI136702_P1 647 2473 365 83.6 globlastp 4 LYD525_H1 aquilegia|I0v2IDT749020_P1 648 2474 365 83.4 globlastp LYD525_H1 eucalyptusI1v2ISRR001659X12 649 2475 365 83.3 globlastp 6 134_P1 LYD525_H1 watermelonIlvlIAM716765 650 2476 365 83.2 globlastp 7 LYD525-HI1 prunusIl~vlICN8998lS 651 2477 365 83.1 globlat 8 ____________________ WO 2013/128448 PCT/IL2013/050172 165 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD525_HI euphorbia|I1vlIDV149525_P1 652 2478 365 82.9 globlastp 9 LYD525_H2 cassava09vlIJGICASSAVA257 653 2479 365 82.5 globlastp 0 2VALIDM1_P1 LYD525_H2 strawberry11vllDV439076 654 2480 365 82.3 globlastp 1 LYD525_H2 tomatol11vllAW032413 655 2481 365 82.3 globlastp 2 LYD525_H4 poppy11vllSRR030259.126125 656 2482 365 82.26 glotblastn 6 T1 LYD525_H4 banana|12vlIMAGEN201203463 657 2483 365 82 globlastp 7 OPi LYD525_H2 vinca|11vllSRR098690X120383 658 2484 365 82 globlastp 3 LYD525_H2 valerianal1lvIlSRR099039X102 659 2485 365 81.87 glotblastn 4 865 LYD525_H2 potatol0vlIBG591483_P1 660 2486 365 81.8 globlastp LYD525_H2 solanumphureja|09vllSPHAWO 661 2486 365 81.8 globlastp 6 32413 LYD525_H4 medicagol12vllBF634704_P1 662 2487 365 81.7 globlastp 8 LYD525_1H2 poplarI10vlICX282997_1 663 2488 365 81.44 glotblastn 7 LYD525_H2 lettucel0vlIlDW064105 664 2489 365 81.2 globlastp 8 LYD525_H4 beet|12v1lBI096237_P1 665 2490 365 81.1 globlastp 9 LYD525_H2 phalaenopsisl 1 lvi ISRR12577 1.1 666 2491 365 81 globlastp 9 000581_P1 LYD525_H3 trigonellallvlISRR066195X105 667 2492 365 80.9 glotblastn 0 848 LYD525_H5 oil-palmIl1vlIEY403951_P1 668 2493 365 80.8 globlastp 0 LYD525_1H5 brachypodium|l2vllBRADI1G41 669 2494 365 80.7 globlastp 1 990_P1 LYD525_H3 brachypodiuml09vll DV479885 670 2494 365 80.7 globlastp 1 LYD525_H3 flaveria|IlvlISRR149229.13485 671 2495 365 80.7 globlastp 2 8_P1 LYD525_H3 flaverial11vllSRR149229.10409 672 2496 365 80.6 globlastp 3 1_Pi LYD525_H3 monkeyflowerIlOvlICV521415_ 673 2497 365 80.5 glotblastn 4 TI LYD525_H3 arnicaIIIvIlSRR099034XI26312 674 2498 365 80.39 glotblastn 5 TI WO 2013/128448 PCT/IL2013/050172 166 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD525_H5 sorghum|12vlISB01GOO1500T_1 675 2499 365 80.26 glotblastn 2 LYD525_H3 sorghumI1vlISB01GOO1500 676 2499 365 80.26 glotblastn 6 LYD525_H3 rice|I1vI|AA749912_P1 677 2500 365 80.1 globlastp 7 LYD525_H3 riceIgbl7010SO3G36780 678 2500 365 80.1 globlastp 7 LYD526_HI arabidopsislyrata|09vllJGIALO1 679 2501 366 94.87 glotblastn 5968_11 LYD526_H2 thellungiella-halophilumllIvIlE 680 2502 366 88.3 globlastp HJGI1 1009328 LYD526_H3 thellungiellaparvulumll IvIlBY 681 2503 366 87.7 globlastp 818477 LYD526_H4 canola|llvlEE446150_1 682 2504 366 85.27 glotblastn LYD526_H5 radishIgb164|EV543432 683 2505 366 84.73 glotblastn LYD526_H8 b rapa|1vI|EE44615O_P1 684 2506 366 84 globlastp LYD526_H9 bjuncea|12v1IE6ANDIZO2HAY 685 2507 366 82.7 globlastp 46_P1 LYD526_H6 canola|llvllSRRO19557.37442_ 686 2508 366 82.55 glotblastn TI LYD526_HI b rapa1vI|CN829199_P1 687 2509 366 82.4 globlastp 0 LYD526_H7 canolaIlvI|EV120639 P1 688 2510 366 81.8 globlastp LYD527_11 arabidopsislyrata|09vllJGIAL01 689 2511 367 86.3 globlastp 6215_P1 LYD527_H2 arabidopsislyratal9 vllCRPAL 690 2512 367 85.9 globlastp E018554_P1 LYD528_11 arabidopsislyrata|09vllJGIAL01 691 2513 368 98.4 globlastp 0051_P1 LYD528_H2 thellungiella-parvuluml IvIEP 692 2514 368 94.9 globlastp CRP009845 LYD528H1 b rapa|1vI|DN9648O7_P1 693 2515 368 94.5 globlastp LYD528_H3 canola|llvllSRR329661.233011 694 2516 368 94.1 globlastp P1 LYD528_H4 thellungiella-halophilumllIvIlE 695 2517 368 93.3 globlastp HJGI11003890 LYD528_H5 canolal11vllS1RR341923.107436 696 2518 368 92.94 glotblastn 0_TI LYD528_H6 canola|11vllSRR29661.212936 697 2519 368 92.55 glotblastn LYD528_H7 canolal11vllSRR329661.203365 698 2520 368 92.16 glotblastn TI LYD528-HI1 b apalllvlEXO967lP1 699 2521 368 89.6 globlastp 8 ____________________ WO 2013/128448 PCT/IL2013/050172 167 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD528_1 brapaI11vIE6ANDIZO1EED7 700 2522 368 89.2 globlastp 9 MP1 LYD528_H8 thellungiella-parvuluml 1 lv IEP 701 2523 368 87.1 globlastp CRPOO2 185 LYD528_H9 arabidopsislyrata09vllJGIAL00 702 2524 368 86.77 glotblastn 4771_11 LYD528H1 arabidopsis|1vllAT1G52700_P 703 2525 368 86.3 globlastp LYD528_11 thellungiellajhalophiluml1ivIlE 704 2526 368 85.5 globlastp 1 HJGI11004658 LYD528_1 canola|llvllSRR341920.125536 705 2527 368 85.1 globlastp 2 P1 LYD528_11 radishIgb164IEW717735 706 2528 368 85.1 globlastp 311 LYD528_H2 bsrapaIlvlIBRA030973_P1 707 2529 368 84.7 globlastp 0 LYD528_H brapalgb162DN964807 708 2530 368 83.9 globlastp 4 LYD528_H2 brapa|IlvlIE6ANDIZOlEBPM 709 2531 368 81.96 glotblastn 1 4_T1 LYD528_1 castorbeanIllvlIEG661187_P1 710 2532 368 81.8 globlastp 5 LYD528_1 poplarIlOvlBU89118l_P1 711 2533 368 80.6 globlastp 6 LYD529_11 arabidopsislyrata09vllJGIALO2 712 2534 369 96.1 globlastp 3826_P1 LYD529_H2 thellungiellafhalophiluml1ivIlE 713 2535 369 90 globlastp HJGI11017680 LYD529_H3 thellungiella-parvulumll IvIlEP 714 2536 369 89.3 globlastp CRP024486 LYD529_H4 canola|llvllEV182687 1 715 2537 369 87.04 glotblastn LYD529_H5 b rapaIl1vlIEV182687 P1 716 2538 369 86.8 globlastp LYD531H1 arabidopsislyrata09vllJGIALO2 717 2539 371 90.2 globlastp 6618_P1 LYD531_H2 canola|llvllEE458414_P1 718 2540 371 83.3 globlastp LYD531_H3 boleraceaIgbl61|EH427989 P1 719 2541 371 80.4 globlastp LYD532_11 arabidopsislyrata09vl ICRPAL 720 2542 372 93 globlastp E021692_P1 LYD532_H2 thellungiellafhalophiluml IvilE 721 2543 372 88.7 globlastp HJGI1 1026551 LYD532_H3 thellungiella-parvuluml IvIlEP 722 2544 372 88.5 globlastp CRP024311II LYD532_H4 brapa|llvlIH07430 P1 723 2545 372 85.5 globlastp LYD533_11 arabidopsislyrata09vllJGIAL02 724 2546 373 95.3 globlastp 0349_P1 LYD533_H2 thellungiellafhalophilum|l1vilD 725 2547 373 85 globlastp N772696 WO 2013/128448 PCT/IL2013/050172 168 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD533_H3 thellungiellap arvulum| 11vlIDN 726 2548 373 85 globlastp 772696 LYD533_H4 b rapa|1vlIDY006448 P1 727 2549 373 80.6 globlastp LYD534_HI arabidopsislyrata|09vllJGIALO2 728 2550 374 94.6 globlastp 8732_P1 LYD534_H2 thellungiella-halophiluml1IvIlE 729 2551 374 83.5 globlastp HJGI1 1028247 LYD534_H3 bjuncea10v2IE6ANDIZ01AUR 730 2552 374 83 globlastp FX_P1 LYD534_H3 bjuncea10v2IE6ANDIZ01AUR 731 - 374 83 globlastp FX LYD534_H4 boleraceaIgb161|AM062082 1 732 2553 374 82.61 glotblastn LYD534_H5 thellungiella halophilumllvIlE 733 2554 374 82.47 glotblastn HPRD125218 LYD534_H6 b rapalgb1621CV546549 734 2555 374 81.91 glotblastn LYD534 H7 radishIgb164|EW725622 735 2556 374 81.91 glotblastn LYD534_HI b rapa1vlICV546549_P1 736 2557 374 81.9 globlastp 211 LYD534_H8 bjuncea10v2IE6ANDIZ01BUS 737 2558 374 81.9 globlastp A3 LYD534_H9 canolaIlvlIEV089507 P1 738 2557 374 81.9 globlastp LYD534_HI canolaIvlIEE446184_P1 739 2559 374 81.5 globlastp 0 LYD534_HI bjuncea|12vIlE6ANDIZ01BUS 740 2560 374 80.9 globlastp 3 A3_P1 LYD534_1 bjunceaI0v2IE6ANDIZ01A0W 741 2561 374 80.9 globlastp 1 7T LYD534_1 b rapa1vlICD829151_P1 742 2562 374 80.2 globlastp 4 LYD534_1 bjrapa|1vlIEE505776_P1 743 2562 374 80.2 globlastp 5 LYD535_H1 arabidopsislyrata|09vllJGIAL02 744 2563 375 89.1 globlastp 8142_P1 LYD536_1 arabidopsislyrata|09vllJGIAL03 745 2564 376 92.6 globlastp 1214_P1 LYD536_H2 thellungiella-halophiluml IvIlE 746 2565 376 88.8 globlastp HJGI11019132 LYD536_H3 thellungiella-parvuluml IvIEP 747 2566 376 87.56 glotblastn CRP006079 LYD536_H4 canolaIvlIDW999348_P1 748 2567 376 87.2 globlastp LYD536_H6 b rapa1vlICD815782 P1 749 2568 376 87 globlastp LYD536_H7 bjuncea|12vIlE6ANDIZ01CHJ 750 2569 376 86.3 globlastp GT_P1 LYD536 H5 radishIgb164|EW715863 751 2570 376 86.3 globlastp LYD537_1 b rapa1vlIEH416474_P1 752 2571 377 97.5 globlastp 0 1 1 1 1 1 1__ ___ __ ___ _1 WO 2013/128448 PCT/IL2013/050172 169 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD537_HI brapalgb162|EX039662 753 2571 377 97.5 globlastp LYD537_H3 b oleraceaIgb161|AM387255_1 754 2572 377 96.45 glotblastn LYD537 H4 canolaIlvlIEV093336 1 755 2573 377 95.43 glotblastn LYD537_H6 thellungiella-halophilum|l1vilD 756 2574 377 89.4 globlastp N774047 LYD537_H7 thellungiellalgbl67IDN774047 757 2574 377 89.4 globlastp LYD537_H9 arabidopsislyrata|09vllJGIAL01 758 2575 377 86 globlastp 1355_P1 LYD538_H2 brapa|11vllD78493_P1 759 378 378 100 globlastp 2 LYD538_H2 brapaIgb162ID78493 760 378 378 100 globlastp LYD538_H2 bjuncea|12vlIE6ANDIZ01A102 761 2576 378 98.3 globlastp 3 HPI LYD538_H3 boleraceaIgb161|AM388274_P1 762 2577 378 98.3 globlastp LYD538_H4 canola|11vllCN829815 P1 763 2578 378 97.9 globlastp LYD538_H2 bjuncea|12vIlE6ANDIZ01A6U 764 2579 378 97.4 globlastp 4 K3_P1 LYD538_H2 bjuncea|l2vlIE6ANDIZ01D1D 765 2580 378 97.4 globlastp 5 A8_P1 LYD538_H5 bjunceal10v2IE6ANDIZ01A102 766 2581 378 97 globlastp H LYD538_H6 bjunceaI0v2IE6ANDIZ01D1D 767 2582 378 97 globlastp A8 LYD538_HI canolaIlvlIDY025281 P1 768 2583 378 96.2 globlastp LYD538_H8 b rapalgb1621CA992498 769 2584 378 94.9 globlastp LYD538 H9 canola|11vlCN732901 P1 770 2585 378 94.9 globlastp LYD538_H2 bjuncea|l2vlIE6ANDIZO1A8Z 771 2586 378 94.4 globlastp 6 ZFPI LYD538_H2 wheat|l2v3|ERR125558X206533 772 2587 378 94.4 globlastp 7 D1_P1 LYD538_H7 bjuncea0v2IE6ANDIZ01AFT 773 2586 378 94.4 globlastp UB LYD538_1 bjunceaI1v2|E6ANDIZO1A8Z 774 2588 378 94.4 globlastp 1 ZF LYD538_H2 bjrapa|1vlICD830505_P1 775 2589 378 94 globlastp 8 LYD538_1 radishIgb164|EX762568 776 2590 378 94 globlastp 2 LYD538_1 radishIgb164|EY906991 777 2591 378 93.6 globlastp 5 LYD538_1 radishIgbI64|EV543577 778 2592 378 93.2 globlastp 4 LYD538_1 thellungiella-halophilum|l1vilD 779 2593 378 92.7 globlastp 6 N773489 LYD538_1 thellungiella-parvuluml1IvIDN 780 2594 378 92.7 globlastp 7 773489 1 1 111 WO 2013/128448 PCT/IL2013/050172 170 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD538_HI thellungiella-parvuluml1vIlEPP 781 2594 378 92.7 globlastp 8 RD115512 LYD538_HI thellungiellalgbl67IDN773489 782 2593 378 92.7 globlastp 9 LYD538_H2 radishIgb164|EV536694 783 2595 378 91.9 globlastp 0 LYD538_HI arabidopsislyrata|09vllJGIALO2 784 2596 378 85.9 globlastp 0 2891_P1 LYD538_H1 arabidopsis|1vllAT4GO9650_P 785 2597 378 85.1 globlastp LYD538_H2 cleome-spinosa|lOvlISRRO1553 786 2598 378 80.1 globlastp 1 1S0004048_P1 LYD539_HI b rapa|11vlES922502_P1 787 2599 379 95.7 globlastp 4 LYD539_H7 canola|11v1lEV186519 P1 788 2600 379 95.7 globlastp LYD539_HI brapalgb162|EX024134 789 2601 379 95.21 glotblastn 0 LYD539_H8 canolaIlvlIEV204662_P1 790 2602 379 93.4 globlastp LYD539_HI bjuncea|l2vlIE6ANDIZO1B2F 791 2603 379 92.8 globlastp 5 LSP1 LYD539_HI b rapa|1vlIEH415044_P1 792 2604 379 92.8 globlastp 6 LYD539_HI canola|llvllEE473969_P1 793 2605 379 92.3 globlastp LYD539_H2 canola|llvllEE431340 P1 794 2606 379 92.3 globlastp LYD539_H4 thellungiella-pavuluml1ivIDN 795 2607 379 91.1 globlastp 772747 LYD539_H3 radishIgbI64|EV546508 796 2608 379 90.2 globlastp LYD539_H6 arabidopsislyratal09vlJGIAL01 797 2609 379 90.2 globlastp 4664_P1I9 69 39 9. lbat LYD539_H9 thellungiella-halophilum|l1vilD 798 2610 379 89.5 globlastp N772747 LYD540_H5 b rapaIIvIlCN830957 P1 799 2611 380 89.5 globlastp LYD540_HI canola|I1vICN830957_P1 800 2612 380 88.7 globlastp LYD541_HI canolaIIvIlES977027 TI 801 2613 381 99.23 glotblastn LYD541_H7 wheat|12v3ITA12V3PRD011584 802 2614 381 92.81 glotblastn T1 LYD541_H2 thellungiella-parvuluml IvIlEP 803 2615 381 88.7 globlastp CRP002741 LYD541_H3 canolaIIvIlES976757_TI 804 2616 381 88.55 glotblastn LYD541_H8 brapa|I1vIlAM395348 P1 805 2617 381 86.8 globlastp LYD541_H4 thellungiella -halophiluml1vIlE 806 2618 381 86.42 glotblastn HJGII 1022196 LYD541_H5 canolaIIIvIlEE503031XXI_P1 807 2619 381 84.1 globlastp LYD541_H6 arabidopsislyrata|09vllJGIAL01 808 2620 381 80.9 globlastp 7560 P1 8 2 3 8 I LYD542 1 barleyl1Ov2|BF622260 809 2621 382 92.3 globlastp WO 2013/128448 PCT/IL2013/050172 171 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD542_H2 wheat|lOv2|BE428760 810 2622 382 92.1 globlastp LYD542_H2 wheat|12v3IBQ579180 P1 811 2622 382 92.1 globlastp LYD542_H3 foxtail milletI1v3IPHY7SI0174 812 2623 382 87.2 globlastp 08M_P1 LYD542_H7 sorghum|12vlSB04G28030 P1 813 2624 382 87 globlastp LYD542_H4 sorghumI11vIlSB04G028030 814 2624 382 87 globlastp LYD542 H5 maizel1OvlIAI600679 P1 815 2625 382 85.6 globlastp LYD542_H6 rice|11vllCA753844_P1 816 2626 382 84.4 globlastp LYD542 H6 riceIgbl7010SO2G51100 817 2627 382 81.8 globlastp LYD542_H8 rye|12vllDRR001012.114491_P 818 2628 382 80.4 globlastp LYD544_HI brachypodium|12vIBRADI2G59 819 2629 384 86.63 glotblastn 740_1 LYD545_HI brachypodium|l2vllBRADI1G39 820 2630 385 95.6 globlastp 4 260_P1 LYD545_HI rice|11vllB1808593_P1 821 2631 385 89.3 globlastp LYD545_HI riceIgbl7010SO6G31100 822 2631 385 89.3 globlastp LYD545_HI sorghum|12vlSB1OG020060_P1 823 2632 385 89.1 globlastp 5 LYD545_H2 sorghumIlvlISB1OG020060 824 2632 385 89.1 globlastp LYD545_H3 foxtail milletI1v3PHY7SI0061 825 2633 385 88.6 globlastp 67M_P1 LYD545_HI rye|12vlIBE587152_P1 826 2634 385 88.4 globlastp 6 LYD545H1 rye|12vllDRR001012.114248_P 827 2635 385 88.4 globlastp LYD545_H1 rye|12vllDRR001012.135473_P 828 2636 385 88.3 globlastp LYD545_H4 sugarcane|lOvllCA093342 829 2637 385 88.3 globlastp LYD545_H5 wheat|12v3BE404680 P1 830 2638 385 88.3 globlastp LYD545_H5 wheat|lOv2|BE403258 831 2639 385 87.9 globlastp LYD545 H6 wheatI0v2IBG906212 832 2640 385 87.6 globlastp LYD545_H7 wheat|lOv2|BE586039 833 2641 385 87.4 globlastp LYD545_H8 leymusIgb166|EG379479_P1 834 2642 385 87.3 globlastp LYD545_H9 maize|lOvlIBG458966_P1 835 2643 385 87.2 globlastp LYD545_H1 wheat|l2v3BE586039_P1 836 2644 385 84.7 globlastp 9 LYD545_H1 switchgrassIgb167FE609538 837 2645 385 80.64 glotblastn 0 LYD5451 maize|lOvlIBG517650_1 838 2646 385 80.28 glotblastn LYD545_H2 sorghum|12vlISB04G009720_1 839 2647 385 80.11 glotblastn 0 LYD545 _1HI sorghumIllvISB4GO972O 840 2647 385 80.11 glotblastn 2 _________________ WO 2013/128448 PCT/IL2013/050172 172 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD545_HI foxtail millet|I11v3|EC613481_P 841 2648 385 80 globlastp 3 184 268 35 8 gobat LYD547_HI b rapa1vI|CD822163_P1 842 387 387 100 globlastp 1 LYD547_HI brapaIgb162|CV545936 843 387 387 100 globlastp LYD547_HI bjuncea|l2vlIE6ANDIZ01BB4 844 2649 387 96.7 globlastp 2 X5_P1 LYD547_H2 boleraceaIgb161|EE535189 P1 845 2650 387 95 globlastp LYD547_H3 radishIgb164|EX749320 846 2651 387 89 globlastp LYD547 H4 radishIgb164|EX772827 847 2652 387 88.4 glotblastn LYD547 H5 radishIgb164|EV524435 848 2653 387 87.8 globlastp LYD547_H6 bjunceaI10v2|E6ANDIZ01BB4 849 2654 387 86.74 glotblastn X5 LYD547_117 arabidopsisl lOvIIAll G10522 P ,LYD547_H 1 850 2655 387 83.5 globlastp 8 LYD547_H7 ,LYD547_H arabidopsisIlOvlIAT1G10522 851 - 387 83.5 globlastp 8 LYD547_H9 thellungiella-halophilum|l1vilB 852 2656 387 82.6 globlastp Y811044 LYD547_HI thellungiellalgbl67IBY811044 853 2656 387 82.6 globlastp 0 LYD548_HI b rapa1vI|CV433382_P1 854 2657 388 99.4 globlastp 5 LYD548_HI canolaIlvlIEV096783_P1 855 2658 388 99.1 globlastp LYD548_H2 brapaIgb162|CV433382 856 2659 388 99.1 globlastp LYD548_HI bjuncea|12vlIE6ANDIZ01BQS 857 2660 388 97.8 globlastp 6 STPI LYD548_H4 radishIgb164|EV524991 858 2661 388 97.5 globlastp LYD548_H5 thellungiella-parvulum|l1vllBI6 859 2662 388 96 globlastp 98654 LYD548_H7 thellungiella-halophilum|l1vilD 860 2663 388 93.8 globlastp N772727 LYD548_H8 thellungiellalgbl67IBI698654 861 2663 388 93.8 globlastp LYD548_H6 arabidopsis|1vllAT4GO9750_P 862 2664 388 92.9 globlastp LYD548_H9 arabidopsislyrata|09vllJGIALO2 863 2665 388 92.9 globlastp 2899_P1 LYD548_1 cleome-spinosa|lOvlISRRO1553 864 2666 388 85.1 globlastp 0 1S0001848_P1 LYD548_1 nasturtiumIlvlISRRO32558.125 865 2667 388 82 globlastp 7 769_P1 LYD548_1 heritiera|lOvlISRROO5794S003 866 2668 388 80 globlastp 8 093_P1 II WO 2013/128448 PCT/IL2013/050172 173 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD549_H2 thellungiellapar vulum| I1vIlBY 867 2669 389 85 globlastp 806948 LYD549_H3 thellungiella-halophilum| 11v llB 868 2670 389 80.7 globlastp Y806948 LYD549_H4 arabidopsislyrata|09vllJGIALO1 869 2671 389 80.7 globlastp 4484_P1 LYD549_H5 arabidopsis|1 vllAT2G33580_P 870 2672 389 80.7 globlastp LYD550_H4 b rapa|1vlICX270458_P1 871 2673 390 95.7 globlastp 6 LYD550_H2 thellungiella-halophilum|l1vilD 872 2674 390 89.2 globlastp N774121 LYD550_H3 thellungiella-parvulum|l1vlIDN 873 2675 390 87.8 globlastp 774121 LYD550_H5 arabidopsislyratal09vllJGIAL01 874 2676 390 87.6 globlastp 0121_P1 LYD551_H9 bjrapa1vlIBQ791522 P1 875 391 391 100 globlastp LYD551_HI b rapaIgb162|BQ791522 876 391 391 100 globlastp LYD551_H2 canola|llvllDYO24382 P1 877 2677 391 98.4 globlastp LYD551_H3 radishIgb164|EV524465 878 2678 391 94 globlastp LYD551_H4 thellungiella-parvuluml IvIlEP 879 2679 391 92.8 globlastp CRP002902 LYD551_H5 thellungiella-halophiluml1ivIlE 880 2680 391 88.8 globlastp HJGI1 1006208 LYD551_H6 arabidopsislyrata|09vllJGIAL0O 881 2681 391 86.4 globlastp 0319_P1 LYD551_H7 arabidopsis|1vl AT1G03870_P 882 2682 391 84.4 globlastp LYD551_H8 thellungiella-parvuluml IvIlEP 883 2683 391 80.08 glotblastn CRP008913_____ LYD552_H4 b rapaI|1vlIEE440823 P1 884 2684 392 94.9 globlastp LYD552_1 radishIgb164|EV537053 885 2685 392 88.5 globlastp LYD552 H5 b rapaIl1vlICD839492_1 886 2686 392 86.64 glotblastn LYD552_H2 b_rapaIgb162|EX018471 887 2687 392 86.4 globlastp LYD552_H3 thellungiellaparvuluml1ivIlBY 888 2688 392 81.35 glotblastn 80061388 268 32 8.5 gobat LYD553_H5 thellungiella halophilumllvIlE 889 2689 393 94.2 globlastp HJGI1 1004320 LYD554_H3 cotton|llvlIAI728201_P1 890 2690 394 99.2 globlastp LYD555_1 cotton|1Ov2|ES850546 891 2691 395 96.68 glotblastn LYD555_H2 gossypiumraimondil12vilDT45 892 2692 395 92.8 globlastp 7613_P1 LYD556_H2 pigeonpeal IvISRRO5458OX11 893 2693 396 80.73 glotblastn LYD56_H1 pS881609_ I 02. LYD556_1HI pigeonpea i0vI ISRRO48SO00 894 2693 396 80.73 glotblastn ___________2555 WO 2013/128448 PCT/IL2013/050172 174 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD558_HI trigonella|I1vlISRRO66194X122 895 2694 397 91.08 glotblastn 160 LYD558_H2 chickpeaI11vlISRR133517.1022 896 2695 397 85.1 globlastp 89_P1 LYD559_H2 chickpea|11vllDY475242_P1 897 2696 398 85.8 globlastp 2 LYD559_H2 chickpea|09v2|DY475242 898 2696 398 85.8 globlastp LYD559_H2 pigeonpea|11v1lSRR054580X12 899 2697 398 84.1 globlastp 3 0956_P1 LYD559_H4 soybean|11vllGLYMA12G1638 900 2698 398 83.7 globlastp 0 LYD559_H5 spurgelgbl6lDV17048 901 2699 398 83 globlastp LYD559_H6 lotus109vIlA1967656 P1 902 2700 398 82.7 globlastp LYD559_H2 cotton|llvllAW186999_P1 903 2701 398 82 globlastp 4 LYD559_H2 gossypiumraimondiill2vllAW1 904 2701 398 82 globlastp 5 86999_P1 LYD559_H8 cotton1l0v21C0071682 905 2701 398 82 globlastp LYD559_H9 eucalyptus|llv2|CD668373 P1 906 2702 398 81.7 globlastp LYD559_H2 cotton|llvlC0069437_P1 907 2703 398 81.4 globlastp 6 LYD559_H2 cotton|llvllDT543683_P1 908 2704 398 81.4 globlastp 7 LYD559_HI euphorbia|llvllDV117048_P1 909 2705 398 81.2 globlastp 0 LYD559_1 peanutIlOvlICDO38760_P1 910 2706 398 81.2 globlastp 1 LYD559_1 valerianal11vllSRR099039X101 911 2707 398 81.1 globlastp 2 600 LYD559_1 pigeonpea|lOvlISRR54580S00 912 2708 398 80.9 globlastp 3 6801 LYD559_1 poplarIlOvlIAI166111_P1 913 2709 398 80.8 globlastp 4 LYD559_1 kiwilgb1661FG427674_P1 914 2710 398 80.6 globlastp 5 LYD559_1 chestnutgb1701SRR006295S002 915 2711 398 80.4 globlastp 6 3483_P1 LYD559_1 primula|llvllSRRO98679XIO12 916 2712 398 80.33 glotblastn 7 26XX1_1 LYD559_1 platanus|llvllAM260510_P1 917 2713 398 80.2 globlastp 8 LYD559_H2 bjuncea|l2vlIE6ANDIZO1A1H 918 2714 398 80.11 glotblastn 8 SYTI LYD559_H2 fraxinus|11vllSRR058827.10336 919 2715 398 80.1 globlastp 0 6_P1 LYD559_H2 scabiosa|11vllSRR063723XIO07 920 2716 398 80.1 globlastp 1 1311111 WO 2013/128448 PCT/IL2013/050172 175 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD560_HI trigonella| 11 vII SRRO66 194X100 921 2717 399 97.6 globlastp 341 LYD560_H3 pea|llvlIY17796_P1 922 2718 399 92.6 globlastp LYD560_HI pigeonpea|11vllSRR05458OX1O 923 2719 399 86.7 globlastp 58 4938_P1 LYD560_HI strawberry|11vllC0378466 924 2720 399 85.4 globlastp 5 LYD560_H2 phyla|11v2|SRR099035X102776 925 2721 399 84.1 globlastp 9 P1 LYD560_H3 euonymusll1vllSRR070038X10 926 2722 399 83.87 glotblastn 4 1097_1 LYD560_H3 euonymusll1vllSRR070038X12 927 2723 399 83.7 globlastp 8 7843_P1 LYD560_H4 tripterygiumllvllSRR098677X1 928 2724 399 83.6 globlastp 3 02820 LYD560_H4 orobanche|lOvlISRRO23189SO01 929 2725 399 83.4 globlastp 8 2604_P1 LYD560_H5 clementinellvllBQ623022_P1 930 2726 399 83.2 globlastp 8 LYD560_H7 citrusIgb166|BQ623022 931 2727 399 83 globlastp LYD560_H9 rice|llvllAA750598_P1 932 2728 399 82.5 globlastp 4 LYD560_H9 ricelgb17010S05G49800 933 2728 399 82.5 globlastp 4 LYD560_H9 clementine|llvlCB293579_P1 934 2729 399 82.4 globlastp 9 LYD560_HI orange|llvllBQ623022_P1 935 2729 399 82.4 globlastp 00 LYD560_HI blueberryl12vllSRR353282X186 936 2730 399 82.31 glotblastn 59 35D1_1 LYD560_HI antirrhinum~gbl66|AJ558721_1 937 2731 399 82.03 glotblastn 06 LYD560_1 cassavaI09v1|CK646362_P1 938 2732 399 82 globlastp 07 LYD560_1 tripterygiumll1vllSRRO98677X1 939 2733 399 81.5 globlastp 23 01139 LYD560_1 cotton|lOv2|BE053665 940 2734 399 80.8 globlastp 31 LYD560_1 poppyll1vllSRR030259.11437_ 941 2735 399 80.72 glotblastn 60 TI LYD560_HI gossypiumraimondiil12vllBE05 942 2736 399 80.6 globlastp 61 3665_P1 LYD560_HI cotton|11vllBE053665_P1 943 2737 399 80.3 globlastp 62 LYD560-HI tobaccolgb I621DWO04467 944 2738 399 80.23 glotblastn 4911 111 WO 2013/128448 PCT/IL2013/050172 176 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD560_HI blueberryI12vIlSRR353282X405 945 2739 399 80 globlastp 63 27D1_P1 LYD561_HI trigonellallvlISRR066194X416 946 2740 400 91.6 globlastp 969 LYD561_H2 cloverlgbl62|BB903437 P1 947 2741 400 83.6 globlastp LYD562_HI soybean|llvllGLYMA16G0107 948 2742 401 83.4 globlastp 0 LYD562_H2 soybean|llvllGLYMA07GO448 949 2743 401 83.1 globlastp 0 LYD562_H4 bean|12vllFG228272_P1 950 2744 401 83 globlastp LYD562H5 pigeonpeal11vllGR464005_P1 951 2745 401 83 globlastp LYD562_H3 pigeonpea|lOvllGR464005 952 2746 401 82.5 globlastp LYD563_HI trigonellallvlISRR066194X190 953 2747 402 92.3 globlastp 527 LYD563_H4 chickpea|llvllGR392227 P1 954 2748 402 87 globlastp LYD563_H2 pea|11vllFG534485_P1 955 2749 402 86.7 globlastp LYD563 H3 lotusI09vlIAV413185 P1 956 2750 402 80 globlastp LYD564_HI trigonellallvlISRR066194X144 957 2751 403 99.5 globlastp 531 LYD564_HI chickpea|llvllGR396842_P1 958 2752 403 95.2 globlastp 30 LYD564_H2 pea|IvlIlFG530295XX1 P1 959 2753 403 94.1 globlastp LYD564_H3 chickpeaI09v2IGR396842 960 2754 403 93.4 globlastp LYD564 H4 cowpea|l2vllFF538026 P1 961 2755 403 92.5 globlastp LYD564_H5 soybean|l1vlIGLYMA04G2580 962 2756 403 92.5 globlastp 0 LYD564_H6 soybean|llvllGLYMAlG1621 963 2757 403 90.5 globlastp 0 LYD564_1 bean|12vllCA896686_P1 964 2758 403 89.5 globlastp 31 LYD564_H7 beanlgbl67|BQ481858 965 2759 403 89.5 globlastp LYD564_H8 cowpea|l2vllFF556286_P1 966 2760 403 89.5 globlastp LYD564_H8 cowpealgbl66|FF556286 967 2760 403 89.5 globlastp LYD564_H9 cirsium|1vllSRR346952.16734 968 2761 403 89.07 glotblastn LYD564_1 sunflower|l2vllDY907147_P1 969 2762 403 88.6 globlastp 32 LYD564_1 fagopyrumIllvlISRR063703Xl0 970 2763 403 88.52 glotblastn 0 4472_1 LYD564_1 orobanche|lOvlISRRO23189S00 971 2764 403 88.52 glotblastn 1 0792_1 LYD564_1 ambrosia|llvllSRR346935.6021 972 2765 403 88.5 globlastp 2 12_P1 LYD564_11 dandelionIlOvllDY824048_P1 973 2766 403 88.5 globlastp 3 ___________________ WO 2013/128448 PCT/IL2013/050172 177 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD564_HI seneciolgbl701DY663921 974 2767 403 88.5 globlastp 4 LYD564_HI tragopogonIOvlISRRO20205SOO 975 2768 403 88.5 globlastp 5 16332 LYD564_HI pigeonpeaI11vIlGW352750_P1 976 2769 403 88.1 globlastp 33 LYD564_HI fagopyruml lvISRR063689X10 977 2770 403 88.04 glotblastn 6 0418_1 LYD564_HI flaveria|11vllSRR149229.11043 978 2771 403 88 globlastp 7 5_PI LYD564_HI safflowerIgbl62|EL407197 979 2772 403 88 globlastp 8 LYD564_HI phyla|11v2|SRR099036X248170 980 2773 403 87.98 glotblastn 9 T1 LYD564_H2 centaureaIgb166|EH717776_P1 981 2774 403 87.6 globlastp 0 LYD564_H2 sunflower1OvllDY907147 982 2775 403 87.6 globlastp 1 LYD564_HI bean12vICA900936_P1 983 2776 403 87.4 globlastp 34 LYD564_12 beanIgb671CA900936 984 2776 403 87.4 globlastp 2 LYD564_HI sunflower|12vlIDY923354_P1 985 2777 403 87.2 globlastp 35 LYD564_HI sunflowers 2vl IDY944220_P1 986 2777 403 87.2 globlastp 36 LYD564_H2 cynaralgb1671GE588051_P1 987 2778 403 87.2 globlastp 3 LYD564_H2 flaveria|l lvI SRR149229.11158 988 2779 403 87.2 globlastp 4 8_P1 LYD564_H2 grape|llvllGSVIVTO103221400 989 2780 403 87.2 globlastp 5 1_Pi LYD564_H2 lotusI09vlILLBG662335_P1 990 2781 403 87.2 globlastp 6 LYD564_H2 sunflowerl10vlIDY923354 991 2777 403 87.2 globlastp 7 LYD564_H2 cleome-gynandra|lOvlISRRO155 992 2782 403 87.1 globlastp 8 32S0011580_P1 LYD564_H2 ambrosia|11vllSRR346943.2874 993 2783 403 87.03 glotblastn 9 16_T1 LYD564_HI sesame|12vIlJK047154_P1 994 2784 403 86.9 globlastp 37 LYD564_H3 artemisia|lOvllEY062833_P1 995 2785 403 86.9 globlastp 0 LYD564_113 petunialgbi17IFN000395_P1 996 2786 403 86.9 globlastp 1 I I I I I I I____________________ WO 2013/128448 PCT/IL2013/050172 178 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD564_H3 flaveriaI11vlISRR149232.13647 997 2787 403 86.7 globlastp 2 _P1 LYD564_H3 triphysaria|IOvlIEY002738 998 2788 403 86.2 globlastp 3 LYD564_H3 sarracenia| 11 vII SRR 192669.103 999 2789 403 86.1 glotblastn 4 612 LYD564_H3 pepperI12vIlCA520536_P1 1000 2790 403 85.9 globlastp 5 LYD564_H3 pepperIgb171|CA520536 1001 2790 403 85.9 globlastp 5 LYD564_H3 salvia|1OvIlCV170107 1002 2791 403 85.9 globlastp 6 LYD564_H3 tobaccoIgb162|DV157807 1003 2792 403 85.9 globlastp 7 LYD564_H3 coffea|IOvlIDV664647_P1 1004 2793 403 85.6 globlastp 8 LYD564_H3 catharanthusI1vllFD660937_P1 1005 2794 403 85.4 globlastp 9 LYD564_H4 citrusIgb166|BQ623391 1006 2795 403 85.35 glotblastn 0 LYD564_H4 clementine|I1vlIBQ623391_T1 1007 2796 403 85.35 glotblastn 1 LYD564_H4 orange|I1vlIBQ623391_T1 1008 2795 403 85.35 glotblastn 21 LYD564_H4 tomatollvllBG643022 1009 2797 403 85.3 globlastp 3 LYD564_H4 ipomoea_nilIlOvlIBJ561525_P1 1010 2798 403 85.2 globlastp 4 LYD564_H4 oakIlOvllDB997519_P1 1011 2799 403 85.1 globlastp 5 LYD564_H4 oakI10vlISRR039735S0009498 1012 2799 403 85.1 globlastp 6 P1 LYD564_H4 tabernaemontana|11vllSRR0986 1013 2800 403 85.1 globlastp 7 89X106773 LYD564_H4 lettuce|IOvlIDWO75465 1014 2801 403 84.9 globlastp 8 LYD564_1 nasturtium|IIvlISRRO32558.116 1015 2802 403 84.82 glotblastn 38 424_1 LYD564_H4 artemisia|IOvlISRRO19254S0026 1016 2803 403 84.8 globlastp 9 008_P1 LYD564_H5 cichoriumlgbl7lEH703642_P1 1017 2804 403 84.8 globlastp 0 LYD564_H5 eggplantIlvlIlFS001669_P1 1018 2805 403 84.8 globlastp 1 LYD564_H5 utriculariallvllSRRO94438.107 1019 2806 403 84.8 globlastp 2 075 WO 2013/128448 PCT/IL2013/050172 179 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD564_HI blueberryI12vISRR353282X270 1020 2807 403 84.7 globlastp 39 16D1_P1 LYD564_H5 dandelionI10vllDY802954_P1 1021 2808 403 84.7 globlastp 3 LYD564_H5 lettucellOvllDWO76259 1022 2809 403 84.7 globlastp 4 LYD564_H5 castorbean|l1vllXM_002517708 1023 2810 403 84.62 glotblastn 5 T1 LYD564_HI plantagoI11v2ISRRO66373X11O2 1024 2811 403 84.6 globlastp 40 82_P1 LYD564_H5 canolallvllEE511611_P1 1025 2812 403 84.6 globlastp 6 LYD564_H5 plantagoIl1vlISRRO66373X11O2 1026 2811 403 84.6 globlastp 7 82 LYD564_HI gossypiumraimondiil12vllAI72 1027 2813 403 84.54 glotblastn 41 7289_1 LYD564_H5 cotton|Iv2BQ412972 1028 2813 403 84.54 glotblastn 8 LYD564_H5 thellungiella-halophiluml1IvIlE 1029 2814 403 84.46 glotblastn 9 HJGI1 1025782 LYD564_H6 potatol1vlIBG592695_P1 1030 2815 403 84.3 globlastp 0 LYD564_H6 solanumphureja|O9vlISPHBG64 1031 2815 403 84.3 globlastp 1 3022 LYD564_H6 chestnutIgb1701SRR006295SOO1 1032 2816 403 84.2 globlastp 2 4027_P1 LYD564_H6 oakIlOvlIFN723381_P1 1033 2816 403 84.2 globlastp 3 LYD564_H6 vinca|I1vlISRRO9869OX111539 1034 2817 403 84.2 globlastp 4 LYD564_H6 valeriana|IlvlISRRO99039X212 1035 2818 403 84.15 glotblastn 5 264 LYD564_1 cotton|IlvlIAI727289_T1 1036 2819 403 84.02 glotblastn 42 LYD564_H6 lettuceI1OvlIDW123070 1037 2820 403 84 globlastp 6 LYD564_H6 strawberryI11vIlEX659306 1038 2821 403 84 globlastp 7 LYD564_H4 8,LYD564_ lettucel12vlIDWO75465_P1 1039 2820 403 84 globlastp H66 LYD564_H6 eucalyptus|llv2ICU394869_1 1040 2822 403 83.92 glotblastn 8 LYD564_HI lettuce|12vlIDWO76259_P1 1041 2823 403 83.6 globlastp 43 LYD564_116 bruguieraIgbl66BP939279_P1 1042 2824 403 83.6 globlastp 9111111 WO 2013/128448 PCT/IL2013/050172 180 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD564_H7 peanut|IOvlIEE124748_P1 1043 2825 403 83.6 globlastp 0 LYD564_H7 platanus|11vllSRR096786X1163 1044 2826 403 83.6 globlastp 1 10_Pi LYD564_H7 radishIgb164|EW715474 1045 2827 403 83.6 globlastp 2 LYD564_H7 tripterygium| 11vl lSRR098677X1 1046 2828 403 83.6 globlastp 3 1813 LYD564_H7 thellungiella-parvuluml IvIEP 1047 2829 403 83.5 globlastp 4 CRP023807 LYD564_H7 humulus|11vllSRR098683X1039 1048 2830 403 83.42 glotblastn 5 67XX1_1 LYD564_H7 boleracealgbl6lES943633_P1 1049 2831 403 83.4 globlastp 6 LYD564_H7 thellungiella halophilumllIvIlE 1050 2832 403 83.4 globlastp 7 HJGI1 1024070 LYD564_H7 kiwilgbl66|FG439670_P1 1051 2833 403 83.2 globlastp 8 LYD564_H7 olea|llvlISRRO14463.26573_P1 1052 2834 403 83.2 globlastp 9 LYD564_H8 arabidopsis|lOvI IAT5GI3780_P 1053 2835 403 83 globlastp 0 1 15 85 43 8 lbat LYD564_H8 papayalgbl65IEX281447_P1 1054 2836 403 83 globlastp 1 LYD564_H8 arabidopsis-lyratal09vllJGIAL02 1055 2837 403 82.9 globlastp 2 1061_P1 LYD564_1 banana|l2vlIFL657740_1 1056 2838 403 82.89 glotblastn 44 LYD564_H8 antirrhinumlgbl66|AJ791317_P1 1057 2839 403 82.8 globlastp 3 LYD564_1 oil-palm|llvlIEY408003_1 1058 2840 403 82.7 glotblastn 45 LYD564_H8 gingerlgbl64DY360679_1 1059 2841 403 82.7 glotblastn 4 LYD564_H8 cassava09vlIDR083932_P1 1060 2842 403 82.6 globlastp 5 LYD564_1 spruce|IlvlIES254811_1 1061 2843 403 82.51 glotblastn 46 LYD564_1 brapaI1vlICD823802_P1 1062 2844 403 82.5 globlastp 4711 LYD564_H8 brapalgbl62|CV546927 1063 2844 403 82.5 globlastp 6 LYD564_H8 teal10vlIGE650599 1064 2845 403 82.4 globlastp 7 c 1 LYD564_118 canolalllvlDYO24886_P1 1065 2846 403 82.3 globlat 8 ____________________ WO 2013/128448 PCT/IL2013/050172 181 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD564_H8 ipomoeabatatasIlOvllBU690124 1066 2847 403 82.3 globlastp 9 P1 LYD564_H9 monkeyflowerIlOvllGO989362_ 1067 2848 403 82.3 globlastp 0 P1 LYD564_H9 aristolochia|lOvlIFD763380_P1 1068 2849 403 82.2 globlastp 1 LYD564_H9 euphorbiaIvlISRR098678X101 1069 2850 403 82.1 globlastp 2 714_P1 LYD564_HI spruceI11vIlES251408_1 1070 2851 403 81.97 glotblastn 48 LYD564_HI spruceI11vIEX364957_1 1071 2851 403 81.97 glotblastn 49 LYD564_H9 spruceIgb1621CO483132 1072 2851 403 81.97 glotblastn 3 LYD564_H9 amorphophallusI1v2SRR08935 1073 2852 403 81.91 glotblastn 4 1X207625_1 LYD564_H9 bjuncea0v2IE6ANDIZ01A14 1074 2853 403 81.9 globlastp 5 OT LYD564_H9 canolaI1vlIDYO24420_P1 1075 2854 403 81.9 globlastp 6 LYD564_H9 curcuma|lOvlDY391831_1 1076 2855 403 81.82 glotblastn 7 LYD564_H9 poplarIlOvlIAI162059_P1 1077 2856 403 81.7 globlastp 8 LYD564_H9 cassavaI09vllDV445645_P1 1078 2857 403 81.6 globlastp 9 LYD564_HI banana|l2vllFL662727_1 1079 2858 403 81.54 glotblastn 50 LYD564_1 oil-palmIlvlIES370541_1 1080 2859 403 81.52 glotblastn 51 LYD564_1 euphorbia|llvllAW821927_P1 1081 2860 403 81.5 globlastp 00 LYD564_1 abies|11v2|SRR098676X107677 1082 2861 403 81.42 glotblastn 01 T1 LYD564_1 distylium|llvlISRRO65077X143 1083 2862 403 81.42 glotblastn 02 14_T1 LYD564_1 podocarpusIlOvlISRRO65014SOO 1084 2863 403 81.42 glotblastn 03 08986_1 LYD564_1 pseudotsuga|lOvlISRRO65119SO 1085 2864 403 81.42 glotblastn 04 002063 LYD564_1 sciadopitysIlOvlISRR65035SOO 1086 2865 403 81.42 glotblastn 05 30946 LYD564_1 euonymus|llvlISRRO70038X11 1087 2866 403 81.3 globlastp 06 2482_P1 LYD564_1 poplarIlOvlIBU833771_P1 1088 2867 403 81.3 globlastp 07 1 _ __ _1__ _1__ __1___1_ WO 2013/128448 PCT/IL2013/050172 182 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD564_HI tripterygium|I1vlISRRO98677X1 1089 2868 403 81.25 glotblastn 08 33407 LYD564_HI cannabisI12vIEW701715_P1 1090 2869 403 81.2 globlastp 09 LYD564_HI phalaenopsisI1vI|CB032868_T1 1091 2870 403 81.18 glotblastn 10 LYD564_HI cleome-spinosa|IOvlIGR931668 1092 2871 403 81 globlastp 11 P1 LYD564_HI chelidoniumI11vIlSRRO84752X1 1093 2872 403 80.83 glotblastn 12 04265_1 LYD564_HI canola|I1vlIEE480839_P1 1094 2873 403 80.8 globlastp 13 LYD564_HI prunusIlOvI|CN489292 1095 2874 403 80.77 glotblastn 14 LYD564_HI spurgeIgb161|AW821927 1096 2875 403 80.7 globlastp 15 LYD564_HI bjrapa|I1vI|CD82396O_P1 1097 2876 403 80.6 globlastp 52 LYD564_HI brapalgb1621CV546937 1098 2876 403 80.6 globlastp 16_ LYD564_HI cacaol1OvI|CA798010_P1 1099 2877 403 80.6 globlastp 17 LYD564_HI flax111vllJG027336_P1 1100 2878 403 80.6 globlastp 18 LYD564_HI flaxIl1vlIJG032028_P1 1101 2879 403 80.6 globlastp 19 LYD564_HI poppy|IIvlISRRO30259.103044 1102 2880 403 80.5 globlastp 53 P1 LYD564_HI poppy|IIvlISRRO30259.106398 1103 2880 403 80.5 globlastp 54 XX1_P1 LYD564_HI euonymusIvlISRR070038X11 1104 2881 403 80.5 globlastp 20 6092_P1 LYD564_HI silene|11vlGH292679 1105 2882 403 80.5 globlastp 21 LYD564_HI silene|11vllSRR096785X122338 1106 2882 403 80.5 globlastp 2211 LYD564_HI aquilegia|lOv2IJGIAC016088_1 1107 2883 403 80.41 glotblastn 23 LYD564_HI spruceI1vlISRR065814X41216 1108 2884 403 80.33 glotblastn 55 6_T1 LYD564_HI cephalotaxusIIIvIlSRR064395X 1109 2885 403 80.33 glotblastn 24 117984_1 LYD564_HI distyliumIIvlISRR065077XII2 1110 2886 403 80.33 glotblastn 25 028_T1 LYD564_HI maritime-pine|10vIlBX254986_ 1111 2887 403 80.33 glotblastn 26 T1 WO 2013/128448 PCT/IL2013/050172 183 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD564_HI roseI12vlISRR397984.111801_P 1112 2888 403 80.3 globlastp 56 1 - 11 88 43 8. lbat LYD564_HI canola|I1vlISRRO19556.1870_P 1113 2889 403 80.2 globlastp 27 1 LYD564_HI poppyI11vlISRR096789.168678 1114 2890 403 80.1 globlastp 57 _P1 LYD564_HI beetIgb162|BI543861 1115 2891 403 80 globlastp 28 LYD564H cynodon|IOvlIES293564_T1 1116 2892 403 80 glotblastn LYD565_H5 chickpeaIllvlIS RR 133517.1162 1117 2893 404 86.65 glotblastn 72 11 LYD565 116 pigeonpeaIllvISRROS458OXlO 1118 2894 404 85.1 globlastp 9139_P1 LYD565_HI pigeonpea|lOvISRR54580SO04 1119 2894 404 85.1 globlastp 6177 LYD565_H7 beanI2vlICA913713_P1 1120 2895 404 83.5 globlastp LYD565_H2 soybeanIvlIGLYMA04G0172 1121 2896 404 82.41 glotblastn 0 LYD565_H3 soybeanIvlIGLYMA06G0181 1122 2897 404 80.58 glotblastn 0 LYD565_H4 peanutIlOvllEGO30338_P1 1123 2898 404 80.2 globlastp LYD566_H2 medicagol12vllAW127599 P1 1124 2899 405 97.5 globlastp LYD566_HI medicagoI09vlIAW127599 1125 2899 405 97.5 globlastp LYD567 HI medicagol09vlILLCO511773 1126 2900 406 93.3 globlastp LYD567_H2 pea|IIvlIAJ308129_P1 1127 2901 406 92 globlastp LYD567_H3 pea|IlvlICD860470_P1 1128 2902 406 92 globlastp LYD567_HI chickpeaIvlIFE669744_P1 1129 2903 406 90.8 globlastp 0 LYD567_H4 chickpeaI09v2IFE669744 1130 2903 406 90.8 globlastp LYD567 H5 peal11vlIAJ308126_P1 1131 2904 406 89.3 globlastp LYD567_H6 cloverlgbl62|BB915852 P1 1132 2905 406 88 globlastp LYD567_H7 trigonellal1lvlISRRO66194X123 1133 2906 406 86.7 globlastp 223 LYD567_HI chickpea|llvlX95708_1 1134 2907 406 85.53 glotblastn 1 LYD567_HI chickpea|llvllSRR133522.1015 1135 2908 406 85.5 globlastp 2 53_P1 LYD567_H8 chickpea09v2ICD051353 1136 2908 406 85.5 globlastp LYD567_H9 trigonella|11vIlSRRO66194X286 1137 2909 406 85.3 globlastp 74 LYD568_HI chickpea|11vIlAJ630657_P1 1138 2910 407 91.6 globlastp LYD568_HI chickpea09v2IAJ630657 1139 2910 407 91.6 globlastp LYD568_HI pigeonpeaIIIvIlSRR054580XI0 1140 2911 407 90.4 globlastp 7 3634 P1 WO 2013/128448 PCT/IL2013/050172 184 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD568_H2 pigeonpeaIOv ISRR054580S000 1141 2911 407 90.4 globlastp 0977 LYD568_H3 liquoriceIgbl71IFS248176_P1 1142 2912 407 89.9 globlastp LYD568_H4 lotus|09v1lAW163923 P1 1143 2913 407 89.9 globlastp LYD568_HI peanutI0vlIlGO266966_1 1144 2914 407 86.52 glotblastn 8 LYD568_H5 soybean|11vlIGLYMA04G0139 1145 2915 407 86.5 globlastp 0 LYD568_H6 cowpea|l2vllFF389144 P1 1146 2916 407 82 globlastp LYD568_H6 cowpealgbl66|FF389144 1147 2916 407 82 globlastp LYD568 H7 flax111vllGW866793 P1 1148 2917 407 81.8 globlastp LYD568_H8 cacaol0vlIlCU490694_P1 1149 2918 407 81.5 globlastp LYD568_H9 flax111v1lEU830291 1 1150 2919 407 81.46 glotblastn LYD568_HI cotton|llvllAI055160_P1 1151 2920 407 80.9 globlastp 9 LYD568_H2 cottonIvlIDT461579_P1 1152 2921 407 80.9 globlastp 0 LYD568_H2 gossypiumraimondiil12vllAI05 1153 2921 407 80.9 globlastp 1 5160_P1 LYD568_H2 nasturtiumIlvlISRRO32558.135 1154 2922 407 80.9 globlastp 2 27_P1 LYD568_1 beanIgb167|CV538261 1155 2923 407 80.9 glotblastn 0 LYD568_1 castorbeanIvlIEE259809_1 1156 2924 407 80.9 glotblastn 1 LYD568_1 cotton|I0v2|AI055160 1157 2921 407 80.9 globlastp 2 LYD568_1 cassavaI09vlICK645402_P1 1158 2925 407 80.7 globlastp 311 LYD568_H2 bean|12vlSRR001334.136593 1159 2926 407 80.34 glotblastn 3 T1 LYD568_1 poplarIlOvllBU813245_P1 1160 2927 407 80.3 globlastp 4 LYD568_1 tomatoIl1vlIBG129131 1161 2928 407 80.3 globlastp LYD570_H1 trigonellallvlISRR066194X239 1162 2929 408 92.9 globlastp 168 LYD570_H2 chickpeaI09v2IEH058717 1163 2930 408 83 globlastp LYD572_1 medicagol12vllEV255012 P1 1164 2931 410 98.2 globlastp LYD573_11 trigonella1IvlISRR66194XI04 1165 2932 411 94 globlastp 366 LYD573_H2 chickpea|11vllSRR133517.1412 1166 2933 411 88.61 glotblastn 59_TI LYD574_H2 chickpea|11vllSRR133517.1288 1167 2934 412 94.9 globlastp 0 64_P1 WO 2013/128448 PCT/IL2013/050172 185 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD574_H2 pigeonpeaI1vlISRR05458OX11 1168 2935 412 91.5 globlastp 1 1703_P1 LYD574_HI soybeanI11vlIGLYMA02GO234 1169 2936 412 90.8 globlastp 0 LYD574_H2 lotusI09vl lLLBG662424 P1 1170 2937 412 90 globlastp LYD574_H2 bean|l2vllCA908921_P1 1171 2938 412 89.5 globlastp 2 LYD574_H3 peanutIlOvlEGO29423 P1 1172 2939 412 87.6 globlastp LYD574_H4 poplarIlOvllBU869776_P1 1173 2940 412 82.3 globlastp LYD574_H5 peanutI0vlIlEC366411 P1 1174 2941 412 82.2 globlastp LYD574_H6 soybeanl11vllGLYMA01G0516 1175 2942 412 82.02 glotblastn 0 LYD574_H7 chestnutIgbl70ISRR006295S002 1176 2943 412 81.9 globlastp 5482_P1 LYD574_H2 bean|l2vllSRR001334.279981 1177 2944 412 81.88 glotblastn 3 T1 LYD574_H8 beanlgbl67|CV542123 1178 2944 412 81.88 glotblastn LYD574_H9 soybeanIllvlIGLYMA08G4092 1179 2945 412 81.6 globlastp 0 LYD574_H2 beechl11vllSRR006293.10412_P 1180 2946 412 81.5 globlastp LYD574_HI prunusIlOvlBU039536 1181 2947 412 81.2 globlastp 0 LYD574_HI poplarIlOvllBU820298_P1 1182 2948 412 81.1 globlastp 1 LYD574_H2 pigeonpeaIllvlSRR054580Xl0 1183 2949 412 80.96 glotblastn 5 0050_1 LYD574_1 pigeonpeal1OviSRR054580S000 1184 2949 412 80.96 glotblastn 2 4056 LYD574_1 soybean|llvllGLYMA18G1606 1185 2950 412 80.9 globlastp 3 0 LYD574_1 oakIlOvlIFPO41194_1 1186 2951 412 80.52 glotblastn 4 LYD574_1 apple|llvllCN864765_P1 1187 2952 412 80.5 globlastp 5 LYD574_1 cacaollOvllCA794423_P1 1188 2953 412 80.5 globlastp 6 LYD574_1 castorbean|llvllGE632527_P1 1189 2954 412 80.5 globlastp 7 LYD574_H2 gossypiumraimondiill2vllAI72 1190 2955 412 80.34 glotblastn 6 8125_TI LYD574_H2 cotton|11vlIAI728125_P1 1191 2956 412 80.3 globlastp 7 LYD574_HI grape|11vllGSVIVTO102004100 1192 2957 412 80.3 globlastp 8 1_Pi LYD574_HI strawberry|11vliC0817255 1193 2958 412 80.1 globlastp 9 WO 2013/128448 PCT/IL2013/050172 186 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD578_HI chickpea|I1vlIFL512454_P1 1194 2959 416 95.4 globlastp 46 LYD578_H2 soybeanI11vIGLYMA16G3450 1195 2960 416 92 globlastp 0 LYD578_HI pigeonpea|I1vlISRR054580X10 1196 2961 416 91.9 globlastp 47 565_P1 LYD578_H3 prunusI0vlIlBU047195 1197 2962 416 91.2 globlastp LYD578_HI bean|l2vllCA910341_P1 1198 2963 416 90.4 globlastp 48 LYD578_H4 flax111v1lCA482751_P1 1199 2964 416 90.2 globlastp LYD578 H5 eucalyptusIv2ICT982512 P1 1200 2965 416 90 globlastp LYD578_H6 appleI1vlICN489546_P1 1201 2966 416 89.8 globlastp LYD578 H7 melon|10v1lAM726472 P1 1202 2967 416 89.8 globlastp LYD578_H8 watermelonIlvlIAM726472 1203 2968 416 89.7 globlastp LYD578 H9 cucumberI09vlIDN910557 P1 1204 2969 416 89.5 globlastp LYD578_HI appleIvlICN996236_P1 1205 2970 416 89.4 globlastp 0 LYD578_HI strawberry|11vllC0380109 1206 2971 416 88.5 globlastp 1 LYD578_HI cacaollOvlICF974101_P1 1207 2972 416 88.4 globlastp 2 LYD578_HI euonymusIvlISRR070038X11 1208 2973 416 88.3 globlastp 3 8639_P1 LYD578_HI euonymusIvlISRR070038X13 1209 2974 416 88.2 globlastp 5 8821_P1 LYD578_HI chestnutIgb170ISRR006295S003 1210 2975 416 88 globlastp 6 2584_P1 LYD578_HI sileneIvlISRR96785X101977 1211 2976 416 88 globlastp 7 LYD578_HI tripterygiumIvlISRRO98677X1 1212 2977 416 88 globlastp 8 18762 LYD578_HI oakIlOvlIFPO33276_P1 1213 2978 416 87.8 globlastp 9 LYD578_H2 peanutIlOvllES712396_1 1214 2979 416 87.59 glotblastn LYD578_H2 grape|llvllGSVIVTO101157400 1215 2980 416 87.3 globlastp 3 1_Pi LYD578_H2 euphorbia|llvllDV112988_P1 1216 2981 416 87.1 globlastp 61 LYD578_HI poppyl11vllSRR030259.373171 1217 2982 416 86.8 globlastp 49 P1 LYD578_H2 tomatoIIIvIlBG131155 1218 2983 416 86.8 globlastp LYD578_HI poppyl11vllSRR030259.105041 1219 2984 416 86.7 globlastp 50 P1 WO 2013/128448 PCT/IL2013/050172 187 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD578_H3 canola|I1vlIEE564982_T1 1220 2985 416 86.61 glotblastn 0 LYD578_HI oil-palm|IIvlIEL687687_P1 1221 2986 416 86.5 globlastp 51 LYD578_H3 arabidopsisjlyrata|09vllJGIALO1 1222 2987 416 86.5 globlastp 1 6352_P1 LYD578_H3 cassavaI09vlIDV443394_P1 1223 2988 416 86.5 globlastp 2 LYD578_HI medicagol12vlIAW684124_P1 1224 2989 416 86.3 globlastp 5211 LYD578_H3 arabidopsisl 10vl IAT2GO1970_P 1225 2990 416 86.3 globlastp 6 1 - 12 90 46 8. lbat LYD578_H3 medicagoI09vlILLAW684124 1226 2989 416 86.3 globlastp 7 LYD578_H3 thellungiella-parvuluml vIDN 1227 2991 416 86.3 globlastp 9 778102 LYD578_H4 canola|IlvlIEE549996_P1 1228 2992 416 86.2 globlastp 0 LYD578_H4 canola|IlvlIEE454097_T1 1229 2993 416 86.13 glotblastn 2 LYD578_H4 canola|IlvlIDY006061_P1 1230 2994 416 86.1 globlastp 3 LYD578_H4 canola|IlvlIDY020128_P1 1231 2995 416 86.1 globlastp 4 LYD578_H4 humulus|IIvlEX520208_P1 1232 2996 416 86.1 globlastp 5 LYD578_H4 thellungiella-halophilumllvllD 1233 2997 416 86.1 globlastp 6 N778102 LYD578_HI bjrapa|llvllCD825207_P1 1234 2998 416 86 globlastp 53 LYD578_1 oilpalmll1vllEL691164_P1 1235 2999 416 85.8 globlastp 5411 LYD578_H4 lotus109vIlA1967723_P1 1236 3000 416 85.8 globlastp 7 LYD578_H4 watermelon|llvllAM739846 1237 3001 416 85.8 globlastp 8 LYD578_1 eschscholzia|llvllCD477858_P1 1238 3002 416 85.7 globlastp 55 LYD578_1 brapa|11vllH74789_P1 1239 3003 416 85.6 globlastp 56 1 LYD578_H4 phyla|11v2|SRRO99035XIO0102 1240 3004 416 85.6 globlastp 9 P1 LYD578_H5 thellungiella-parvulumllvllBY 1241 3005 416 85.6 globlastp 0 807072 LYD578_H5 applel11vllCX024719_P1 1242 3006 416 85.5 globlastp 1I__________________________ WO 2013/128448 PCT/IL2013/050172 188 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD578_H5 arabidopsi1 vlAT1G14670_P 1243 3007 416 85.5 globlastp LYD578_H5 prunusIlOvlICN492032 1244 3008 416 85.4 globlastp 4 LYD578_H5 tabernaemontanal Iv SRR0986 1245 3009 416 85.4 globlastp 5 89X101380 LYD578_H5 thellungiella-halophilum| 11v lB 1246 3010 416 85.4 globlastp 6 Y809962 LYD5781 H5 solanum phureja|09vlISPHBG13 1247 3011 416 85.3 globlastp 8 1155 LYD578_H5 triphysaria|IvlIDR175111 1248 3012 416 85.3 globlastp 9 LYD578_H6 artemisiaI10vIlEY072332_P1 1249 3013 416 85.2 globlastp 0 LYD578_HI sunflowerIl2vlIDY905094_P1 1250 3014 416 85.1 globlastp 57 LYD578_HI oil-palm|IIvlISRR190698.1079 1251 3015 416 85.06 glotblastn 58 91_T1 LYD578_H6 apple|I1vlICN492032_P1 1252 3016 416 85 globlastp 3 LYD578_H6 solanumphureja|09vlISPHDB72 1253 3017 416 85 globlastp 5 1762 LYD578_H6 strawberryI11vIlDY674763 1254 3018 416 85 globlastp 6 LYD578_H6 solanumphureja|09vlISPHBG13 1255 3019 416 84.9 globlastp 8 4887 LYD578_H6 tomatollvllBG134887 1256 3020 416 84.9 globlastp 9 LYD578_HI bananaIl2vlIFF557959_P1 1257 3021 416 84.7 globlastp 59 LYD578_1 banana|12vlIFL660505_P1 1258 3022 416 84.7 globlastp 60 LYD578_H7 artemisia|l0vlIEYO43221_P1 1259 3023 416 84.6 globlastp 4 LYD578_H7 vinca|IlvlISRRO9869OX121789 1260 3024 416 84.6 globlastp 5 LYD578_H7 cacaol10vlICU588720_T1 1261 3025 416 84.55 glotblastn 6 LYD578_H7 catharanthus|I1vlIEG557449_1 1262 3026 416 84.55 glotblastn 711 LYD578_H7 amsonia|IIvlISRRO98688X1110 1263 3027 416 84.5 globlastp 8 96_P1 LYD578_H8 flaveriaIIvlISRR149229.11484 1264 3028 416 84.5 globlastp 0 5_PI LYD578_H8 sunflower10vllIDY903830 1265 3029 416 84.5 globlastp 2 1 1 1 1 1__ __ __ __ __ __1_ WO 2013/128448 PCT/IL2013/050172 189 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD578_HI banana|12vllMAGEN201203539 1266 3030 416 84.4 globlastp 61 1_Pi LYD578_HI sunflowerI12v1IDY903830_P1 1267 3031 416 84.4 globlastp 62 LYD578_HI sunflower|10vlDY939736P1 1268 3032 416 84.4 globlastp 63 LYD578_118 sunflowerIl~vlDY90736l 1269 3032 416 84.4 globlastp 4 LYD578_H8 tobaccolgbl62|DW003003 1270 3033 416 84.4 globlastp 5 LYD578_H8 vinca|11vllSRRO98690X103710 1271 3034 416 84.4 globlastp 61 LYD578_H8 tripterygium|IIvlISRRO98677X1 1272 3035 416 84.38 glotblastn 7 17684 LYD578_H8 cucumberI09vlIAM739846_P1 1273 3036 416 84.3 globlastp 811 LYD578_H9 ambrosial 1 lv ISRR346935.3835 1274 3037 416 84.21 glotblastn 0 T11 LYD578_HI banana|12vlIBBS1314T3_P1 1275 3038 416 84.1 globlastp 64 LYD578_H9 chestnutgb1701SRROO6295SO04 1276 3039 416 84.1 globlastp 1 5171_P1 LYD578_H9 euonymus|IIvlISRRO70038X11 1277 3040 416 84.1 globlastp 2 3826_P1 LYD578_H9 catharanthus|IIvlISRRO98691X 1278 3041 416 84.03 glotblastn 3 104034_1 LYD578_HI sunflower|12vlIDY907361_P1 1279 3042 416 84 globlastp 6511 LYD578_H9 arnica|IIvlISRRO99034X111318 1280 3043 416 84 globlastp 4 P11 LYD578_H9 lettuce|IOvlIDW111094 1281 3044 416 84 globlastp 5 LYD578_H9 poplar|IOvlIAI166075_P1 1282 3045 416 84 globlastp 611 LYD578_H9 poplar|IOvlIBIl28092_P1 1283 3046 416 84 globlastp 7 LYD578_HI plantagolI1v2|SRR066373X1023 1284 3047 416 83.9 globlastp 66 61_P1 LYD578_H9 plantagolIIvIlSRRO66373X1023 1285 3047 416 83.9 globlastp 8 61 LYD578_H9 tabernaemontanal Iv 1 lSRRO986 1286 3048 416 83.9 globlastp 9 89X100108 LYD578_HI vinca|IIvIlSRRO9869OX110217 1287 3049 416 83.9 glotblastn 01 LYD578_-HI canolaIIivI IEE485698TIi 1288 3050 416 83.87 glotblastn 03__ _ _ _ _ _ _ _ _ _ _ _ _ _ WO 2013/128448 PCT/IL2013/050172 190 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD578_HI nasturtium|IIvlISRRO32558.117 1289 3051 416 83.8 globlastp 67 106_P1 LYD578_HI cassavaI09vllJGICASSAVA180 1290 3052 416 83.8 globlastp 04 83VALIDM1_P1 LYD578_HI tomatollvllDB721762 1291 3053 416 83.8 globlastp 05 LYD578_HI banana|12vlIES436693_P1 1292 3054 416 83.6 globlastp 68 LYD578_HI ambrosia|IlvlISRR346935.1013 1293 3055 416 83.4 globlastp 10 84_P1 LYD578_HI oakIlOvlIFN730940_P1 1294 3056 416 83.4 globlastp 11 LYD578_HI ambrosia|IlvlISRR346935.1014 1295 3057 416 83.33 glotblastn 12 06_T1 LYD578_HI bjuncea|12vIlE6ANDIZO1AHJJ 1296 3058 416 83.31 glotblastn 69 JTI LYD578_HI centaurealgbl66|EH717543_P1 1297 3059 416 83.3 globlastp 13 LYD578_HI arnica|IlvlISRRO99034X103662 1298 3060 416 83.28 glotblastn 14 T1 LYD578_HI rice|I1vlIAA751885_P1 1299 3061 416 83.2 globlastp 15 LYD578_HI riceIgbl701OSO3G13380 1300 3061 416 83.2 globlastp 15 LYD578_HI brachypodium|12vlIBRADI1G68 1301 3062 416 82.9 globlastp 70 750_P1 LYD578_HI phalaenopsis|IlvlISRR125771 1 302 3063 416 82.9 globlastp 16 004728_P1 LYD578_HI silene|I1vlISRRO96785XI15898 1303 3064 416 82.9 globlastp 17 LYD578_HI sunflower12vlIDY903937_P1 1304 3065 416 82.7 globlastp 71 LYD578_HI sunflowers vl IDY903937 1305 3066 416 82.7 globlastp 18 LYD578_HI oatIvlIAA231831_P1 1306 3067 416 82.5 globlastp 19 LYD578_HI poplarl10vlIAI164784_P1 1307 3068 416 82.4 globlastp 21 LYD578_HI flaveria|IlvlISRR149229.25937 1308 3069 416 82.1 globlastp 24 P1 LYD578_HI arabidopsislyrata|09vllJGIAL02 1309 3070 416 82 globlastp 26 7304_P1 LYD578_HI ambrosia|IIvIlSRR346935.5664 1310 3071 416 81.8 globlastp 27 63_P1 LYD578_HI arnica|IIvIlSRRO99034X115318 1311 3072 416 81.8 globlastp 28 _P1 WO 2013/128448 PCT/IL2013/050172 191 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD578_HI arabidopsis| 1Ov IlAT5G37310_P 1312 3073 416 81.6 globlastp 30,LGP44 1 LYD578_HI oil-palm|IIvIEL692338_P1 1313 3074 416 81.5 globlastp 72 LYD578_HI phalaenopsisIIIvlISRR125771. 1 314 3075 416 81.5 globlastp 32 010602_P1 LYD578_HI flaveria|I1vlISRR149229.12252 1315 3076 416 81.46 glotblastn 33 8_T1 LYD578_HI canola|llvllEE543932_P1 1316 3077 416 81.2 globlastp 3511 LYD578_HI flaverial11vllSRR149229.12505 1317 3078 416 80.95 glotblastn 37 5 T1 LYD578_HI bjrapallvllCD825294_P1 1318 3079 416 80.9 globlastp 73 LYD578_HI cannabisIl2vlISOLX00055372 1319 3080 416 80.6 globlastp 38 P1 LYD578_HI eschscholzial11vllCD48051OXX 1320 3081 416 80.5 globlastp 74 1_P1 LYD578_HI maritime-pine|lOvlIAL750688 1321 3082 416 80.5 globlastp 39 P1 LYD578_HI amorphophallusIllv2SRR08935 1322 3083 416 80.4 globlastp 40 1X125537_P1 LYD578_HI vinca|llvllSRRO9869OX112534 1323 3084 416 80.3 globlastp 42 LYD578_HI abiesIllv2|SRRO98676Xl00567 1324 3085 416 80.1 globlastp 43 P1 LYD578_HI sequoia|lOvlISRRO65044SO0141 1325 3086 416 80.1 globlastp 44 46 LYD578_HI brachypodiumI09vlIDV486133 1326 3087 416 80.07 glotblastn 45 LYD579_H7 chickpea|llvllFE670056 P1 1327 3088 417 87.7 globlastp LYD579_H8 pigeonpeaIllvlISRR054580X44 1328 3089 417 84.3 globlastp 7982_P1 LYD579_HI lotusI09vlIAV410218_P1 1329 3090 417 84 globlastp LYD579_H2 cowpea|l2vllFC461356_P1 1330 3091 417 83.6 globlastp LYD579_H2 cowpealgbl66|FC461356 1331 3091 417 83.6 globlastp LYD579_H9 bean|l2vllSRROO1336.56224_P1 1332 3092 417 83 globlastp LYD579_H3 beanlgbl67|CV530490 1333 3092 417 83 globlastp LYD579_H4 soybeanIllvlIGLYMA05G3857 1334 3093 417 82.7 globlastp 0 LYD579_H5 soybean|11vllGLYMA08GO106 1335 3094 417 82.5 globlastp 0 LYD579_H6 peanutIOvIlCDO37684_P1 1336 3095 417 80.7 globlastp LYD58OH3 medicagol12vllXM_003597757 1337 3096 418 95 globlastp LYD580 H4 chickpea|11vllGR911819 P1 1338 3097 418 86.7 globlastp WO 2013/128448 PCT/IL2013/050172 192 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD585_HI medicagol09vlILLBE942833 1339 3098 422 98.2 globlastp LYD585_H2 trigonellallvlISRRO66194X116 1340 3099 422 90 globlastp 540 LYD585_H3 chickpea|llvllSRR133517.1033 1341 3100 422 80.3 globlastp 17 P1I3130 2 8. lbat LYD586_H2 chickpea|llvllSRR133518.1258 1342 3101 423 81.5 globlastp 6_P1 LYD586_HI lotus09vlIAW719808_P1 1343 3102 423 80.6 globlastp LYD588_HI medicagoI09vlICRPMT003032 1344 3103 425 87.08 glotblastn LYD588_H3 medicagoll2vllXM_003615634 1345 3104 425 80.6 globlastp P1 LYD590_HI chickpealllvlSRR133517.1344 1346 3105 427 88.06 glotblastn 94_11 LYD591_HI chickpea|llvllSRR133517.1666 1347 3106 428 83.9 globlastp 72_P1 LYD592_H2 soybean|llvllGLYMA19G3727 1348 3107 429 81.6 globlastp 0_P1 LYD592_H3 soybeanIllvlIGLYMA03G3458 1349 3108 429 80.6 globlastp 0_P1 LYD594_HI medicagoI09vlILLBF633538 1350 3109 431 97 globlastp LYD598_HI wheatIl0v2BE400730XX2 1351 3110 435 85.4 globlastp LYD598_HI wheat|l2v3BT009540_P1 1352 3110 435 85.4 globlastp LYD598_H6 rye|12vllDRR001012.100407_P 1353 3111 435 85.1 globlastp LYD598_H7 sorghum|l2vllSBOG042010 P1 1354 3112 435 84.9 globlastp LYD598_H2 sorghumllvllSBOG042010 1355 3112 435 84.9 globlastp LYD598 H3 maize|lOvlIAI586617 1 1356 3113 435 81.84 glotblastn LYD598_H4 foxtail milletIllv3PHY7SIO357 1357 3114 435 81.4 globlastp 80M_P1 LYD598 H5 switchgrassIgbl67|FL903075 1358 3115 435 80.7 globlastp LYD601 rice|llvllBI306238_P1 1359 3116 438 98.9 globlastp LYD601 rice|llvllCK007248_P1 1360 3116 438 98.9 globlastp LYD601_1 wheat|lOv2|BE400601 1361 3117 438 83.1 globlastp LYD601_H8 sorghum|l2vllSB1OG002190 P1 1362 3118 438 82.5 globlastp LYD601_H2 sorghumll1vllSB1OG002190 1363 3118 438 82.5 globlastp LYD601_11 wheat|l2v3ICD931110 P1 1364 3119 438 82.2 globlastp LYD601_H3 foxtail milletIllv3PHY7SI0068 1365 3120 438 81.1 globlastp 04M_P1 LYD601_H4 switchgrassIgbl67|FL690669 1366 3121 438 81.1 globlastp LYD601_H5 sugarcanellOvllCA084453 1367 3122 438 80.8 globlastp LYD601_H9 brachypodiuml12vllBRADIG50 1368 3123 438 80.29 glotblastn 140_T1 LYD601_H6 barleyllOv2|AW982216 1369 3124 438 80.29 glotblastn LYD601_H7 brachypodiuml09vl ISRRO31798 1370 3123 438 80.29 glotblastn S 0 0 5 16 9 4 1 755_ LYD603 1 wheatIl0v2IBG906907 1371 3125 440 80.05 glotblastn WO 2013/128448 PCT/IL2013/050172 193 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD603_HI wheat|12v3IBE591745 1 1372 3125 440 80.05 glotblastn LYD604_HI maize|l0vlIBM896111_P1 1373 3126 441 90.4 globlastp LYD604 H2 sugarcane|lOvlIBQ533093 1374 3127 441 90.34 glotblastn LYD604_H3 foxtail milletI1v3IPHY7SI0141 1375 3128 441 84.9 globlastp 87M_P1 LYD604_H4 switchgrassIgb167|FL751571 1376 3129 441 82.61 glotblastn LYD604_H5 foxtail milletI1v3IPHY7SI0143 1377 3130 441 82.2 globlastp 32M_P1 LYD605_HI maize|l0vlIAI395969 P1 1378 3131 442 90.2 globlastp LYD605_H3 foxtail milletI1v3IPHY7SI0324 1379 3132 442 85.4 globlastp 02M_P1 LYD606_HI maize|l0vlICD998192 P1 1380 3133 443 88.9 globlastp LYD606_H2 foxtail milletI1v3IPHY7SI0033 1381 3134 443 85.9 globlastp 55M_P1 LYD606_H3 switchgrassIgb167IFE620000 1382 3135 443 82 globlastp LYD607_HI sugarcane|IOvlICA090822 1383 3136 444 98.3 globlastp LYD607_H2 maize|l0vlIAI461578_P1 1384 3137 444 97 globlastp LYD607_H3 foxtail milletIlv3IEC613899 P 1385 3138 444 88.4 globlastp 1 LYD607_H4 milletI0vlIlEVO454PM019085_ 1386 3139 444 87.9 globlastp P1 LYD607_H5 switchgrassIgb167|FL736062 1387 3140 444 87.9 globlastp LYD607_H6 rice|11vlCA756435_P1 1388 3141 444 84.5 globlastp LYD607 H6 ricelgb17010S01G59500 1389 3141 444 84.5 globlastp LYD607_HI brachypodium|12vlIBRADI2G52 1390 3142 444 81.9 globlastp 0 910_P1 LYD607_H7 brachypodium09vlIDV477071 1391 3142 444 81.9 globlastp LYD607_H8 cynodonI0vlIlES293393_1 1392 3143 444 81.9 glotblastn LYD607_H9 oatIvlICN815678_P1 1393 3144 444 81 globlastp LYD608_11 foxtail milleti1v3IPHY7SI0096 1394 3145 445 91.6 globlastp 30M_P1 LYD608_H2 maize|l0vlIBM498393_P1 1395 3146 445 91.3 globlastp LYD608_H3 rice|11vlCB629440_P1 1396 3147 445 82.1 globlastp LYD608_H3 riceIgbl7010SO9G32840 1397 3147 445 82.1 globlastp LYD608_H4 milletIlOvllEVO454PM008964_ 1398 3148 445 80.7 globlastp P1 LYD609_1 maize|lOvllAWO91479 P1 1399 3149 446 90.8 globlastp LYD609_H2 foxtail milletI1v3IPHY7SIO215 1400 3150 446 87.8 globlastp 03M_P1 LYD609_H3 maize|lOvllAW066176 P1 1401 3151 446 84.3 globlastp LYD610_1 maize|lOvllAW313273_P1 1402 3152 447 93.4 globlastp LYD610 H2 maize|lOvlICD941624 P1 1403 3153 447 93.2 globlastp LYD610_H3 foxtail_milletI1v3IPHY7SI0341 1404 3154 447 91.2 globlastp 80M_P1 LYD610_H4 milletIlOvllEVO454PM000391_ 1405 3155 447 89.61 glotblastn T1 WO 2013/128448 PCT/IL2013/050172 194 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD610_H8 rice|llvllOSCRP015914 P1 1406 3156 447 84.8 globlastp LYD610_H5 ricel11vllCA767059_P1 1407 3157 447 84.8 globlastp LYD610 H5 riceIgbl7010SO1G56330 1408 3157 447 84.8 globlastp LYD610_H9 brachypodiuml|12vllBRADI1G63 1409 3158 447 83.8 globlastp 320_P1 LYD610_H6 brachypodiumIO9vlIGT772226 1410 3158 447 83.8 globlastp LYD610_HI rye|12vllDRROO1012.101001_P 1411 3159 447 82.8 globlastp 0 1 11 19 47 8. lbat LYD610_H1 rye|12vllDRR001012.103223_P 1412 3160 447 82.6 globlastp LYD610_HI riceI1vlIOSCRP079749_P1 1413 3161 447 81.3 globlastp 2 LYD610_H7 rice|llvlIC22581_P1 1414 3161 447 81.3 globlastp LYD610_H7 ricelgb17010S03G21540 1415 3161 447 81.3 globlastp LYD610_HI wheat|12v3|BE637867_P1 1416 3162 447 80.4 globlastp 3 LYD610_HI wheat|12v3IBI751671T1 1417 3163 447 80.36 glotblastn 4 LYD611_HI soybean|llvllGLYMA09G3370 1418 3164 448 92.8 globlastp 0 LYD611_H2 cowpea|l2vllFG852821_P1 1419 3165 448 87.8 globlastp LYD611_H2 cowpealgbl66|FG852821 1420 3165 448 87.8 globlastp LYD611_H3 bean|12vlISRROO1335.371744P 1421 3166 448 87.3 globlastp 1 LYD611 H4 pigeonpea|IlvI|CCIIPG1100762 1422 3167 448 86.5 globlastp 3_P1 LYD612_HI soybean|llvllGLYMA10G0221 1423 3168 449 91.9 globlastp 0 LYD612H6 pigeonpea|llvllGR466527 P1 1424 3169 449 90.8 globlastp LYD612_H2 pigeonpea|lOvlIGW351945 1425 3169 449 90.8 globlastp LYD612 H7 bean|l2vlCA910393 P1 1426 3170 449 84 globlastp LYD612_H3 cowpea|l2vllFF384755_P1 1427 3171 449 82.8 globlastp LYD612_H3 cowpeaIgbl66|VIRARG2 1428 3171 449 82.8 globlastp LYD612_H4 beanIgb167|CA910393 1429 3172 449 82 globlastp LYD612_H5 beanIgb167ICB540659 1430 3173 449 82 glotblastn LYD613_1 pigeonpeaIllvlISRR054580X1 1431 3174 450 82.9 globlastp 0249_P1I LYD613_H2 beanI12vlISRRO90491.1230988 1432 3175 450 80.2 globlastp LYD614_11 soybean|I1vlIGLYMA14GO664 1433 3176 451 86 globlastp 0 LYD615_11 soybean|I1vlIGLYMA19G3066 1434 3177 452 94.4 globlastp 0 LYD615_H4 bean|l2vlCB543286 P1 1435 3178 452 88.9 globlastp LYD615_H5 pigeonpeaIllvIySRR054580X16 1436 3179 452 88.5 globlastp ____________3954_P1I__ WO 2013/128448 PCT/IL2013/050172 195 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD615_H2 lotus09vlIBP070765 P1 1437 3180 452 81.5 globlastp LYD615_H6 medicagol12vllAW684979_P1 1438 3181 452 81.4 globlastp LYD615 H3 medicagoI09vIAW684979 1439 3181 452 81.4 globlastp LYD616_H4 bean|12vlISRR00l334.260126 1440 3182 453 88.4 glotblastn LYD616_H5 pigeonpeaIlll ISRRO5458OX11 1441 3183 453 87.88 glotblastn 2099_11 LYD616_H6 chickpea|llvllFE671275 1 1442 3184 453 84.37 glotblastn LYD616_HI lotusI09vlICRPLJO28046 1 1443 3185 453 82.69 glotblastn LYD616 H7 medicagol12vllBG450022 P1 1444 3186 453 82.5 globlastp LYD616 H2 medicago09vlIBG450022 1445 3186 453 82.5 globlastp LYD616_H3 soybean|IlvlIGLYMA19G3956 1446 3187 453 80.8 globlastp 0 LYD617_HI cyamopsisIlOvllEG979147 P1 1447 3188 454 93.3 globlastp LYD617_H2 liquoricelgbl7lFS251251_P1 1448 3189 454 93.3 globlastp LYD617 H3 cowpea|l2vllFF382757 P1 1449 3190 454 91.3 globlastp LYD617_HI chickpea|llvllSRR133517.1185 1450 3191 454 91 globlastp 9 02_P1 LYD617_H3 cowpealgbl66|FF382757 1451 3192 454 90.2 globlastp LYD617_H2 pigeonpea|llvllGR470046_P1 1452 3193 454 88.8 globlastp 0 LYD617_H4 pigeonpea|lOvllGR470046 1453 3193 454 88.8 globlastp LYD617_H2 medicagol12vlIAW329294_P1 1454 3194 454 87.6 globlastp 1 LYD617 H5 medicagoI09vlIAW329294 1455 3194 454 87.6 globlastp LYD617_H2 medicagol12vlIBF632685_P1 1456 3195 454 85.4 globlastp 2 LYD617_H6 trigonella|IlvlISRR066194X345 1457 3196 454 85.4 globlastp 953 LYD617_H2 medicagol12vlIAL381382_P1 1458 3197 454 84.3 globlastp 3 LYD617_H7 lotus109vIlAW428820_P1 1459 3198 454 84.3 globlastp LYD617_H8 medicagoI09vlIAL381382 1460 3197 454 84.3 globlastp LYD617_H2 chickpea|llvllGR394427_P1 1461 3199 454 83.1 globlastp 4 LYD617_H9 soybeanllvllGLYMA10G0243 1462 3200 454 83.1 globlastp 0 LYD617_H2 bean|l2vllCA898865_P1 1463 3201 454 82 globlastp LYD617_H2 pigeonpea|11vllSRR05458OX13 1464 3202 454 82 globlastp 6 373_P1 LYD617_1 beanlgb167|CA898865 1465 3201 454 82 globlastp 0 LYD617-HI1 cloverlgbi62IBB92i888_P1 1466 3203 454 82 globlat 1I__________________________ WO 2013/128448 PCT/IL2013/050172 196 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD617_HI pigeonpea|lOvlISRR54580SO01 1467 3202 454 82 globlastp 2 3374 LYD617_HI soybean|11vllGLYMA02G1737 1468 3204 454 82 globlastp 3 0 LYD617_HI cassavaI09vIDV442613_P1 1469 3205 454 80.9 globlastp 4 LYD617_HI cowpea|l2vllFF385220_P1 1470 3206 454 80.9 globlastp 5 LYD617_HI cucurbita|11vllSRR091276X104 1471 3207 454 80.9 glotblastn 6 51_T1 LYD617_HI oakl10vllFP034480_P1 1472 3208 454 80.9 globlastp 7 LYD617_HI trigonellaI11vIlSRRO66194X186 1473 3209 454 80.9 globlastp 8 437 LYD620_HI soybeanIlvllGLYMA17G0866 1474 3210 457 92.9 globlastp 0 LYD620_H2 bean|l2vllCA902170_P1 1475 3211 457 84.2 globlastp LYD620_H3 pigeonpeaIllvlSRR054580Xl0 1476 3212 457 82.4 globlastp 0276_P1 LYD621_HI soybeanIllvlGLYMA08G0504 1477 3213 458 96 globlastp 0 LYD621_H5 bean|l2vllCB542975 P1 1478 3214 458 92.1 globlastp LYD621_H6 pigeonpeaIllvlISRR054580Xl0 1479 3215 458 91.4 globlastp 5242_P1 LYD621_H2 pigeonpea|lOvIISRR54580SO01 1480 3216 458 91.35 glotblastn 8657 LYD621_H3 lotus109vllG0024264 P1 1481 3217 458 86 globlastp LYD621_H7 chickpealllvlSRR133517.1332 1482 3218 458 85.77 glotblastn 12lI9 LYD621_H8 medicagoll2vlIAI974296_PI 1483 3219 458 84.3 globlastp LYD621_114 medicagoIO9vl IA1974296 1484 3219 458 84.3 globlastp LYD622_HI soybean|IlvlIGLYMA04GO368 1485 3220 459 97.8 globlastp 0 LYD622_HI pigeonpea|I1vlISRR5458OX10 1486 3221 459 91.4 globlastp 2 3966_P1 LYD622_H2 cowpea|l2vllFF543494_P1 1487 3222 459 90 globlastp LYD622_H2 cowpealgbl66|FF543494 1488 3222 459 90 globlastp LYD622_H3 pigeonpea|lOvISRRO54580SO03 1489 3223 459 87.5 globlastp 7538 LYD622_HI bean|12vlIFE899993_P1 1490 3224 459 87.1 globlastp 3 LYD622_H4 lotusI09vIlCB828440 P1 1491 3225 459 84 globlastp LYD622_HI chickpea|11vllGR396021_P1 1492 3226 459 83.5 globlastp 4 LYD622_H5 peanutI1OvIlGO338761 P1 1493 3227 459 82.4 globlastp LYD622_H6 liquoricelgbl71|FS241834 P1 1494 3228 459 81.9 globlastp WO 2013/128448 PCT/IL2013/050172 197 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD622_H7 cassavaI09vlIDV454935 P1 1495 3229 459 81.4 globlastp LYD622_H8 cloverlgbl62|BB911490_P1 1496 3230 459 81.4 globlastp LYD622 H9 beanlgb1671FE899993 1497 3231 459 81.03 glotblastn LYD622_HI medicagoI09vlILLBF646969 1498 3232 459 80.8 globlastp 0 LYD622_HI medicagol12vlIBF646969_T1 1499 3233 459 80.34 glotblastn 5 LYD622_HI trigonella|IlvlISRR066194X120 1500 3234 459 80.3 globlastp 1 913 LYD623_HI soybeanI11vIlGLYMA04GO589 1501 3235 460 85 globlastp 0 LYD624_H3 bean|l2vllGFXX53603X1_P1 1502 3236 461 83.6 globlastp LYD624_HI beanlgbl671GFXX53603X1 1503 3236 461 83.6 globlastp LYD624_H2 soybeanIllvlIGLYMAl3GO25l 1504 3237 461 80.4 globlastp 0 LYD625_HI pigeonpeaIllvlISRR054580X38 1505 3238 462 84.8 globlastp 7827_P1 LYD625_H2 bean|l2vllFE703801 P1 1506 3239 462 81.5 globlastp LYD626_H5 pigeonpeaIllvlISRR054580Xl2 1507 3240 463 90 globlastp 0385_P1 LYD626_HI pigeonpeal1OvI ISRRO54580S007 1508 3240 463 90 globlastp 9586 LYD626_112 cowpeall2vlIEE384OlS P1 1509 3241 463 84 globlastp LYD626_H2 cowpealgbl66|FF384015 1510 3241 463 84 globlastp LYD626 H6 bean|l2vllFE683652 P1 1511 3242 463 82.7 globlastp LYD626_H3 beanlgbl67|CV530073 1512 3242 463 82.7 globlastp LYD626 H7 medicagol12vlIAW776098 P1 1513 3243 463 80.8 globlastp LYD626_H4 medicagoI09vlIAW776098 1514 3243 463 80.8 globlastp LYD627_HI soybean|IlvlIGLYMA18G1905 1515 3244 464 94.46 glotblastn 0 11 LYD627_H8 pigeonpeal lvI ISRRO5458OX 10 1516 3245 464 88.69 glotblastn 3254_16 LYD627_H9 beangl2vlCK901542_TI 1517 3246 464 88.53 glotblastn LYD627_112 beanlgbl671CK901542 1518 3246 464 88.53 glotblastn LYD627_H3 pigeonpeal1Ovi ISRRO54580S000 1519 3247 464 87.69 glotblastn 2136 11 27 44 8.9 gobat LYD627_H4 cowpea|l2vllFC461147 1 1520 3248 464 86.65 glotblastn LYD627_H4 cowpealgbl66|FC461147 1521 3248 464 86.65 glotblastn LYD627 H5 lotusl09vIlAV775154 TI 1522 3249 464 85.93 glotblastn LYD627_1 chickpea|11vllSRR133517.1069 1523 3250 464 84.54 glotblastn 0 23_T1 LYD627H6 peanutIOvIlGO263794_1 1524 3251 464 83.29 glotblastn LYD627_H7 cloverlgb162|BB914886_1 1525 3252 464 81.86 glotblastn LYD628_H2 pigeonpea|11vllCCIIPG1102635 1526 3253 465 88.95 glotblastn 1_4_TIII4_11 WO 2013/128448 PCT/IL2013/050172 198 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD628_HI soybean|I1vlIGLYMA16G3260 1527 3254 465 88 globlastp 0 LYD628_H3 bean|12vllCV534892 P1 1528 3255 465 86.6 globlastp LYD629_HI soybean|11vllGLYMA07G1203 1529 3256 466 96.8 globlastp 0 LYD629_HI pigeonpea|11vllSRR05458OX11 1530 3257 466 90.5 globlastp 2 9400_P1 LYD629_H2 pigeonpea|l0vlISRR054580S000 1531 3257 466 90.5 globlastp 0470 LYD629_H3 cowpeal12v6EG594224 P1 1532 3258 466 89.3 globlastp LYD629_113 cowpealgb166IEG594224 1533 3258 466 89.3 globlastp LYD629 H4 beanlgb1671CV543026 1534 3259 466 88.4 globlastp LYD629_HI bean|l2vllSRR001334.139650_P 1535 3260 466 88.1 globlastp 3 1 13 20 46 8. lbat LYD629_HI chickpea|llvllGR393168_P1 1536 3261 466 86.4 globlastp 4 LYD629_H5 lotusl09vllBF177689 P1 1537 3262 466 85.2 globlastp LYD629_H6 trigonella|llvlISRR066194X308 1538 3263 466 84.2 globlastp 576 LYD629_HI medicagol12vlIAW256951_P1 1539 3264 466 83.3 globlastp 5 LYD629_H7 medicagol09vlILLAW256951 1540 3264 466 83.3 globlastp LYD629_HI medicagol12vllBI311156_P1 1541 3265 466 83 globlastp 6 LYD629_H8 medicagoI09vlILLBI311156 1542 3265 466 83 globlastp LYD629_H9 trigonella|IlvlISRR066194X184 1543 3266 466 83 globlastp 937 LYD629_HI peanut|l0vlISRRO42413S001197 1544 3267 466 81.4 globlastp 0 7_P1 LYD629_HI soybean|IlvlIGLYMA08G0610 1545 3268 466 81.4 globlastp 1 0 LYD630_11 soybean|IlvlIGLYMA12G0160 1546 3269 467 96.6 globlastp 0 LYD630_H5 pigeonpeall v ISRRO5458OX11 1547 3270 467 90.2 globlastp 6473 b LYD630_H6 beangl2vlCB280685P1 1548 3271 467 87.5 globlastp LYD630_112 beanlgbl671CB280685 1549 3272 467 87.3 globlastp LYD630 H3 lotus09vlIBPO40921 P1 1550 3273 467 84.5 globlastp LYD630 H7 medicagol12vlIAW256804 TI 1551 3274 467 80.59 glotblastn LYD630 H4 medicagoI09vIlLLAW776894 1552 3275 467 80.4 glotblastn LYD631_HI soybean|IIvIlGLYMA12G064 1553 3276 468 94 globlastp 0 LYD631_H2 cowpea|12vllFG816078_P1 1554 3277 468 92 globlastp LYD631H8 bean|12vllEG562963 P1 1555 3278 468 91.1 globlastp LYD631_H2 cowpealgb166|FG816078 1556 3279 468 87.7 globlastp WO 2013/128448 PCT/IL2013/050172 199 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD631_H9 pigeonpea|I1vlICCIIPG1102182 1557 3280 468 87.4 globlastp 6_P1 LYD631_HI pigeonpeaIllvlSRR054580X55 1558 3280 468 87.4 globlastp 0 5062_P1 LYD631_H3 peanutI0vlIlES712405_P1 1559 3281 468 85.8 globlastp LYD631_H4 beanlgbl67|CV530804 1560 3282 468 84.2 globlastp LYD631_H5 lotusI09vlILLAW720068_P1 1561 3283 468 83 globlastp LYD6311H6 medicagol09vllBE239557 1562 3284 468 81.9 glotblastn LYD631_HI chickpea|llvllSRR133517.1076 1563 3285 468 81.8 globlastp 1 9_P1 LYD631_HI medicagol12vllBE239557_1 1564 3286 468 81.61 glotblastn 2 LYD631_H7 trigonellal1lvIlSRR066194X150 1565 3287 468 81.38 glotblastn 691 16 27 48 8.8 gobat LYD632_H3 soybean|llvllGLYMA03G3610 1566 3288 469 95 globlastp 0 LYD632_H6 pigeonpea|llvllGR464470 P1 1567 3289 469 90.1 globlastp LYD632_H7 bean|12vllFE693882_P1 1568 3290 469 89.1 globlastp LYD632 H4 beanlgbl67|CV541137 1569 3291 469 88.8 globlastp LYD632_H5 cowpeal12vllFF390940_P1 1570 3292 469 88.4 globlastp LYD632 H5 cowpealgbl661FF390940 1571 3292 469 88.4 globlastp LYD634_HI soybean|llvllGLYMAlG1846 1572 3293 471 89.9 globlastp 0 LYD634_H2 cowpeall2vl6FF384860 P1 1573 3294 471 87.6 globlastp LYD634_112 cowpealgbl661FF384860 1574 3294 471 87.6 globlastp LYD634 H6 bean|l2vllFE899187 P1 1575 3295 471 86.6 globlastp LYD634_H3 beanlgbl67|CV532868 1576 3295 471 86.6 globlastp LYD634_H7 pigeonpea|llvllEE605085_P1 1577 3296 471 83.7 globlastp LYD634_H4 pigeonpea|lOvllEE605085 1578 3296 471 83.7 globlastp LYD634_H5 soybeanIllvlIGLYMAl3G3904 1579 3297 471 80.71 glotblastn 0 LYD635_11 soybeanIlvllGLYMA19G0191 1580 3298 472 95 globlastp 0 LYD635_H4 bean|12vllSRR001334.123668_P 1581 3299 472 84.1 globlastp LYD635_H5 pigeonpeaIllvlSRR054580Xl0 1582 3300 472 83.6 globlastp 4907_P1 LYD635_H2 beanlgbl671FE680073 1583 3301 472 83.55 glotblastn LYD635_H3 cowpea|12vllFF391308_P1 1584 3302 472 81.8 globlastp LYD635_H3 cowpealgbl66|FF391308 1585 3303 472 81.2 globlastp LYD636_H3 bean|12vllCA908996_P1 1586 3304 473 92.5 globlastp LYD636_1 soybean|11vllGLYMA10G0466 1587 3305 473 91.6 globlastp 0 LYD636_H4 pigeonpeaI1vlISRR054580X16 1588 3306 473 89.8 globlastp ___________507_P1I__ WO 2013/128448 PCT/IL2013/050172 200 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD636_H2 pigeonpeaIOv IS RR054580S001 1589 3307 473 87 globlastp 6508 LYD636_H5 chickpeaIlll ISRR133517.1313 1590 3308 473 84.2 globlastp 66_P1 LYD636_H6 medicagol12vllAW256943 P1 1591 3309 473 81.2 globlastp LYD638_HI soybeanIvlIGLYMA15G0382 1592 3310 475 98.9 globlastp 0 LYD638_H2 cowpea|l2vllFF394689_P1 1593 3311 475 97.1 globlastp LYD638_H2 cowpealgbl66|FF394689 1594 3311 475 97.1 globlastp LYD638_H8 pigeonpeaIvlISRR054580X10 1595 3312 475 96.4 globlastp 1 2130_P1 LYD638_H8 bean112vllFG229632_P1 1596 3313 475 95.7 globlastp 2 LYD638_H3 beanIgb167|CV530755 1597 3313 475 95.7 globlastp LYD638_H8 chickpea|llvllSRR133517.1122 1598 3314 475 93.8 globlastp 3 19_P1 LYD638_H4 trigonellallvlISRR066194X121 1599 3315 475 91.7 globlastp 07 LYD638_H5 medicagoI09vlIDY618321 1600 3316 475 91.3 globlastp LYD638_H6 castorbean|11vlGE635823 P1 1601 3317 475 89.9 globlastp LYD638_H7 monkeyflowerIlOvllGO987981_ 1602 3318 475 89.9 globlastp P1 LYD638H8 beechIlvlISRR006293.6452_1 1603 3319 475 89.13 glotblastn LYD638_H8 orobanche|lOvlISRRO23189S00 1604 3320 475 89.1 globlastp 2399_P1 LYD638_H9 cacaollOv1ICF974571_P1 1605 3321 475 88.8 globlastp LYD638_1 grape|llvllGSVIVTO102530200 1606 3322 475 88.8 globlastp 0 1_Pi LYD638_1 watermelon|I1vICV004917 1607 3323 475 88.8 globlastp 1 LYD638_1 cotton|lOv2|DV849102 1608 3324 475 88.41 glotblastn 2 LYD638_1 cotton|10v2ISRR032878S008245 1609 3325 475 88.41 glotblastn 3 1 LYD638_1 fagopyrumIvlISRR063689X12 1610 3326 475 88.41 glotblastn 4 5403_1 LYD638_1 cotton|I1v2IC0088742 1611 3327 475 88.4 globlastp 5 LYD638_1 cotton|Iv2IDT053039 1612 3327 475 88.4 globlastp 61 LYD638H1 cotton60v2|SRR032878S000110 1613 3328 475 88.4 globlastp LYD638_1 cassavaI09vllJGICASSAVA306 1614 3329 475 88 globlastp 8 84VALIDM1 P1 WO 2013/128448 PCT/IL2013/050172 201 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD638_HI oakl10v1lFP073589_P1 1615 3330 475 88 globlastp 9 LYD638_H2 cucumberI09vlICV004917_P1 1616 3331 475 87.7 globlastp 0 LYD638_H2 flaveriaI11vlISRR149229.15365 1617 3332 475 87.7 globlastp 1 5_P1 LYD638_H2 fagopyrumI11vISRR063689X11 1618 3333 475 87.32 glotblastn 2 5245_1 LYD638_H8 lettuce|l2vllDY981698_P1 1619 3334 475 87.3 globlastp LYD638_H2 artemisia|lOvllEYO93426_P1 1620 3335 475 87.3 globlastp 3 LYD638_H2 citrusIgb166ICB290538 1621 3336 475 87.3 globlastp 4 LYD638_H2 orangeIvlICB290538_P1 1622 3336 475 87.3 globlastp 5 LYD638_H2 strawberry|11vllC0381546 1623 3337 475 87.3 globlastp 61 LYD638_H2 valerianaI1vlISRRO99039X104 1624 3338 475 87.3 globlastp 7 058 LYD638_H8 nasturtiumIlvlISRRO32558.128 1625 3339 475 87 globlastp 6 316_P1 LYD638_H2 aquilegia|l0v2|DR946895_P1 1626 3340 475 87 globlastp 8 LYD638_H2 cannabisI12vlIJK501697_P1 1627 3341 475 87 globlastp 9 LYD638_H3 clementine|11vlCB290538_P1 1628 3342 475 87 globlastp 0 LYD638_H3 flaverial11vllSRR149229.22921 1629 3343 475 87 globlastp 1 7_P1 LYD638_H3 poplarIlOvllBU869270_P1 1630 3344 475 87 globlastp 2 LYD638_H3 potatollOvlIBQ118035_P1 1631 3345 475 87 globlastp 3 LYD638_H3 primulaI1vlISRRO98679X1025 1632 3346 475 87 globlastp 4 65_P1 LYD638_H3 solanumphureja09vlISPHBG12 1633 3345 475 87 globlastp 5 6806 LYD638_H3 tragopogonIlOvlISRR20205SOO 1634 3347 475 87 globlastp 6 00931 LYD638_H3 cirsiuml11vllSRR346952.10266 1635 3348 475 86.6 globlastp 7 9_P1 LYD638_H3 sunflowerIlOvllEE615497 1636 3349 475 86.6 globlastp 8 LYD638_113 eucalyptusll v2IES5886l7_P1 1637 3350 475 86.2 globlastp 9 _________________ WO 2013/128448 PCT/IL2013/050172 202 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD638_H4 euphorbia|I1vlIDV126968_P1 1638 3351 475 86.2 globlastp 0 LYD638_H4 tomatollvllBG126806 1639 3352 475 86.2 globlastp 1 LYD638_H8 sunflowerI12vIEE615497_P1 1640 3353 475 85.9 globlastp 7 LYD638_H4 apple|11vllCV129099_P1 1641 3354 475 85.9 globlastp 2 LYD638_H4 centaureaIgb166|EH713237_P1 1642 3355 475 85.9 globlastp 3 LYD638_H4 cirsiumI11vlISRR346952.10237 1643 3355 475 85.9 globlastp 4 75_P1 LYD638_H4 prunus|10vllBU039771 1644 3356 475 85.9 globlastp 5 LYD638_H4 silene|I1vlISRR096785X108818 1645 3357 475 85.9 globlastp 6 LYD638_H4 ambrosia 11 vl lSRR346935.3547 1646 3358 475 85.87 glotblastn 7 46_T1 LYD638_H4 aristolochiaI0vlISRRO39082S00 1647 3359 475 85.6 globlastp 8 02743_P1 LYD638_H8 oil-palm|IIvlIEL687196_P1 1648 3360 475 85.5 globlastp 8 LYD638_H4 ambrosia 11 vl lSRR346935.1087 1649 3361 475 85.14 glotblastn 9 72_T1 LYD638_H5 flaveriaIl1vlISRR149232.11389 1650 3362 475 85.14 glotblastn 0 0_T1 LYD638_H8 poppyI11vlISRR030259.114169 1651 3363 475 85.1 globlastp 9 P1 LYD638_H9 amborella| 12v3|SRR038634.23364 475 84.8 globlastp 0 30_P1 LYD638_H5 poplarl10vllXM002303855_P1 1653 3365 475 84.8 globlastp 1 LYD638_H5 riceIl1vlIAU031876_P1 1654 3366 475 84.8 globlastp 2 LYD638_H5 ricelgb17010S02G10230 1655 3366 475 84.8 globlastp 2 LYD638_H5 thellungiella-parvulum| I1vIlBY 1656 3367 475 84.8 globlastp 3 812134 LYD638_H9 onionIl2vlICF441304_T1 1657 3368 475 84.78 glotblastn LYD638_H5 monkeyflowerIlOvlISRRO37227 1658 3369 475 84.6 globlastp 4 S0052581_P1 LYD638_H9 beetIl2vlIBQ593198_P1 1659 3370 475 84.5 globlastp 2 LYD638_H9 poppyI11vlISRRO30259.110127 1660 3371 475 84.42 glotblastn 3 T1 WO 2013/128448 PCT/IL2013/050172 203 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD638_H5 cirsiuml11vlISRR346952.10125 1661 3372 475 84.42 glotblastn 5 72_T1 LYD638_H5 tripterygiumI11vISRR098677X1 1662 3373 475 84.4 globlastp 6 70048 LYD638_H9 bean|l2vllSRRO90491.1076536 1663 3374 475 84.1 globlastp 4 P1 LYD638_H9 poppyll1vllSRR033668.365155 1664 3375 475 84.1 globlastp 5 P1 LYD638_H5 soybeanI11vlIGLYMA11G1409 1665 3376 475 84.1 globlastp 7 0 LYD638H5 cucurbital11vlISRR091276X112 1666 337 475 84.06 glotblastn 8 061_T1 LYD638_H9 bjuncea|l2vlIE6ANDIZ01A97 1667 3378 475 83.7 globlastp 6 YXP1 LYD638_H5 bjunceaIl0v2IE6ANDIZ01A97 1668 3378 475 83.7 globlastp 9 YX LYD638_H6 canolaIvlIEE439609_P1 1669 3378 475 83.7 globlastp 0 LYD638_H6 canolaIvlIEE473348_P1 1670 3378 475 83.7 globlastp 1 LYD638_H6 canola|llvllSRR019557.21478_ 1671 3378 475 83.7 globlastp 2 P1 LYD638_H6 phalaenopsisIvlISRR125771.1 1672 3379 475 83.7 globlastp 3 013801_P1 LYD638_H6 brapalgb162|EE519713 1673 3380 475 83.33 glotblastn 4 LYD638_H6 radishIgb1641EV530173 1674 3381 475 83.3 globlastp 5 LYD638_H9 b rapa1vlICD813392_P1 1675 3382 475 83.1 globlastp 7 LYD638_H9 gossypiumraimondiil12vllDV8 1676 3383 475 83 globlastp 8 49102_P1 LYD638_H6 thellungiella-halophiluml lvI lB 1677 3384 475 82.7 globlastp 6 Y812134 LYD638_H6 amorphophallus|I1v2SRR08935 1678 3385 475 82.61 glotblastn 7 1X167144_1 LYD638_H6 phyla|l 1v2ISRR099037X109540 1679 3386 475 82.61 glotblastn 8 T1 LYD638_H9 chickpea|IlvlISRR133517.2146 1680 3387 475 82.25 glotblastn 9 58_T1 LYD638_H6 ambrosial 1 lvi SRR346935.2348 1681 3388 475 82.2 globlastp 9 8_P1 LYD638_H7 arabidopsislyrata|09vllJGIAL01 1682 3389 475 82.2 globlastp 0 0678_P1 LYD638_H7 triphysarial10vlIEY128050 1683 3390 475 82.2 globlastp WO 2013/128448 PCT/IL2013/050172 204 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD638_HI bjunceaI12vlIE6ANDIZO1EK3 1684 3391 475 81.5 globlastp 00 W2_P1 LYD638_HI medicagol12vIlBE324303_P1 1685 3392 475 81.5 globlastp 01 LYD638_H7 arabidopsis|10v lAT3G20870-P 1686 3393 475 81.5 globlastp LYD638_H7 lotus|09vllBPO48291_P1 1687 3394 475 81.5 globlastp 3 LYD638_H7 podocarpus|10vlISRR065014S00 1688 3395 475 80.94 glotblastn 4 46390_1 LYD638_HI pigeonpea|IlvlICCIIPG1100024 1689 3396 475 80.9 globlastp 02 8_P1 LYD638_H7 dandelion|10vlIDY818839_P1 1690 3397 475 80.9 globlastp 5 LYD638_HI spruce|IlvlIEX419926_P1 1691 3398 475 80.8 globlastp 03 LYD638_H7 sprucelgb1621CO487657 1692 3398 475 80.8 globlastp 6 LYD638_HI brachypodium|12vlIBRADI3GO7 1693 3399 475 80.5 globlastp 04 080T2_P1 LYD638_H7 brachypodiumI09vlIDV486023 1694 3399 475 80.5 globlastp 7 LYD638_H7 peanutl10vlISRRO42413SO01443 1695 3400 475 80.4 globlastp 8 2_P1 LYD638_HI rye|12vlIDRROO1012.1356_P1 1696 3401 475 80.1 globlastp 05 LYD638_H7 barleyllOv2|BG417171 1697 3402 475 80.1 globlastp 9 LYD638_H8 wheat|lOv2|BE213609 1698 3403 475 80.1 globlastp 0 LYD639_HI soybean|IlvlIGLYMA19G1 177 1699 3404 476 88.6 globlastp 0 LYD639_H3 pigeonpeaIll vISRRO5458OX15 1700 3405 476 81.8 globlastp 2862_P1 LYD639_H2 cowpea|l2vllFF389274_1 1701 3406 476 81.38 glotblastn LYD639_H2 cowpealgbl66|FF389274 1702 3407 476 80.87 glotblastn LYD640_HI soybean|1vlIGLYMA02G3740 1703 3408 477 93.4 globlastp 0 LYD640_H4 pigeonpeaI1vlISRR054580X16 1704 3409 477 87.1 globlastp 367_P1 LYD640_H2 cowpea|l2vllVIRPSAS1 1705 3410 477 87.07 glotblastn LYD640_H2 cowpealgbl66|VIRPSAS 1706 3410 477 87.07 glotblastn LYD640_H5 bean112vllSRR001334.200990_P 1707 3411 477 86.8 globlastp LYD640 H3 beanIgb167|CV535087 1708 3412 477 86.34 glotblastn LYD642_H9 pigeonpea|llvllEE604557 P1 1709 3413 479 91.1 globlastp WO 2013/128448 PCT/IL2013/050172 205 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD642_HI beanlgbl67|FD785160 1710 3414 479 91.1 globlastp LYD642_H2 cowpea|l2vllFF540232 P1 1711 3415 479 91.1 globlastp LYD642_H2 cowpealgbl66|FF540232 1712 3415 479 91.1 globlastp LYD642_H3 pigeonpea|lOvllEE604557 1713 3413 479 91.1 globlastp LYD642_H4 soybean|llvllGLYMA09GO435 1714 3416 479 90.3 globlastp 0 LYD642_HI bean|l2vllSRR001335.120177_P 1715 3417 479 90 globlastp 0 1 11 47 49 9 lbat LYD642_H5 lotus09vlILLGO008153_P1 1716 3418 479 87.9 globlastp LYD642H6 liquoricelgbl7lFS239800 P1 1717 3419 479 87 globlastp LYD642_HI medicagol12vllAL377555_1 1718 3420 479 83.52 glotblastn 1 LYD642_H7 medicagoI09vlIAL377555 1719 3421 479 83.5 globlastp LYD642_HI chickpea|llvllSRR133517.1178 1720 3422 479 81.3 globlastp 2 51_PI LYD642_H8 prunusl0vlIlCO416682 1721 3423 479 80.43 glotblastn LYD643_HI soybean|llvllGLYMA07G0655 1722 3424 480 93.1 globlastp 0 LYD643_H8 pigeonpea|llvllGR470036 P1 1723 3425 480 91.6 globlastp LYD643_H2 pigeonpea|lOvllGR470036 1724 3425 480 91.6 globlastp LYD643 H3 cowpealgbl66|FF540040 1725 3426 480 89.3 globlastp LYD643_H9 bean|12vllCB542964_P1 1726 3427 480 88.4 globlastp LYD643_H4 beanlgb1671CB542736 1727 3428 480 88 globlastp LYD643_HI cowpea|l2vllFF540040_P1 1728 3429 480 87.9 globlastp 0 LYD643_HI medicagoll2vllBG452896_P1 1729 3430 480 85.6 globlastp 1 LYD643_115 medicagoIO9vl IBG452896 1730 3430 480 85.6 globlastp LYD643_H6 lotusIO9vlILLGO012566 1 1731 3431 480 85.05 glotblastn LYD643_1 chickpea|llvllSRR133517.1132 1732 3432 480 83.2 globlastp 2 64_P1 LYD643_H7 cloverlgbl62|BB918052 P1 1733 3433 480 82.7 globlastp LYD644_11 soybean|llvllGLYMA07G3932 1734 3434 481 98.2 globlastp 0 LYD644_H6 bean|12vllSRR001334.118891_P 1735 3435 481 91.4 globlastp LYD644_H2 trigonella|llvlISRRO66194X104 1736 3436 481 87.4 globlastp 241 LYD644_H7 medicagol12vllBE204178_P1 1737 3437 481 86.6 globlastp LYD644_H8 medicagol12vllBF641611 P1 1738 3437 481 86.6 globlastp LYD644_H4 soybeanIllvlIGLYMAl3Gl049 1739 3438 481 85.7 globlastp 0 LYD644H5 soybean|llvlIGLYMA20G623 1740 3439 481 85.5 globlastp LYD644 119 pigeonpeaIllvlISRROS458OXl2 1741 3440 481 84.3 globlastp 1__ __ _ _ 4197_P1 I I I WO 2013/128448 PCT/IL2013/050172 206 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD644_HI beanI12vlISRR001334.288940_P 1742 3441 481 83.5 globlastp 0 1 14 41 41 8. lbat LYD645_HI soybeanI11vIGLYMA07G3834 1743 3442 482 92.2 globlastp 0 LYD645_H6 beangl2vlCB542096_P1 1744 3443 482 87.4 globlastp LYD645_H2 beanIgbl67ICB42196 1745 3443 482 87.4 globlastp LYD645_H3 cowpeall2vl6FF383417 P1 1746 3444 482 86.6 globlastp LYD645_1H3 cowpealgbl661FF383417 1747 3444 482 86.6 globlastp LYD645_H7 pigeonpeaI1vlISRR054580X16 1748 3445 482 86 globlastp 291_P1 LYD645_H4 pigeonpea|l0vlISRR054580S001 1749 3445 482 86 globlastp 6292 LYD645_H5 lotusl09vllCB827458 P1 1750 3446 482 80.5 globlastp LYD647_HI soybeanIvlIGLYMA08G4104 1751 3447 484 83.9 globlastp 0 LYD648_HI potatollOvlIBF153552_P1 1752 3448 485 95.4 globlastp LYD648_H2 solanumphurejaI09vlISPHAI78 1753 3449 485 95.1 globlastp 0847 LYD648_H7 pepper|l2vllGD067902 P1 1754 3450 485 92.2 globlastp LYD648_H3 eggplantI0vlIlFS007304_P1 1755 3451 485 91.9 globlastp LYD648 H4 tobaccolgbl62|EB443178 1756 3452 485 83.7 globlastp LYD648_H5 nicotianabenthaianalgb1621C 1757 3453 485 82.9 globlastp K281577_P1 LYD648_H6 nicotianabenthaianalgbl62|C 1758 3454 485 82.2 globlastp K282667_P1 LYD650_HI solanumphureja|09vl ISPHAF20 1759 3455 486 95.5 globlastp 4783 LYD650_H2 potatol0vlICV494921_1 1760 3456 486 93.33 glotblastn LYD650_H4 eggplantI0vlIlFS037047 P1 1761 3457 486 85.8 globlastp LYD650_H5 pepperl12vllBM066147_P1 1762 3458 486 84.9 globlastp LYD650 H5 pepperIgbl71IBM066147 1763 3458 486 84.9 globlastp LYD651_H2 tobaccolgb162|AF211738 1764 3459 487 80.7 globlastp LYD653_HI tomatoIl1vlIBG123578 1765 3460 489 85.33 glotblastn LYD653_H2 petunialgbl71|CV294459_P1 1766 3461 489 83.1 globlastp LYD653_H3 potatollOvlIBQ516821_1 1767 3462 489 81.33 glotblastn LYD653_H4 solanumphureja09vlISPHBG12 1768 3463 489 81.33 glotblastn 3578 LYD654_11 solanumphureja09vlISPHAI78 1769 3464 490 98 globlastp 2247 LYD654_H2 pepper|l2vllBM063093 P1 1770 3465 490 95 globlastp LYD655_H1 solanumphureja09vlISPHAI89 1771 3466 491 95.6 globlastp 6168 LYD655_H2 pepper|l2vlICO909199 P1 1772 3467 491 88.4 globlastp LYD655_H2 pepperIgb171ICO909199 1773 3467 491 88.4 globlastp LYD655_H3 potatollOvlIBF460284 P1 1774 3468 491 85.9 globlastp LYD655_H4 tobaccolgbl62|CV019561 1775 3469 491 85.58 glotblastn WO 2013/128448 PCT/IL2013/050172 207 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD655_H5 petunialgbl7lCV295783 P1 1776 3470 491 81.3 globlastp LYD657_HI solanumphurejal09vllSPHAWO 1777 3471 492 96.9 globlastp 30194 LYD658_HI solanumphureja09vllSPHAWO 1778 3472 493 94.6 globlastp 94631 LYD658_H2 potatol0vlIBF187607 P1 1779 3473 493 81.7 globlastp LYD658_H3 nicotianabenthamianalgbl62|C 1780 3474 493 80.46 glotblastn K280675_TI LYD658_H4 nicotiana benthaianalgbl62|C 1781 3475 493 80.2 globlastp K288269_P1 LYD659_HI solanumphureja|09vllSPHAW2 1782 3476 494 97 globlastp 17526 LYD659_H2 amsonial 1 lv ISRRO98688X1409 1783 3477 494 80.71 glotblastn 68_ 1 1 LYD660-HI solanumiphurej al09vlIlSPllAW6 1784 3478 495 97.4 globlastp 16260 LYD661_HI solanumphureja|09vllSPHAW6 1785 3479 496 98.3 globlastp 16620 LYD661_H2 cacaollOvlCU538010 P1 1786 3480 496 82 globlastp LYD661_H3 cassava09vlIDB937952 P1 1787 3481 496 81.9 globlastp LYD661_H4 poplarI0vlIlBI069117 P1 1788 3482 496 81.3 globlastp LYD661 H5 eucalyptusI1v2|ES591203 P1 1789 3483 496 81 globlastp LYD661_H6 grape|llvllGSVIVTO103316800 1790 3484 496 80.9 globlastp 1_P1 LYD661_HI cotton|llvllDW488153_P1 1791 3485 496 80.7 globlastp 0 LYD661_HI gossypiumraimondiill2vllDR45 1792 3486 496 80.7 globlastp 1 4811_P1 LYD661_H7 castorbeanlllvllXM_002515320 1793 3487 496 80.7 globlastp P1 LYD661_H8 cotton|lOv2|DR454811 1794 3488 496 80.6 globlastp LYD661_HI cotton|llvlIAI727236_1 1795 3489 496 80.43 glotblastn 2 LYD661_HI cotton|llvllBE054582_1 1796 3490 496 80.43 glotblastn 3 LYD661_HI cotton|llvllDR454811_P1 1797 3491 496 80.4 globlastp 4 LYD661_1 gossypiumraimondiill2vllAI72 1798 3492 496 80.4 globlastp 5 7236_P1 LYD661H9 cotton|I1v2|AI727236 1799 3493 496 80.3 globlastp LYD662_HI solanumphureja09vlISPHAW6 1800 3494 497 96.5 globlastp 18546 180 44 47 9. lbat LYD662_H2 eggplantIlOvllFSO33651_P1 1801 3495 497 89 globlastp LYD663_HI solanumphureja|09vllSPHAY3 1802 3496 498 90.5 globlastp LD_ H2 pto0lV 22T 137768514 LYD663 112 potatoliOviICV5O262i TI 1803 3497 498 88.51 glotblastn WO 2013/128448 PCT/IL2013/050172 208 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD664_HI solanumphureja09vlISPHBE46 1804 3498 499 90 globlastp 0507 LYD666_H3 pepperll2v1BM061649 P1 1805 3499 501 91.6 globlastp LYD666_113 pepperIgb 171 IBM061649 1806 3499 501 91.6 globlastp LYD666 H4 tobaccolgbl62|AY639146 1807 3500 501 87.5 globlastp LYD667_HI solanumphureja09vlISPHBG12 1808 3501 502 98.2 globlastp 3287 LYD667_H2 pepper|l2vllCA522829_P1 1809 3502 502 86.6 globlastp LYD667_H2 pepperIgbl71ICA522829 1810 3502 502 86.6 globlastp LYD667_H3 potatollOvlIBG350145 P1 1811 3503 502 85.7 globlastp LYD667_H4 solanumphureja09vlISPHBG12 1812 3503 502 85.7 globlastp 6102 LYD667 H5 tomatollvllBG126102 1813 3504 502 85.7 globlastp LYD669_HI solanumphurejaI09vlISPHBG12 1814 3505 504 99.1 globlastp 7852 LYD669_H2 pepper|l2vllBM063343 P1 1815 3506 504 96.2 globlastp LYD669_H3 catharanthus|llvllEG555968_P1 1816 3507 504 86.8 globlastp LYD669 H4 vincaI1vlISRRO98690X137330 1817 3508 504 86.55 glotblastn LYD669_H5 tabernaemontanallvllSRR0986 1818 3509 504 86.5 globlastp 89X113952 LYD669_H6 amsoniaIvlISRRO98688X1236 1819 3510 504 86.1 globlastp 59_P1 LYD669_H7 vincaIvlISRRO98690X130330 1820 3511 504 85.23 glotblastn LYD669_H8 valeriana|llvlISRR99039X100 1821 3512 504 85 globlastp 383 LYD669_H9 kiwilgbl66|FG397105 P1 1822 3513 504 84.1 globlastp LYD669_1 potatollOvlIBF459943_P1 1823 3514 504 84.1 globlastp 0 LYD669H3 beechl11vIlSRR006293.14617 T 1824 3515 504 83.18 glotblastn 3 1 LYD669_1 chestnutIgb170ISRR006295S002 1825 3516 504 83 globlastp 1 1602_P1 LYD669_1 citrusIgb166IBE205717 1826 3517 504 83 globlastp 2 LYD669_1 clementine|llvllBE205717_P1 1827 3518 504 83 globlastp 311 LYD669_1 orange|llvllBE205717_P1 1828 3519 504 82.7 globlastp 4 LYD669_1 watermelon|l1viIVMELOOO7033 1829 3520 504 82.1 globlastp 5 8543255 LYD669_H3 beechIIIvlIFR603623_1 1830 3521 504 81.84 glotblastn 4 LYD669_1 oakIlOvllDN950840_P1 1831 3522 504 81.8 globlastp LYD669_1 phylaIIIv2ISRR099035XIII901 1832 3523 504 81.8 globlastp 7 P1 WO 2013/128448 PCT/IL2013/050172 209 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD669_H3 gossypiumraimondiil12vllCA99 1833 3524 504 81.4 globlastp 5 3556_P1 LYD669_HI apple|I1vlICN578861_P1 1834 3525 504 81.4 globlastp 8 LYD669_H3 gossypiumraimondiil12vllDR45 1835 3526 504 81.2 globlastp 6 2577_P1 LYD669_HI cotton1I0v2|CO116252 1836 3527 504 81.2 globlastp 9 LYD669_H2 prunusI0vlIlBU047497 1837 3528 504 81.2 globlastp 0 LYD669_H2 strawberryI11vllC0380648 1838 3529 504 81.2 globlastp 1 LYD669_H3 lettuceIl2vlILSl2vlCRP084179 1839 3530 504 81 globlastp 7 P1 LYD669_H3 cotton|I1vlICA993556_P1 1840 3531 504 80.9 globlastp 8 LYD669_H2 cacaoIl0vlICU483136_P1 1841 3532 504 80.9 globlastp 2 LYD669_H2 cucumberI09vlIBGI454G016992 1842 3533 504 80.9 globlastp 3 7_P1 LYD669_H2 poplarI0vlIBU879857_P1 1843 3534 504 80.9 globlastp 4 LYD669_H3 cotton|I1vlIDR452577XX1T1 1844 3535 504 80.72 glotblastn LYD669_H2 cotton|lOv2|CA993556 1845 3536 504 80.7 globlastp 5 LYD669_H2 euonymus|I1vlISRR070038X10 1846 3537 504 80.7 globlastp 6 4702_P1 LYD669_H2 melon| 10 vII VMELOO070338543 1847 3538 504 80.7 globlastp 7 255_P1 LYD669_H2 aristolochia|IOvllFD752757_P1 1848 3539 504 80.5 globlastp 8 LYD669_H2 euonymus|I1vlISRR070038X15 1849 3540 504 80.5 globlastp 9 1093_P1 LYD669_H3 tripterygium|I1vlISRRO98677X1 1850 3541 504 80.5 globlastp 0 23156 LYD669_H3 poplar|IOvlIBU820108_P1 1851 3542 504 80.3 globlastp LYD669_H3 apple|I1vlICN496454_P1 1852 3543 504 80 globlastp 2 LYD670_H1 solanumphureja|09vlISPHBG12 1853 3544 505 93.7 globlastp 6384 LYD670_H2 potatollOvllBE922534 1 1854 3545 505 90.66 glotblastn LYD672_11 solanumphurejaIO9vllSPHBG13 1855 3546 507 95.3 globlastp 4039 LYD672_H2 pepper|l2vllCA519411_P1 1856 3547 507 88.3 globlastp LYD672_H2 pepperlgbl7lCA519411 1857 3547 507 88.3 globlastp WO 2013/128448 PCT/IL2013/050172 210 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD672_H3 tobaccolgb162|DWO04996 1858 3548 507 82.57 glotblastn LYD674_HI potatol0vlIlBE921584 P1 1859 3549 509 93 globlastp LYD674_H2 solanumphureja|09vlISPHBG13 1860 3550 509 93 globlastp 3722 LYD674_H3 eggplant1OvIlFS004197 P1 1861 3551 509 87.3 globlastp LYD674_H4 nicotianabenthaianalgbl62|C 1862 3552 509 81.8 globlastp K293409_P1 LYD677_HI solanumphureja|09vlISPHBG59 1863 3553 512 96 globlastp 2613 LYD678_HI potatol0vlIBG598437_P1 1864 3554 513 97.5 globlastp LYD678_H2 solanumphureja|09vlISPHBG62 1865 3555 513 96.8 globlastp 6546 LYD68OH2 tabernaemontanallvllSRR0986 1866 3556 515 80.77 glotblastn 89X 1160121 LYD681_HI solanumphureja09vlISPHBG63 1867 3557 516 98.6 globlastp 0045 LYD681_H2 potatollOvlIBF053994 P1 1868 3558 516 98.4 globlastp LYD681_H3 amsoniaIvlISRRO98688X1010 1869 3559 516 89.7 globlastp 55_P1 LYD681_H4 catharanthusI1vlISRRO98691X 1870 3560 516 89.7 globlastp 104148_P1 LYD681_H5 tabernaemontanal11vIlSRR0986 1871 3561 516 89.1 globlastp 89X106474 LYD681H6 vincaIvlISRRO98690X10387 1872 3562 516 87.7 globlastp LYD681_H7 phylaIv2ISRR099035X141015 1873 3563 516 87.3 glotblastn T1 LYD681_H8 orobanche|lOvlISRRO23189SO00 1874 3564 516 86.3 globlastp 4460_P1 LYD681_H9 monkeyflowerIlOvlDV211803_ 1875 3565 516 85.7 globlastp P1 LYD681_1 arnicaIvlISRR099034X102089 1876 3566 516 85.5 globlastp 0 P1 LYD681_H5 sunflowerl2vlDY921230_P1 1877 3567 516 85.1 globlastp 8 LYD681_1 arabidopsislyrata|09vllJGIAL02 1878 3568 516 85.1 globlastp 1 7489_P1 LYD681_1 sunflowerIlOvllDY921230 1879 3567 516 85.1 globlastp 2 LYD681_H1 arabidopsislyrata|09vllJGIALOO 1880 3569 516 84.9 globlastp 3 5462_P1 LYD681H1 arabidopsis|1vllAT1G64190_P 1881 3570 516 84.9 globlastp LYD681_H1 thellungiella-halophiluml1IvIlB 1882 3571 516 84.9 globlastp 5 Y804243 LYD681_H1 canola|11vllEE413371_Ti 1883 3572 516 84.88 glotblastn 6 __________________ WO 2013/128448 PCT/IL2013/050172 211 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD681_HI canola|I1vlIEE415072_T1 1884 3573 516 84.88 glotblastn 7 LYD681_H5 bjrapaIl1vlIBG54393O_P1 1885 3574 516 84.7 globlastp 9 LYD681_H6 bjrapaI1vlICV433796_P1 1886 3575 516 84.7 globlastp 0 LYD681_HI brapalgb1621CV433796 1887 3575 516 84.7 globlastp 8 LYD681_HI canola|llvllEE417941_P1 1888 3575 516 84.7 globlastp 9 LYD681_H2 canola|11vllES911843_P1 1889 3575 516 84.7 globlastp 0 LYD681_H6 b-rapa|11vlCD814820_1 1890 3576 516 84.68 glotblastn 1 LYD681_H2 arabidopsis|lOvIAT5G41670_P 1891 3577 516 84.5 globlastp LYD681_H2 lettuce|lOvllDW169046 1892 3578 516 84.5 globlastp 2 LYD681_H2 ambrosia|llvllSRR346935.2040 1893 3579 516 84.48 glotblastn 3 66_T1 LYD681_H2 ambrosia|llvllSRR346935.4043 1894 3580 516 84.48 glotblastn 4 37_T1 LYD681_H2 lettuce|l2vlIDW166137_P1 1895 3581 516 84.1 globlastp 2 LYD681_H2 cirsiumIvlISRR346952.13802 1896 3582 516 84.07 glotblastn 5 T1 LYD681_H2 vincaIvlISRRO98690X113839 1897 3583 516 84.07 glotblastn 6 LYD681_H6 nasturtium|l1vlISRRO32558.171 1898 3584 516 83.5 globlastp 2 608_P1 LYD681_H2 cacaol0vlIlCU508968_P1 1899 3585 516 83.1 globlastp 7 LYD681_H2 citrusIgb166ICN190890 1900 3586 516 83.06 glotblastn 8 LYD681_H2 ambrosial11vllSRR346935.4021 1901 3587 516 82.9 glotblastn 9 52_T1 LYD681_H3 cucumberI09vlIEB716020_P1 1902 3588 516 82.9 globlastp 0 LYD681_H3 cynaralgbl671GE577931_1 1903 3589 516 82.86 glotblastn LYD681H6 pigeonpeaIIIvIlGW359493_P1 1904 3590 516 82.8 globlastp 3 LYD68I1H3 castorbean|I1vlIGE634479_P1 1905 3591 516 82.7 globlastp 2 s LYD68I_113 soybeanIIIvIIGLYMAO8GO24i 1906 3592 516 82.7 globlastp 3 0 _ WO 2013/128448 PCT/IL2013/050172 212 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD681_H6 cotton|I1vlIBQ410946_P1 1907 3593 516 82.5 globlastp 4 LYD681_H3 castorbean|11vllXM_002509856 1908 3594 516 82.5 globlastp 4 P1 LYD681_H3 euonymus|I1vlISRR070038X10 1909 3595 516 82.5 globlastp 5 8968_P1 LYD681_H3 grape|I1vlIGSVIVT0101946700 1910 3596 516 82.5 globlastp 6 1_PI LYD681_H3 tripterygiumI11vIlSRR098677X1 1911 3597 516 82.5 globlastp 7 11190 LYD681_H6 gossypiumraimondiil12vllAI73 1912 3598 516 82.3 globlastp 5 0491_P1 LYD681_H3 cotton|10v21C0076294 1913 3599 516 82.3 globlastp 8 LYD681_H3 watermelon|I1vlIAM715537 1914 3600 516 82.3 globlastp 9 LYD681_H4 strawberryI11vIlEX672776 1915 3601 516 82.2 globlastp 0 LYD681_H4 soybean|I1vlIGLYMA05G3717 1916 3602 516 82.1 globlastp 1 0 LYD681_H4 trigonella|llvlISRRO66194X112 1917 3603 516 82.1 globlastp 2 434 LYD681_H4 medicagol09vlILLAL384701 1918 3604 516 82.06 glotblastn 3 LYD681_H4 clementine|11vlCN190890_P1 1919 3605 516 81.9 globlastp 4 LYD681_H4 prunusIlOvlICN863535 1920 3606 516 81.9 globlastp 5 LYD681_H4 thellungiella-halophilumllIvIlE 1921 3607 516 81.9 globlastp 6 HJGI1 1021359 LYD681_H4 euonymus|IlvlISRRO70038X1O 1922 3608 516 81.8 globlastp 7 7038_P1 LYD681_H4 platanus|IlvlISRRO96786X1407 1923 3609 516 81.7 globlastp 8 80_P1 LYD681_H4 lotusI09vlILLAV410725_P1 1924 3610 516 81.5 globlastp 9 LYD681_H5 oakIlOvlIFPO25719_P1 1925 3611 516 81.5 globlastp 0 LYD68 1_H6 beechl 11 vI SRR006293.12520_P 1926 3612 516 81.4 globlastp 6 1 - 12 62 56 8. lbat LYD681_H6 chickpea|IlvlIGR912701_P1 1927 3613 516 81.3 globlastp 7 LYD681_H6 poppyllvlISRRO30259.136321 1928 3614 516 81.3 globlastp 8 P1 LYD681_H5 aquilegiallOv2DR920343_P1 1929 3615 516 81.3 globlastp 1I__________________________ WO 2013/128448 PCT/IL2013/050172 213 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD681_H5 poplarIlOvlIBU829466_P1 1930 3616 516 81.3 globlastp 2 LYD681_H6 poppyIl1vlIFE965679_P1 1931 3617 516 81.1 globlastp 9 LYD681_H5 chestnutIgb170SRROO629SS004 1932 3618 516 81.1 globlastp 3 4488_P1 LYD681_H7 poppyllvllSRR096789.181966 1933 3619 516 81.05 glotblastn 0 T1 LYD681_H7 poppyllvllSRR030259.353240 1934 3620 516 80.9 globlastp 1 P1 LYD681_H5 poplarIlOvlIAI165699_P1 1935 3621 516 80.8 globlastp 4 LYD681_H5 aristolochia|lOvlIFD755163_1 1936 3622 516 80.65 glotblastn 5 LYD681_H7 bean|l2vlCA900025_1 1937 3623 516 80.52 glotblastn 2 LYD681_H7 amborella|12v3ISRR038635.703 1938 3624 516 80.5 globlastp 3 40_P1 LYD681_H5 orangel1vlCN190890_P1 1939 3625 516 80.5 globlastp 6 LYD681H5 sileneIl1vlISRRO96785X102909 1940 3626 516 80.24 glotblastn LYD682_HI solanumphureja09vlISPHBG63 1941 3627 517 95.9 globlastp 0298 LYD684_HI solanumphurejaI09vlISPHBG73 1942 3628 519 96.2 globlastp 4982 LYD684_H2 pepperIgbl7I|CA524110 1943 3629 519 85.5 globlastp LYD685_11 solanumphurejaI09vlISPHS701 1944 3630 520 91.05 glotblastn 86 LYD685_H2 potatollOvlIS70186 P1 1945 3631 520 89.8 globlastp LYD686_11 solanumphurejaI09vlISPHBI40 1946 3632 521 96.4 globlastp 5665 LYD686_H2 solanumphureja09vlISPHBG13 1947 3633 521 83.1 globlastp 0034 LYD686_H3 tomatoIl1vlIBG130034 1948 3634 521 81.1 globlastp LYD686_H4 amsoniaIvlISRRO98688X1255 1949 3635 521 80.2 globlastp 11_P1 LYD687_11 solanumphurejaI09vlISPHSRRO 1950 3636 522 98.5 globlastp 15435S0022465 LYD689_11 solanumphurejaI09vlISPHBQ51 1951 3637 524 91.9 globlastp 2926 LYD689_H2 potatollOvlIBQ512926_P1 1952 3638 524 91.4 globlastp LYD689_H3 eggplantIlOvllFS050105_P1 1953 3639 524 82.7 globlastp LYD689_H4 pepper|l2vllGDO93486 P1 1954 3640 524 81.8 globlastp LYD689_H5 tobaccolgbl62|EB425168 1955 3641 524 80.8 globlastp WO 2013/128448 PCT/IL2013/050172 214 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD690_HI solanumphureja|09vllSPHDN9 1956 3642 525 81.2 globlastp 78843 LYD538_H2 bjunceaI12vlIE6ANDIZO1DI5V 1957 3643 528 85.4 globlastp 9 0_Pi LYD539_H5 arabidopsislyrata09vllJGIALO3 1958 3644 529 94.23 glotblastn 2238_11 LYD539_HI boleraceaIgb161|EH415045_P1 1959 3645 529 87.7 globlastp 2 LYD539_HI cleome-spinosaI1OvlIGR933964 1960 3646 529 82.28 glotblastn 3 T1 LYD540_H2 thellungiella-parvuluml lvIBM 1961 3647 530 84.57 glotblastn 986015 LYD540_H3 thellungiella-halophilum| 11v llB 1962 3648 530 81.91 glotblastn Y819763 LYD540_H4 arabidopsislyrata|09vllJGIALOO 1963 3649 530 81.38 glotblastn 6775_11 LYD548_HI euphorbia|I1vlIDV124286_P1 1964 3650 533 82.5 globlastp 1 LYD548_HI spurgeIgb161|DV124286 1965 3651 533 82.1 globlastp 2 LYD548_HI beechIl1vlISRR006293.7878_T1 1966 3652 533 80 glotblastn 9 LYD548_HI papayaIgb165|EX247662_T1 1967 3653 533 80 glotblastn 3 LYD548_HI prunusI0vlIlBU039510 1968 3654 533 80 glotblastn 4 LYD549_HI b rapaIgb162|BG544752 1969 3655 534 98.89 glotblastn LYD550 HI canolaIvlIEV151262 1 1970 3656 535 97.94 glotblastn LYD550_H4 arabidopsis|1vllAT3G16290_T 1971 3657 535 95.46 glotblastn LYD550H_6 radishIgb164|EV569321 1972 3658 535 92.4 globlastp LYD550H_7 cacaollOvllCU477476 1 1973 3659 535 88.25 glotblastn LYD550H_8 poplarIlOvllCA924970_1 1974 3660 535 87.63 glotblastn LYD550 H9 appleI1vlICN496155T1 1975 3661 535 86.8 glotblastn LYD550_H1 castorbeanI1vlIEE255437_1 1976 3662 535 86.8 glotblastn LYD550_HI prunusIlOvllBU043895 1977 3663 535 86.8 glotblastn 1 LYD550H_4 gossypiumraimondiili2vilAI72 1978 3664 535 86.39 glotblastn 7 5752_TI LYD550H1 cassavaIO9viICK643710_Ti 1979 3665 535 86.39 glotblastn LYD550_HI eucalyptusIIIv2ISRR001659XI3 1980 3666 535 86.39 glotblastn 3 0634_TI LYD550_HI vincaIIIvIlSRRO98690X123915 1981 3667 535 86.39 glotblastn 4 ________________ WO 2013/128448 PCT/IL2013/050172 215 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD550H_4 cotton|I1vlIAI725752_T1 1982 3668 535 86.19 glotblastn 8 LYD550_HI grapeI11vIlGSVIVT0101702900 1983 3669 535 86.19 glotblastn 5 1_T1 LYD550_HI cottonI10v2|SRRO32367S010901 1984 3670 535 86.01 glotblastn 6 7 LYD550_H4 pigeonpeaI1vlISRR05458OX10 1985 3671 535 85.77 glotblastn 9 4890_1 LYD550_HI clementineI11vICD574164_T1 1986 3672 535 85.77 glotblastn 7 LYD550_HI orange|11vIlCD574164_T1 1987 3673 535 85.77 glotblastn 8 LYD550_HI pigeonpea|I0vlISRR054580S001 1988 3674 535 85.77 glotblastn 9 5969 LYD550_H2 prunusI0vlICN934625 1989 3675 535 85.77 glotblastn 0 LYD550_H2 tripterygium| 11vl lSRR098677X1 1990 3676 535 85.77 glotblastn 1 01640 LYD550_H2 oakl10vllFP027246_1 1991 3677 535 85.57 glotblastn 2 LYD550_H2 watermelon|I1vlIAM733953 1992 3678 535 85.36 glotblastn 3 LYD550_H5 sesamel12vlISESI12V1405091_ 1993 3679 535 85.15 glotblastn 0 T1 LYD550_H2 strawberryI11vIlDV439362 1994 3680 535 85.15 glotblastn 4 LYD550_H2 amsonia|I1vlISRR098688X1154 1995 3681 535 84.95 glotblastn 5 80_T1 LYD550_H2 monkeyflower|IOvlIDV209912 1996 3682 535 84.95 glotblastn 6 T1 LYD550_H2 tabernaemontana|11vllSRR0986 1997 3683 535 84.95 glotblastn 7 89X108650 LYD550_H2 artemisia|IOvlIEYO90642_T1 1998 3684 535 84.74 glotblastn 8 LYD550_H5 bean|12vllCA902012T1 1999 3685 535 84.33 glotblastn LYD550H_2 soybean|I1vlIGLYMA15G0217 2000 3686 535 84.33 glotblastn 9 0 LYD550H_3 soybeanIIIvIlGLYMA13G4318 2001 3687 535 83.92 glotblastn 0 0 LYD550H_3 cottonII0v2|SRRO32367S109589 2002 3688 535 83.8 globlastp LYD550_1H3 solanumphureja|09vlISPHAI78 2003 3689 535 83.78 glotblastn 2 1891 LYD550H_3 flaveriaIIIvIlSRR149229.15630 2004 3690 535 83.71 glotblastn 3 8_1 WO 2013/128448 PCT/IL2013/050172 216 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD550H_3 cucumberI09v1IAM733953_T1 2005 3691 535 83.51 glotblastn 4 LYD550H_3 flaveria|I1vlISRR149229.18761 2006 3692 535 83.51 glotblastn 5 1_T1 LYD550H3 tomatol11v1|A1781891 2007 3693 535 83.16 glotblastn LYD550_H3 melon|10v1|AM733953_T1 2008 3694 535 82.79 glotblastn 7 LYD550_H5 beechl11vllSRR006293.13266_P 2009 3695 535 82.7 globlastp 2 1 - 20 65 55 8. lbat LYD550_H3 sunflowerI1Ov1IDY912854 2010 3696 535 82.68 glotblastn 8 LYD550H_5 oil-palml11vllEL930445_T1 2011 3697 535 82.47 glotblastn 3 LYD550H_3 ambrosiaI11vlISRR346935.1307 2012 3698 535 82.47 glotblastn 9 19_T1 LYD550_1H5 bananal 12vl IMAGEN201203404 2013 3699 535 82.27 glotblastn 4 6_T1 LYD550H_4 ambrosia|IlvlISRR346935.1230 2014 3700 535 82.27 glotblastn 0 18_T1 LYD550H_4 silene|IlvlISRRO96785X132229 2015 3701 535 81.44 glotblastn 1 LYD550H4 aristolochia|l0vlIFD762492_1 2016 3702 535 81.03 glotblastn LYD550H_4 cirsium|IlvlISRR346952.10611 2017 3703 535 81 globlastp 3 50_PI LYD550H_4 aquilegia|l0v2|DR915316_T1 2018 3704 535 80.82 glotblastn 4 LYD550_H5 poppyl1IvllSRR130259.168193 2019 3705 535 80.41 glotblastn 5 T1 LYD550_1H4 cirsium|IlvlISRR346952.10492 2020 3706 535 80.41 glotblastn 5 24_T1 LYD553_H3 canolal 1 lvI SRR341920.517375 2021 3707 536 92.8 glotblastn TI LYD553_H6 canola|llvlEE475615 P1 2022 3708 536 90.5 globlastp LYD584_11 trigonellallvlISRR066194X103 2023 3709 537 92.46 glotblastn 417 LYD584_H2 soybeanIllvlGLYMA08G4449 2024 3710 537 81.26 glotblastn 0 LYD584_H3 pigeonpeaIllvlSRR054580X10 2025 3711 537 80.67 glotblastn 6211_T1 LYD592_1 medicagoI09vlICRPMT037344 2026 3712 539 94.1 globlastp LYD619_1 soybean|llvllGLYMA06G1629 2027 3713 540 80.6 globlastp 0 LYD633_1 soybean|llvllGLYMAlG1030 2028 3714 543 89 globlastp 0 WO 2013/128448 PCT/IL2013/050172 217 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD633_H2 be an12vllSRR01334.148755 -P 2029 3715 543 86 globlastp 1 LYD633_H3 pigeonpeal IvIISRR05458OX35 2030 3716 543 83.8 globlastp 2353_P1 LYD537_H2 radishIgb164|EV525517 2031 3717 550 98 globlastp LYD537_H5 thellungiellaparvuluml1ivIDN 2032 3718 550 93.1 globlastp 774047 LYD537_H8 arabidopsis|1vllAT2GO4039_P 2033 3719 550 86.6 globlastp LYD548_H2 pigeonpeaI1vlISRR054580X12 2034 3720 553 80.7 globlastp 0 1566_P1 LYD549_H6 brapa1vlIBG544752_P1 2035 3721 554 99.1 globlastp LYD553_H9 b rapa1vlIBQ704191 P1 2036 556 556 100 globlastp LYD553_HI b rapaIgb162|EX029238 2037 3722 556 98.9 glotblastn LYD553 H2 radishIgb164|EW723928 2038 3723 556 97.8 globlastp LYD553_H4 thellungiella-parvuluml IvIlEP 2039 3724 556 95.3 globlastp CRP010138 LYD553_HI bjrapa11vIlE6ANDIZ01AZWQ 2040 3725 556 93.1 globlastp 0 BP1 LYD553_H7 arabidopsislyratal09vllJGIAL01 2041 3726 556 92.3 globlastp 0738_P1 LYD553_H8 arabidopsis|1vllAT3G21420_P 2042 3727 556 92.3 globlastp LYD554_H4 gossypiumraimondiil12vllC008 2043 3728 557 99.6 globlastp 7573_P1 LYD554_1 cacaollOvllCU507663_P1 2044 3729 557 88.3 globlastp LYD554_H2 pteridiumIvlISRR043594X132 2045 3730 557 85.48 glotblastn 113 LYD559_1 trigonella|llvlISRRO66194X140 2046 3731 559 97.4 globlastp 992 LYD559_H2 chickpea|llvllSRR133517.1159 2047 3732 559 87.7 globlastp 9 58_P1 LYD559_H3 soybeanI1vlIGLYMA06G4208 2048 3733 559 84.2 globlastp 0 LYD559_H3 bean|12vlICA896695_P1 2049 3734 559 82.8 globlastp 0 LYD559_H7 cacaollOvllCA794256 P1 2050 3735 559 82.5 globlastp LYD559_1 kiwiIgb166|FG404235_1 2051 3736 559 80.45 glotblastn 9 LYD559_H3 kiwilgb1661FG396783_P1 2052 3737 559 80.2 globlastp 1 LYD559_H3 orange|11vlIZ82983_P1 2053 3738 559 80 globlastp 2 LYD560_1 chickpeaIIIvIlFL518933_P1 2054 3739 560 93.3 globlastp 64 liquricegbl7|FS294_ P 25 4 6 93 oa LYD560 112 liguoriceIgbI7iIES249643-P1 2055 3740 560 193.3 1globlat WO 2013/128448 PCT/IL2013/050172 218 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD560_H4 soybean| 11 v IGLYMA 13G3673 2056 3741 560 87.5 globlastp 0 LYD560_H5 trigonellaIl1vlISRRO66194X108 2057 3742 560 87.4 globlastp 453 LYD560_HI chickpeaI11vIGR395239_P1 2058 3743 560 87.2 globlastp 65 LYD560_H6 cowpea|l2vllFC458592_P1 2059 3744 560 87.2 globlastp LYD560 H6 cowpealgb166|CK151399 2060 3744 560 87.2 globlastp LYD560_H7 soybean|11vllGLYMA12G3376 2061 3745 560 87.2 globlastp 0 LYD560_HI bean|12vllCA896625_P1 2062 3746 560 86.3 globlastp 66 LYD560_H8 apple|11vllCN491810_P1 2063 3747 560 86.2 globlastp LYD560_H9 beanlgb1671CA896625 2064 3748 560 86.13 glotblastn LYD560_HI peanutI1OvIlCDO37768_P1 2065 3749 560 86.1 globlastp 1 LYD560_HI pigeonpea|11vllSRR05458OX1O 2066 3750 560 86 globlastp 67 1487_P1 LYD560_HI humulusI11vIlCD527124_P1 2067 3751 560 86 globlastp 0 LYD560_HI beechl11vllDT317640_P1 2068 3752 560 85.9 globlastp 6811 LYD560_HI cannabis|l2vllGR220771_P1 2069 3753 560 85.9 globlastp 2 LYD560_HI humulus|I1vlISRRO98683X1040 2070 3754 560 85.67 glotblastn 3 55_T1 LYD560_HI rose|l2vllBQ105339_P1 2071 3755 560 85.6 globlastp 69 LYD560_HI grape|llvllGSVIVTO102068900 2072 3756 560 85.6 globlastp 4 1_Pi LYD560_HI cowpea|l2vllFC461925_P1 2073 3757 560 85.4 globlastp 70 LYD560_HI sesame|l2vllJK065449_P1 2074 3758 560 85.4 globlastp 71 LYD560_HI soybean|llvllGLYMA12G1442 2075 3759 560 85.4 globlastp 6 0 LYD560_HI prunusIlOvllBU039550 2076 3760 560 85.4 globlastp 7 LYD560_HI bean|l2vllCB539455_P1 2077 3761 560 85.3 globlastp 72 LYD560_HI platanus|11vllAM260502_P1 2078 3762 560 85.3 globlastp 8 LYD560_HI triphysaria|1OvIlBE574775 2079 3763 560 85.2 globlastp 9 LY50H 1ahrnhslllH069- 2080 3764 560 85.1 globlastp WO 2013/128448 PCT/IL2013/050172 219 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD560_H2 eucalyptus|11v2ICD669407_P1 2081 3765 560 85 globlastp 2 LYD560_H2 amsonia|11vllSRRO98688X1013 2082 3766 560 84.9 globlastp 1 5_PI LYD560_H2 flaveria|l lvI ISRR149229.11602 2083 3767 560 84.66 glotblastn 5 5_ T LYD560_H2 cichoriumIgbl71IDT211113_P1 2084 3768 560 84.6 globlastp 3 LYD560_H2 poplar|10v1lBI068438_P1 2085 3769 560 84.6 globlastp 4 LYD560_H2 watermelon|IIvlIAI563215 2086 3770 560 84.4 globlastp 6 LYD560_H2 triphysaria|IOvlIBM356564 2087 3771 560 84.4 globlastp 7 LYD560_HI bjuncea|12vlIE6ANDIZO1A281 2088 3772 560 84.3 globlastp 73 4_P1 LYD560_H3 platanus|IIvlISRRO96786X1096 2089 3773 560 84.3 globlastp 0 71_P1 LYD560_HI sunflower|12vlIDY904533_P1 2090 3774 560 84.2 globlastp 74 LYD560_H2 euphorbia|IIvlIBI946379_P1 2091 3775 560 84.2 globlastp 8 LYD560_H3 sunflower|IOvlIDY905884 2092 3774 560 84.2 globlastp 2 LYD560_HI lettuce|12vlIDWO56546_P1 2093 3776 560 84.2 globlastp 46 LYD560_H3 monkeyflowerl 1vlIDV206354 2094 3777 560 84.1 globlastp 1 P1 LYD560_1H3 oakIlOvlICN725669_P1 2095 3778 560 84.1 globlastp 3 LYD560_H3 melonl10vlIDV632098_P1 2096 3779 560 84 globlastp 5 LYD560_1H3 sunflowerl10vlIDY904533 2097 3780 560 84 globlastp 6 LYD560_H3 radishIgb1641EV525375 2098 3781 560 83.9 globlastp 9 LYD560_H3 chestnutIgb1701SRROO6295S00 2099 3782 560 83.8 globlastp 7 2507_P1 LYD560_H4 arnica|IIvIlSRRO99034X101317 2100 3783 560 83.8 globlastp 0 _P1 LYD560_1H4 flaveria|IIvIlSRR149229.17385 2101 3784 560 83.8 globlastp 1 P1 LYD560_1H4 tabernaemontanalIvllSRRO986 2102 3785 560 83.8 globlastp 2 89X103361 LYD560_1H4 aquilegia|1Ov2|DR912607_P1 2103 3786 560 83.7 globlastp 4 ________________ WO 2013/128448 PCT/IL2013/050172 220 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD560_H4 vincaI1vlISRRO9869OX101887 2104 3787 560 83.6 globlastp 5 LYD560_H4 canola|11v1|CN831246_P1 2105 3788 560 83.6 globlastp 6 LYD560_H4 poplarI0vI|CA923778_P1 2106 3789 560 83.6 globlastp 9 LYD560_H4 chelidoniumI11vISRR084752X1 2107 3790 560 83.5 globlastp 7 01401_P1 LYD560_H5 potatol1OvlIBF153344_P1 2108 3791 560 83.5 globlastp 0 LYD560_H5 cleome-gynandrallOvlISRRO155 2109 3792 560 83.5 glotblastn 1 32SO001111_1 LYD560_H5 ambrosial11vllSRR346935.1286 2110 3793 560 83.48 glotblastn 2 56_T1 LYD560_H5 ambrosiallvllSRR346943.1747 2111 3794 560 83.48 glotblastn 3 8_T1 LYD560_H5 flaverial11vllSRR149232.78867 2112 3795 560 83.45 glotblastn 5 T1 LYD560_HI gossypiumraimondiil12vllAI72 2113 3796 560 83.4 globlastp 75 8816_P1 LYD560_H5 castorbeanIvlIEG661185_P1 2114 3797 560 83.4 globlastp 4 LYD560_H5 arabidopsislOvilAT3G58610_P 2115 3798 560 83.4 globlastp 6 1 - 21 78 50 8. lbat LYD560_H5 canolaIl1vlICN829948_P1 2116 3799 560 83.4 globlastp 7 LYD560_H5 cucumberI09vlIAI563215_P1 2117 3800 560 83.4 globlastp 9 LYD560_H6 plantagoIl1vlISRR066373X1127 2118 3801 560 83.4 globlastp 0 12 LYD560_H6 potatollOvlIBF153566_P1 2119 3802 560 83.4 globlastp 1 LYD560_1H6 switchgrassIgb167FE598038 2120 3803 560 83.4 globlastp 2 LYD560_H6 foxtail milleti1v3IPHY7SIO215 2121 3804 560 83.3 globlastp 6 28M P1 LYD560_H6 switchgrassIgb167IDN146770 2122 3805 560 83.3 globlastp 7 LYD560_H6 flaveria|llvllSRR149232.19624 2123 3806 560 83.22 glotblastn 8 3_T1 LYD560_1 bjrapa1vlIBG732247_P1 2124 3807 560 83.2 globlastp 76 LYD560_H6 cacaol1OvI|CA796626_P1 2125 3808 560 83.2 globlastp 3 LYD56O_116 F canolaIIIvIICN7267i3_P1 2126 3809 560 83.2 globlastp 4 ________________ WO 2013/128448 PCT/IL2013/050172 221 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD560_H6 flaveriaIIIvIlSRR149229.10104 2127 3810 560 83.2 globlastp 5 3_P1 LYD560_H6 brapalgb1621CA992458 2128 3807 560 83.2 globlastp 9 LYD560_H7 tragopogonI10vISRR020205S00 2129 3811 560 83.2 globlastp 2 20857 LYD560_HI cotton|llvlIAI728816_P1 2130 3812 560 83.1 globlastp 77 LYD560_HI cottonI1vlIBE054370_P1 2131 3813 560 83.1 globlastp 78 LYD560_H7 canola|11v1lDY006367_P1 2132 3814 560 83.1 globlastp 01 LYD560_H7 canolaIvlICX278693_1 2133 3815 560 83.1 glotblastn 3 LYD560_H7 cottonI0v2ISRR032367SO20165 2134 3812 560 83.1 globlastp 4 3 LYD560_H7 flaverial11vllSRR149229.15424 2135 3816 560 83.1 globlastp 5 6_P1 LYD560_H7 brapalgb162|L33635 2136 3817 560 83.05 glotblastn 6 LYD560_H7 switchgrassIgb167IDN140714 2137 3818 560 83.05 glotblastn 7 LYD560_HI sunflower|12vlCD852201_P1 2138 3819 560 83 globlastp 79 LYD560_HI sunflower|12vlCD858388_P1 2139 3820 560 83 globlastp 80 LYD560_H7 arabidopsislyrata|09vllJGIAL01 2140 3821 560 83 globlastp 8 9161_P1 LYD560_H7 oil-palmIgb166ICN599790 2141 3822 560 83 globlastp 9 LYD560_H8 sunflowerI1OvIlCD852201 2142 3823 560 83 globlastp 0 LYD560_H8 tabernaemontanalIvIlSRR0986 2143 3824 560 82.91 glotblastn 1 89X102834 LYD560_H8 tabernaemontanalliv11SRR0986 2144 3825 560 82.91 glotblastn 2 89X103761 LYD560_H1 brapaIIIvIlL33635_P1 2145 3826 560 82.9 globlastp 81_ LYD560_H8 aristolochia|1OvIFD748169_P1 2146 3827 560 82.9 globlastp 311 LYD560_H8 euphorbiaIIIvIlSRRO98678XI00 2147 3828 560 82.8 globlastp 4 620_P1 LYD560_H8 maize|1OvIlAI391790_P1 2148 3829 560 82.8 globlastp LYD560_H8 wheat|I1v2ICA605463 2149 3829 560 82.8 globlastp 6 __________________ WO 2013/128448 PCT/IL2013/050172 222 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD560_H8 aquilegia|IOv2IDR937512_P1 2150 3830 560 82.7 globlastp 8 LYD560_H8 cirsiumI11vlISRR346952.10484 2151 3831 560 82.7 globlastp 9 1_Pi LYD560_H9 fescueIgb161IDT685772_P1 2152 3832 560 82.7 globlastp 0 LYD560_H9 peanutI0vlIEL966584_P1 2153 3833 560 82.7 globlastp 1 LYD560_H9 vinca|11v1SRR098690X104754 2154 3834 560 82.7 globlastp 7 LYD560_H8 arnica|11vl1SRR099034X101454 2155 3835 560 82.69 glotblastn 7 XX1_T1 LYD560_HI oil-palmI11vlISRR190698.1226 2156 3836 560 82.68 glotblastn 82 2_T1 LYD560_HI bjrapa11vlIBQ791335_P1 2157 3837 560 82.6 globlastp 83 LYD560_HI sorghumI12vlISB03G029720_P1 2158 3838 560 82.6 globlastp 84 LYD560_H9 pepperIgbl71IBM063882 2159 3839 560 82.6 globlastp 2 LYD560_H9 riceI11vlIBE228654_P1 2160 3840 560 82.6 globlastp 3 LYD560_H9 riceIgbl7010SO1G46380 2161 3840 560 82.6 globlastp 3 LYD560_H9 sorghumI11vlISB03G029720 2162 3838 560 82.6 globlastp 5 LYD560_H9 thellungiella-parvuluml vIBM 2163 3841 560 82.6 globlastp 6 985551 LYD560_HI oil-palmI11vlISRR190698.1000 2164 3842 560 82.5 glotblastn 85 20_T1 LYD560_HI rye|l2vllDRROO1012.115524_P 2165 3843 560 82.5 globlastp 86 1 - 26 83 50 8. lbat LYD560_H9 canola|llvllSRRO23610.26048_ 2166 3844 560 82.5 globlastp 8 P1 LYD560_1 brachypodiumI09vlIDV469933 2167 3845 560 82.5 globlastp 02 LYD560_H1 poppy|IlvlISRRO30259.10325 2168 3846 560 82.4 globlastp 87 P1 LYD560_H1 brapalgb162|BQ791335 2169 3847 560 82.4 globlastp 01 1 LYD560_HI barleyl1Ov2|BE413220 2170 3848 560 82.4 globlastp 03 LYD560_HI eschscholzia|IIvIlCD478497_P1 2171 3849 560 82.3 globlastp 88 LYD560OHI onions i2vi IBI095623_P1 2172 3850 560 82.3 globlastp 89 1 1___ _ _ __ _ _ __ _ _ _ WO 2013/128448 PCT/IL2013/050172 223 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD560_HI ryeIl2vlIDRR001012.11842_P1 2173 3851 560 82.3 globlastp 90 LYD560_HI sugarcaneIIOvICA069523 2174 3852 560 82.3 globlastp 05 LYD560_HI flaveria| 11vl lSRR149241.12451 2175 3853 560 82.29 glotblastn 04 0_T1 LYD560_HI oilpalm|11vllCN600787_P1 2176 3854 560 82.2 globlastp 91 LYD560_HI thellungiella-halophilumllvllB 2177 3855 560 82.2 globlastp 08 M985551 LYD560_HI tomatol11vllBG124037 2178 3856 560 82.2 globlastp 09 LYD560_HI wheat1Ov2BE399048 2179 3857 560 82.2 globlastp 101 LYD560-HI wheatll2v3IBE399O48_P1 2180 3857 560 82.2 globlastp 10 LYD560_HI foxtail millet|IIv3|EC612034P 2181 3858 560 82.1 globlastp 11 1 28 88 50 8. lbat LYD560_HI leymuslgbl66|EG374815_P1 2182 3859 560 82.1 globlastp 12 1 LYD560_HI wheatlOv2BE413925 2183 3860 560 82.1 globlastp 13 LYD560-HI wheatll2v3IBE4l3925_P1 2184 3860 560 82.1 globlastp 13 LYD560_HI poppyll1vllSRR030259.155979 2185 3861 560 82.03 glotblastn 92 T1 LYD560_HI banana|l2vllFF557878_P1 2186 3862 560 82 globlastp 931 LYD560_HI cassavaI09vlIDV4460ll_P1 2187 3863 560 82 globlastp 14 LYD560_HI artemisia|lOvllEYO32298_P1 2188 3864 560 82 globlastp 15 LYD560_HI banana|12vlIFL659215_P1 2189 3865 560 81.9 globlastp 94 LYD560_HI plantagol11v2|SRR066373X1127 2190 3866 560 81.9 globlastp 95 12_P1 LYD560_HI poppyll1vllSRR030259.101863 2191 3867 560 81.8 globlastp 96 P1 LYD560_HI sorghum|l2vllSB09GO29170_P1 2192 3868 560 81.8 globlastp 97 LYD560_HI flaverial11vllSRR149229.26461 2193 3869 560 81.8 globlastp 17 8_P1 LYD560_HI solanumphureja|09vllSPHBGl2 2194 3870 560 81.8 globlastp 18 4037 LYD560_HI sugarcane|IOvlICA069008 2195 3871 560 81.8 globlastp 19 1 _ _ _ _ _ _ _ _ _ _ _ _ _ _ WO 2013/128448 PCT/IL2013/050172 224 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD560_HI wheat|lOv2|BE402709 2196 3872 560 81.8 globlastp 20 LYD560_HI wheat|12v3BE402709_P1 2197 3872 560 81.8 globlastp 20 LYD560_HI sorghumI1vlISB09G029170 2198 3868 560 81.8 globlastp 53 LYD560_HI ambrosia|I1vlISRR346935.1247 2199 3873 560 81.79 glotblastn 16 09_T1 LYD560_HI flaveria|11vllSRR149232.69233 2200 3874 560 81.76 glotblastn 21 T1 LYD560_HI milletI0vlIlEVO454PM006129_ 2201 3875 560 81.7 globlastp 22 P1 LYD560_HI hornbeam|12vlISRR364455.102 2202 3876 560 81.6 globlastp 98 657_P1 LYD560_HI onionIgb162|BI095623 2203 3877 560 81.57 glotblastn 24 LYD560_HI cassava|0vlCK643930_T1 2204 3878 560 81.55 glotblastn LYD560_HI oil-palmI1vlIEY407536_P1 2205 3879 560 81.5 globlastp 99 LYD560_HI castorbeanIvlIEE257398_P1 2206 3880 560 81.5 globlastp 26 LYD560_HI cirsiumi1vlISRR346952.10141 2207 3881 560 81.5 globlastp 27 9_ P LYD560_HI oatI1vlIGO589350_P1 2208 3882 560 81.5 globlastp 28 LYD560_H2 brachypodium|l2vllBRADI2G15 2209 - 560 81.48 glotblastn 00 790_1 LYD560_HI flaverial11vllSRR149229.44395 2210 3883 560 81.4 globlastp 30 P12 LYD560_HI artemisia|lOvlEY057322_P1 2211 3884 560 81.3 globlastp 29 LYD560_H2 oil-palmI1vlICN599858_P1 2212 3885 560 81.2 globlastp 011 LYD560_H2 gossypiumraimondiil12vllDW2 2213 3886 560 81.1 globlastp 02 33183_P1 LYD560_H2 oil-palmI1vlIEL683104_1 2214 3887 560 81.07 glotblastn 03 LYD560_H2 cotton|llvlICO494385_1 2215 3888 560 81.03 glotblastn 0411 LYD560_H2 amborella|12v3CK756678_P1 2216 3889 560 81 globlastp 05 LYD560_HI potatol1OvIBF153113_P1 2217 3890 560 81 globlastp 32 LYD560_HI solanumphureja|09vllSPHAA8 2218 3890 560 81 globlastp 33 24938 1 1 111 WO 2013/128448 PCT/IL2013/050172 225 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD560_H2 banana|12vlIES435770_P1 2219 3891 560 80.9 globlastp 06 LYD560_HI valeriana|I1vlISRRO99039X100 2220 3892 560 80.9 globlastp 34 132 LYD560_HI cacaol10vI|CA794506_T1 2221 3893 560 80.88 glotblastn 35 LYD560_H2 brachypodium|12vlIBRADI2G45 2222 3894 560 80.8 globlastp 07 330_P1 LYD560_HI brachypodiumI09vlIDV472499 2223 3894 560 80.8 globlastp 37 LYD560_HI flaveria|IlvlISRR149229.11539 2224 3895 560 80.8 globlastp 38 5_P1 LYD560_HI silene|IlvlISRRO96785XIO1730 2225 3896 560 80.8 globlastp 40 LYD560_HI tomatollvllAA824938 2226 3897 560 80.78 glotblastn 361 LYD560_HI ambrosial 1 lvi SRR346935.6365 2227 3898 560 80.76 glotblastn 41 2_T1 LYD560_HI flaveria|IlvlISRR149229.15094 2228 3899 560 80.7 globlastp 39 2_P1 LYD560_HI cottonI10v2IBF268414 2229 3900 560 80.7 globlastp 42 LYD560_H2 beet|12vllBE590351_T1 2230 3901 560 80.61 glotblastn LYD560_H2 cotton|IlvlICO107572_P1 2231 3902 560 80.6 globlastp 09 LYD560_HI ambrosia|IlvlISRR346935.1091 2232 3903 560 80.6 globlastp 43 61_P1 LYD560_HI ambrosial lvISRR346935.3957 2233 3904 560 80.6 globlastp 44 23XX2_P1 LYD560_HI flaveria|llvllSRR149232.11282 2234 3905 560 80.6 globlastp 45 7_P1 LYD560_HI lettuce|lOvllDWO56546 2235 3906 560 80.6 globlastp 46 LYD560_HI milletIlOvllEVO454PM014502_ 2236 3907 560 80.52 glotblastn 47 T1 LYD560_HI canolaI1vI|CN725975_P1 2237 3908 560 80.5 globlastp 48 LYD560_HI chelidoniumIIIvIlSRR084752XI 2238 3909 560 80.4 globlastp 51 00065_P1 LYD560_HI momordica|1OvIlSRRO71315SOO 2239 3910 560 80.4 globlastp 52 02438_P1 LYD560_HI fagopyrumIIIvIlSRR063689XI0 2240 3911 560 80.38 glotblastn 50 4708_TI LYD560_HI flaveria|11vllSRR149241.10921 2241 3912 560 80.3 glotblastn 54 7_T1 WO 2013/128448 PCT/IL2013/050172 226 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD560_H2 bjuncea|l2vlIE6ANDIZO1A9Y 2242 3913 560 80.2 globlastp 10 9ZP1 LYD560_H2 nasturtiumIlvllGH167255_1 2243 3914 560 80.2 glotblastn LYD560_HI amorphophallusIllv2SRR08935 2244 3915 560 80.2 globlastp 55 1X10005_P1 LYD560_HI fagopyrumI11vlIGO496319_1 2245 3916 560 80.17 glotblastn 56 LYD560_HI pseudoroegnerialgbl671FF34925 2246 3917 560 80.17 glotblastn 57 6 LYD560_H2 grape|11vllGSVIVTO102120400 2247 3918 560 80.03 glotblastn 12 1_T1 LYD560_1H2 humulus|11vllSRR098683X1093 2248 3919 560 80.03 glotblastn 13 13_T1 LYD560_H2 flaveria|llvllSRR149229.13949 2249 3920 560 80 globlastp 14 7_P1 LYD571_HI trigonella|llvlISRRO66194X103 2250 3921 563 97.04 glotblastn 623 LYD571_H8 chickpea|llvllGR915346 P1 2251 3922 563 94.4 globlastp LYD571_H9 pigeonpeaIllvlSRR054580X10 2252 3923 563 88.5 globlastp 2540_P1 LYD571_H2 lotusI09vlIAW720127_P1 2253 3924 563 87.2 globlastp LYD571_H3 cowpea|l2vllFF390005_P1 2254 3925 563 86.8 globlastp LYD571_H3 cowpealgbl66|FF390005 2255 3925 563 86.8 globlastp LYD571_H4 soybean|llvllGLYMA09GO819 2256 3926 563 86.33 glotblastn 0 LYD571H1 bean|12vllSRR001334.141366_P 2257 3927 563 86.1 globlastp LYD571_H5 citrusIgb166ICB250284 2258 3928 563 81 globlastp LYD571_H6 clementine|I1vICB250284_P1 2259 3928 563 81 globlastp LYD571_H7 orange|llvl1CB250284_P1 2260 3928 563 81 globlastp LYD572_H2 cloverlgbl62|BB915599 1 2261 3929 564 80.35 glotblastn LYD575_H1 trigonella|llvlISRRO66194X189 2262 3930 565 81.2 globlastp 015 LYD575_H2 lotusI09vlIAV416874_P1 2263 3931 565 80.1 globlastp LYD577_1 chickpea|llvllSRR133517.1116 2264 3932 566 92.6 globlastp 9 44_P1 LYD577_H2 pigeonpeaIllvlSRR054580Xl0 2265 3933 566 89.6 globlastp 0 3980_P1 LYD577_11 soybeanIllvlIGLYMA04G3998 2266 3934 566 89.3 globlastp 0 LYD577_H2 soybean|llvllGLYMA06G1487 2267 3935 566 88.7 globlastp 0 LYD577_H2 bean|12v1|CA898729_P1 2268 3936 566 87.9 globlastp LYD577_H3 oakIlOvlIFPO43216 P1 2269 3937 566 85.6 globlastp WO 2013/128448 PCT/IL2013/050172 227 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD577_H4 grape|I1vlIGSVIVT0102230000 2270 3938 566 83.5 globlastp 1_P1 LYD577_H6 prunusIlOvlICN862404 2271 3939 566 83.2 globlastp LYD577_H5 applel11vllCN911043_P1 2272 3940 566 83.1 globlastp LYD577_H7 eucalyptusII1v2|CD668107 P1 2273 3941 566 82.5 globlastp LYD577_H8 castorbeanlllvllXM_002521692 2274 3942 566 82.4 globlastp P1 LAB627_HI beet|12vIlBQ584887_1 2275 3943 566 82.12 glotblastn 9 LYD577_H9 watermelonIlvlIAM720533 2276 3944 566 82.1 globlastp LYD577_HI cassavaI09vlICK645412_P1 2277 3945 566 82 globlastp 0 LYD577_HI aquilegia|lOv2|DR932473_P1 2278 3946 566 81.6 globlastp 1 LYD577_HI clementine|11vlCK701542_1 2279 3947 566 81.56 glotblastn 3 LYD577_HI cucumberI09vlIDV737259_P1 2280 3948 566 81.5 globlastp 2 LYD577_HI valerianaIvlISRR099039X110 2281 3949 566 81.48 glotblastn 4 137 LAB627_H2 sunflower|l2vllDY906340_P1 2282 3950 566 81.2 globlastp 6 LYD577_HI sunflowerI0vlIlDY906340 2283 3951 566 81 globlastp 5 LYD577_HI thellungiella-halophilumll1vIlB 2284 3952 566 80.7 globlastp 6 Y808300 LAB627_HI oil_palmI1vlIEY396859_P1 2285 3953 566 80.4 globlastp 1 LYD577_HI arabidopsislyrata|09vllJGIAL01 2286 3954 566 80.4 globlastp 7 2212_P1 LYD577_H2 b rapa|1vlIDY009615_P1 2287 3955 566 80.3 globlastp 2 LYD577_HI poplarIlOvllBI129795_P1 2288 3956 566 80.3 globlastp 8 LYD577_H2 monkeyflowerIlOvllGRO46028 2289 3957 566 80.2 globlastp 3 P1 LYD577_H2 canolaI1vlIES905120_1 2290 3958 566 80.13 glotblastn 411 LYD578_HI trigonellal1lvlISRRO66194X120 2291 3959 567 98.6 globlastp 334 LYD578_HI aquilegia|1Ov2|DR913123_P1 2292 3960 567 88.6 globlastp 4 LYD578_HI cotton|0v2|AI05562iP1 2293 3961 567 88.3 globlastp 75 LYD578_112 cottonIMvIAIOSS62i 2294 3961 567 88.3 globlastp 2 _________________ WO 2013/128448 PCT/IL2013/050172 228 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD578_HI gossypiumraimondiil12vllAI05 2295 3962 567 88.1 globlastp 76 5621_P1 LYD578_HI cotton|I1vlIAI727988_P1 2296 3963 567 87.9 globlastp 77 LYD578_H2 cassava09vlIDV444573_P1 2297 3964 567 87.9 globlastp 0 LYD578_H2 cotton1l0v21CO119212 2298 3963 567 87.9 globlastp 5 LYD578_H2 chelidoniumI11vlISRRO84752X1 2299 3965 567 87.69 glotblastn 4 02130_1 LYD578_HI cotton|IvllAI055263_P1 2300 3966 567 87.4 globlastp 78 LYD578_HI gossypiumraimondiil2vllAI05 2301 3967 567 87.2 globlastp 79 5263_P1 LYD578_H2 cassavaI09vlIDV449138_P1 2302 3968 567 87.2 globlastp 7 LYD578_H2 cotton|l0v2|BG444918 2303 3969 567 87.2 globlastp 8 LYD578_H3 soybean|I1vlIGLYMA08G0974 2304 3970 567 86.7 globlastp 5 0 LYD578_H3 citrusgb166ICB250290 2305 3971 567 86.6 globlastp 3 LYD578_H3 clementine|I1vlICD574218_P1 2306 3972 567 86.6 globlastp 4 LYD578_H3 soybeanI1vlIGLYMA05G2675 2307 3973 567 86.5 globlastp 8 0 LYD578_H4 clementineI1vlICB25029O_P1 2308 3974 567 86.5 globlastp 1 LYD578_H6 trigonella|I1vlISRRO66194X119 2309 3975 567 85.8 globlastp 7 293 LYD578_HI pigeonpeaI1vlISRR05458OX10 2310 3976 567 85.7 globlastp 80 5689_P1 LYD578_H5 canolaIl1vlIEG021317_P1 2311 3977 567 85.7 globlastp 311 LYD578_H5 monkeyflowerIlOvlIDV207594_ 2312 3978 567 85.7 globlastp 7 P1 LYD578_H6 monkeyflowerIl OvlIDV208027 2313 3979 567 85.5 globlastp 1 P1 LYD578_H7 castorbean|I1vlIT23277_P1 2314 3980 567 85.5 globlastp 011 LYD578_H6 orobanche|IOvlISRRO23189S000 2315 3981 567 85.2 globlastp 2 0345_P1 LYD578_H6 euonymus|I1vlISRRO70038X10 2316 3982 567 85.2 globlastp 4 094_P1 LYD578_H8 oakIlOvlIFPO30675_P1 2317 3983 567 85.2 globlastp 1I__________________________ WO 2013/128448 PCT/IL2013/050172 229 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD578_H7 eucalyptus|I1v2ICT987127_P1 2318 3984 567 85.1 globlastp 9 LYD578_H8 eucalyptusI1v2ICT984993_P1 2319 3985 567 85.1 globlastp 9 LYD578_H7 valerianaI11vlISRR099039X102 2320 3986 567 85 globlastp 1 744 LYD578_H7 amsonia|I1vlISRR098688X1034 2321 3987 567 84.9 globlastp 2 50_PI LYD578_H7 zostera|10vIlAM767776 2322 3988 567 84.8 globlastp 3 LYD578_HI gossypiumraimondiilI2vilAI05 2323 3989 567 84.5 globlastp 81 4718_P1 LYD578_H8 euonymusIvlISRR070038X16 2324 3990 567 84.49 glotblastn 3 6372_1 LYD578_HI oil-palm|11v1lEL695363_P1 2325 3991 567 84.4 globlastp 82 LYD578_HI nasturtium|l1vIlSRR032558.101 2326 3992 567 84.15 glotblastn 83 620_T1 LYD578_HI cotton|llvlIAI054718_P1 2327 3993 567 84.1 globlastp 84 LYD578_HI zostera|l0vlISRR057351S00059 2328 3994 567 84.1 globlastp 02 12 LYD578_HI barley|12vllB1946608_P1 2329 3995 567 84 globlastp 85 LYD578_HI rye|l2vllDRR001012.100198_P 2330 3995 567 84 globlastp 86 1 - 23 95 57 8 lbat LYD578_HI valeriana|llvlISRR099039X113 2331 3996 567 84 globlastp 00 494 LYD578_HI foxtail milletI1v3IPHY7SI0348 2332 3997 567 84 globlastp 07 06M P1 LYD578_HI barleyl10v2|BI946608 2333 3995 567 84 globlastp 08 LYD578_HI wheat|l0v2|BF291626 2334 3995 567 84 globlastp 09 LYD578_HI wheat|12v3|BE444286_P1 2335 3995 567 84 globlastp 09 LYD578_HI oil palm|11v1lEL684249_P1 2336 3998 567 83.8 globlastp 871 LYD578_HI centaurealgbl66|EH713185_P1 2337 3999 567 83.8 globlastp 06 LYD578_HI lettuce|12vIlDWO52763_P1 2338 4000 567 83.4 globlastp 88 LYD578_HI maize|10vIlAI987493_P1 2339 4001 567 82.7 globlastp 23 1 2 LYD578-HI amborellal 1203IFD429782_P1 2340 4002 567 82.6 globlastp 89 1_ _ _ _ _ _ _ __ _ _ _ _ _ _ WO 2013/128448 PCT/IL2013/050172 230 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD578_HI aristolochia|lOvlISRRO39083SOO 2341 4003 567 82.6 globlastp 20 92867_P1 LYD578_HI maize|10vllA1601039_P1 2342 4004 567 82.5 globlastp 22 LYD578_HI sugarcane|lOvlIBQ533651 2343 4005 567 82.5 globlastp 25 LYD578_HI sorghumI1v1ISB01G041650_P1 2344 4006 567 82.2 globlastp 90 LYD578_HI sorghumI11v1ISB01G041650 2345 4006 567 82.2 globlastp 29 LYD578_HI amorphophallusI1v2SRR08935 2346 4007 567 81.7 globlastp 31 1X155622_P1 LYD578_HI ambrosia|11vllSRR346935.1179 2347 4008 567 81.7 globlastp 34 8_P1 LYD578_HI amborella|12v3ICK743344_P1 2348 4009 567 81.4 globlastp 91 LYD578_HI thellungiella-halophilum|l1vIlB 2349 4010 567 81.1 globlastp 36 Y807071 LYD578_HI pine|I0v2|AI725121_P1 2350 4011 567 80.8 globlastp 41 LYD578_HI podocarpusIlOvlISRRO65014SOO 2351 4012 567 80.1 globlastp 92 03582_P1 LYD580_HI cloverlgbl62|BB906292 P1 2352 4013 569 84.7 globlastp LYD58OH5 pigeonpeaIllvlISRR054580X13 2353 4014 569 80.1 globlastp 3160_P1 LYD58OH2 pigeonpea|lOvISRRO54580SO02 2354 4014 569 80.1 globlastp 7058 LYD583_HI pigeonpeall 1vISRR054581X20 2355 4015 570 80.4 globlastp 8104 P1I3541 7 8. lbat LYD587_HI chickpealllvlSRR133517.1288 2356 4016 571 83.4 globlastp 22_ P LYD588_H4 medicagoll2vlBE32203l P1 2357 4017 572 86.3 globlastp LYD588_112 medicagoIOWvlIBE322031 2358 4018 572 84.7 globlastp LYD588 H5 medicagol12vlBI272020 P1 2359 4019 572 80.9 globlastp LYD589_HI soybean|11vlGLYMA09G3275 2360 4020 573 83.7 globlastp 0 LYD589_H2 beanIgb167|EC911408 2361 4021 573 83 globlastp LYD589_H4 pigeonpeaI1vlISRR054580X14 2362 4022 573 81.9 globlastp 159_P1 LYD589_H3 soybeanIIIvIlGLYMA16G2131 2363 4023 573 81.5 globlastp 0 LYD589_H5 bean|12vllEC911765_P1 2364 4024 573 81.2 globlastp LYD593_HI trigonella|1IvIlSRRO66194XII6 2365 4025 576 96.3 globlastp 418 LYD593_115 chickpeallvllSRR133517.1774 2366 4026 576 87.3 globlastp __ _ _ _ _ _93_P1 III_ WO 2013/128448 PCT/IL2013/050172 231 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD593_H6 pigeonpeaI1vlISRR05458OX10 2367 4027 576 85.8 globlastp 3481_P1 LYD593_H2 soybeanI11vIlGLYMA17G1850 2368 4028 576 85.2 globlastp 0 LYD593_H7 bean| 12vl lSRR001334.19 1933 2369 4029 576 83.08 glotblastn TI LYD593_H3 peanut|10vllGO330608 P1 2370 4030 576 82.2 globlastp LYD593_H4 cowpea|12vllFG826472_P1 2371 4031 576 80.4 globlastp LYD593 H4 cowpealgb166|FG826472 2372 4031 576 80.4 globlastp LYD605_H2 foxtail milletI11v3IPHY7SI0294 2373 4032 578 86.2 globlastp 08M_P1 LYD618_H3 bean|12v1|CB542893 P1 2374 4033 579 88.5 globlastp LYD618_H4 pigeonpealllvlSRR05458OX16 2375 4034 579 88 globlastp 9953_P1 LYD618_HI cowpealgbl66|FF547523 2376 4035 579 87.12 glotblastn LYD618_H2 lotusI09vlIBW622754 P1 2377 4036 579 81.9 globlastp LYD632_H2 soybean|llvllGLYMA19G3874 2378 4037 581 99.8 globlastp 0 LYD637_HI soybeanIllvlGLYMA0084S002 2379 4038 582 96.2 globlastp 10 LYD637_H4 pigeonpeaIllvlISRR054580X52 2380 4039 582 88.2 globlastp 8923_P1 LYD637_H2 beanlgbl67|CV530100 2381 4040 582 87.2 globlastp LYD637_H3 cowpea|l2vllFF546955_1 2382 4041 582 84.66 glotblastn LYD637_H3 cowpealgbl66|FF546955 2383 4042 582 84.4 globlastp LYD637_H5 bean|12vllSRR001334.120242_P 2384 4043 582 81.1 globlastp 1 LYD641_11 soybean|llvllGLYMA13G4274 2385 4044 583 95.2 globlastp 0 LNU337_H3 pigeonpea|llvllSRR05458OX1O 2386 4045 583 86.1 globlastp 3 8382_P1 LYD641_H2 bean|l2vlCA902313 P1 2387 4046 583 85.5 globlastp LYD646_11 soybean|llvllGLYMA05GO165 2388 4047 584 90.6 globlastp 0 LYD646_H2 pigeonpealllvlISRR05458OX1O 2389 4048 584 89.2 globlastp 8829_P1 LYD646_H3 bean|12vllSRR001334.187433_P 2390 4049 584 88.1 globlastp LYD650_H3 tobaccolgbl62|DV157531 2391 4050 585 87 globlastp LYD651_11 solanumphureja09vlISPHAI48 2392 4051 586 94 globlastp 5479 LYD652_1 solanumphureja09vlISPHAI77 2393 4052 587 98 globlastp 1255 LYD652_12 eggplantIlOvllFSO71038 P1 2394 4053 587 81.6 globlastp LYD652_H3 solanumphurej aI09v 1ISPHBG13 2395 4054 587 80.1 globlastp _____________0927_P1I__ WO 2013/128448 PCT/IL2013/050172 232 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD660_H2 solanumphurejao9vl ISPHCRP 2396 4055 588 82 globlastp SP0I0629 LYD660_H3 tomatollvllAW223948 2397 4056 588 81.65 glotblastn LYD665_HI solanumphureja|09vlISPHBF09 2398 4057 589 91.27 glotblastn 7728 29 07 59 9.7 gobat LYD665_H2 solanumphureja|09vl ISPHDN5 2399 4058 589 85.28 glotblastn 89048 LYD665_H3 eggplantI0vlIlFS008366 1 2400 4059 589 82.48 glotblastn LYD666_HI solanumphureja|09vllSPHBG12 2401 4060 590 96 globlastp 3259 LYD666_H2 potatol10vIBF153474 P1 2402 4061 590 95.8 globlastp LYD668_HI solanumphureja09vlISPHBG12 2403 4062 592 97.4 globlastp 53901 LYD668_H2 ipomoeanill10vllBJ560832 P1 2404 4063 592 86.5 globlastp LYD668_H3 amsonia|11vllSRRO98688X1058 2405 4064 592 85.9 globlastp LYD668_H4 tabernaemontanallvllSRR0986 2406 4065 592 85.1 globlastp 89XII8673 LYD668_H5 phylal1v2ISRR099035X102114 2407 4066 592 84.7 globlastp P1 LYD668_HI blueberryI12vISRR353282X100 2408 4067 592 83 globlastp 1 511DI_P1 LYD668_H6 monkeyflowerIlOvllGO963338 2409 4068 592 83 globlastp P1 LYD668_H7 triphysaria|lOvllEY170500 2410 4069 592 81.8 globlastp LYD668_H8 cacaollOvllCU484627 P1 2411 4070 592 81 globlastp LYD668_H9 cirsiumIvlISRR346952.10520 2412 4071 592 80.4 globlastp 9_P1 LYD668_HI phyla|1v2ISRR099035X106776 2413 4072 592 80.4 globlastp 0 P1 LYD668_1 valeriana|llvlISRRO99039X108 2414 4073 592 80.2 globlastp 2 687_P1 LYD668_1 prunusIlOvlICN947564_1 2415 4074 592 80.12 glotblastn 3 LYD668_1 sarraceniallvlISRR192669.149 2416 4075 592 80.12 glotblastn 4 59_ T LYD671_11 solanumphurejaI09vlISPHBG12 2417 4076 593 90.8 globlastp 9734 LYD671_H2 potatollOvlIBG350219 P1 2418 4077 593 90 globlastp LYD673_HI solanumphureja09vlISPHBG13 2419 4078 594 94.7 globlastp 2287 LYD675_HI potatollOvlIBQ515816 P1 2420 4079 595 92.5 globlastp LYD675_H2 solanumphurejaI09vlISPHBG13 2421 4080 595 91.9 globlastp 4175 LYD676_HI solanumiphurejaIO9vlISPHBGl3 2422 4081 596 92.5 globlastp ____________5207 _ _ WO 2013/128448 PCT/IL2013/050172 233 Hom. % To globa Gene Name Organism / Cluster tag P.N. P.P. SEQ I Algor. ID identi NO: ty LYD679_HI solanumphureja|09vllSPHBG62 2423 4082 597 92.4 globlastp 8242 LYD680_HI solanumphureja|09vllSPHBG62 2424 4083 598 97.1 globlastp 8985 LYD680_H3 ipomoea nill10vllBJ560522_P1 2425 4084 598 80.7 globlastp LYD683_HI potatol10v1|CK248027 P1 2426 4085 599 92.3 globlastp LYD683_H2 solanumphureja|09vllSPHlBG64 2427 4085 599 92.3 globlastp 3762 LYD688_HI solanumphureja|09vllSPHBG59 2428 4086 601 98.2 globlastp 3254 Table 54: Provided are polynucleotides (P.N.) and polypeptides (P.P.) which are homologous to the identified polynucleotides or polypeptides of Table 53. Hom. = homologue; Algor. = Algorithm; 5 EXAMPLE 14 GENE CLONING AND GENERATION OF BINARY VECTORS FOR PLANT EXPRESSION To validate their role in improving plant yield, oil content, seed yield, biomass, growth rate, fiber yield, fiber quality, ABST, NUE and/or vigor, selected genes were 10 over-expressed in plants, as follows. Cloning strategy Selected genes from those listed in Examples 1-13 hereinabove were cloned into binary vectors for the generation of transgenic plants. For cloning, the full-length open reading frame (ORF) was first identified. In case of ORF-EST clusters and in some 15 cases already published mRNA sequences were analyzed to identify the entire open reading frame by comparing the results of several translation algorithms to known proteins from other plant species. To clone the full-length cDNAs, reverse transcription (RT) followed by polymerase chain reaction (PCR; RT-PCR) was performed on total RNA extracted from leaves, flowers, siliques or other plant tissues, growing under 20 normal and different treated conditions. Total RNA was extracted as described in "GENERAL EXPERIMENTAL AND BIOINFORMATICS METHODS" above. Production of cDNA and PCR amplification was performed using standard protocols described elsewhere (Sambrook J., E.F. Fritsch, and T. Maniatis. 1989. Molecular Cloning. A Laboratory Manual., 2nd Ed. Cold Spring Harbor Laboratory Press, New WO 2013/128448 PCT/IL2013/050172 234 York.), which are well known to those skilled in the art. PCR products were purified using PCR purification kit (Qiagen). In case where the entire coding sequence was not found, RACE kit from Invitrogen (RACE = Rapid Amplification of cDNA Ends) was used to access the full cDNA transcript of the gene from the RNA samples described 5 above. RACE products were cloned into high copy vector followed by sequencing or directly sequenced. The information from the RACE procedure was used for cloning of the full length ORF of the corresponding genes. In case genomic DNA was cloned, the genes are amplified by direct PCR on 10 genomic DNA extracted from leaf tissue using the DNAeasy kit (Qiagen Cat. No. 69104). Usually, 2 sets of primers were synthesized for the amplification of each gene from a cDNA or a genomic sequence; an external set of primers and an internal set (nested PCR primers). When needed (e.g., when the first PCR reaction does not result 15 in a satisfactory product for sequencing), an additional primer (or two) of the nested PCR primers is used. To facilitate cloning of the cDNAs/ genomic sequences, an 8-12 bp extension was added to the 5' of each primer. The primer extension includes an endonuclease restriction site. The restriction sites were selected using two parameters: (a). The site 20 does not exist in the cDNA sequence; and (b). The restriction sites in the forward and reverse primers were designed such that the digested cDNA was inserted in the sense formation into the binary vector utilized for transformation. PCR products were digested with the restriction endonucleases (New England BioLabs Inc) according to the sites designed in the primers. Each digested PCR product 25 was inserted into a high copy vector pUC19 (New England BioLabs Inc], or into plasmids originating from this vector or into CloneJet (Thermo Scientific). In some cases the undigested PCR product was inserted into pCR-Blunt 1I-TOPO (Invitrogen) or directly into the binary vector. Sequencing of the amplified PCR products was performed, using ABI 377 30 sequencer (Amersham Biosciences Inc). In some cases, after confirming the sequences of the cloned genes, the cloned cDNA was introduced into a modified pGI binary vector containing the At6669 promoter via digestion with appropriate restriction WO 2013/128448 PCT/IL2013/050172 235 endonucleases. The digested products and the linearized plasmid vector were ligated using T4 DNA ligase enzyme (Roche, Switzerland). High copy plasmids containing the cloned genes were digested with the restriction endonucleases (New England BioLabs Inc) according to the sites designed in 5 the primers and cloned into binary vectors. Several DNA sequences of the selected genes were synthesized by a commercial supplier GeneArt (Life Technologies) [Hypertext Transfer Protocol://World Wide Web (dot) geneart (dot) com]. Synthetic DNA was designed in silico. Suitable restriction enzymes sites were added to the cloned sequences at the 5' end and at the 3' end to 10 enable later cloning into the pQFNc or other required binary vector downstream of the At6669 promoter (SEQ ID NO: 4111). Binary vectors usedfor cloning: The plasmid pPI was constructed by inserting a synthetic poly-(A) signal sequence, originating from pGL3 basic plasmid vector (Promega, Acc No U47295; bp 4658-4811) into the HindIII restriction site of the binary 15 vector pB101.3 (Clontech, Acc. No. U12640). pGI (pBXYN) was similar to pPI, but the original gene in the backbone, the GUS gene, was replaced by the GUS-Intron gene followed by the NOS terminator (SEQ ID NO: 4122) (Vancanneyt. G, et al MGG 220, 245-50, 1990). pGI was used in the past to clone the polynucleotide sequences, initially under the control of 35S promoter [Odell, JT, et al. Nature 313, 810 - 812 (28 February 20 1985); SEQ ID NO:4109]. The modified pGI vectors [QXNc (Figure 8); or pQFN (Figure 2), pQFNc (Figure 2) or pQYN_6669 (Figure 1)] were modified versions of the pGI vector in which the cassette was inverted between the left and right borders so the gene and its corresponding promoter were close to the right border and the NPTII gene was close to 25 the left border. At6669, the Arabidopsis thaliana promoter sequence (SEQ ID NO: 4111) was inserted in the modified pGI binary vector, upstream to the cloned genes, followed by DNA ligation and binary plasmid extraction from positive E. coli colonies, as described above. 30 Colonies were analyzed by PCR using the primers covering the insert which are designed to span the introduced promoter and gene. Positive plasmids were identified, isolated and sequenced.
WO 2013/128448 PCT/IL2013/050172 236 Selected genes cloned by the present inventors are provided in Table 55 below.
WO 2013/128448 PCT/1L2013/050172 c ocCT ho37C ' - C) 0C, "IVh1C I- .r#t . ~ .c ~ t ~ . o . - - -t -) -7 -7 -75 -75 75 75 -5 -7 -7 I-1 WO 2013/128448 PCT/1L2013/050172 -i - - - - - 7 --- 7- - -- 75 7 7 I-t I I I II I I I I I WO 2013/128448 PCT/1L2013/050172 -- 016 C Z C- ci 4 ti c- 9 C - C~ C - tcC I- - C Z - C ) c~~~c~C C4 cr ccc r ~~c c ~c tt 0 0 0 0000 C C C C 0 C C tn - V- V V - V- WO 2013/128448 PCT/1L2013/050172 - cl~it fl o4 zr - 06 C I- M z tV - cr 0 0- C - C I- M- t V ::3 > CN ::3 ::3~ C C4C4C I ) ) I-l CL C- C~ ~ LCoCo LC-C- lC L 000, WO 2013/128448 PCT/1L2013/050172 -. ~~~~~~~ -fC -f~ - -~Z - - 2 ltf~ -- -~ -~i~ C)- - r It~l~ V> 1C m UU 0000 -- - - - - - - It V- 1C V- - jV V C" C " C" Il I I I CL I) ) ) ) ) l C L C- c l C- C- WO 2013/128448 PCT/1L2013/050172 %)- "C ) /5 C'n I0 ; tri~~~~~~ ~ ~ ~ 01 C 4Cif 4t:r- 1 C 4CiM t i , , tn n n t t tntnV- V- V 1C 1C11C"C"C C C 2i 0. ::3 ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ / :: : : : : : : : : : : : : : : : : : : : : : WO 2013/128448 PCT/IL2013/050172 243 EXAMPLE 15 EVALUATION OF TRANSGENIC ARABIDOPSIS FOR SEED YIELD AND PLANT GROWTH RATE UNDER NORMAL CONDITIONS IN GREENHOUSE ASSAYS (GH -SM Assays) 5 Assay 1: Seed yield plant biomass and plant growth rate under normal greenhouse conditions - This assay follows seed yield production, the biomass formation and the rosette area growth of plants grown in the greenhouse at non-limiting nitrogen growth conditions. Transgenic Arabidopsis seeds were sown in agar media supplemented with MS medium and a selection agent (Kanamycin). The T 2 10 transgenic seedlings were then transplanted to 1.7 trays filled with peat and perlite in a 1:1 ratio. The trays were irrigated with a solution containing 6 mM inorganic nitrogen in the form of KNO 3 with 1 mM KH 2
PO
4 , 1 mM MgSO 4 , 2 mM CaCl 2 and microelements. All plants were grown in the greenhouse until mature seeds. Seeds were harvested, extracted and weight. The remaining plant biomass (the above ground tissue) was also 15 harvested, and weighted immediately or following drying in oven at 50'C for 24 hours. Each construct was validated at its T 2 generation. Transgenic plants transformed with a construct conformed by an empty vector carrying the At6669 promoter and the selectable marker was used as control. The plants were analyzed for their overall size, growth rate, flowering, seed 20 yield, 1,000-seed weight, dry matter and harvest index (HI- seed yield/dry matter). Transgenic plants performance was compared to control plants grown in parallel under the same conditions. Mock- transgenic plants expressing the uidA reporter gene (GUS Intron) or with no gene at all, under the same promoter were used as control. The experiment was planned in nested randomized plot distribution. For each 25 gene of the invention three to five independent transformation events were analyzed from each construct. Digital imaging - A laboratory image acquisition system, which consists of a digital reflex camera (Canon EOS 300D) attached with a 55 mm focal length lens (Canon EF-S series), mounted on a reproduction device (Kaiser RS), which includes 4 30 light units (4 x 150 Watts light bulb) was used for capturing images of plant samples. The image capturing process was repeated every 2 days starting from day 1 after transplanting till day 15. Same camera, placed in a custom made iron mount, was used WO 2013/128448 PCT/IL2013/050172 244 for capturing images of larger plants sawn in white tubs in an environmental controlled greenhouse. The tubs are square shape include 1.7 liter trays. During the capture process, the tubs were placed beneath the iron mount, while avoiding direct sun light and casting of shadows. 5 An image analysis system was used, which consists of a personal desktop computer (Intel P4 3.0 GHz processor) and a public domain program - ImageJ 1.39 [Java based image processing program which was developed at the U.S. National Institutes of Health and freely available on the internet at Hypertext Transfer Protocol://rsbweb (dot) nih (dot) gov/]. Images were captured in resolution of 10 Mega 10 Pixels (3888 x 2592 pixels) and stored in a low compression JPEG (Joint Photographic Experts Group standard) format. Next, analyzed data was saved to text files and processed using the JMP statistical analysis software (SAS institute). Leaf analysis - Using the digital analysis leaves data was calculated, including leaf number, rosette area, rosette diameter, and leaf blade area. 15 Vegetative growth rate: the relative growth rate (RGR) of leaf number [Formula IX (described above)], rosette area [Formula VIII (described above)], plot coverage (Formula XIV, below) and harvest index [Formula IV (described above)] was calculated with the indicated formulas. Formula XIV 20 Relative growth rate of plot coverage = Regression coefficient of plot coverage along time course. Seeds average weight - At the end of the experiment all seeds were collected. The seeds were scattered on a glass tray and a picture was taken. Using the digital analysis, the number of seeds in each sample was calculated. 25 Dry weight and seed yield - On about day 80 from sowing, the plants were harvested and left to dry at 30'C in a drying chamber. The biomass and seed weight of each plot were measured and divided by the number of plants in each plot. Dry weight = total weight of the vegetative portion above ground (excluding roots) after drying at 30'C in a drying chamber; Seed yield per plant = total seed weight per plant (gr); 1000 30 seed weight (the weight of 1000 seeds) (gr.). The harvest index (HI) was calculated using Formula IV as described above.
WO 2013/128448 PCT/IL2013/050172 245 Oil percentage in seeds - At the end of the experiment all seeds from each plot were collected. Seeds from 3 plots were mixed grounded and then mounted onto the extraction chamber. 210 ml of n-Hexane (Cat No. 080951 Biolab Ltd.) were used as the solvent. The extraction was performed for 30 hours at medium heat 50'C. Once the 5 extraction has ended the n-Hexane was evaporated using the evaporator at 35'C and vacuum conditions. The process was repeated twice. The information gained from the Soxhlet extractor (Soxhlet, F. Die gewichtsanalytische Bestimmung des Milchfettes, Polytechnisches J. (Dingler's) 1879, 232, 461) was used to create a calibration curve for the Low Resonance NMR. The content of oil of all seed samples was determined using 10 the Low Resonance NMR (MARAN Ultra- Oxford Instrument) and its MultiQuant software package Silique length analysis - On day 50 from sowing, 30 siliques from different plants in each plot were sampled in block A. The chosen siliques were green-yellow in color and were collected from the bottom parts of a grown plant's stem. A digital 15 photograph was taken to determine silique's length. Statistical analyses - To identify outperforming genes and constructs, results from the independent transformation events tested were analyzed separately. Data was analyzed using Student's t-test and results are considered significant if the p value was less than 0.1. The JMP statistics software package was used (Version 5.2.1, SAS 20 Institute Inc., Cary, NC, USA). Tables 56-60 summarize the observed phenotypes of transgenic plants exogenously expressing the gene constructs using the seed maturation (GH-SM) assays under normal conditions. Transgenic plants expressing these genes exhibit higher biomass (Tables 56, 57, 59), yield (Tables 59 and 60), vigor (Table 58), growth rate 25 (Table 58), as compared to control plants grown under identical growth conditions. The evaluation of each gene was performed by testing the performance of different number of events. Event with p-value <0.1 was considered statistically significant.
WO 2013/128448 PCT/IL2013/050172 246 Table 56 Genes showing improved plant performance at Normal growth conditions under regulation of At6669 promoter 5 Dry Weight [mg] Flowering (days) Inflorescence Gene Event # Emergence (days) Name P- % P- % P- % Ave. Val. Incr. Ave. Val. Incr. Ave. Val. Incr. LYD689 72710.2 - - - 39.7 0.25 -3 34.1 0.07 -3 LYD689 72711.2 1157.7 0.15 12 37.9 L -8 34.1 0.06 -3 LYD689 72713.1 - - - 40.3 0.22 -2 34.5 0.17 -2 LYD677 72223.1 - - - - - - 34.2 0.08 -3 LYD677 72223.6 - - - 39.3 0.10 -4 34.3 0.12 -3 LYD677 72227.1 - - - 39.5 0.13 -4 34.1 0.07 -3 LYD675 72644.3 - - - - - - 34.6 0.23 -2 LYD648 72834.2 1073.6 0.28 4 - - - - - LYD641 72632.2 - - - - - - 34.1 0.07 -3 LYD641 72635.2 - - - - - - 34.2 0.09 -3 LYD636 72204.1 - - - 40.4 0.28 -2 34.1 0.06 -3 LYD625 72752.4 - - - 40.3 0.23 -2 34.5 0.17 -2 LYD625 72755.1 1166.7 0.05 13 - - - - - LYD611 71991.1 - - - - - - 34.5 0.18 -2 LYD611 71992.6 - - - - - - 34.7 0.28 -2 LYD602 72613.3 - - - - - - 34.3 0.12 -3 LYD599 72270.5 - - - 39.3 0.05 -4 34.5 0.18 -2 CONT. - 1033.1 - - 41.0 - - 35.3 - LYD667 72030.1 1106.2 0.02 19 - - - - - LYD667 72035.2 - - - - - - 34.1 0.21 -5 LYD667 72035.6 - - - - - - 34.5 0.13 -4 LYD635 72626.1 1004.8 0.22 8 - - - - - LYD635 72626.2 1100.0 0.02 18 - - - - - LYD635 72630.2 1081.2 0.13 16 42.8 0.19 -2 35.2 0.29 -2 LYD635 72630.4 1083.8 0.04 16 42.0 0.13 -4 34.5 0.10 -4 LYD632 72771.1 1086.5 0.07 17 - - - - - LYD632 72774.4 1129.4 0.02 21 - - - - - LYD631 72542.3 - - - 41.4 0.13 -5 33.2 L -7 LYD627 72764.3 1070.4 0.21 15 - - - - - LYD627 72765.1 1031.9 0.16 11 - - - - - LYD627 72766.1 1190.6 0.08 28 - - - - - LYD623 71970.2 1049.4 0.07 13 41.5 L -5 34.5 0.01 -4 LYD623 71970.4 1027.5 0.14 10 42.2 0.06 -3 34.3 0.26 -4 LYD623 71972.3 1057.5 0.09 14 - - - - - LYD623 71974.1 1199.4 L 29 - - - - - LYD621 72573.3 - - - 42.6 0.07 -2 33.9 0.02 -5 WO 2013/128448 PCT/IL2013/050172 247 Dry Weight [mg] Flowering (days) Inflorescence Gene Event # Emergence (days) Name Av. P- % Av. P- % Av. P- % Ave. Val. Incr. Val. Incr.Ave. Val. Incr. LYD621 72574.1 1111.9 0.27 19 - - - - - LYD618 72622.2 1121.2 0.02 20 - - - - - LYD618 72623.1 1026.5 0.25 10 - - - - - LYD618 72624.4 1070.6 0.11 15 41.3 0.08 -5 34.3 0.14 -4 LYD612 71818.3 1065.5 0.05 14 42.8 0.18 -2 - - LYD603 72536.2 1036.2 0.10 11 - - - - - LYD603 72537.3 - - - 42.8 0.19 -2 35.2 0.16 -2 LYD603 72537.5 - - - 41.1 0.20 -5 - - LYD603 72537.7 1131.9 0.03 22 - - - - - LYD593 71953.4 1041.2 0.10 12 - - - - - LYD585 72986.1 1158.8 0.16 24 43.0 0.25 -1 - - LYD585 72986.2 1137.5 L 22 42.9 0.19 -1 - - LYD585 72986.4 1116.2 0.02 20 - - - - - LYD585 72988.1 1083.1 0.22 16 - - - - - LYD585 72988.3 1048.8 0.08 13 - - - - - LYD572 72385.1 1126.9 0.01 21 41.8 0.29 -4 34.4 L -4 LYD571 72357.5 - - - 41.5 0.18 -5 33.6 0.02 -6 LYD571 72358.3 - - - 40.6 L -7 32.6 L -9 LYD571 72360.2 1095.0 0.06 18 41.4 L -5 - - LYD551 71984.1 1171.9 0.17 26 - - - - - LYD551 71986.4 1185.0 0.06 27 40.5 L -7 33.1 L -8 LYD551 71986.7 1078.8 0.03 16 42.8 0.19 -2 35.0 0.07 -2 LYD551 71986.9 1027.5 0.14 10 - - - - - LYD548 72656.1 1006.9 0.21 8 42.8 0.19 -2 - - LYD548 72656.2 1117.6 0.13 20 - - - - - LYD548 72676.1 - - - 42.9 0.21 -1 35.1 0.15 -2 LYD548 72677.1 1168.8 L 26 - - - - - LYD531 71916.1 - - - - - - 34.1 0.21 -5 LYD531 71917.1 1026.9 0.13 10 41.9 0.07 -4 33.5 0.05 -7 LYD531 71917.2 1160.6 0.06 25 - - - - - LYD531 71921.2 - - - 41.4 L -5 33.5 L -7 LYD527 72241.3 1016.9 0.28 9 41.9 0.15 -4 33.9 0.25 -5 LYD527 72243.3 - - - 42.4 0.05 -2 35.1 0.14 -2 LYD527 72245.2 - - - 42.1 0.02 -3 34.2 0.28 -5 LYD527 72246.3 1131.9 L 22 41.6 0.10 -4 33.9 0.18 -5 CONT. - 930.8 - - 43.5 - - 35.9 - LYD684 72271.2 - - - 40.5 0.21 -4 - - LYD684 72274.3 - - - 39.9 L -5 32.3 0.29 -7 LYD666 72391.3 - - - 41.1 0.11 -3 - - LYD666 72393.1 - - - 40.5 0.10 -4 - - - WO 2013/128448 PCT/IL2013/050172 248 Dry Weight [mg] Flowering (days) Inflorescence Gene Event # Emergence (days) Name Av. P- % Av. P- % Av. P- % Ave. Val. Incr. Val. Incr.Ave. Val. Incr. LYD666 72394.5 - - - 40.2 0.01 -5 33.0 0.05 -5 LYD666 72396.2 1208.1 0.19 7 - - - 33.3 0.11 -4 LYD662 72008.3 - - - 39.8 0.03 -6 32.0 0.16 -7 LYD662 72011.2 - - - 41.0 0.10 -3 - - LYD662 72011.4 - - - 40.3 0.14 -4 - - LYD658 72279.1 - - - 41.0 0.08 -3 - - LYD645 72341.2 - - - 41.3 0.15 -2 33.4 0.12 -3 LYD632 72771.1 - - - - - - 33.4 0.12 -3 LYD632 72774.3 1219.4 0.04 8 - - - - - LYD631 72541.2 - - - - - - 33.6 0.17 -3 LYD631 72544.1 - - - 40.7 0.06 -4 - - LYD631 72544.4 - - - 41.3 0.22 -2 33.3 0.11 -4 LYD627 72766.1 - - - 40.3 0.02 -5 32.0 0.16 -7 LYD627 72766.2 - - - - - - 33.6 0.17 -3 LYD627 72767.1 - - - 40.2 0.18 -5 - - LYD586 71947.4 - - - - - - 33.4 0.12 -3 LYD586 71949.6 - - - 40.6 0.07 -4 33.3 0.09 -4 LYD586 71949.7 - - - 40.5 0.10 -4 33.0 0.05 -5 LYD571 72357.5 - - - 40.8 0.13 -3 - - LYD571 72358.3 1205.0 0.07 7 39.9 0.24 -6 30.6 L -12 LYD571 72358.4 - - - 39.3 L -7 32.1 0.23 -7 LYD571 72360.2 - - - 40.6 0.07 -4 - - LYD570 71934.2 - - - - - - 33.4 0.12 -3 LYD570 71936.2 - - - 40.7 0.15 -3 33.3 0.09 -4 LYD570 71938.2 - - - 40.2 0.01 -5 33.3 0.11 -4 LYD564 72182.4 - - - 39.6 L -6 31.7 0.29 -8 LYD564 72182.5 - - - - - - 33.3 0.09 -4 LYD564 72185.1 - - - 40.7 0.06 -4 33.3 0.11 -4 LYD564 72186.2 - - - 40.5 0.10 -4 - - LYD560 71924.1 - - - - - - 33.6 0.17 -3 LYD560 71925.1 - - - 39.9 L -5 33.0 0.05 -5 LYD560 71926.1 - - - 41.2 0.12 -2 - - LYD560 71927.1 - - - 40.9 0.26 -3 - - LYD545 72510.2 - - - 40.0 0.01 -5 33.1 0.06 -4 LYD543 72251.2 - - - - - - 31.8 0.28 -8 LYD543 72252.1 - - - 39.6 L -6 31.8 0.20 -8 CONT. - 1124.2 - - 42.2 - - 34.6 - LYD672 72346.4 - - - 41.5 0.14 -2 32.9 0.10 -5 LYD672 72347.3 - - - 40.7 0.06 -4 32.8 0.03 -6 LYD672 72348.1 - - - 41.0 0.21 -4 33.2 0.06 -5 WO 2013/128448 PCT/IL2013/050172 249 Dry Weight [mg] Flowering (days) Inflorescence Gene Event # Emergence (days) Name Av. P- % Av. P- % Av. P- % Ave. Val. Incr. Val. Incr.Ave. Val. Incr. LYD668 72020.2 1169.4 L 15 - - - - - LYD664 72015.2 - - - 40.9 0.04 -4 32.8 L -6 LYD664 72016.2 - - - 40.6 0.24 -5 31.6 0.28 -9 LYD664 72017.8 1065.6 0.12 5 - - - - - LYD661 72325.1 1112.5 0.20 10 - - - - - LYD661 72325.4 - - - 40.1 L -6 33.1 0.06 -5 LYD661 72326.1 - - - 40.1 L -6 32.4 L -7 LYD661 72328.2 - - - 40.0 0.28 -6 32.5 0.14 -7 LYD661 72329.2 - - - 40.2 0.25 -5 32.8 0.12 -6 LYD657 72400.3 - - - 39.4 0.11 -7 32.4 L -7 LYD657 72402.1 - - - 41.4 0.01 -3 33.6 0.02 -3 LYD580 72188.2 1070.0 0.09 5 40.2 L -6 32.8 L -6 LYD580 72189.1 - - - - - - 33.6 0.28 -3 LYD580 72189.2 1090.2 0.23 7 - - - - - LYD573 72973.3 - - - 41.6 0.11 -2 34.3 0.25 -1 LYD561 72178.1 - - - 40.7 0.12 -4 - - LYD554 72169.2 - - - 41.4 L -3 33.9 0.16 -2 LYD553 72741.2 - - - 40.1 L -6 32.5 L -6 LYD553 72742.3 1073.1 0.21 6 - - - 33.7 0.09 -3 LYD547 71978.2 - - - 40.2 L -6 32.8 L -6 LYD547 71978.3 - - - - - - 33.1 0.09 -5 LYD547 71980.1 - - - 39.8 0.08 -6 32.9 L -5 LYD547 71980.3 - - - 40.6 0.06 -5 33.4 0.22 -4 LYD538 72839.5 - - - 40.8 0.03 -4 33.7 0.20 -3 LYD528 72311.1 - - - 40.5 0.02 -5 32.5 0.07 -7 LYD528 72312.3 - - - - - - 34.2 0.16 -1 LYD522 72720.1 - - - 40.9 0.15 -4 - - LYD521 72607.1 - - - 40.0 L -6 32.4 0.10 -7 LYD521 72611.3 - - - 41.1 0.17 -3 33.4 0.01 -4 CONT. - 1014.5 - - 42.5 - - 34.8 - LYD682 72566.1 - - - 41.5 0.05 -2 34.8 0.03 -3 LYD682 72568.2 - - - 41.0 0.02 -3 - - LYD665 72211.2 - - - 40.2 0.06 -5 34.6 0.14 -4 LYD665 72216.5 1077.6 0.18 6 - - - - - LYD650 72641.2 - - - 40.5 0.26 -5 - - LYD644 72775.2 - - - 40.6 0.23 -4 - - LYD644 72780.2 - - - 41.9 0.22 -1 35.3 0.27 -2 LYD639 72548.4 - - - 41.1 0.06 -3 - - LYD639 72549.3 1111.9 0.01 9 - - - - - LYD630 72404.3 1102.1 0.07 8 40.0 L -6 34.7 0.09 -3 WO 2013/128448 PCT/IL2013/050172 250 Dry Weight [mg] Flowering (days) Inflorescence Gene Event # Emergence (days) Name Av. P- % Av. P- % Av. P- % Ave. Val. Incr. Val. Incr.Ave. Val. Incr. LYD626 72002.1 1074.4 0.25 5 40.6 L -4 - - LYD606 72500.2 - - - 40.8 0.19 -4 - - LYD606 72500.5 - - - 41.7 0.15 -2 - - LYD577 72745.4 - - - 41.0 0.09 -3 35.3 0.27 -2 LYD577 72750.4 - - - 40.7 0.19 -4 34.7 0.09 -3 LYD542 72733.2 1153.8 L 13 - - - - - LYD526 72164.4 1081.9 0.07 6 - - - - - LYD526 72167.4 - - - 39.6 0.14 -7 35.3 0.27 -2 LYD526 72168.1 - - - 40.6 L -4 - - CONT. - 1019.8 - - 42.5 - - 35.9 - LYD683 72867.2 - - - - - - 30.7 0.19 -3 LYD683 72867.4 1178.1 0.27 4 - - - - - LYD674 72253.6 - - - 38.9 0.05 -2 30.2 0.06 -5 LYD674 72255.1 - - - - - - 30.5 0.12 -4 LYD664 72015.2 - - - - - - 30.7 0.19 -3 LYD664 72016.2 - - - - - - 30.3 0.07 -4 LYD664 72017.8 - - - 38.2 0.14 -4 30.1 0.05 -5 LYD643 72333.6 1229.9 0.17 8 - - - - - LYD643 72336.3 - - - - - - 30.1 0.04 -5 LYD642 71820.2 - - - - - - 30.3 0.09 -4 LYD642 71824.5 1192.5 0.18 5 - - - 30.0 0.04 -5 LYD642 71825.1 - - - 38.4 0.25 -3 30.4 0.09 -4 LYD634 71995.1 1339.4 0.04 18 37.7 L -5 30.1 0.05 -5 LYD634 71996.2 1319.4 L 16 - - - - - LYD634 71999.3 - - - 38.4 0.25 -3 30.4 0.09 -4 LYD629 72198.2 - - - 38.9 0.05 -2 30.1 0.04 -5 LYD629 72198.5 - - - - - - 30.0 0.04 -5 LYD622 72024.3 - - - 37.7 L -5 30.2 0.06 -5 LYD622 72027.5 - - - 38.2 0.14 -4 30.3 0.09 -4 LYD617 71966.6 - - - 38.7 0.02 -2 30.2 0.06 -5 LYD603 72537.3 - - - - - - 30.2 0.05 -5 LYD603 72537.5 - - - 39.2 0.20 -1 - - LYD603 72537.7 - - - - - - 30.8 0.21 -3 LYD567 72495.3 - - - - - - 30.5 0.10 -4 LYD567 72496.2 - - - 39.0 0.08 -2 30.6 0.19 -3 LYD561 72177.1 - - - 38.2 0.14 -4 30.1 0.04 -5 LYD561 72178.2 - - - - - - 30.5 0.10 -4 LYD553 72743.1 1282.5 0.22 13 - - - - - LYD553 72743.2 - - - - - - 30.5 0.10 -4 LYD547 71978.3 - - - - - - 30.1 0.04 -5 WO 2013/128448 PCT/IL2013/050172 251 Dry Weight [mg] Flowering (days) Inflorescence Gene Event # Emergence (days) Name P- % P- % P- % Ave. Vi I Ave. Ave. Vl nr Val. Incr. Val. Incr. Val. Incr. LYD547 71980.3 - - - - - - 30.5 0.10 -4 LYD547 71981.2 - - - 37.6 L -5 30.1 0.04 -5 LYD534 72414.3 1199.4 0.12 6 - - - - - LYD531 71917.1 - - - - - - 30.1 0.04 -5 LYD531 71917.2 - - - - - - 30.1 0.04 -5 LYD531 71921.2 1236.9 0.04 9 - - - 30.1 0.04 -5 LYD521 72610.2 - - - - - - 30.6 0.19 -3 CONT. - 1135.4 - - 39.7 - - 31.7 - Table 56. "CONT." - Control; "Ave." - Average; "% Incr." = % increment; "p-val." value, L- p< 0
.
0 1. The transgenes were under the transcriptional regulation of the new At6669 promoter (SEQ ID NO: 4111). "-" = results are still unavailable. Table 57 5 Genes showing improved plant performance at Normal growth conditions under regulation of At6669 promoter Leaf Blade Area2 Leaf Blede A Leaf Number Plot Coverage [cm 2 ] Gene Eet#[cm 2 ] Name EvtP- % P- % P- % Val. Incr. Val. Incr. Val. Incr. LYD689 72711.2 0.9 0.01 19 - - - 46.8 0.29 15 LYD689 72713.1 0.8 0.11 9 10.0 0.14 5 46.3 0.08 13 LYD677 72223.3 0.8 0.05 13 - - - 46.4 0.16 14 LYD677 72223.6 0.9 L 25 - - - 51.9 L 27 LYD677 72227.1 0.8 0.17 8 - - - - - LYD675 72644.3 - - - - - - 46.4 0.27 14 LYD671 72880.1 0.8 0.26 6 - - - - - LYD648 72831.3 0.8 0.23 8 - - - - - LYD641 72635.2 0.8 0.03 15 - - - 46.1 0.19 13 LYD636 72204.1 0.8 0.09 10 - - - 44.4 0.21 9 LYD625 72752.4 0.8 0.21 7 - - - 44.4 0.25 9 LYD625 72755.1 - - - 10.2 0.05 7 - - LYD625 72755.4 0.8 0.22 13 - - - - - LYD602 72613.3 0.8 0.26 6 - - - - - LYD599 72270.5 - - - 10.1 0.16 5 46.1 0.28 13 LYD598 72421.2 - - - - - - 44.3 0.26 8 LYD585 72986.1 0.8 0.15 16 - - - - - LYD573 72977.1 0.8 0.05 16 10.2 0.10 7 49.7 0.02 22 CONT. - 0.7 - - 9.6 - - 40.8 - LYD635 72630.2 - - - 12.4 0.16 14 69.9 0.28 18 WO 2013/128448 PCT/IL2013/050172 252 Leaf Blade Area2 Leaf Blede A Leaf Number Plot Coverage [cm 2 ] Gene [cm 2 ] Name Event # P -P NaeAve. p- % Ave. p- % Ave. Val %nr A Val. Incr. Val. Incr. Val. Incr. LYD635 72630.4 1.1 L 24 - - - 74.1 0.13 25 LYD632 72769.2 1.0 0.15 6 - - - - - LYD631 72542.3 1.2 L 31 11.9 0.16 10 85.9 L 45 LYD627 72764.3 1.0 0.02 11 - - - 66.8 0.01 12 LYD627 72765.1 1.1 L 16 - - - 67.6 L 14 LYD623 71970.2 1.1 0.03 18 - - - 71.0 0.09 19 LYD623 71970.4 1.0 0.17 14 - - - 68.2 L 15 LYD623 71972.3 1.1 0.14 23 11.4 0.03 6 74.9 0.19 26 LYD621 72571.1 1.0 0.27 4 - - - 63.8 0.12 7 LYD621 72573.3 1.2 0.19 29 11.8 0.22 9 80.2 0.20 35 LYD621 72574.3 - - - 11.5 0.03 6 65.5 0.05 10 LYD618 72621.2 1.0 0.10 8 - - - - - LYD618 72622.2 - - - 11.2 0.15 3 - - LYD618 72622.3 - - - 11.3 0.07 4 - - LYD618 72624.4 1.1 0.06 18 11.7 0.15 8 79.0 0.04 33 LYD612 71817.3 - - - - - - 67.5 0.01 14 LYD612 71819.1 - - - 11.2 0.28 3 64.0 0.14 8 LYD603 72535.2 1.0 0.08 8 - - - 67.9 0.03 14 LYD603 72536.2 - - - 11.2 0.14 4 - - LYD603 72537.5 1.0 0.20 10 - - - - - LYD585 72986.1 1.1 0.05 22 - - - 71.7 L 21 LYD585 72986.2 1.0 0.05 9 - - - 65.6 0.11 10 LYD585 72988.3 1.1 0.15 17 12.0 L 11 74.4 0.20 25 LYD572 72385.1 1.0 0.22 10 11.8 0.22 9 70.1 0.22 18 LYD572 72386.1 - - - 11.1 0.28 3 - - LYD571 72357.5 1.1 L 20 - - - 75.0 0.02 26 LYD571 72358.1 1.0 0.14 11 - - - 70.9 0.03 19 LYD571 72358.3 1.3 L 41 11.7 L 8 86.4 L 45 LYD571 72358.4 1.0 0.14 9 - - - 65.6 0.03 11 LYD571 72360.2 - - - 11.6 0.01 7 70.5 0.04 19 LYD551 71984.1 - - - 11.2 0.28 3 - - LYD551 71986.4 1.1 L 19 - - - - - LYD551 71986.7 1.0 0.05 9 11.7 L 8 66.4 0.02 12 LYD551 71986.9 - - - - - - 63.2 0.27 6 LYD548 72656.1 1.0 0.26 10 11.8 0.08 8 - - LYD548 72673.3 - - - 11.7 0.04 8 64.7 0.06 9 LYD548 72676.1 1.0 L 15 - - - 70.8 L 19 LYD548 72677.1 1.0 0.13 6 - - - - - LYD531 71916.1 1.0 0.23 9 - - - 67.9 0.20 14 LYD531 71917.1 1.1 L 18 11.5 0.15 6 72.6 L 22 WO 2013/128448 PCT/IL2013/050172 253 Leaf Blade Area2 Leaf Blede A Leaf Number Plot Coverage [cm 2 ] Gene [cm 2 ] Name Event # P -P NaeAve. p- % Ave. p- % Ave. Val %nr A Val. Incr. Val. Incr. Val. Incr. LYD531 71917.2 - - - 11.9 L 10 72.0 0.06 21 LYD531 71921.2 1.1 0.02 18 11.9 0.06 10 76.7 L 29 LYD527 72241.3 1.1 0.14 21 11.4 0.25 6 72.3 0.06 22 LYD527 72243.3 1.0 L 14 11.4 0.07 5 68.8 L 16 LYD527 72243.4 - - - - - - 63.0 0.19 6 LYD527 72245.2 1.0 0.05 9 - - - 69.9 L 18 LYD527 72246.3 1.1 L 18 12.0 0.05 11 72.6 0.01 22 CONT. - 0.9 - - 10.8 - - 59.4 - LYD684 72271.2 - - - 10.4 0.22 4 48.0 0.25 9 LYD684 72274.3 0.9 0.03 13 10.4 0.05 3 50.7 0.08 15 LYD666 72391.3 0.8 0.14 7 - - - - - LYD666 72393.1 0.9 0.17 12 - - - 50.8 0.04 15 LYD666 72396.2 - - - 10.3 0.11 3 - - LYD662 72008.3 0.9 0.03 14 - - - 51.5 0.01 17 LYD662 72011.4 0.9 0.02 12 - - - 46.9 0.24 6 LYD658 72277.2 0.8 0.18 7 - - - 47.5 0.17 7 LYD658 72282.1 0.8 0.04 11 - - - 50.0 0.04 13 LYD645 72340.2 - - - 10.2 0.17 2 - - LYD645 72341.2 0.9 0.10 14 - - - 51.6 0.14 17 LYD632 72771.1 0.8 0.06 10 - - - 48.6 0.24 10 LYD632 72774.4 0.8 0.27 7 - - - - - LYD631 72544.1 0.8 0.13 8 - - - - - LYD631 72544.3 - - - 10.4 0.03 4 - - LYD631 72544.4 0.9 0.03 11 - - - 50.9 0.02 15 LYD627 72764.3 0.8 0.16 7 - - - - - LYD627 72765.1 - - - 10.8 L 7 49.7 0.08 13 LYD627 72766.1 1.0 0.04 30 - - - 58.7 L 33 LYD601 72872.2 0.9 0.02 13 - - - 51.0 0.04 16 LYD586 71949.6 0.8 0.09 8 - - - - - LYD586 71949.7 0.9 0.03 11 10.6 0.14 5 53.1 0.02 20 LYD571 72357.5 0.8 0.25 8 - - - 51.1 0.07 16 LYD571 72358.3 1.0 L 30 11.4 0.06 13 60.9 0.03 38 LYD571 72358.4 0.9 0.21 15 - - - 49.9 0.10 13 LYD564 72182.4 0.9 0.09 17 - - - 55.5 0.11 26 LYD564 72182.5 0.8 0.15 6 - - - - - LYD564 72185.1 0.8 0.10 8 10.7 0.25 6 50.0 0.04 13 LYD564 72186.2 - - - 10.3 0.11 3 - - LYD560 71925.1 0.9 0.01 14 - - - 50.4 0.04 14 LYD545 72510.2 0.9 0.15 13 10.2 0.17 2 52.3 0.12 18 LYD543 72252.1 0.8 0.27 5 - - - 49.4 0.06 12 WO 2013/128448 PCT/IL2013/050172 254 Leaf Blade Area2 Leaf Blede A Leaf Number Plot Coverage [cm 2 ] Gene [cm 2 ] Name Event # P -P NaeAve. p- % Ave. p- % Ave. Val %nr A Val. Incr. Val. Incr. Val. Incr. CONT. - 0.8 - - 10.0 - - 44.2 - LYD672 72346.4 0.8 0.12 7 - - - 47.5 0.18 14 LYD672 72347.3 - - - 10.5 L 9 54.2 0.16 30 LYD668 72023.3 0.8 0.29 8 - - - 46.7 0.04 12 LYD664 72012.1 0.8 0.13 7 - - - 45.9 0.07 10 LYD664 72015.2 - - - - - - 44.8 0.22 8 LYD664 72016.2 0.9 L 20 10.1 0.05 6 53.1 L 28 LYD664 72017.8 0.8 0.22 13 9.9 0.25 3 47.3 0.16 14 LYD661 72325.1 - - - 10.1 0.16 5 - - LYD661 72325.4 - - - 10.2 0.10 6 - - LYD661 72326.1 0.8 0.08 8 - - - - - LYD661 72328.2 0.9 0.14 21 10.4 0.24 8 56.0 0.28 35 LYD661 72329.2 0.9 0.05 16 - - - 51.4 0.07 23 LYD657 72400.3 0.9 0.17 27 10.5 L 9 54.8 0.26 32 LYD580 72188.2 0.9 0.11 16 - - - 51.8 L 24 LYD580 72189.1 0.8 0.05 12 10.3 0.06 8 48.7 0.01 17 LYD580 72192.3 0.9 L 20 9.8 0.29 2 51.9 L 25 LYD561 72177.1 0.8 0.30 13 - - - - - LYD561 72178.1 0.9 0.11 17 - - - 51.4 0.19 23 LYD560 71925.1 0.8 0.12 7 - - - 48.6 0.25 17 LYD554 72169.2 0.8 0.16 7 - - - - - LYD553 72741.2 0.8 0.09 8 - - - 45.1 0.29 8 LYD547 71978.2 0.9 0.16 29 10.9 0.04 13 57.5 0.12 38 LYD547 71978.3 - - - 10.0 0.12 4 50.9 0.29 22 LYD547 71980.1 0.8 0.22 9 10.2 0.15 7 47.3 0.08 14 LYD547 71980.3 0.8 0.09 8 10.1 0.05 6 47.6 0.07 14 LYD538 72835.2 0.8 0.06 9 - - - 45.0 0.13 8 LYD538 72839.5 - - - 10.1 0.04 5 - - LYD528 72311.1 0.8 0.03 10 - - - 45.7 0.12 10 LYD528 72312.3 0.8 0.06 14 - - - 45.5 0.11 9 LYD522 72715.2 - - - 9.8 0.29 2 - - LYD522 72720.1 0.9 L 16 10.1 0.03 6 49.8 0.02 20 LYD522 72720.2 - - - - - - 49.2 0.30 18 LYD521 72607.1 0.9 0.03 23 10.2 0.15 7 55.1 0.07 32 LYD521 72610.1 - - - 9.9 0.25 3 - - LYD521 72610.2 - - - 10.1 0.03 6 58.3 0.22 40 LYD521 72611.3 0.8 0.28 7 - - - - - CONT. - 0.7 - - 9.6 - - 41.6 - LYD683 72870.1 0.8 0.02 16 - - - 44.3 0.05 26 LYD682 72566.1 0.8 L 26 - - - 46.7 L 33 WO 2013/128448 PCT/IL2013/050172 255 Leaf Blade Area2 Leaf Blede A Leaf Number Plot Coverage [cm 2 ] Gene Eet#[cm 2 ] Name P- % P- % P- % A Val. Incr. Val. Incr. Val. Incr. LYD682 72568.2 0.8 L 21 - - - 45.9 0.02 31 LYD678 72787.2 0.7 0.08 7 9.8 0.12 5 41.5 0.03 18 LYD665 72211.2 0.8 L 20 - - - 44.6 L 27 LYD650 72639.4 0.7 0.04 13 - - - 41.2 0.02 18 LYD644 72775.1 0.7 0.01 13 - - - 41.1 0.03 17 LYD644 72775.2 0.8 0.24 20 9.9 0.11 5 45.1 0.17 29 LYD644 72780.2 0.7 0.03 13 - - - 42.3 0.12 21 LYD639 72548.4 0.7 0.22 13 9.8 0.20 4 44.0 L 26 LYD639 72548.6 - - - - - - 40.6 0.29 16 LYD639 72549.3 - - - - - - 41.2 0.02 17 LYD639 72551.1 0.7 0.21 13 - - - 40.9 0.22 17 LYD639 72551.2 0.8 0.01 24 - - - 44.7 L 27 LYD630 72404.3 0.9 L 34 - - - 50.9 L 45 LYD626 72002.1 0.7 0.06 10 - - - 40.3 0.04 15 LYD626 72004.4 - - - - - - 40.6 0.08 16 LYD606 72500.5 0.8 L 14 - - - 40.5 0.03 16 LYD606 72501.1 0.7 0.16 7 - - - - - LYD577 72745.4 0.8 L 19 - - - 42.0 0.01 20 LYD577 72747.4 0.7 0.11 7 - - - 38.4 0.11 10 LYD577 72748.2 0.7 0.02 12 - - - 40.9 0.02 17 LYD577 72750.4 - - - - - - 44.2 0.29 26 LYD536 72529.2 - - - - - - 44.2 0.20 26 LYD536 72529.5 0.8 0.15 15 - - - 44.1 L 26 LYD536 72534.2 0.7 0.07 7 - - - 39.9 0.05 14 LYD526 72164.4 0.8 0.24 21 - - - 47.5 0.13 36 LYD526 72167.4 0.9 L 31 10.4 0.01 11 53.8 L 53 LYD526 72168.1 0.7 0.02 12 - - - 42.4 0.01 21 CONT. - 0.7 - - 9.4 - - 35.1 - LYD683 72867.2 1.0 0.20 8 - - - 57.7 0.20 10 LYD674 72253.6 - - - 10.9 0.25 6 58.4 0.24 11 LYD664 72015.2 - - - 10.8 0.17 4 - - LYD664 72016.2 1.0 0.13 12 - - - 57.9 0.21 10 LYD664 72017.8 1.1 0.03 27 11.6 L 12 69.3 L 32 LYD643 72336.3 - - - - - - 68.0 0.22 30 LYD642 71820.2 - - - 10.9 0.05 6 - - LYD642 71824.5 1.0 0.17 10 11.4 0.05 10 58.2 0.16 11 LYD634 71995.1 - - - 11.1 0.10 8 60.9 0.13 16 LYD629 72195.1 - - - 11.1 0.19 7 58.9 0.13 12 LYD629 72198.2 - - - - - - 62.3 0.27 19 LYD629 72198.5 1.1 0.02 28 11.6 L 12 71.0 L 35 WO 2013/128448 PCT/IL2013/050172 256 Leaf Blade Area2 Leaf Blede Ae [CMLeaf Number Plot Coverage [cm 2 ] Gene [cm 2 ] Name P- % P- % P- % Ave. Ave. Ave. Vl nr Val. Incr. Val. Incr. Val. Incr. LYD622 72028.3 - - - 10.6 0.28 3 - - LYD617 71966.6 1.0 0.08 12 - - - - - LYD603 72535.2 - - - 10.6 0.28 3 - - LYD595 72907.4 1.0 0.18 9 - - - - - LYD595 72909.1 1.0 0.18 13 - - - 61.3 0.18 17 LYD595 72910.3 1.0 0.18 9 11.1 0.10 8 59.0 0.13 12 LYD567 72496.2 1.1 0.04 20 11.3 0.21 9 63.6 0.02 21 LYD561 72175.4 - - - 11.2 0.02 8 - - LYD561 72177.1 0.9 0.30 7 - - - 59.5 0.12 13 LYD561 72178.2 - - - 10.9 0.05 6 - - LYD553 72743.2 1.0 0.28 13 - - - 58.8 0.21 12 LYD547 71978.3 1.0 0.23 8 - - - 61.1 0.06 16 LYD547 71981.2 1.0 0.04 17 11.9 0.08 15 65.3 0.01 24 LYD531 71921.2 1.0 0.04 16 11.6 0.16 12 65.4 0.06 25 CONT. - 0.9 - - 10.3 - - 52.5 - Table 57. "CONT." - Control; "Ave." - Average; "% Incr." = % increment; "p-val." - p value, L- p< 0
.
0 1. The transgenes were under the transcriptional regulation of the new At6669 promoter (SEQ ID NO: 4111). "-"= results are still unavailable. 5 Table 58 Genes showing improved plant performance at Normal growth conditions under regulation of At6669 promoter RGR Of Leaf RGR Of Plot RGR Of Rosette Gene Coverage (cm 2 lday) Diameter (cm/day) Name Event # (number/day) Ave. Val. Incr. Ave. Val. Incr. Ave. Val. Incr. LYD689 72711.2 - - - - - - 0.4 0.14 15 LYD677 72223.6 - - - 6.4 0.08 26 0.4 0.29 10 LYD625 72755.1 - - - 6.4 0.12 27 0.4 0.23 13 LYD573 72977.1 - - - 6.2 0.14 22 - - CONT. - - - - 5.1 - - 0.4 - LYD635 72626.1 - - - 8.5 0.17 17 - - LYD635 72626.2 - - - 8.2 0.29 13 - - LYD635 72630.2 - - - 8.4 0.18 16 - - LYD635 72630.4 - - - 9.0 0.04 24 0.5 0.09 17 LYD632 72770.2 - - - 8.5 0.16 18 - - LYD631 72542.3 0.8 0.27 16 10.6 L 46 0.5 0.04 20 LYD627 72765.1 - - - 8.3 0.21 14 0.5 0.27 10 LYD623 71970.2 - - - 8.7 0.08 20 0.5 0.25 11 WO 2013/128448 PCT/IL2013/050172 257 RGR Of Leaf RGR Of Plot RGR Of Rosette Gene Number Coverage (cm 2 lday) Diameter (cm/day) Name Event # (number/day) Ave. Val. Incr. Ave. Val. Incr. Ave. Val. Incr. LYD623 71970.4 - - - 8.4 0.16 16 - - LYD623 71972.3 - - - 9.0 0.04 25 0.5 0.21 13 LYD621 72573.3 - - - 9.8 L 36 0.5 0.19 13 LYD618 72624.4 - - - 9.5 0.01 31 - - LYD612 71817.3 - - - 8.2 0.27 13 - - LYD612 71818.3 0.8 0.23 19 - - - - - LYD603 72535.2 - - - 8.4 0.16 16 - - LYD585 72986.1 - - - 8.8 0.05 22 0.5 0.30 10 LYD585 72988.3 0.8 0.11 24 9.1 0.04 25 - - LYD572 72385.1 - - - 8.6 0.10 20 - - LYD572 72387.1 - - - 8.9 0.08 22 - - LYD571 72357.5 - - - 9.1 0.03 26 0.5 0.21 12 LYD571 72358.1 0.8 0.27 16 8.6 0.10 19 - - LYD571 72358.3 - - - 10.5 L 45 0.5 0.04 20 LYD571 72360.2 - - - 8.7 0.08 20 - - LYD551 71986.2 0.8 0.26 16 - - - - - LYD551 71986.4 - - - 8.5 0.13 18 0.5 0.25 11 LYD551 71986.7 0.8 0.26 17 - - - - - LYD548 72656.1 - - - 8.3 0.20 15 - - LYD548 72673.3 0.8 0.25 16 - - - - - LYD548 72676.1 - - - 8.6 0.11 18 - - LYD531 71916.1 - - - 8.2 0.24 13 - - LYD531 71917.1 - - - 8.8 0.06 22 0.5 0.21 13 LYD531 71917.2 - - - 8.7 0.08 20 0.5 0.21 12 LYD531 71921.2 - - - 9.4 0.02 29 0.5 0.12 15 LYD527 72241.3 - - - 8.8 0.06 22 0.5 0.27 11 LYD527 72243.3 - - - 8.4 0.14 17 - - LYD527 72245.2 - - - 8.5 0.14 17 - - LYD527 72246.3 - - - 8.9 0.04 23 0.5 0.24 11 CONT. - 0.7 - - 7.2 - - 0.4 - LYD684 72274.3 - - - 6.3 0.11 15 - - LYD666 72393.1 - - - 6.2 0.14 14 - - LYD662 72008.3 - - - 6.3 0.08 17 0.4 0.21 9 LYD662 72008.5 - - - - - - 0.4 0.15 14 LYD658 72277.2 0.7 0.28 14 - - - - - LYD658 72282.1 - - - - - - 0.4 0.30 8 LYD645 72341.2 - - - 6.3 0.09 16 0.4 0.29 8 LYD632 72771.1 - - - 6.0 0.21 12 - - LYD631 72544.1 0.6 0.30 12 - - - - - - WO 2013/128448 PCT/IL2013/050172 258 RGR Of Leaf RGR Of Plot RGR Of Rosette Gene Number Coverage (cm 2 lday) Diameter (cm/day) Name Event # (number/day) Ave. Val. Incr. Ave. Val. Incr. Ave. Val. Incr. LYD631 72544.4 - - - 6.2 0.11 15 0.4 0.16 11 LYD627 72764.3 0.7 0.27 14 - - - 0.4 0.18 11 LYD627 72765.1 - - - 6.0 0.23 11 - - LYD627 72766.1 - - - 7.1 L 30 0.4 0.13 12 LYD601 72872.2 - - - 6.2 0.11 15 - - LYD586 71949.7 - - - 6.5 0.04 20 - - LYD571 72357.5 - - - 6.2 0.12 15 0.4 0.28 8 LYD571 72358.3 - - - 7.5 L 38 0.4 0.02 19 LYD571 72358.4 - - - 6.2 0.14 14 - - LYD570 71934.2 0.7 0.23 15 - - - - - LYD570 71936.4 0.7 0.04 25 - - - - - LYD564 72182.4 - - - 6.6 0.03 23 - - LYD564 72182.5 - - - 6.0 0.28 11 - - LYD564 72185.1 - - - 6.1 0.18 13 0.4 0.20 10 LYD560 71925.1 - - - 6.1 0.17 13 0.4 0.26 8 LYD545 72510.2 - - - 6.5 0.05 20 - - LYD543 72252.1 - - - 6.0 0.22 12 - - CONT. - 0.6 - - 5.4 - - 0.3 - LYD672 72346.4 - - - 6.0 0.26 16 - - LYD672 72347.3 - - - 6.7 0.05 29 0.4 0.19 15 LYD664 72012.1 - - - - - - 0.4 0.27 12 LYD664 72016.2 - - - 6.6 0.06 28 - - LYD661 72325.1 - - - 6.2 0.20 19 - - LYD661 72326.1 - - - - - - 0.4 0.30 11 LYD661 72328.2 - - - 6.9 0.04 34 0.4 0.30 13 LYD661 72329.2 - - - 6.4 0.10 24 0.4 0.22 13 LYD657 72400.3 0.7 0.29 16 6.8 0.05 31 0.4 0.15 18 LYD580 72188.2 - - - 6.4 0.10 24 0.4 0.22 14 LYD580 72189.1 - - - 6.0 0.24 16 - - LYD580 72192.3 - - - 6.4 0.10 25 - - LYD561 72177.1 - - - 6.0 0.29 15 - - LYD561 72178.1 - - - 6.4 0.11 24 - - LYD560 71925.1 - - - 6.0 0.28 16 - - LYD554 72174.4 - - - 6.2 0.27 19 - - LYD547 71978.2 - - - 7.1 0.01 38 0.4 0.14 16 LYD547 71978.3 - - - 6.3 0.13 22 0.4 0.24 13 LYD547 71981.2 - - - 6.4 0.14 23 - - LYD538 72838.3 - - - 6.3 0.20 22 - - LYD522 72715.2 - - - 6.2 0.23 19 - - - WO 2013/128448 PCT/IL2013/050172 259 RGR Of Leaf RGR Of Plot RGR Of Rosette Gene Number Coverage (cm 2 lday) Diameter (cm/day) Name Event # (number/day) Ave. Val. Incr. Ave. Val. Incr. Ave. Val. Incr. LYD522 72720.1 - - - 6.1 0.21 18 0.4 0.28 12 LYD522 72720.2 - - - 6.2 0.20 19 - - LYD521 72607.1 - - - 6.9 0.03 33 0.4 0.16 16 LYD521 72610.2 - - - 7.2 0.02 39 0.4 0.29 12 CONT. - 0.6 - - 5.2 - - 0.3 - LYD683 72866.4 - - - 5.1 0.28 17 - - LYD683 72870.1 - - - 5.5 0.09 27 0.4 0.23 11 LYD682 72566.1 - - - 5.7 0.06 31 - - LYD682 72568.2 - - - 5.6 0.05 30 0.4 0.14 13 LYD678 72787.2 - - - 5.2 0.18 20 - - LYD665 72211.2 - - - 5.4 0.08 26 - - LYD650 72639.4 - - - 5.1 0.21 18 0.4 0.17 12 LYD644 72775.1 - - - 5.1 0.20 19 0.4 0.15 12 LYD644 72775.2 - - - 5.6 0.06 30 - - LYD644 72780.2 - - - 5.2 0.17 21 - - LYD639 72548.4 - - - 5.4 0.11 25 0.4 0.19 12 LYD639 72549.3 - - - 5.1 0.24 17 - - LYD639 72551.1 - - - 5.1 0.23 18 - - LYD639 72551.2 - - - 5.5 0.06 28 0.4 0.03 19 LYD630 72404.3 - - - 6.3 L 45 0.4 0.03 20 LYD626 72002.1 - - - 5.0 0.28 15 0.4 0.23 11 LYD626 72004.4 - - - 5.1 0.24 17 - - LYD606 72500.2 - - - 5.2 0.21 20 - - LYD606 72500.5 - - - 5.2 0.18 19 0.4 0.06 16 LYD577 72745.4 - - - 5.2 0.18 20 0.4 0.15 13 LYD577 72748.2 - - - 5.1 0.21 18 0.4 0.14 13 LYD577 72750.4 - - - 5.5 0.09 27 0.4 0.27 10 LYD536 72529.2 - - - 5.5 0.08 27 0.4 0.20 12 LYD536 72529.5 - - - 5.5 0.07 27 - - LYD536 72534.2 - - - 5.0 0.30 15 - - LYD526 72164.4 - - - 5.9 0.03 36 0.4 0.22 12 LYD526 72167.4 - - - 6.6 L 53 0.4 0.04 18 LYD526 72168.1 - - - 5.3 0.14 21 - - CONT. - - - - 4.3 - - 0.3 - LYD664 72017.8 - - - 8.5 0.03 29 0.4 0.20 14 LYD643 72336.3 - - - 8.3 0.05 27 - - LYD629 72198.2 - - - 7.6 0.19 17 0.4 0.29 12 LYD629 72198.5 0.7 0.28 17 8.7 0.01 33 0.4 0.11 17 LYD595 72909.1 - - - 7.5 0.23 15 - - - WO 2013/128448 PCT/IL2013/050172 260 RGR Of Leaf RGR Of Plot RGR Of Rosette Gene Coverage (cm 2 /day) Diameter (cm/day) Name Event # (number/day) Ave. Val. Incr. Ave. Val. Incr. Ave. Val. Incr. LYD567 72496.2 - - - 8.0 0.08 22 0.4 0.21 13 LYD561 72175.4 0.7 0.26 17 - - - - - LYD553 72743.2 - - - - - - 0.4 0.20 14 LYD547 71978.3 - - - 7.4 0.27 14 - - LYD547 71981.2 0.7 0.21 21 8.0 0.08 22 0.4 0.14 16 LYD531 71921.2 - - - 8.0 0.07 23 0.4 0.29 11 CONT. - 0.6 - - 6.5 - - 0.4 - Table 58. "CONT." - Control; "Ave." - Average; "% Incr." = % increment; "p-val." - p value, L- p<0.01. RGR = relative growth rate. The transgenes were under the transcriptional regulation of the new At6669 promoter (SEQ ID NO: 4111). "-"= results are still unavailable. 5 Table 59 Genes showing improved plant performance at Normal growth conditions under regulation of At6669 promoter Rosette Diameter Harvest Index Rosette Area [cm 2 ] [im] Gene Event # [cm] Name P- % P- % P- % Ave. Ave. Ave. Vl nr Val. Incr. Val. Incr. Val. Incr. LYD689 72711.2 - - - 6.2 0.02 22 4.5 0.04 14 LYD689 72713.1 - - - 5.8 0.08 13 4.2 0.09 7 LYD677 72223.3 - - - 5.8 0.16 14 4.3 0.05 9 LYD677 72223.6 0.2 0.21 14 6.5 L 27 4.5 0.03 13 LYD677 72227.1 0.2 0.22 17 - - - - - LYD675 72643.1 0.2 0.15 21 - - - - - LYD675 72644.3 0.2 0.03 32 5.8 0.27 14 4.2 0.28 6 LYD648 72831.3 - - - - - - 4.1 0.23 5 LYD641 72632.2 0.2 0.04 27 - - - - - LYD641 72635.2 0.2 0.04 27 5.8 0.19 13 4.3 0.04 10 LYD636 72204.1 - - - 5.6 0.21 9 - - LYD625 72752.4 0.2 0.03 29 5.6 0.25 9 4.1 0.20 5 LYD625 72755.4 - - - - - - 4.3 0.18 8 LYD611 71991.1 0.2 0.25 50 - - - - - LYD599 72270.5 0.2 0.18 15 5.8 0.28 13 - - LYD598 72421.2 0.2 0.13 21 5.5 0.26 8 - - LYD573 72977.1 0.2 0.05 26 6.2 0.02 22 4.3 0.08 9 CONT. - 0.2 - - 5.1 - - 3.9 - LYD667 72031.1 - - - - - - 5.4 0.27 6 LYD635 72626.1 - - - - - - 5.6 0.21 11 LYD635 72630.2 - - - 8.7 0.28 18 - - - WO 2013/128448 PCT/IL2013/050172 261 Harvest Index Rosette Area [cm2 Rosette Diameter Gene Event # [cm] Name Av. P- % Av. P- % Av. P- % Ave. Va.Ic.Ave. Va.Ic.Ave. Val. Incr. Val Incr. Val Incr. a Inr LYD635 72630.4 - - - 9.3 0.13 25 5.8 L 16 LYD632 72769.2 0.2 0.09 9 - - - 5.2 0.02 4 LYD631 72541.5 - - - - - - 5.3 0.01 4 LYD631 72542.3 0.2 0.02 12 10.7 L 45 6.0 L 19 LYD631 72544.1 0.2 0.02 13 - - - 5.2 0.14 3 LYD627 72764.3 - - - 8.4 0.01 12 5.4 L 7 LYD627 72765.1 - - - 8.4 L 14 5.5 0.11 8 LYD627 72766.2 - - - - - - 5.3 0.01 4 LYD623 71970.2 - - - 8.9 0.09 19 5.6 0.20 11 LYD623 71970.4 - - - 8.5 L 15 5.4 0.17 8 LYD623 71972.2 0.2 0.12 11 - - - - - LYD623 71972.3 - - - 9.4 0.19 26 5.8 0.21 14 LYD621 72571.1 - - - 8.0 0.12 7 5.3 L 6 LYD621 72573.3 - - - 10.0 0.20 35 5.8 0.19 15 LYD621 72574.3 0.2 0.06 9 8.2 0.05 10 5.5 L 8 LYD618 72621.2 - - - - - - 5.3 0.20 6 LYD618 72622.2 0.2 0.12 9 - - - - - LYD618 72622.3 - - - - - - 5.2 0.06 3 LYD618 72623.1 - - - - - - 5.2 0.05 4 LYD618 72624.4 0.2 0.22 10 9.9 0.04 33 5.8 L 14 LYD612 71817.3 0.2 L 16 8.4 0.01 14 5.4 0.03 7 LYD612 71819.1 - - - 8.0 0.14 8 - - LYD603 72535.2 - - - 8.5 0.03 14 5.5 0.06 8 LYD603 72537.3 0.2 0.07 17 - - - - - LYD593 71957.5 - - - - - - 5.2 0.06 3 LYD585 72986.1 0.2 0.07 9 9.0 L 21 5.6 L 10 LYD585 72986.2 0.2 0.10 8 8.2 0.11 10 5.3 L 5 LYD585 72988.3 - - - 9.3 0.20 25 5.5 0.21 10 LYD572 72385.1 - - - 8.8 0.22 18 - - LYD572 72387.1 0.2 0.16 7 - - - - - LYD571 72357.5 0.2 L 26 9.4 0.02 26 5.7 L 12 LYD571 72358.1 - - - 8.9 0.03 19 5.4 0.02 8 LYD571 72358.3 0.2 0.08 26 10.8 L 45 6.0 L 20 LYD571 72358.4 - - - 8.2 0.03 11 5.4 0.16 6 LYD571 72360.2 - - - 8.8 0.04 19 5.4 0.06 8 LYD551 71986.4 0.2 0.15 7 - - - 5.5 L 9 LYD551 71986.7 - - - 8.3 0.02 12 - - LYD551 71986.9 0.2 0.03 21 7.9 0.27 6 5.2 0.17 2 LYD548 72673.3 - - - 8.1 0.06 9 5.3 L 6 LYD548 72676.1 - - - 8.9 L 19 5.5 0.10 8 WO 2013/128448 PCT/IL2013/050172 262 Harvest Index Rosette Area [cm2 Rosette Diameter Gene Event # [cm] Name Av. P- % Av. P- % Av. P- % Ave. Va.Ic.Ave. Va.Ic.Ave. Val. Incr. Val Incr. Val Incr. a Inr LYD548 72677.1 - - - - - - 5.3 0.24 5 LYD531 71916.1 - - - 8.5 0.20 14 5.4 0.19 7 LYD531 71917.1 0.2 0.23 13 9.1 L 22 5.6 0.03 11 LYD531 71917.2 - - - 9.0 0.06 21 5.6 L 11 LYD531 71921.2 - - - 9.6 L 29 5.7 L 14 LYD527 72241.3 0.2 0.19 17 9.0 0.06 22 5.5 0.17 10 LYD527 72243.3 - - - 8.6 L 16 5.4 0.04 7 LYD527 72243.4 - - - 7.9 0.19 6 5.2 0.27 3 LYD527 72245.2 0.2 L 34 8.7 L 18 5.4 L 7 LYD527 72246.3 - - - 9.1 0.01 22 5.5 0.07 9 CONT. - 0.2 - - 7.4 - - 5.0 - LYD684 72271.2 - - - 6.0 0.25 9 4.3 0.17 3 LYD684 72274.3 0.2 0.07 29 6.3 0.08 15 4.3 0.07 5 LYD666 72391.3 - - - - - - 4.2 0.28 2 LYD666 72393.1 0.1 0.22 19 6.3 0.04 15 - - LYD662 72008.3 - - - 6.4 0.01 17 4.5 0.11 10 LYD662 72011.4 0.2 0.06 31 5.9 0.24 6 4.2 0.25 3 LYD658 72277.2 - - - 5.9 0.17 7 4.3 0.15 4 LYD658 72279.3 0.2 0.08 28 - - - - - LYD658 72282.1 - - - 6.2 0.04 13 4.5 L 8 LYD645 72341.2 - - - 6.4 0.14 17 4.4 0.05 8 LYD632 72771.1 0.1 0.27 18 6.1 0.24 10 4.3 0.06 5 LYD631 72541.2 0.1 0.25 17 - - - - - LYD631 72544.3 - - - - - - 4.2 0.27 3 LYD631 72544.4 - - - 6.4 0.02 15 4.5 0.05 9 LYD627 72764.3 - - - - - - 4.4 0.04 6 LYD627 72765.1 - - - 6.2 0.08 13 - - LYD627 72766.1 - - - 7.3 L 33 4.8 0.05 15 LYD618 72622.3 - - - - - - 4.4 0.05 6 LYD601 72872.2 - - - 6.4 0.04 16 4.5 0.13 8 LYD586 71949.7 - - - 6.6 0.02 20 4.4 0.05 7 LYD571 72357.5 - - - 6.4 0.07 16 4.5 0.15 8 LYD571 72358.3 - - - 7.6 0.03 38 4.8 L 17 LYD571 72358.4 0.2 0.04 38 6.2 0.10 13 4.3 0.24 5 LYD571 72360.2 0.1 0.25 16 - - - - - LYD570 71936.2 0.1 0.30 19 - - - - - LYD564 72182.4 0.1 0.19 22 6.9 0.11 26 4.6 0.14 11 LYD564 72182.5 - - - - - - 4.3 0.19 4 LYD564 72185.1 - - - 6.2 0.04 13 4.4 0.03 7 LYD560 71925.1 0.2 0.07 29 6.3 0.04 14 4.4 0.01 8 WO 2013/128448 PCT/IL2013/050172 263 Harvest Index Rosette Area [cm2 Rosette Diameter Gene Event # [cm] Name Av. P- % Av. P- % Av. P- % Ave. Va.Ic.Ave. Va.Ic.Ave. Val. Incr. Val Incr. Val Incr. a Inr LYD560 71926.1 0.2 0.20 24 - - - - - LYD560 71927.1 0.2 0.10 26 - - - - - LYD545 72510.2 0.2 0.21 39 6.5 0.12 18 4.4 0.15 6 LYD543 72251.2 0.2 0.11 34 - - - - - LYD543 72252.1 - - - 6.2 0.06 12 4.3 0.10 4 CONT. - 0.1 - - 5.5 - - 4.1 - LYD672 72346.4 0.2 0.28 26 5.9 0.18 14 4.2 0.17 5 LYD672 72347.3 - - - 6.8 0.16 30 4.5 0.20 14 LYD668 72020.4 0.2 0.14 13 - - - - - LYD668 72023.3 0.2 0.02 25 5.8 0.04 12 4.1 0.26 4 LYD664 72012.1 0.3 0.10 37 5.7 0.07 10 4.3 0.06 7 LYD664 72015.2 - - - 5.6 0.22 8 - - LYD664 72016.2 - - - 6.6 L 28 4.4 0.01 11 LYD664 72017.7 0.2 0.26 15 - - - - - LYD664 72017.8 0.2 0.09 22 5.9 0.16 14 - - LYD661 72326.1 0.2 0.20 11 - - - - - LYD661 72328.2 - - - 7.0 0.28 35 4.6 0.27 14 LYD661 72329.2 0.3 0.01 32 6.4 0.07 23 4.4 0.13 10 LYD657 72400.1 0.2 0.01 22 - - - - - LYD657 72400.3 - - - 6.8 0.26 32 4.6 0.29 15 LYD657 72401.2 0.3 L 29 - - - 4.2 0.27 5 LYD657 72402.1 0.3 0.07 30 - - - - - LYD580 72188.2 0.2 0.03 18 6.5 L 24 4.5 0.08 12 LYD580 72189.1 - - - 6.1 0.01 17 4.3 0.05 7 LYD580 72191.1 0.2 0.10 17 - - - - - LYD580 72192.3 0.3 0.14 48 6.5 L 25 4.5 L 12 LYD573 72973.2 0.2 0.11 12 - - - - - LYD573 72977.1 0.2 0.17 19 - - - - - LYD561 72177.1 0.2 0.28 12 - - - 4.2 0.28 6 LYD561 72177.2 0.2 0.16 23 - - - - - LYD561 72178.1 - - - 6.4 0.19 23 4.3 0.15 9 LYD560 71922.1 0.3 L 29 - - - - - LYD560 71925.1 0.2 0.11 16 6.1 0.25 17 - - LYD560 71926.1 0.2 0.01 21 - - - - - LYD554 72174.4 0.2 0.10 24 - - - - - LYD553 72741.2 0.2 0.06 15 5.6 0.29 8 4.2 0.09 6 LYD553 72743.2 0.2 0.26 9 - - - - - LYD547 71978.2 - - - 7.2 0.12 38 4.7 0.06 17 LYD547 71978.3 - - - 6.4 0.29 22 4.4 0.28 12 LYD547 71980.1 0.2 0.19 24 5.9 0.08 14 - - - WO 2013/128448 PCT/IL2013/050172 264 Harvest Index Rosette Area [cm2 Rosette Diameter Gene Event # [cm] Name Av. P- % Av. P- % Av. P- % Ave. Va.Ic.Ave. Va.Ic.Ave. Val. Incr. Val Incr. Val Incr. a Inr LYD547 71980.3 0.2 0.25 21 5.9 0.07 14 4.2 0.14 5 LYD538 72835.2 0.2 L 25 5.6 0.13 8 4.2 0.15 5 LYD528 72310.1 0.3 L 39 - - - - - LYD528 72311.1 - - - 5.7 0.12 10 4.2 0.21 5 LYD528 72312.2 0.2 0.07 24 - - - - - LYD528 72312.3 - - - 5.7 0.11 9 4.3 0.12 7 LYD528 72312.4 0.2 0.16 18 - - - - - LYD522 72716.6 0.2 0.25 25 - - - - - LYD522 72720.1 - - - 6.2 0.02 20 4.3 0.02 9 LYD522 72720.2 - - - 6.2 0.30 18 - - LYD521 72607.1 0.3 0.24 34 6.9 0.07 32 4.5 0.10 13 LYD521 72610.1 0.2 0.24 12 - - - - - LYD521 72610.2 0.3 0.23 28 7.3 0.22 40 - - LYD521 72611.1 0.2 0.01 22 - - - - - CONT. - 0.2 - - 5.2 - - 4.0 - LYD683 72870.1 - - - 5.5 0.05 26 4.1 L 13 LYD682 72565.1 - - - - - - 3.9 0.14 7 LYD682 72566.1 - - - 5.8 L 33 4.2 L 15 LYD682 72568.2 0.1 0.26 14 5.7 0.02 31 4.2 L 16 LYD678 72787.2 - - - 5.2 0.03 18 3.9 0.05 8 LYD665 72211.2 - - - 5.6 L 27 4.0 L 11 LYD665 72216.5 - - - - - - 3.8 0.07 5 LYD650 72639.4 - - - 5.2 0.02 18 4.1 L 13 LYD644 72775.1 - - - 5.1 0.03 17 3.9 0.03 8 LYD644 72775.2 - - - 5.6 0.17 29 4.1 0.15 14 LYD644 72780.2 0.1 0.19 42 5.3 0.12 21 4.0 0.03 10 LYD639 72548.4 - - - 5.5 L 26 4.1 L 12 LYD639 72548.6 - - - 5.1 0.29 16 3.9 0.22 8 LYD639 72549.3 - - - 5.1 0.02 17 4.0 0.01 10 LYD639 72551.1 - - - 5.1 0.22 17 - - LYD639 72551.2 0.1 0.27 18 5.6 L 27 4.2 L 17 LYD630 72404.3 - - - 6.4 L 45 4.5 L 23 LYD626 72002.1 0.1 0.11 49 5.0 0.04 15 4.0 0.02 9 LYD626 72004.4 0.1 0.23 26 5.1 0.08 16 3.9 0.07 8 LYD606 72500.5 - - - 5.1 0.03 16 4.0 L 11 LYD606 72501.1 - - - - - - 3.8 0.26 4 LYD577 72745.4 - - - 5.2 0.01 20 4.1 L 13 LYD577 72747.4 - - - 4.8 0.11 10 3.9 0.03 8 LYD577 72748.2 - - - 5.1 0.02 17 4.1 L 12 LYD577 72750.4 0.1 0.26 32 5.5 0.29 26 4.1 0.21 13 WO 2013/128448 PCT/IL2013/050172 265 Rosette Diameter Harvest Index Rosette Area [cm 2 R tm Gene Eet#[cm] Nae Event # Name Av. P- % Av. P- % Av. P- % Ave. Ave. Ave. Vl nr Val. Incr. Val. Incr. VaL Incr. LYD536 72529.2 - - - 5.5 0.20 26 4.2 0.17 15 LYD536 72529.5 - - - 5.5 L 26 4.1 L 13 LYD536 72534.2 - - - 5.0 0.05 14 3.9 0.04 8 LYD526 72164.4 - - - 5.9 0.13 36 4.2 0.11 17 LYD526 72167.4 - - - 6.7 L 53 4.5 L 23 LYD526 72168.1 0.1 0.07 33 5.3 0.01 21 4.0 0.10 9 CONT. - 0.1 - - 4.4 - - 3.6 - LYD683 72867.2 - - - 7.2 0.20 10 4.7 0.20 5 LYD674 72253.6 0.2 0.12 17 7.3 0.24 11 - - LYD674 72255.1 0.2 0.10 23 - - - - - LYD664 72016.2 - - - 7.2 0.21 10 4.7 0.23 5 LYD664 72017.8 0.2 L 25 8.7 L 32 5.1 0.05 13 LYD643 72336.3 0.2 0.02 10 8.5 0.22 30 - - LYD642 71824.5 - - - 7.3 0.16 11 4.8 0.12 7 LYD642 71825.1 0.2 L 14 - - - - - LYD634 71995.1 - - - 7.6 0.13 16 - - LYD634 71999.3 0.2 L 17 - - - - - LYD629 72195.1 - - - 7.4 0.13 12 4.7 0.17 6 LYD629 72198.2 0.2 L 19 7.8 0.27 19 4.9 0.27 9 LYD629 72198.5 - - - 8.9 L 35 5.2 L 16 LYD622 72027.5 0.2 L 24 - - - - - LYD617 71966.6 - - - - - - 4.7 0.22 5 LYD595 72909.1 - - - 7.7 0.18 17 4.8 0.17 8 LYD595 72910.3 - - - 7.4 0.13 12 - - LYD567 72496.2 0.2 0.02 12 8.0 0.02 21 4.8 0.09 7 LYD567 72496.3 0.2 0.20 5 - - - - - LYD561 72175.4 0.2 0.11 11 - - - - - LYD561 72177.1 - - - 7.4 0.12 13 4.7 0.26 5 LYD553 72743.2 0.2 0.01 16 7.4 0.21 12 4.9 0.10 9 LYD547 71978.3 - - - 7.6 0.06 16 4.8 0.13 8 LYD547 71981.2 - - - 8.2 0.01 24 5.0 0.02 12 LYD531 71921.2 - - - 8.2 0.06 25 4.9 0.04 10 CONT. - 0.2 - - 6.6 - - 4.5 - Table 59. "CONT." - Control; "Ave." - Average; "% Incr." = % increment; "p-val." - p value, L- p< 0
.
0 1. The transgenes were under the transcriptional regulation of the new At6669 promoter (SEQ ID NO: 4111). "-"= results are still unavailable.
WO 2013/128448 PCT/IL2013/050172 266 Table 60 Genes showing improved plant performance at Normal growth conditions under regulation of At6669 promoter 5 Gne Event Seed Yield [mg] 1000 Seed Weight [mg] Name Ave. P-Val. % Incr. Ave. P-Val. % Incr. LYD689 72711.2 205.6 0.26 33 27.5 0.25 19 LYD689 72713.1 171.1 0.25 10 25.2 0.02 9 LYD677 72227.1 191.4 0.04 23 24.3 0.21 6 LYD675 72643.1 175.7 0.16 13 - - LYD675 72644.3 173.1 0.21 12 - LYD641 72632.2 198.5 0.10 28 - - LYD641 72635.2 179.0 0.14 15 23.8 0.14 3 LYD636 72204.1 - - - 27.0 0.27 17 LYD625 72752.4 187.9 0.05 21 - - LYD625 72756.2 - - - 25.3 0.21 10 LYD599 72270.5 183.2 0.07 18 - - LYD573 72977.1 186.6 0.25 20 - CONT. - 155.2 - - 23.1 - LYD667 72030.4 - - - 18.8 0.30 3 LYD667 72035.6 175.8 0.11 13 - - LYD635 72626.1 185.3 0.27 20 - - LYD635 72630.2 - - - 21.7 0.22 19 LYD632 72769.2 170.0 0.22 10 - - LYD632 72770.2 - - - 19.3 0.06 5 LYD632 72771.1 - - - 20.2 L 10 LYD632 72774.4 204.8 0.05 32 - - LYD631 72542.3 180.0 0.07 16 20.2 0.21 11 LYD631 72544.1 174.3 0.26 13 - - LYD631 72544.4 - - - 21.3 L 17 LYD627 72764.3 - - - 20.3 0.14 11 LYD627 72765.1 - - - 19.6 0.02 7 LYD627 72766.1 - - - 19.8 0.06 8 LYD623 71970.2 185.5 0.08 20 - - LYD623 71974.1 215.8 0.26 39 19.1 0.12 4 LYD618 72621.2 - - - 19.3 0.09 5 LYD618 72622.2 202.6 0.04 31 - - LYD618 72624.4 196.1 0.18 27 21.4 0.29 17 LYD612 71817.3 186.8 0.07 21 - - LYD603 72536.2 196.2 0.20 27 - - LYD603 72537.3 180.7 0.06 17 - - LYD603 72537.7 209.6 0.19 35 - - LYD585 72986.1 209.3 0.09 35 - - LYD585 72986.2 203.8 L 32 - - - WO 2013/128448 PCT/IL2013/050172 267 Gne Event Seed Yield [mg] 1000 Seed Weight [mg] Name Ave. P-Val. % Incr. Ave. P-Val. % Incr. LYD585 72986.4 188.1 0.02 21 - - LYD585 72988.3 186.2 0.25 20 19.8 0.05 8 LYD572 72387.1 176.6 0.24 14 - - LYD572 72388.2 185.3 0.24 20 - LYD571 72357.5 210.4 L 36 - - LYD571 72358.3 199.2 0.05 29 20.8 L 14 LYD551 71986.4 209.9 0.02 35 - - LYD551 71986.7 203.3 0.11 31 - LYD551 71986.9 206.2 0.04 33 - - LYD531 71916.1 - - - 20.7 L 13 LYD531 71917.1 193.3 0.11 25 - - LYD531 71917.2 - - - 20.0 0.03 9 LYD527 72241.3 197.2 L 27 - - LYD527 72245.2 207.2 0.17 34 - LYD527 72246.3 190.5 0.04 23 - CONT. - 154.9 - - 18.3 LYD684 72274.3 166.6 0.25 19 - LYD666 72393.1 163.6 0.29 17 - LYD662 72011.4 188.5 0.05 35 - - LYD658 72282.1 - - - 20.6 0.02 5 LYD632 72771.1 - - - 22.7 L 15 LYD632 72774.3 - - - 20.5 0.05 4 LYD631 72544.4 - - - 21.8 0.02 10 LYD627 72764.3 - - - 21.7 0.18 10 LYD627 72765.1 - - - 23.3 0.07 18 LYD601 72872.2 - - - 20.2 0.23 2 LYD571 72358.1 - - - 21.1 0.16 7 LYD571 72358.3 173.9 0.28 24 22.8 0.03 16 LYD571 72358.4 190.9 0.06 36 20.3 0.25 3 LYD570 71935.1 - - - 20.8 L 6 LYD570 71936.2 - - - 20.6 0.26 4 LYD564 72182.4 172.7 0.28 23 - - LYD564 72182.5 - - - 21.0 0.07 7 LYD560 71925.1 179.4 0.10 28 - - LYD560 71927.1 170.0 0.20 21 - - LYD545 72510.2 183.4 0.23 31 - - LYD543 72251.2 175.6 0.23 25 - - CONT. - 140.1 - - 19.7 - LYD672 72347.2 268.4 L 36 - - LYD672 72347.3 - - - 22.7 0.10 13 LYD672 72348.1 220.3 0.15 11 - - LYD668 72020.2 - - - 21.5 0.25 7 WO 2013/128448 PCT/IL2013/050172 268 Gne Event Seed Yield [mg] 1000 Seed Weight [mg] Name Ave. P-Val. % Incr. Ave. P-Val. % Incr. LYD668 72023.1 - - - 21.6 0.16 8 LYD668 72023.3 218.8 0.15 11 - - LYD664 72012.1 244.8 0.01 24 - - LYD664 72015.2 225.2 0.07 14 - - LYD664 72017.7 227.5 0.06 15 - - LYD664 72017.8 254.0 0.04 28 - - LYD661 72325.1 - - - 23.6 0.11 18 LYD661 72329.2 258.5 L 31 - - LYD657 72400.1 222.1 0.15 12 - - LYD657 72401.2 233.5 0.03 18 - - LYD657 72402.1 249.7 0.04 26 - - LYD580 72188.2 246.1 L 24 21.6 0.08 8 LYD580 72189.2 248.5 0.24 26 - - LYD580 72192.3 277.0 0.13 40 - - LYD561 72177.2 246.7 L 25 - - LYD561 72179.1 221.4 0.19 12 - - LYD560 71922.1 239.6 0.14 21 - - LYD560 71925.1 243.7 0.01 23 - - LYD560 71926.1 238.5 0.06 20 - - LYD554 72174.4 241.0 0.02 22 - - LYD547 71978.2 - - - 22.5 0.06 12 LYD547 71980.3 215.7 0.21 9 - - LYD538 72835.2 243.9 0.02 23 - - LYD528 72310.1 277.8 L 40 - - LYD528 72312.2 236.6 0.17 19 - - LYD528 72312.4 237.6 0.28 20 - - LYD522 72716.2 244.8 0.19 24 - - LYD522 72716.6 247.0 0.21 25 - - LYD521 72611.1 237.8 0.28 20 - - CONT. - 198.0 - - 20.0 - LYD682 72566.1 - - - 25.2 0.29 6 LYD682 72568.2 100.2 0.17 17 - - LYD665 72211.2 - - - 26.3 0.01 11 LYD644 72780.2 126.2 0.29 48 - - LYD630 72404.3 116.1 0.28 36 26.6 0.04 12 LYD626 72002.1 134.7 0.05 58 - - LYD626 72004.4 105.6 0.07 24 - - LYD606 72500.2 - - - 24.9 0.12 5 LYD577 72750.4 106.8 0.06 25 - - LYD526 72167.4 - - - 24.8 0.14 5 LYD526 72168.1 113.5 0.03 33 - - CONT. - 85.5 - - 23.7 - WO 2013/128448 PCT/IL2013/050172 269 Gne Event Seed Yield [mg] 1000 Seed Weight [mg] Name Ave. P-Val. % Incr. Ave. P-Val. % Incr. LYD683 72866.4 - - - 20.4 0.29 4 LYD674 72255.1 246.4 0.16 28 - - LYD664 72015.2 208.6 L 9 20.1 0.24 3 LYD664 72016.2 197.0 0.30 3 21.1 0.01 8 LYD643 72333.2 - - - 20.1 0.25 3 LYD643 72336.3 - - - 22.9 0.08 17 LYD643 72336.6 - - - 21.4 0.05 9 LYD642 71824.5 - - - 24.0 0.13 23 LYD634 71995.1 - - - 25.0 0.08 28 LYD634 71999.3 230.6 0.04 20 - - LYD629 72195.1 - - - 20.4 0.29 4 LYD629 72198.5 200.8 0.08 5 21.8 L 12 LYD622 72027.5 - - - 20.9 0.17 7 LYD622 72028.3 - - - 20.9 0.02 7 LYD617 71964.2 - - - 20.0 0.26 3 LYD617 71966.6 219.6 0.28 14 - - LYD603 72537.3 215.9 0.21 12 - LYD595 72909.1 - - - 21.6 0.11 11 LYD595 72910.3 206.8 0.04 8 - - LYD567 72495.3 - - - 20.2 0.19 4 LYD567 72496.2 217.3 L 13 - - LYD561 72175.4 212.5 0.21 11 - LYD561 72177.1 215.3 0.04 12 - - LYD561 72177.2 - - - 20.5 0.28 5 LYD553 72743.1 252.4 0.29 31 - - LYD547 71978.3 209.6 L 9 - - LYD547 71980.3 - - - 20.3 0.19 4 LYD547 71981.2 - - - 22.8 0.23 17 LYD534 72411.2 - - - 20.3 0.12 4 LYD534 72414.3 224.6 0.27 17 20.9 0.03 7 LYD521 72607.1 - - - 20.2 0.22 4 LYD521 72610.2 - - - 20.1 0.24 3 CONT. - 192.1 - - 19.5 - Table 60. "CONT." - Control; "Ave." - Average; "9 Incr." = % increment; "p-val." -p value, L- p< 0
.
0 1. The transgenes were under the transcriptional regulation of the new At6669 promoter (SEQ ID NO: 4111). "-" = results are still unavailable.
WO 2013/128448 PCT/IL2013/050172 270 EXAMPLE 16 EVALUATION OF TRANSGENIC ARABIDOPSIS FOR SEED YIELD AND PLANT GROWTH RATE UNDER NORMAL CONDITIONS IN GREENHOUSE ASSAYS UNTIL BOLTING (GH -SB Assays) 5 Assay 2: Plant performance improvement measured until bolting stage: plant biomass and plant growth rate under normal greenhouse conditions (GH -SB Assays) - This assay follows the plant biomass formation and the rosette area growth of plants grown in the greenhouse under normal growth conditions. Transgenic Arabidopsis seeds were sown in agar media supplemented with MS medium and a selection agent 10 (Kanamycin). The T 2 transgenic seedlings were then transplanted to 1.7 trays filled with peat and perlite in a 1:1 ratio. The trays were irrigated with a solution containing of 6 mM inorganic nitrogen in the form of KNO 3 with 1 mM KH 2
PO
4 , 1 mM MgSO 4 , 2 mM CaCl 2 and microelements. All plants were grown in the greenhouse until bolting stage. Plant biomass (the above ground tissue) was weight in directly after harvesting the 15 rosette (plant fresh weight [FW]). Following plants were dried in an oven at 50 'C for 48 hours and weighted (plant dry weight [DW]). Each construct was validated at its T 2 generation. Transgenic plants transformed with a construct conformed by an empty vector carrying the 35S promoter and the selectable marker was used as control. 20 The plants were analyzed for their overall size, growth rate, fresh weight and dry matter. Transgenic plants performance was compared to control plants grown in parallel under the same conditions. Mock- transgenic plants expressing the uidA reporter gene (GUS-Intron) or with no gene at all, under the same promoter were used as control. 25 The experiment was planned in nested randomized plot distribution. For each gene of the invention three to five independent transformation events were analyzed from each construct. Digital imaging - A laboratory image acquisition system, which consists of a digital reflex camera (Canon EOS 300D) attached with a 55 mm focal length lens 30 (Canon EF-S series), mounted on a reproduction device (Kaiser RS), which includes 4 light units (4 x 150 Watts light bulb) was used for capturing images of plant samples.
WO 2013/128448 PCT/IL2013/050172 271 The image capturing process was repeated every 2 days starting from day 1 after transplanting till day 15. Same camera, placed in a custom made iron mount, was used for capturing images of larger plants sawn in white tubs in an environmental controlled greenhouse. The tubs were square shape include 1.7 liter trays. During the capture 5 process, the tubes were placed beneath the iron mount, while avoiding direct sun light and casting of shadows. An image analysis system was used, which consists of a personal desktop computer (Intel P4 3.0 GHz processor) and a public domain program - ImageJ 1.39 [Java based image processing program which was developed at the U.S. National 10 Institutes of Health and freely available on the internet at Hypertext Transfer Protocol://rsbweb (dot) nih (dot) gov/]. Images were captured in resolution of 10 Mega Pixels (3888 x 2592 pixels) and stored in a low compression JPEG (Joint Photographic Experts Group standard) format. Next, analyzed data was saved to text files and processed using the JMP statistical analysis software (SAS institute). 15 Leaf analysis - Using the digital analysis leaves data was calculated, including leaf number, rosette area, rosette diameter, and leaf blade area. Vegetative growth rate: the relative growth rate (RGR) of leaf number (Formula IX, described above), rosette area (Formula VIII described above) and plot coverage (Formula XIV, described above) were calculated using the indicated formulas. 20 Plant Fresh and Dry weight - On about day 80 from sowing, the plants were harvested and directly weight for the determination of the plant fresh weight (FW) and left to dry at 50 'C in a drying chamber for about 48 hours before weighting to determine plant dry weight (DW). Statistical analyses - To identify outperforming genes and constructs, results 25 from the independent transformation events tested were analyzed separately. Data was analyzed using Student's t-test and results are considered significant if the p value was less than 0.1. The JMP statistics software package was used (Version 5.2.1, SAS Institute Inc., Cary, NC, USA). Experimental results: 30 Tables 61-63 summarize the observed phenotypes of transgenic plants expressing the genes constructs using the GH -SB Assays.
WO 2013/128448 PCT/IL2013/050172 272 The genes listed in Tables 61-63 improved plant performance when grown at normal conditions. These genes produced larger plants with a larger photosynthetic area, biomass (fresh weight, dry weight, rosette diameter, rosette area and plot coverage), and relative growth rate (of leaf number, plot coverage and rosette diameter) 5 as compared to control plants grown under identical growth conditions. The genes were cloned under the regulation of a constitutive At6669 promoter (SEQ ID NO:41 11). The evaluation of each gene was performed by testing the performance of different number of events. Event with p-value <0.1 was considered statistically significant 10 Table 61 Genes showing improved plant performance at Normal growth conditions under regulation of At6669 promoter Dry Weight [mg] Fresh Weight [mg] Leaf Number Name Event # .P- % P- % P- % Val. Incr. Val. Incr. Val. Incr. LYD684 72271.4 377.2 0.04 13 4795.5 0.01 11 - - LYD684 72274.1 379.4 L 14 4718.8 L 9 11.1 0.03 7 LYD672 72347.3 364.8 L 9 4987.5 L 15 - - LYD667 72030.1 368.8 0.07 11 4643.8 L 7 - - LYD667 72031.1 371.9 0.03 11 4575.0 0.02 6 - - LYD661 72325.1 366.2 L 10 4831.2 L 12 11.9 0.17 14 LYD661 72328.1 358.3 0.02 7 - - - 11.1 0.23 6 LYD661 72328.2 - - - - - - 10.8 0.11 4 LYD651 73026.4 - - - 4675.0 L 8 - - LYD626 72004.4 - - - - - - 11.2 0.01 8 LYD620 73066.3 359.4 L 8 4681.2 L 8 11.4 0.07 9 LYD617 71966.2 349.4 0.05 5 4581.2 0.10 6 - - LYD617 71966.3 358.1 0.04 7 4600.0 0.11 6 - - LYD617 71966.6 345.6 0.11 4 4568.8 0.15 6 11.4 0.02 10 LYD612 71814.5 - - - 4618.8 0.01 7 - - LYD612 71818.3 350.6 0.07 5 - - - - - LYD609 73124.4 - - - 4943.8 0.01 14 11.2 0.22 8 LYD609 73125.3 - - - 4581.2 0.29 6 - - LYD609 73125.4 365.6 0.10 10 4543.8 0.06 5 10.9 0.05 5 LYD596 73639.1 360.0 0.01 8 4506.2 0.19 4 - - LYD593 71952.1 365.0 0.03 9 4593.8 0.02 6 - - LYD593 71957.5 347.1 0.09 4 - - - - - LYD574 73118.4 376.9 0.02 13 4783.0 L 11 11.1 0.03 7 LYD574 73122.3 371.9 L 11 4625.0 L 7 - - LYD564 72182.4 - - - 4437.5 0.23 3 - - - WO 2013/128448 PCT/IL2013/050172 273 Dry Weight [mg] Fresh Weight [mg] Leaf Number Name Event # P- % P- % ve. - % Val. Incr. Val. Incr. Val. Incr. LYD558 73112.3 390.0 0.16 17 5143.8 L 19 11.4 0.18 9 LYD558 73114.3 - - - 4600.9 L 6 11.2 0.01 8 LYD527 72241.3 - - - 4662.5 0.22 8 - - LYD527 72243.4 - - - 4581.2 0.07 6 - - LYD527 72246.3 378.1 0.11 13 4781.2 L 11 - - LYD526 72164.4 367.5 0.17 10 4518.8 0.13 5 - - LYD526 72164.5 - - - - - - 10.8 0.11 4 LYD526 72167.4 - - - 4687.5 0.06 8 10.9 0.27 4 LYD526 72168.1 - - - 4475.0 0.10 4 - - CONT. - 333.6 - - 4322.7 - - 10.4 - LYD680 72230.2 - - - - - - 9.8 0.26 5 LYD680 72232.1 - - - - - - 10.2 0.06 10 LYD668 72019.2 - - - - - - 9.8 L 6 LYD668 72019.3 - - - - - - 9.9 0.03 7 LYD668 72020.2 257.1 0.03 15 3474.1 0.29 11 9.6 0.02 4 LYD668 72023.3 262.0 0.07 17 3536.6 0.17 13 - - LYD664 72012.1 277.9 0.12 24 3435.7 0.28 9 9.9 0.20 7 LYD664 72015.2 - - - - - - 9.9 0.03 7 LYD664 72016.2 235.0 0.30 5 3450.0 0.01 10 9.9 0.03 7 LYD664 72017.8 260.0 0.03 16 3356.2 0.05 7 9.9 0.10 7 LYD661 72325.1 - - - 3386.6 0.17 8 9.6 0.12 4 LYD661 72325.4 236.9 0.28 6 3400.0 0.19 8 - - LYD661 72328.2 258.1 0.01 15 3700.0 L 18 9.9 0.03 7 LYD661 72329.2 - - - 3481.2 0.29 11 - - LYD657 72400.1 236.2 0.26 6 - - - - - LYD657 72400.3 - - - 3630.4 0.13 16 - - LYD657 72401.1 280.5 0.04 25 3461.6 0.16 10 - - LYD657 72401.2 - - - 3325.0 0.14 6 - - LYD642 71820.2 - - - - - - 9.7 0.02 5 LYD642 71824.5 290.0 0.23 30 3868.8 0.23 23 10.8 0.15 17 LYD642 71825.1 - - - 3368.8 0.28 7 9.9 0.03 7 LYD642 71825.3 - - - 3356.2 0.06 7 9.7 0.20 5 LYD631 72541.2 - - - - - - 9.6 0.07 3 LYD631 72544.3 268.2 0.10 20 3484.5 0.08 11 - - LYD631 72544.4 - - - 3318.8 0.17 6 - - LYD621 72571.1 248.1 0.06 11 3431.2 0.17 9 - - LYD621 72573.6 272.5 0.01 22 3681.2 0.21 17 9.8 0.25 6 LYD621 72574.1 - - - 3468.8 0.14 11 - - LYD618 72621.2 - - - 3393.8 0.03 8 9.6 0.02 4 LYD618 72622.2 - - - 3562.5 0.20 13 - - LYD618 72622.3 247.5 0.14 11 3550.0 0.16 13 - - - WO 2013/128448 PCT/IL2013/050172 274 Dry Weight [mg] Fresh Weight [mg] Leaf Number Name Event # P- % P- % ve. - % Val. Incr. Val. Incr. Val. Incr. LYD618 72624.4 255.7 0.13 14 3592.9 0.03 14 9.9 0.03 7 LYD603 72535.2 - - - 3393.8 0.05 8 - - LYD603 72536.1 - - - 3318.8 0.17 6 - - LYD603 72537.7 - - - 3487.5 L 11 - - LYD572 72388.2 240.6 0.18 8 - - - 9.4 0.25 2 LYD572 72390.3 - - - - - - 9.9 L 7 LYD568 71930.1 240.6 0.16 8 3487.5 L 11 9.7 0.02 5 LYD568 71931.2 - - - 3406.2 0.20 9 - - LYD568 71931.4 - - - 3581.2 L 14 9.6 0.12 4 LYD561 72175.4 - - - - - - 9.8 L 6 LYD561 72177.1 - - - 3362.5 0.24 7 10.1 0.20 9 LYD561 72179.1 - - - - - - 9.8 0.06 5 LYD551 71986.9 238.1 0.20 6 3312.5 0.11 6 10.0 0.02 8 LYD531 71916.3 - - - 3343.8 0.06 7 9.8 0.26 5 LYD531 71917.1 - - - 3406.2 0.06 9 - - LYD531 71917.2 - - - 3400.0 0.22 8 9.8 L 6 LYD531 71918.1 258.8 0.08 16 3562.5 0.03 13 10.4 0.09 12 LYD531 71921.2 255.0 0.03 14 3418.8 0.04 9 9.9 0.20 7 LYD528 72310.1 - - - 3325.9 0.08 6 - - LYD528 72312.4 245.6 0.12 10 3556.2 0.19 13 9.5 0.27 3 LYD522 72716.2 - - - 3456.2 0.27 10 10.1 0.01 9 LYD522 72716.6 274.9 L 23 3799.1 0.12 21 - - LYD522 72720.1 - - - 3437.5 0.11 10 - - LYD522 72720.2 241.9 0.12 8 3450.0 0.02 10 9.9 0.03 7 CONT. - 223.6 - - 3138.8 - - 9.3 - LYD688 73129.1 - - - - - - 11.4 0.30 5 LYD688 73133.1 371.2 0.01 15 4818.8 0.04 11 11.8 0.04 8 LYD688 73133.3 - - - - - - 11.4 0.30 5 LYD688 73133.6 368.1 0.17 14 4987.5 0.01 15 - - LYD670 73346.2 350.0 0.20 8 4675.0 0.17 7 - - LYD670 73347.4 - - - 4912.5 0.07 13 - - LYD670 73348.1 - - - - - - 12.2 0.28 12 LYD670 73350.2 376.2 0.12 16 5050.0 L 16 11.5 0.08 5 LYD662 72008.3 - - - 4637.5 0.17 7 11.8 0.02 8 LYD643 72336.3 354.8 0.10 10 4816.7 0.21 11 - - LYD629 72198.3 - - - - - - 11.8 0.03 8 LYD623 71972.3 - - - 4575.0 0.28 5 - - LYD606 72500.2 - - - - - - 11.5 0.10 5 LYD606 72500.5 341.2 0.25 6 - - - - - LYD599 72266.2 375.0 0.01 16 4831.2 0.04 11 12.1 L 11 LYD594 73307.4 - - - - - - 11.4 0.28 4 WO 2013/128448 PCT/IL2013/050172 275 Dry Weight [mg] Fresh Weight [mg] Leaf Number Name Event # P- % P- % ve. - % Val. Incr. Val. Incr. Val. Incr. LYD562 73484.1 - - - - - - 11.4 0.17 5 LYD562 73484.2 351.2 0.16 9 4781.2 0.06 10 11.5 0.10 5 LYD562 73486.3 350.0 0.13 8 4756.2 0.13 9 - - LYD562 73489.1 352.5 0.09 9 4687.5 0.13 8 - - LYD549 73029.2 363.1 0.03 12 4806.2 0.07 10 - - LYD549 73032.1 - - - - - - 11.5 0.19 5 CONT. - 323.4 - - 4352.3 - - 10.9 - LYD669 72217.2 - - - 4262.5 0.11 17 - - LYD660 73929.2 395.6 0.23 30 - - - 11.9 0.17 13 LYD660 73933.5 374.4 0.11 23 4137.5 0.01 13 12.2 0.05 16 LYD654 73924.4 328.8 0.15 8 3875.0 0.29 6 - - LYD643 72333.1 - - - 3843.8 0.29 5 - - LYD643 72333.2 - - - - - - 11.0 0.19 4 LYD643 72333.6 - - - 4231.2 0.03 16 - - LYD643 72336.3 - - - - - - 11.2 0.11 6 LYD634 71995.1 - - - 4012.5 0.07 10 11.4 0.04 8 LYD634 71996.1 - - - 3829.2 0.23 5 - - LYD634 71996.2 - - - 3931.2 0.19 8 - - LYD629 72195.1 - - - 4075.0 0.15 12 11.9 L 13 LYD629 72198.3 328.8 0.17 8 - - - 11.4 0.20 8 LYD622 72024.3 - - - 3868.8 0.21 6 - - LYD614 73916.4 340.6 0.12 12 4231.2 0.04 16 - - LYD614 73917.1 - - - 4156.2 0.05 14 - - LYD614 73917.3 337.5 0.18 11 - - - - - LYD609 73125.4 - - - - - - 11.4 0.09 8 LYD609 73128.5 - - - 3875.0 0.16 6 - - LYD603 72537.7 330.0 0.13 8 4131.2 0.01 13 - - LYD584 73915.2 - - - - - - 11.4 0.09 8 LYD584 73915.4 - - - - - - 11.3 0.07 7 LYD580 72188.2 - - - 4237.5 L 16 10.9 0.23 4 LYD580 72189.1 - - - 3837.5 0.23 5 - - LYD570 71937.3 323.1 0.29 6 4043.8 0.06 11 12.1 0.20 15 LYD561 72177.2 - - - 3868.8 0.21 6 - - LYD556 72903.5 - - - - - - 11.4 0.09 8 LYD556 72903.6 - - - 4062.5 0.02 11 - - LYD556 72904.3 - - - 4131.2 0.01 13 - - LYD534 72409.2 - - - 3912.5 0.15 7 - - CONT. - 305.2 - - 3651.8 - - 10.6 - LYD674 72254.1 - - - 3581.2 0.14 8 - - LYD672 72347.3 - - - - - - 9.6 0.03 6 LYD635 72626.2 - - - 3737.5 0.03 13 9.4 0.21 4 WO 2013/128448 PCT/IL2013/050172 276 Dry Weight [mg] Fresh Weight [mg] Leaf Number Name Event # P- % P- % ve. - % Val. Incr. Val. Incr. Val. Incr. LYD635 72630.1 - - - - - - 9.7 0.01 7 LYD635 72630.2 - - - - - - 10.1 0.06 12 LYD635 72630.4 - - - - - - 9.6 0.02 7 LYD632 72770.2 - - - 3617.9 0.10 9 9.4 0.11 4 LYD627 72765.1 - - - - - - 10.1 L 12 LYD627 72767.1 - - - 3568.8 0.16 8 - - LYD623 71970.2 - - - - - - 9.9 L 10 LYD623 71972.2 - - - - - - 9.4 0.07 4 LYD623 71972.3 - - - - - - 9.8 0.13 8 LYD623 71974.3 271.9 0.19 15 - - - 9.8 L 8 LYD593 71957.1 - - - 3714.3 0.06 12 9.6 0.13 6 LYD593 71957.5 283.1 0.11 20 - - - 9.3 0.19 3 LYD580 72188.2 - - - - - - 9.9 L 10 LYD580 72189.1 - - - - - - 9.7 0.08 7 LYD580 72189.2 288.8 0.02 22 3793.8 0.02 15 9.9 L 9 LYD571 72357.5 - - - - - - 9.6 0.18 7 LYD571 72358.1 278.1 0.12 18 3675.0 0.06 11 - - LYD571 72358.3 287.0 0.22 22 3955.4 0.03 20 10.1 L 12 LYD571 72360.2 - - - - - - 9.4 0.07 4 LYD560 71925.1 265.9 0.19 13 - - - 9.5 0.26 5 LYD554 72169.2 - - - - - - 9.6 0.04 7 LYD554 72173.2 - - - - - - 9.6 0.13 6 LYD553 72742.1 - - - - - - 9.6 0.18 7 LYD553 72743.2 - - - - - - 9.3 0.19 3 LYD548 72656.1 - - - - - - 9.6 0.30 6 LYD548 72656.2 - - - - - - 9.5 0.26 5 LYD548 72673.3 - - - - - - 9.5 0.04 5 LYD548 72677.1 276.9 0.28 17 - - - - - LYD547 71978.3 - - - - - - 9.8 L 9 LYD547 71980.1 - - - - - - 10.0 0.08 11 LYD547 71980.3 - - - 3590.2 0.26 9 - - LYD547 71981.2 - - - - - - 10.0 L 11 LYD538 72835.2 273.8 0.08 16 3837.5 0.17 16 9.9 0.22 9 LYD538 72835.4 262.9 0.16 11 - - - 9.4 0.18 4 LYD538 72839.1 - - - - - - 9.7 0.23 7 LYD538 72839.5 - - - - - - 9.7 0.08 7 LYD527 72241.3 - - - - - - 9.6 0.30 6 LYD527 72243.4 - - - - - - 9.3 0.19 3 LYD527 72245.2 - - - - - - 9.4 0.18 4 LYD527 72246.3 - - - - - - 9.5 0.08 5 LYD521 72607.1 - - - - - - 9.8 0.13 8 WO 2013/128448 PCT/IL2013/050172 277 Dry Weight [mg] Fresh Weight [mg] Leaf Number Name Event # P- % P- % ve. - % Val. Incr. Val. Incr. Val. Incr. LYD521 72610.2 - - - - - - 9.9 0.22 9 LYD521 72611.3 - - - - - - 9.4 0.21 4 CONT. - 236.0 - - 3306.4 - - 9.0 - LYD680 72230.2 - - - 3043.8 0.03 15 - - LYD680 72231.2 281.9 L 30 3675.0 L 39 - - LYD680 72232.1 275.6 L 27 3568.8 L 35 9.8 0.13 6 LYD678 72787.2 304.4 L 41 3562.5 0.01 35 - - LYD678 72788.1 - - - 3081.2 0.25 17 - - LYD678 72790.1 - - - - - - 9.6 0.15 4 LYD674 72254.3 - - - 3387.5 0.17 28 - - LYD674 72255.1 261.2 0.03 21 3550.0 L 34 9.7 0.04 4 LYD674 72256.3 244.4 0.06 13 - - - - - LYD664 72015.2 250.6 0.10 16 3455.4 0.16 31 - - LYD664 72017.7 286.9 L 33 3668.8 L 39 9.6 0.15 4 LYD642 71821.4 275.0 L 27 3662.5 L 39 - - LYD642 71824.5 - - - - - - 9.7 0.21 4 LYD642 71825.1 270.0 0.03 25 3568.8 L 35 - - LYD642 71825.3 - - - - - - 9.7 0.04 4 LYD641 72632.2 - - - 2881.2 0.08 9 9.5 0.19 2 LYD641 72633.4 302.5 L 40 3950.0 L 50 - - LYD641 72635.2 244.4 0.08 13 3256.2 0.01 23 - - LYD637 73684.1 273.1 L 26 3475.0 L 32 - - LYD637 73685.1 271.9 0.14 26 3781.2 L 43 - - LYD637 73685.2 - - - 3231.2 L 22 - - LYD637 73685.3 262.5 L 21 3293.8 L 25 - - LYD624 73382.3 - - - 3256.2 0.11 23 - - LYD624 73385.3 264.9 0.14 22 - - - - - LYD621 72571.1 - - - - - - 9.8 0.07 5 LYD621 72574.1 245.8 0.19 14 - - - - - LYD621 72574.3 - - - - - - 9.6 0.06 4 LYD617 71964.2 - - - 3437.5 L 30 - - LYD617 71966.2 264.4 0.25 22 3525.0 0.06 33 - - LYD617 71966.6 258.1 L 19 3243.8 L 23 9.5 0.19 2 LYD617 71967.1 244.4 0.03 13 3268.8 L 24 - - LYD616 73057.1 239.4 0.13 11 2981.2 0.21 13 - - LYD616 73057.4 - - - 3425.0 L 30 9.5 0.19 2 LYD616 73058.4 265.6 L 23 3425.0 L 30 - - LYD616 73059.1 - - - 3475.0 0.09 32 - - LYD616 73059.4 - - - - - - 9.6 0.12 3 LYD588 73852.1 233.8 0.15 8 - - - - - LYD588 73852.2 241.9 0.14 12 3062.5 0.01 16 - - - WO 2013/128448 PCT/IL2013/050172 278 Dry Weight [mg] Fresh Weight [mg] Leaf Number Name Event # P- % P- % ve. - % Val. Incr. Val. Incr. Val. Incr. LYD572 72387.1 258.1 L 19 3381.2 L 28 - - LYD572 72390.3 276.2 L 28 3625.0 L 37 - - LYD567 72495.3 255.6 0.20 18 3637.5 0.08 38 - - LYD567 72495.4 - - - - - - 10.0 0.28 8 LYD567 72496.2 - - - - - - 9.5 0.19 2 LYD567 72496.3 259.4 0.04 20 3518.8 0.01 33 - - LYD559 73623.3 - - - 3412.5 0.22 29 - - LYD559 73624.1 - - - - - - 9.6 0.15 4 LYD559 73626.1 - - - 2916.1 0.29 10 - - LYD538 72835.4 260.0 L 20 3281.2 L 24 9.8 0.07 5 LYD537 73628.1 279.4 0.02 29 3631.2 L 37 - - LYD537 73633.1 265.6 0.01 23 3212.5 L 22 - - LYD537 73633.4 238.3 0.06 10 2902.1 0.08 10 - - LYD537 73633.5 248.8 0.12 15 2981.2 0.02 13 - - LYD521 72607.1 277.5 L 28 3368.8 L 28 - - LYD521 72610.1 240.0 0.05 11 3043.8 0.03 15 9.8 0.27 5 LYD521 72610.2 - - - - - - 9.6 0.06 4 LYD521 72611.1 241.2 0.04 12 - - - 9.7 0.04 4 LYD521 72611.3 294.4 L 36 3406.2 L 29 - - CONT. - 216.3 - - 2641.6 - - 9.3 - LYD689 72711.2 - - - 5537.5 0.02 12 10.6 0.05 5 LYD689 72712.3 465.0 0.01 17 5575.0 0.11 13 - - LYD689 72713.1 446.2 0.26 12 5656.2 0.04 15 10.4 0.16 3 LYD682 72566.2 460.6 0.05 16 5618.8 0.02 14 - - LYD682 72568.2 474.3 L 19 5596.4 0.01 13 - - LYD677 72223.6 - - - - - - 10.8 0.18 8 LYD677 72223.7 461.1 0.04 16 5209.8 0.21 6 - - LYD677 72227.1 - - - - - - 10.5 0.27 4 LYD669 73327.1 471.4 0.09 19 5750.0 L 17 10.9 0.25 9 LYD666 72394.3 - - - 5631.2 0.01 14 - - LYD657 72400.1 453.8 0.29 14 5868.8 0.01 19 - - LYD657 72400.3 426.4 0.19 7 5291.1 0.13 7 - - LYD657 72401.1 421.9 0.27 6 5293.8 0.12 7 - - LYD620 73063.3 - - - 5291.1 0.19 7 - - LYD620 73066.3 - - - 5262.5 0.30 7 10.6 0.14 5 LYD602 72613.1 - - - 5443.8 0.04 10 - - LYD602 72613.2 429.3 0.17 8 - - - - - LYD598 72421.1 - - - 5250.0 0.28 6 - - LYD598 72446.4 446.9 0.09 12 5187.5 0.24 5 - - LYD595 72907.4 - - - - - - 10.5 0.07 4 LYD595 72907.5 434.4 0.16 9 5743.8 L 16 - - - WO 2013/128448 PCT/IL2013/050172 279 Dry Weight [mg] Fresh Weight [mg] Leaf Number Name Event # P- % P- % ve. - % Val. Incr. Val. Incr. Val. Incr. LYD574 73118.3 447.5 0.22 13 5300.0 0.12 7 - - LYD574 73118.4 - - - 5237.5 0.18 6 - - LYD574 73119.1 463.8 0.25 17 5525.0 0.05 12 10.9 0.22 8 LYD574 73121.2 461.0 0.28 16 5226.8 0.22 6 10.3 0.26 3 LYD574 73122.3 466.9 0.15 17 5881.2 L 19 - - LYD562 73484.2 - - - - - - 10.7 0.02 6 LYD549 73029.1 - - - - - - 10.3 0.26 3 LYD549 73029.4 457.1 0.02 15 - - - - - LYD549 73032.1 424.8 0.20 7 - - - - - LYD549 73032.2 - - - 5481.2 0.06 11 - - LYD542 72733.2 425.6 0.25 7 5425.0 0.04 10 - - LYD542 72735.4 426.7 0.23 7 5600.0 0.01 13 10.3 0.26 3 LYD542 72736.3 423.8 0.29 7 - - - - - LYD542 72736.4 - - - - - - 10.6 0.03 6 LYD542 72736.7 433.0 0.11 9 5530.4 0.02 12 - - LYD536 72531.3 424.4 0.24 7 5493.8 0.07 11 - - LYD533 72726.2 - - - 5268.8 0.18 7 - - CONT. - 397.4 - - 4934.9 - - 10.1 - LYD688 73133.1 449.2 0.02 11 5805.4 0.08 5 - - LYD688 73134.6 455.0 0.07 13 5831.2 0.03 6 10.5 0.02 7 LYD681 73184.1 - - - - - - 10.6 L 8 LYD681 73184.3 - - - - - - 10.4 0.11 6 LYD681 73186.2 - - - 5762.5 0.06 5 10.5 0.02 7 LYD675 72644.1 435.0 0.02 8 5893.8 0.01 7 11.1 0.12 13 LYD675 72644.3 - - - - - - 10.4 0.04 6 LYD675 72648.1 460.0 0.15 14 - - - - - LYD671 72877.1 427.5 0.21 6 - - - - - LYD671 72878.2 425.0 0.25 5 - - - - - LYD671 72879.2 464.4 0.29 15 5862.5 0.13 6 - - LYD665 72216.5 435.6 0.29 8 - - - - - LYD665 72216.6 426.9 0.06 6 - - - - - LYD652 72559.1 - - - - - - 10.1 0.17 3 LYD652 72560.1 - - - 5817.0 0.03 6 - - LYD651 73021.3 451.2 0.10 12 6031.2 L 10 - - LYD648 72831.3 420.0 0.23 4 - - - - - LYD648 72832.2 442.2 0.02 10 - - - - - LYD644 72775.1 476.6 L 18 5875.9 0.01 7 - - LYD644 72778.1 420.6 0.11 4 - - - - - LYD644 72778.2 421.3 0.28 4 - - - - - LYD639 72548.4 - - - - - - 10.0 0.20 2 LYD639 72549.3 - - - - - - 10.2 0.08 4 WO 2013/128448 PCT/IL2013/050172 280 Dry Weight [mg] Fresh Weight [mg] Leaf Number Gene Event # P- % P- % P- % Val. Incr. Val. Incr. Val. Incr. LYD639 72551.3 440.6 L 9 - - - - - LYD596 73635.1 - - - 5756.2 0.06 5 - - LYD596 73635.3 - - - 5700.0 0.15 4 - - LYD596 73636.1 453.6 0.25 12 - - - - - LYD596 73637.1 440.0 0.18 9 6206.2 L 13 - - LYD594 73303.1 416.2 0.21 3 - - - - - LYD594 73307.1 462.5 0.21 15 6068.8 0.11 10 - - LYD594 73307.3 434.4 0.02 8 - - - - - LYD594 73307.4 475.0 0.08 18 - - - 10.2 0.03 4 LYD577 72747.4 481.2 L 19 - - - - - LYD577 72748.2 - - - - - - 10.1 0.17 3 LYD577 72748.3 - - - - - - 10.2 0.24 4 LYD577 72750.4 430.0 0.06 7 - - - - - LYD545 72506.2 448.8 L 11 5956.2 L 8 - - LYD545 72508.2 429.2 0.10 6 - - - - - LYD545 72508.5 428.8 0.19 6 - - - - - LYD541 72729.1 432.3 0.25 7 - - - - - LYD541 72729.2 439.4 0.15 9 - - - - - LYD541 72732.1 452.7 0.03 12 - - - - - LYD534 72409.2 - - - - - - 10.2 0.24 4 LYD534 72414.3 - - - - - - 10.1 0.05 3 LYD522 72715.2 474.4 0.23 18 - - - - - LYD522 72720.1 - - - - - - 10.2 0.03 4 CONT. - 403.4 - - 5506.6 - - 9.8 - Table 61. "CONT." - Control; "Ave." - Average; "% Incr." = % increment; "p-val." - p value, L- p<0.01. The transgenes were under the transcriptional regulation of the new At6669 promoter (SEQ ID NO:41 11). "-"= results are still unavailable. 5 Table 62 Genes showing improved plant performance at Normal growth conditions under regulation of At6669 promoter Plot Coverage [cm 2 ] Rosette Area [cm 2 ] Rosette Diameter Gene Event # [cm] Name P- % P- % P- % Ave. Val. Incr. Ave. Val. Incr. Ave. Val. Incr. LYD684 72271.4 - - - - - - 4.8 0.24 7 LYD684 72272.3 57.6 0.17 9 7.2 0.17 9 - - LYD684 72274.1 73.6 0.13 39 9.2 0.13 39 5.1 0.14 13 LYD681 73188.3 62.4 0.24 18 7.8 0.24 18 4.8 0.22 6 LYD667 72030.4 58.0 0.22 9 7.2 0.22 9 - - - WO 2013/128448 PCT/IL2013/050172 281 Plot Coverage [cm 2 ] Rosette Area [cm 2 Rosette Diameter Gene Event # [cm] Name P- % P- % P- % Val. Incr. Val. Incr. Val. Incr. LYD661 72325.1 63.0 L 19 7.9 L 19 4.9 0.07 7 LYD661 72328.1 70.3 L 32 8.8 L 32 5.1 0.01 14 LYD661 72328.2 67.7 0.04 28 8.5 0.04 28 5.1 0.12 13 LYD651 73026.4 60.2 0.11 13 7.5 0.11 13 - - LYD626 72002.1 - - - - - - 4.8 0.27 7 LYD626 72003.1 - - - - - - 4.9 0.14 9 LYD620 73066.3 67.2 L 26 8.4 L 26 5.1 L 13 LYD617 71964.2 58.2 0.12 10 7.3 0.12 10 4.8 0.22 6 LYD617 71966.3 56.1 0.28 6 7.0 0.28 6 - - LYD617 71966.6 70.1 L 32 8.8 L 32 5.0 L 11 LYD612 71818.3 58.0 0.08 9 7.3 0.08 9 4.7 0.12 5 LYD609 73125.3 61.6 0.28 16 7.7 0.28 16 4.9 0.22 7 LYD609 73125.4 61.1 0.08 15 7.6 0.08 15 4.8 0.14 5 LYD609 73128.5 59.9 0.23 13 7.5 0.23 13 4.9 0.05 7 LYD596 73635.1 - - - - - - 5.1 0.02 12 LYD596 73639.1 61.5 0.08 16 7.7 0.08 16 5.1 0.03 12 LYD593 71952.1 62.5 0.26 18 7.8 0.26 18 - - LYD593 71952.2 58.4 0.06 10 7.3 0.06 10 4.7 0.28 4 LYD593 71957.5 58.9 0.05 11 7.4 0.05 11 - - LYD574 73118.4 70.3 L 32 8.8 L 32 5.1 L 13 LYD574 73119.1 58.2 0.17 10 7.3 0.17 10 - - LYD564 72182.4 62.0 0.17 17 7.8 0.17 17 - - LYD564 72182.5 56.0 0.26 5 7.0 0.26 5 - - LYD558 73112.3 71.0 0.07 34 8.9 0.07 34 5.2 L 15 LYD558 73113.1 60.3 0.02 14 7.5 0.02 14 4.7 0.19 4 LYD558 73114.3 58.1 0.21 9 7.3 0.21 9 - - LYD558 73114.6 58.5 0.17 10 7.3 0.17 10 4.7 0.19 4 LYD527 72246.1 56.0 0.27 5 7.0 0.27 5 - - LYD527 72246.3 67.2 0.29 26 8.4 0.29 26 - - LYD526 72164.5 63.0 L 19 7.9 L 19 4.9 0.01 9 LYD526 72167.4 67.9 0.10 28 8.5 0.10 28 5.1 0.03 13 LYD526 72168.1 59.6 0.06 12 7.5 0.06 12 4.8 0.25 6 LYD526 72168.4 64.1 L 21 8.0 L 21 4.9 0.02 9 CONT. - 53.1 - - 6.6 - - 4.5 - LYD680 72232.1 53.7 0.29 16 6.7 0.29 16 - - LYD664 72012.1 52.0 0.02 12 6.5 0.02 12 4.3 0.11 4 LYD664 72015.2 54.4 0.29 17 6.8 0.29 17 4.5 0.25 8 LYD661 72325.1 54.7 0.25 18 6.8 0.25 18 4.4 0.28 6 LYD661 72328.2 57.9 0.01 25 7.2 0.01 25 4.5 0.06 8 LYD657 72401.1 50.7 0.02 9 6.3 0.02 9 - - - WO 2013/128448 PCT/IL2013/050172 282 2 2 Rosette Diameter Plot Coverage [cm 2 ] Rosette Area [cm 2 ] ]tm Gene Eet#[cm] Name P- % P- % P- % Ave. Ave. Ave. Vl nr Val. Incr. Val. Incr. Val. Incr. LYD642 71820.2 49.8 0.14 7 6.2 0.14 7 4.4 0.10 6 LYD642 71821.4 51.0 0.02 10 6.4 0.02 10 4.5 0.01 7 LYD642 71824.5 64.5 0.08 39 8.1 0.08 39 4.9 0.06 17 LYD642 71825.1 48.2 0.25 4 6.0 0.25 4 - - LYD631 72544.4 54.4 0.20 17 6.8 0.20 17 4.5 0.09 8 LYD621 72571.1 53.2 L 15 6.7 L 15 4.5 L 9 LYD618 72621.2 57.2 0.20 23 7.1 0.20 23 4.6 0.29 10 LYD618 72622.2 49.8 0.23 7 6.2 0.23 7 - - LYD572 72390.3 54.2 L 17 6.8 L 17 4.5 0.04 8 LYD568 71930.1 57.5 0.22 24 7.2 0.22 24 4.7 0.13 13 LYD568 71931.4 53.7 0.01 16 6.7 0.01 16 4.4 0.12 7 LYD561 72177.1 51.2 0.01 10 6.4 0.01 10 4.3 0.14 4 LYD551 71984.1 50.0 0.27 8 6.2 0.27 8 - - LYD551 71986.9 52.7 L 14 6.6 L 14 4.4 0.15 5 LYD531 71917.1 52.2 0.10 13 6.5 0.10 13 4.6 0.01 9 LYD531 71917.2 52.6 0.17 13 6.6 0.17 13 4.4 0.10 5 LYD531 71918.1 59.7 0.15 29 7.5 0.15 29 4.7 0.03 13 LYD531 71921.2 - - - - - - 4.4 0.21 5 LYD528 72312.2 49.5 0.08 7 6.2 0.08 7 4.3 0.16 3 LYD522 72715.2 48.9 0.13 6 6.1 0.13 6 4.3 0.21 3 LYD522 72720.1 51.5 0.29 11 6.4 0.29 11 - - LYD522 72720.2 53.8 0.12 16 6.7 0.12 16 - - CONT. - 46.4 - - 5.8 - - 4.2 - LYD688 73129.1 74.6 0.07 22 9.3 0.07 22 5.4 0.05 13 LYD688 73133.1 75.8 0.03 24 9.5 0.03 24 5.3 0.04 10 LYD688 73133.3 - - - - - - 5.2 0.27 8 LYD688 73133.6 67.7 0.26 11 8.5 0.26 11 - - LYD670 73346.2 70.3 0.17 15 8.8 0.17 15 5.2 0.08 9 LYD670 73347.4 - - - - - - 5.1 0.20 5 LYD670 73348.1 77.6 0.22 27 9.7 0.22 27 5.4 0.10 11 LYD662 72008.3 74.8 0.04 22 9.4 0.04 22 5.5 L 14 LYD646 73040.5 - - - - - - 5.0 0.24 5 LYD646 73042.4 75.7 0.07 24 9.5 0.07 24 5.4 0.09 13 LYD643 72336.3 72.6 0.07 19 9.1 0.07 19 5.3 0.07 9 LYD643 72336.6 72.1 0.12 18 9.0 0.12 18 5.3 0.03 10 LYD629 72198.3 72.8 0.07 19 9.1 0.07 19 5.3 0.15 10 LYD623 71972.3 70.0 0.15 15 8.8 0.15 15 5.2 0.10 7 LYD622 72026.1 68.2 0.26 12 8.5 0.26 12 5.1 0.17 6 LYD599 72266.2 81.3 0.04 33 10.2 0.04 33 5.5 0.11 15 LYD594 73307.4 71.2 0.22 16 8.9 0.22 16 5.2 0.26 8 WO 2013/128448 PCT/IL2013/050172 283 Plot Coverage [cm 2 ] Rosette Area [cm 2 Rosette Diameter Gene Event # [cm] Name P- % P- % P- % Val. Incr. Val. Incr. Val. Incr. LYD562 73484.1 71.5 0.15 17 8.9 0.15 17 5.2 0.29 8 LYD562 73484.2 74.9 0.10 23 9.4 0.10 23 5.4 0.08 12 LYD562 73486.3 - - - - - - 5.1 0.12 7 LYD551 71986.9 71.9 0.08 18 9.0 0.08 18 5.4 0.02 12 LYD549 73029.4 - - - - - - 5.3 0.06 11 LYD549 73032.1 - - - - - - 5.3 0.03 10 LYD528 72312.4 - - - - - - 5.2 0.10 8 CONT. - 61.1 - - 7.6 - - 4.8 - LYD669 73330.2 65.0 0.19 11 8.1 0.19 11 - - LYD660 73929.2 70.6 0.05 21 8.8 0.05 21 4.9 0.25 9 LYD660 73933.4 - - - - - - 4.8 0.05 7 LYD660 73933.5 78.5 L 34 9.8 L 34 5.2 L 16 LYD654 73924.5 - - - - - - 4.9 0.04 9 LYD654 73926.3 63.7 0.20 9 8.0 0.20 9 4.8 0.11 6 LYD643 72336.3 67.8 0.08 16 8.5 0.08 16 4.8 0.24 8 LYD634 71995.1 64.0 0.13 9 8.0 0.13 9 - - LYD629 72195.1 69.2 0.05 18 8.7 0.05 18 - - LYD629 72198.2 65.7 0.15 12 8.2 0.15 12 4.8 0.08 6 LYD629 72198.3 73.0 0.02 25 9.1 0.02 25 4.9 0.02 9 LYD629 72198.5 65.6 0.17 12 8.2 0.17 12 - - LYD614 73916.4 68.0 0.02 16 8.5 0.02 16 4.8 0.18 6 LYD614 73916.5 - - - - - - 5.0 0.28 10 LYD614 73917.3 63.0 0.20 8 7.9 0.20 8 - - LYD609 73125.4 63.8 0.15 9 8.0 0.15 9 4.8 0.11 6 LYD584 73912.3 - - - - - - 4.7 0.14 5 LYD584 73915.2 66.8 0.15 14 8.3 0.15 14 4.8 0.28 8 LYD584 73915.4 68.4 0.02 17 8.5 0.02 17 4.8 0.05 7 LYD580 72188.2 67.7 0.03 16 8.5 0.03 16 4.8 0.12 7 LYD570 71937.3 71.1 L 22 8.9 L 22 4.9 0.08 9 LYD561 72177.2 - - - - - - 4.9 0.26 10 LYD556 72903.5 - - - - - - 4.7 0.27 4 LYD534 72414.4 62.8 0.22 7 7.9 0.22 7 - - CONT. - 58.5 - - 7.3 - - 4.5 - LYD672 72348.2 - - - - - - 4.1 0.06 7 LYD635 72626.2 44.4 0.02 13 5.5 0.02 13 4.0 0.02 6 LYD632 72771.1 45.1 0.07 15 5.6 0.07 15 4.1 0.01 7 LYD632 72774.3 - - - - - - 4.1 0.12 7 LYD632 72774.4 42.8 0.25 9 5.3 0.25 9 - - LYD627 72766.1 44.0 0.09 12 5.5 0.09 12 4.0 0.25 5 LYD627 72767.1 - - - - - - 4.2 0.25 11 WO 2013/128448 PCT/IL2013/050172 284 Plot Coverage [cm 2 ] Rosette Area [cm 2 Rosette Diameter Gene Event # [cm] Name P- % P- % P- % Val. Incr. Val. Incr. Val. Incr. LYD593 71957.5 42.8 0.05 9 5.3 0.05 9 4.0 0.06 5 LYD580 72188.2 44.2 0.10 12 5.5 0.10 12 - - LYD571 72357.5 47.7 L 21 6.0 L 21 4.1 L 8 LYD571 72358.1 47.9 L 22 6.0 L 22 4.2 L 11 LYD571 72358.3 54.2 0.20 38 6.8 0.20 38 4.4 0.18 17 LYD571 72358.4 46.7 0.08 19 5.8 0.08 19 4.1 0.19 8 LYD554 72174.4 45.3 0.18 15 5.7 0.18 15 - - LYD553 72741.2 44.2 0.15 12 5.5 0.15 12 4.1 0.03 6 LYD548 72656.2 - - - - - - 4.0 0.13 4 LYD548 72677.1 43.9 0.27 12 5.5 0.27 12 - - LYD547 71980.1 47.4 L 20 5.9 L 20 - - LYD538 72835.2 52.6 L 34 6.6 L 34 4.5 0.07 18 LYD538 72835.4 41.7 0.06 6 5.2 0.06 6 - - LYD538 72839.5 41.4 0.10 5 5.2 0.10 5 - - LYD527 72246.3 44.2 L 12 5.5 L 12 4.2 L 10 LYD521 72610.2 42.6 0.02 8 5.3 0.02 8 - - CONT. - 39.4 - - 4.9 - - 3.8 - LYD680 72231.2 - - - - - - 3.4 0.26 5 LYD680 72232.1 32.4 0.11 11 4.0 0.11 11 - - LYD680 72232.4 31.3 0.29 7 3.9 0.29 7 3.6 0.07 9 LYD678 72787.2 32.1 0.13 10 4.0 0.13 10 - - LYD678 72790.1 33.7 0.15 16 4.2 0.15 16 3.5 0.07 6 LYD664 72016.2 - - - - - - 3.4 0.23 4 LYD664 72017.7 35.1 0.06 20 4.4 0.06 20 3.5 0.11 8 LYD642 71824.5 33.3 0.05 14 4.2 0.05 14 3.7 L 13 LYD642 71825.1 31.4 0.22 8 3.9 0.22 8 3.4 0.16 4 LYD641 72632.2 31.4 0.24 8 3.9 0.24 8 - - LYD641 72633.4 41.0 0.11 41 5.1 0.11 41 3.9 0.08 19 LYD637 73683.1 32.6 0.17 12 4.3 0.02 19 3.6 0.01 11 LYD637 73685.3 - - - - - - 3.4 0.12 5 LYD624 73382.4 - - - - - - 3.6 0.02 10 LYD621 72571.1 32.2 0.11 11 4.0 0.11 11 3.5 0.03 8 LYD621 72573.6 32.3 0.11 11 4.0 0.11 11 3.5 0.24 6 LYD621 72574.3 32.5 0.09 12 4.1 0.09 12 3.5 0.08 6 LYD617 71966.6 - - - - - - 3.4 0.28 4 LYD616 73058.4 36.6 L 26 4.6 L 26 3.6 0.02 10 LYD616 73059.4 - - - - - - 3.5 0.14 6 LYD588 73855.2 35.1 0.23 20 4.4 0.23 20 3.6 0.20 12 LYD588 73855.3 32.5 0.14 11 4.1 0.14 11 3.5 0.04 8 LYD567 72495.3 - - - - - - 3.4 0.19 4 WO 2013/128448 PCT/IL2013/050172 285 Plot Coverage [cm 2 ] Rosette Area [cm 2 Rosette Diameter Gene Event # [cm] Name P- % P- % P- % Val. Incr. Val. Incr. Val. Incr. LYD567 72495.4 31.6 0.19 9 4.0 0.19 9 3.4 0.11 5 LYD567 72496.3 32.4 0.09 11 4.1 0.09 11 3.4 0.11 5 LYD559 73624.1 32.6 0.08 12 4.1 0.08 12 3.5 0.09 6 LYD538 72839.2 31.8 0.15 9 4.0 0.15 9 - - LYD537 73630.3 - - - - - - 3.5 0.12 8 LYD521 72611.1 32.0 0.21 10 4.0 0.21 10 - - LYD521 72611.3 33.0 0.28 13 4.1 0.28 13 3.5 0.19 7 CONT. - 29.1 - - 3.6 - - 3.3 - LYD689 72711.2 58.6 0.29 10 7.3 0.29 10 - - LYD689 72713.1 64.0 0.03 20 8.0 0.03 20 5.0 0.02 8 LYD682 72566.2 60.5 0.24 14 7.6 0.24 14 - - LYD677 72223.6 64.3 0.03 21 8.0 0.03 21 4.9 0.05 7 LYD669 72217.2 61.8 0.06 16 7.7 0.06 16 4.9 0.04 8 LYD669 73330.1 64.3 0.29 21 8.0 0.29 21 - - LYD666 72394.3 64.7 L 22 8.1 L 22 5.0 0.02 9 LYD666 72396.2 60.8 0.04 14 7.6 0.04 14 4.8 0.15 6 LYD650 72640.1 57.3 0.18 8 7.2 0.18 8 4.7 0.26 3 LYD620 73066.3 65.2 0.12 23 8.1 0.12 23 5.1 0.08 11 LYD620 73068.2 58.0 0.14 9 7.3 0.14 9 - - LYD602 72613.1 58.5 0.10 10 7.3 0.10 10 4.8 0.14 5 LYD598 72421.1 62.7 0.01 18 7.8 0.01 18 4.9 0.09 8 LYD598 72445.1 62.0 0.13 17 7.8 0.13 17 4.9 0.14 6 LYD598 72446.4 61.4 0.02 16 7.7 0.02 16 4.9 0.05 7 LYD574 73118.4 - - - - - - 5.0 0.05 9 LYD574 73119.1 67.1 0.04 26 8.4 0.04 26 5.0 0.07 9 LYD562 73484.2 62.5 0.27 18 7.8 0.27 18 - - LYD562 73489.4 65.4 L 23 8.2 L 23 5.0 0.28 8 LYD549 73029.4 63.4 0.06 19 7.9 0.06 19 4.9 0.06 6 CONT. - 53.1 - - 6.6 - - 4.6 - LYD688 73129.1 - - - - - - 4.6 0.27 9 LYD688 73133.1 68.7 L 45 8.6 L 45 5.2 L 24 LYD688 73134.6 62.9 0.13 33 7.9 0.13 33 4.9 L 16 LYD681 73184.1 58.5 L 24 7.3 L 24 4.7 L 11 LYD681 73184.2 56.7 0.27 20 7.1 0.27 20 4.7 0.09 12 LYD681 73184.3 55.2 0.02 17 6.9 0.02 17 4.5 0.04 7 LYD681 73186.2 58.5 0.21 24 7.3 0.21 24 4.8 0.19 13 LYD681 73188.3 54.6 0.20 15 6.8 0.20 15 4.6 0.04 8 LYD675 72644.1 64.2 0.12 36 8.0 0.12 36 4.9 0.07 16 LYD675 72644.3 59.0 L 25 7.4 L 25 4.7 0.01 12 LYD671 72878.2 54.3 0.16 15 6.8 0.16 15 4.6 0.09 8 WO 2013/128448 PCT/IL2013/050172 286 2 Rosette Diameter Plot Coverage [cm 2 ] Rosette Area [cm 2 ] R tm Gene Eet#[cm] Name P- % P- % P- % Ave. Ave. Ave. Vl nr Val. Incr. Val. Incr. Val. Incr. LYD665 72216.5 - - - - - - 4.6 0.07 8 LYD652 72559.1 53.6 0.05 13 6.7 0.05 13 4.7 0.14 11 LYD652 72560.1 53.6 0.05 13 6.7 0.05 13 4.5 0.12 6 LYD652 72563.1 51.9 0.26 10 6.5 0.26 10 4.4 0.16 5 LYD651 73021.3 57.4 L 21 7.2 L 21 4.7 L 11 LYD651 73021.5 55.3 0.02 17 6.9 0.02 17 4.6 0.01 9 LYD651 73026.4 55.9 0.18 18 7.0 0.18 18 4.6 0.09 10 LYD648 72834.1 - - - - - - 4.4 0.22 5 LYD644 72775.1 55.7 0.10 18 7.0 0.10 18 4.6 0.02 9 LYD639 72548.4 - - - - - - 4.7 0.22 11 LYD639 72549.3 52.6 0.10 11 6.6 0.10 11 4.5 0.11 7 LYD596 73635.1 - - - - - - 4.4 0.22 4 LYD596 73637.1 50.7 0.26 7 6.3 0.26 7 4.6 0.02 9 LYD594 73307.1 57.6 0.19 22 7.2 0.19 22 4.9 0.18 15 LYD594 73307.4 56.0 0.12 19 7.0 0.12 19 4.6 0.06 8 LYD577 72745.4 - - - - - - 4.5 0.17 7 LYD577 72748.3 57.1 0.11 21 7.1 0.11 21 4.8 0.14 13 LYD545 72506.2 - - - - - - 4.6 0.13 8 LYD545 72508.5 50.6 0.25 7 6.3 0.25 7 4.4 0.21 4 LYD541 72729.1 52.6 0.18 11 6.6 0.18 11 4.5 0.06 7 LYD534 72409.1 59.7 0.29 26 7.5 0.29 26 4.9 0.11 16 LYD534 72414.3 55.1 0.06 17 6.9 0.06 17 4.6 0.15 8 LYD524 72859.3 57.6 L 22 7.2 L 22 4.8 L 14 LYD524 72864.4 - - - - - - 4.5 0.11 5 LYD522 72716.2 - - - - - - 4.7 0.10 11 CONT. - 47.3 - - 5.9 - - 4.2 - Table 62. "CONT." - Control; "Ave." - Average; "% Incr." = % increment; "p-val." - p value, L- p<0.01. The transgenes were under the transcriptional regulation of the new At6669 promoter (SEQ ID NO: 4111). "-" = results are still unavailable. Table 63 5 Genes showing improved plant performance at Normal growth conditions under regulation of At6669 promoter RGR Of Leaf RGR Of Plot RGR Of Rosette Number Gene Number Coverage (cm 2 lday) Diameter (cm/day) Nae Event # (number/day) NameT Ave. P- % Ave. P- % Ave. P Val. Incr. Val. Incr. Val. Incr. LYD684 72274.1 - - - 8.6 0.02 39 0.4 0.17 15 LYD681 73186.2 - - - 7.6 0.16 23 - - - WO 2013/128448 PCT/IL2013/050172 287 RGR Of Leaf RGR Of Plot RGR Of Rosette Gene Number Coverage (cm 2 lday) Diameter (cm/day) Name Event # (number/day) Ave. Val. Incr. Ave. Val. Incr. Ave. Val. Incr. LYD681 73188.3 - - - 7.2 0.23 18 - - LYD672 72347.3 - - - 7.6 0.20 24 - - LYD667 72030.1 - - - 7.2 0.26 17 - - LYD661 72325.1 0.7 0.13 21 7.3 0.19 19 - - LYD661 72328.1 - - - 8.4 0.02 37 0.4 0.23 13 LYD661 72328.2 - - - 7.8 0.08 27 - - LYD626 72002.1 0.7 0.29 16 - - - - - LYD626 72003.1 - - - - - - 0.4 0.27 13 LYD620 73066.3 0.7 0.25 15 7.8 0.07 27 0.4 0.21 13 LYD620 73066.5 0.7 0.10 22 - - - - - LYD617 71966.6 0.7 0.11 21 8.2 0.03 34 0.4 0.24 13 LYD617 71967.1 0.7 0.23 16 - - - - - LYD609 73124.4 0.7 0.28 15 8.0 0.08 29 0.4 0.29 12 LYD609 73125.3 - - - 7.3 0.24 18 - - LYD609 73125.4 0.7 0.18 18 7.2 0.25 17 - - LYD596 73639.1 - - - 7.2 0.22 18 - - LYD593 71952.1 - - - 7.3 0.21 19 - - LYD593 71952.2 0.7 0.27 15 - - - - - LYD574 73118.3 - - - 7.3 0.24 19 - - LYD574 73118.4 - - - 8.2 0.03 33 - - LYD574 73122.3 - - - 7.2 0.28 17 - - LYD564 72182.4 - - - 7.1 0.28 16 - - LYD564 72184.1 - - - 7.8 0.17 26 - - LYD558 73112.3 - - - 8.2 0.03 33 0.4 0.25 13 LYD558 73113.1 - - - 7.1 0.26 16 - - LYD558 73114.3 0.7 0.12 21 - - - - - LYD527 72246.3 - - - 7.8 0.09 26 - - LYD526 72164.5 - - - 7.3 0.22 18 - - LYD526 72167.4 - - - 8.1 0.03 31 - - LYD526 72168.1 0.7 0.19 17 - - - - - LYD526 72168.4 - - - 7.4 0.16 21 - - CONT. - 0.6 - - 6.2 - - 0.4 - LYD680 72232.1 0.7 0.28 13 6.6 0.19 15 0.4 0.12 13 LYD668 72023.3 - - - 7.1 0.07 24 - - LYD664 72012.1 - - - 6.5 0.27 12 - - LYD664 72015.2 - - - 6.7 0.14 17 0.4 0.16 11 LYD661 72325.1 - - - 6.7 0.17 16 - - LYD661 72328.2 - - - 7.2 0.04 24 - - LYD642 71820.2 - - - - - - 0.4 0.26 9 WO 2013/128448 PCT/IL2013/050172 288 RGR Of Leaf RGR Of Plot RGR Of Rosette Gene Number Coverage (cm 2 lday) Diameter (cm/day) Name Event # (number/day) Ave. Val. Incr. Ave. Val. Incr. Ave. Val. Incr. LYD642 71821.4 0.7 0.23 14 - - - 0.4 0.11 12 LYD642 71824.5 0.7 0.09 21 8.0 L 38 0.4 0.01 20 LYD642 71825.1 0.7 0.16 17 - - - - - LYD631 72544.4 - - - 6.6 0.18 15 - - LYD621 72571.1 - - - 6.5 0.22 13 0.4 0.21 10 LYD621 72574.3 0.7 0.29 13 - - - - - LYD618 72621.2 - - - 7.1 0.04 24 0.4 0.10 13 LYD572 72390.3 - - - 6.8 0.13 17 0.4 0.09 13 LYD568 71930.1 - - - 7.2 0.04 25 0.4 0.03 17 LYD568 71931.4 - - - 6.7 0.15 16 0.4 0.27 8 LYD568 71932.2 0.7 0.27 13 - - - - - LYD561 72175.4 - - - 6.7 0.15 17 - - LYD561 72177.1 0.7 0.27 13 - - - - - LYD561 72177.2 - - - 6.8 0.12 19 0.4 0.25 9 LYD561 72179.1 - - - 6.6 0.19 15 - - LYD551 71986.9 - - - 6.6 0.18 14 0.4 0.26 8 LYD531 71916.3 0.7 0.29 13 - - - - - LYD531 71917.1 - - - 6.4 0.29 12 0.4 0.07 14 LYD531 71918.1 - - - 7.3 0.03 27 0.4 0.08 13 LYD531 71921.2 - - - 6.4 0.30 12 - - LYD528 72312.4 0.7 0.22 15 - - - - - LYD522 72715.2 - - - - - - 0.4 0.24 8 LYD522 72716.6 - - - 6.6 0.23 14 0.4 0.18 11 LYD522 72720.1 - - - - - - 0.4 0.27 8 LYD522 72720.2 0.7 0.21 15 6.7 0.15 16 - - CONT. - 0.6 - - 5.8 - - 0.3 - LYD688 73129.1 - - - 8.7 0.27 22 - - LYD688 73133.1 - - - 8.8 0.23 24 - - LYD670 73348.1 - - - 9.1 0.19 27 - - LYD662 72008.3 - - - 8.7 0.26 22 - - LYD646 73042.4 - - - 8.7 0.30 21 - - LYD599 72266.2 - - - 9.4 0.13 31 - - LYD562 73484.2 - - - 8.8 0.25 23 - - CONT. - - - - 7.2 - - - - LYD660 73929.2 0.8 0.09 21 8.5 0.14 21 - - LYD660 73933.5 0.8 0.30 14 9.4 0.03 34 0.4 0.18 15 LYD629 72195.1 0.8 0.13 20 8.2 0.22 18 - - LYD629 72198.3 - - - 8.7 0.09 25 - - LYD614 73916.4 - - - 8.1 0.27 16 - - - WO 2013/128448 PCT/IL2013/050172 289 RGR Of Leaf RGR Of Plot RGR Of Rosette Gene Number Coverage (cm 2 lday) Diameter (cm/day) Name Event # (number/day) Ave. Val. Incr. Ave. Val. Incr. Ave. Val. Incr. LYD614 73916.5 - - - 8.2 0.26 17 0.4 0.18 16 LYD609 73128.5 - - - 8.4 0.21 19 0.4 0.13 19 LYD584 73915.4 - - - 8.1 0.25 16 - - LYD570 71937.3 0.8 0.16 18 8.5 0.15 21 - - LYD561 72177.2 - - - - - - 0.4 0.28 13 CONT. - 0.7 - - 7.0 - - 0.3 - LYD672 72348.2 - - - - - - 0.3 0.18 10 LYD635 72626.2 - - - 5.5 0.17 14 0.3 0.07 12 LYD632 72770.2 - - - 5.7 0.10 19 0.3 0.17 11 LYD632 72771.1 - - - 5.6 0.11 17 0.3 0.07 13 LYD632 72774.4 - - - 5.3 0.27 11 - - LYD627 72765.1 - - - 6.0 0.04 25 - - LYD627 72766.1 - - - 5.4 0.20 13 - - LYD627 72767.1 - - - 5.8 0.06 22 0.3 0.08 14 LYD623 71970.2 0.7 0.21 21 - - - - - LYD623 71974.3 0.7 0.28 18 - - - - - LYD580 72188.2 - - - 5.4 0.24 12 - - LYD580 72189.2 - - - 5.5 0.16 15 0.3 0.06 14 LYD571 72357.5 - - - 5.9 0.04 23 0.3 0.09 11 LYD571 72358.1 - - - 5.9 0.04 22 0.3 0.05 14 LYD571 72358.3 - - - 6.7 L 39 0.4 0.02 18 LYD571 72358.4 - - - 5.7 0.06 20 0.3 0.29 7 LYD560 71925.1 - - - 6.2 0.02 28 0.3 0.16 12 LYD554 72174.4 - - - 5.6 0.11 17 - - LYD553 72741.2 - - - 5.4 0.20 13 0.3 0.22 8 LYD553 72741.3 - - - - - - 0.3 0.22 10 LYD548 72656.1 - - - 5.7 0.07 19 0.3 0.13 12 LYD548 72677.1 - - - 5.4 0.20 13 - - LYD547 71980.1 - - - 5.8 0.04 21 - - LYD538 72835.2 - - - 6.4 L 33 0.4 L 20 LYD527 72241.3 - - - 5.4 0.21 13 - - LYD527 72245.2 - - - 5.5 0.19 14 - - LYD527 72246.3 - - - 5.4 0.24 12 0.3 0.06 14 LYD521 72610.1 - - - 5.8 0.07 20 0.3 0.22 10 CONT. - 0.6 - - 4.8 - - 0.3 - LYD678 72790.1 - - - 4.2 0.27 16 - - LYD664 72017.7 - - - 4.4 0.17 21 - - LYD641 72633.4 - - - 5.0 0.01 39 0.3 0.15 14 LYD641 72635.2 0.7 0.23 14 - - - - - - WO 2013/128448 PCT/IL2013/050172 290 RGR Of Leaf RGR Of Plot RGR Of Rosette Gene Number Coverage (cm 2 lday) Diameter (cm/day) Name Event # (number/day) Ave. Val. Incr. Ave. Val. Incr. Ave. Val. Incr. LYD624 73382.4 - - - - - - 0.3 0.27 10 LYD616 73058.4 - - - 4.5 0.09 25 - - LYD588 73855.2 - - - 4.4 0.18 21 - - LYD567 72495.4 0.7 0.29 14 - - - - - LYD559 73624.1 0.7 0.22 14 - - - - - LYD538 72835.4 0.7 0.28 13 - - - 0.3 0.25 11 LYD537 73630.3 - - - - - - 0.3 0.22 12 LYD521 72607.1 - - - 4.3 0.21 19 - - CONT. - 0.6 - - 3.6 - - 0.3 - LYD689 72713.1 - - - 7.5 0.23 19 - - LYD682 72568.2 0.7 0.28 14 - - - - - LYD677 72223.6 - - - 7.6 0.19 21 - - LYD669 72217.2 - - - 7.4 0.24 18 - - LYD669 73327.1 0.7 0.14 21 - - - - - LYD669 73330.1 - - - 7.8 0.15 24 0.4 0.20 12 LYD666 72394.3 - - - 7.6 0.20 21 0.4 0.28 9 LYD650 72642.5 0.7 0.11 21 - - - - - LYD620 73066.3 - - - 7.7 0.15 22 0.4 0.26 10 LYD598 72421.1 - - - 7.3 0.27 17 0.4 0.30 9 LYD598 72445.1 - - - 7.4 0.27 18 - - LYD574 73119.1 0.7 0.29 14 8.0 0.10 27 - - LYD574 73121.2 0.7 0.26 15 - - - - - LYD562 73484.2 0.7 0.27 15 7.4 0.26 18 - - LYD562 73489.4 - - - 7.8 0.13 24 - - LYD549 73029.4 - - - 7.5 0.21 20 - - LYD542 72733.2 0.7 0.24 17 7.4 0.27 18 - - LYD542 72735.4 0.7 0.19 18 - - - - - LYD542 72736.4 0.7 0.21 16 - - - - - LYD536 72531.3 0.7 0.09 23 - - - - - CONT. - 0.6 - - 6.3 - - 0.4 - LYD688 73133.1 - - - 8.1 0.01 44 0.4 0.03 25 LYD688 73134.6 - - - 7.4 0.05 33 0.4 0.12 17 LYD681 73184.1 - - - 6.8 0.18 22 0.4 0.16 15 LYD681 73184.2 - - - 6.7 0.23 20 0.4 0.21 14 LYD681 73186.2 - - - 6.9 0.16 24 - - LYD675 72644.1 - - - 7.6 0.04 36 0.4 0.14 16 LYD675 72644.3 0.7 0.22 17 6.9 0.15 24 0.4 0.23 13 LYD675 72648.1 0.7 0.20 18 6.9 0.20 24 - - LYD671 72882.3 0.7 0.14 19 - - - - - - WO 2013/128448 PCT/IL2013/050172 291 RGR Of Leaf RGR Of Plot RGR Of Rosette Gene Coverage (cm 2 /day) Diameter (cm/day) Name Event # (number/day) Ave. P_ % Ave. P_ % Ave. P Val. Incr. Val. Incr. Val. Incr. LYD651 73021.3 - - - 6.7 0.22 20 - - LYD651 73026.4 - - - 6.6 0.27 18 0.4 0.27 12 LYD644 72775.1 0.7 0.25 16 6.5 0.29 17 - - LYD639 72548.4 - - - 6.6 0.28 19 0.4 0.23 13 LYD594 73307.1 - - - 6.8 0.18 22 0.4 0.20 15 LYD594 73307.3 - - - 6.6 0.28 19 - - LYD594 73307.4 - - - 6.6 0.26 18 - - LYD577 72748.3 - - - 6.7 0.21 21 0.4 0.24 13 LYD545 72508.2 0.7 0.30 13 - - - - - LYD534 72409.1 - - - 7.0 0.15 25 0.4 0.15 16 LYD534 72414.3 - - - 6.6 0.28 18 - - LYD524 72859.3 - - - 6.8 0.20 21 0.4 0.21 13 LYD524 72859.4 0.7 0.12 20 - - - - - LYD522 72720.1 0.7 0.27 14 - - - - - CONT. - 0.6 - - 5.6 - - 0.3 - Table 63. "CONT." - Control; "Ave." - Average; "% Incr." = % increment; "p-val." - p value, L- p< 0
.
0 1. The transgenes were under the transcriptional regulation of the new At6669 promoter (SEQ ID NO: 4111). "-" = results are still unavailable. 5 EXAMPLE 17 EVALUATING TRANSGENIC ARABIDOPSIS UNDER NORMAL CONDITIONS USING IN VITRO ASSAYS [TISSUE CULTURE T2 AND Ti PLANTS, TC -T2 AND TC-T1 ASSAYS] Surface sterilized seeds were sown in basal media [50 % Murashige-Skoog 10 medium (MS) supplemented with 0.8 % plant agar as solidifying agent] in the presence of Kanamycin (used as a selecting agent). After sowing, plates were transferred for 2-3 days for stratification at 4 'C and then grown at 25 'C under 12-hour light 12-hour dark daily cycles for 7 to 10 days. At this time point, seedlings randomly chosen were carefully transferred to plates containing MS media (15 mM N). For experiments 15 performed in T 2 lines, each plate contained 5 seedlings of the same transgenic event, and 3-4 different plates (replicates) for each event. For each polynucleotide of the invention at least four-five independent transformation events were analyzed from each construct. For experiments performed in T 1 lines, each plate contained 5 seedlings of 5 WO 2013/128448 PCT/IL2013/050172 292 independent transgenic events and 3-4 different plates (replicates) were planted. In total, for T 1 lines, 20 independent events were evaluated. Plants expressing the polynucleotides of the invention were compared to the average measurement of the control plants (empty vector or GUS reporter gene under the same promoter) used in the 5 same experiment. Digital imaging - A laboratory image acquisition system, which consists of a digital reflex camera (Canon EOS 300D) attached with a 55 mm focal length lens (Canon EF-S series), mounted on a reproduction device (Kaiser RS), which includes 4 light units (4 x 150 Watts light bulb) and located in a darkroom, was used for capturing 10 images of plantlets sawn in agar plates. The image capturing process was repeated every 3-4 days starting at day 1 till day 10 (see for example the images in Figures 3A-F). An image analysis system was used, which consists of a personal desktop computer (Intel P4 3.0 GHz processor) and a public domain program - ImageJ 1.39 [Java based image processing program which was 15 developed at the U.S. National Institutes of Health and freely available on the internet at Hypertext Transfer Protocol://rsbweb (dot) nih (dot) gov/]. Images were captured in resolution of 10 Mega Pixels (3888 x 2592 pixels) and stored in a low compression JPEG (Joint Photographic Experts Group standard) format. Next, analyzed data was saved to text files and processed using the JMP statistical analysis software (SAS 20 institute). Seedling analysis - Using the digital analysis seedling data was calculated, including leaf area, root coverage and root length. The relative growth rate for the various seedling parameters was calculated according to the following formulas XV (RGR leaf area), and XVI (RGR root length). 25 Formula XV: Relative growth rate of leaf area = Regression coefficient of leaf area along time course. Formula XVI: Relative growth rate of root length = Regression coefficient of root length along 30 time course. At the end of the experiment, plantlets were removed from the media and weighed for the determination of plant fresh weight. Plantlets were then dried for 24 WO 2013/128448 PCT/IL2013/050172 293 hours at 60'C, and weighed again to measure plant dry weight for later statistical analysis. The fresh and dry weights are provided for each Arabidopsis plant. Growth rate was determined by comparing the leaf area coverage, root coverage and root length, between each couple of sequential photographs, and results were used to resolve the 5 effect of the gene introduced on plant vigor under optimal conditions. Similarly, the effect of the gene introduced on biomass accumulation, under optimal conditions, was determined by comparing the plants' fresh and dry weight to that of control plants (containing an empty vector or the GUS reporter gene under the same promoter). From every construct created, 3-5 independent transformation events were examined in 10 replicates. Statistical analyses - To identify genes conferring significantly improved plant vigor or enlarged root architecture, the results obtained from the transgenic plants were compared to those obtained from control plants. To identify outperforming genes and constructs, results from the independent transformation events tested were analyzed 15 separately. To evaluate the effect of a gene event over a control the data was analyzed by Student's t-test and the p value was calculated. Results were considered significant if p < 0.1. The JMP statistics software package was used (Version 5.2.1, SAS Institute Inc., Cary, NC, USA). Experimental results: 20 Results from T2 plants Tables 64-66 summarize the observed phenotypes of transgenic plants expressing the gene constructs using the TC -T2 Assays. The genes presented in Table 64 showed a significant improvement as they produced larger plant biomass (plant fresh and dry weight) in T2 generation when 25 grown under normal growth conditions, as compared to control plants grown under identical growth conditions. The genes were cloned under the regulation of a constitutive promoter (At6669, SEQ ID NO:41 11). The evaluation of each gene was carried out by testing the performance of different number of events. Some of the genes were evaluated in more than one tissue 30 culture assay. The results obtained in these second experiments were significantly positive as well.
WO 2013/128448 PCT/IL2013/050172 294 Table 64 Genes showing improved plant performance at Normal growth conditions under regulation of At6669 promoter 5 Gene Dry Weight [mg] Fresh Weight [mg] Name Event # r egt[g Name Ave. P-Val. % Incr. Ave. P-Val. % Incr. LYD686 72796.2 6.6 L 83 119.8 0.01 51 LYD686 72798.1 6.8 L 88 127.7 L 61 LYD685 72458.3 5.8 0.22 61 - - LYD685 72458.5 6.5 0.06 80 116.9 0.09 48 LYD685 72459.1 5.5 0.11 52 125.7 0.27 59 LYD685 72462.4 - - - 105.5 0.09 33 LYD685 72462.5 4.8 0.14 33 103.3 0.12 30 LYD673 72662.2 5.2 0.02 44 - - LYD673 72664.1 4.8 0.24 33 - LYD673 72666.1 4.5 0.23 23 - - LYD663 72856.3 5.4 L 48 102.2 0.29 29 LYD663 72856.5 5.6 0.01 54 106.3 0.03 34 LYD663 72858.1 5.6 L 55 98.7 0.07 25 LYD663 72858.3 4.9 0.07 34 - - LYD655 72209.1 - - - 106.5 0.21 34 LYD655 72210.1 4.8 0.26 33 - - LYD640 72556.3 6.6 0.01 81 106.2 0.07 34 LYD640 72557.2 4.6 0.07 27 - - LYD640 72558.2 6.2 L 71 105.2 0.04 33 LYD638 72451.1 6.3 L 73 109.6 0.02 38 LYD638 72456.2 4.2 0.25 17 - - LYD615 72260.1 6.1 0.06 68 104.8 0.17 32 LYD615 72264.2 5.3 0.02 46 92.9 0.22 17 LYD613 72512.3 5.0 0.08 37 - - LYD613 72514.2 6.1 0.16 68 109.0 0.29 38 LYD613 72515.4 4.9 0.13 34 99.0 0.24 25 LYD608 72883.2 5.9 L 63 95.7 0.12 21 LYD608 72888.2 6.4 L 77 119.5 L 51 LYD607 71961.1 7.3 L 103 133.1 L 68 LYD607 71963.1 6.3 0.02 73 119.2 0.04 51 LYD607 71963.2 5.7 0.09 58 128.8 0.11 63 LYD607 71963.4 5.1 0.08 40 - - LYD597 72419.1 5.1 0.18 41 - LYD597 72419.2 4.1 0.17 13 - - LYD597 72419.3 6.6 L 81 106.7 0.01 35 LYD597 72420.1 4.9 L 34 - - LYD597 72443.4 5.8 0.23 59 - LYD583 71943.1 4.7 0.04 30 - - WO 2013/128448 PCT/IL2013/050172 295 Gene Dry Weight [ng] Fresh Weight [mg] Name Event # r egt[g Name Ave. P-Val. % Incr. Ave. P-Val. % Incr. LYD579 72350.3 5.1 0.03 40 92.1 0.23 16 LYD579 72354.1 5.7 0.14 57 104.6 0.15 32 LYD563 72319.2 4.1 0.19 13 - - LYD563 72319.4 6.5 0.02 78 110.3 0.12 39 LYD563 72321.2 4.8 0.17 32 - - LYD563 72323.1 5.0 0.07 38 - CONT. - 3.6 - - 79.2 - LYD676 73880.1 4.9 0.17 43 97.8 0.17 41 LYD676 73884.1 - - - 85.6 0.16 23 LYD660 73932.1 5.1 0.03 49 107.4 L 54 LYD654 73924.4 4.7 0.06 36 96.9 0.05 39 LYD654 73926.3 4.3 0.17 25 84.0 0.20 21 LYD647 72784.3 5.6 0.09 64 116.9 0.07 68 LYD647 72785.2 4.8 0.04 38 103.7 L 49 LYD628 73678.3 4.5 0.25 30 92.9 0.15 34 LYD628 73679.2 7.6 0.11 120 136.4 0.11 96 LYD614 73917.1 4.8 0.04 38 106.8 0.04 54 LYD614 73919.3 6.2 0.04 78 128.1 0.05 84 LYD611 71988.3 4.6 0.07 35 93.1 0.04 34 LYD611 71992.5 5.2 0.02 51 104.8 0.13 51 LYD611 71992.6 5.7 0.07 66 92.1 0.13 32 LYD605 73643.1 5.8 0.05 67 104.0 0.07 50 LYD605 73644.2 5.1 0.04 47 106.8 0.07 54 LYD605 73645.2 - - - 79.8 0.29 15 LYD598 72421.2 5.8 L 67 104.4 0.04 50 LYD598 72423.2 4.6 0.07 33 - - LYD598 72423.3 4.8 0.16 38 92.8 0.04 33 LYD591 73907.3 5.0 0.04 46 91.2 0.24 31 LYD589 73898.1 5.5 L 61 119.7 0.08 72 LYD589 73902.3 4.6 0.24 35 - - LYD589 73903.3 5.5 L 61 111.2 0.02 60 LYD588 73852.2 4.7 0.22 37 - - LYD588 73854.1 5.2 0.10 51 111.9 0.03 61 LYD588 73855.3 5.8 0.03 69 115.6 0.04 66 LYD584 73910.2 4.5 0.08 30 99.5 0.01 43 LYD584 73915.4 - - - 84.7 0.24 22 LYD566 73482.4 6.4 L 85 127.5 L 83 LYD566 73483.5 4.8 0.13 40 101.1 0.11 45 LYD535 72850.5 5.0 0.21 45 95.7 0.29 38 LYD535 72851.6 4.9 0.04 43 98.1 0.06 41 LYD535 72852.1 6.2 L 79 121.1 L 74 CONT. - 3.4 - - 69.5 -- WO 2013/128448 PCT/IL2013/050172 296 Gene Dry Weight [ng] Fresh Weight [mg] Name Event # r egt[g Name Ave. P-Val. % Incr. Ave. P-Val. % Incr. LYD682 72565.2 - - - 83.8 0.10 23 LYD682 72566.1 - - - 91.7 0.02 35 LYD665 72215.2 4.5 0.22 18 - - LYD665 72216.4 5.3 0.18 39 95.8 0.03 41 LYD650 72641.2 - - - 86.2 0.21 27 LYD644 72775.1 - - - 96.4 0.03 41 LYD644 72780.2 - - - 92.4 0.11 36 LYD626 72001.1 - - - 82.2 0.10 21 LYD626 72001.3 5.1 0.15 35 96.4 0.09 42 LYD626 72002.1 - - - 102.3 L 50 LYD555 74193.5 - - - 92.1 0.02 35 LYD555 74194.1 4.8 0.17 26 100.6 L 48 LYD555 74197.1 - - - 95.5 L 40 LYD542 72733.1 4.9 0.17 28 96.4 0.15 41 LYD542 72733.2 - - - 99.1 0.15 45 LYD542 72736.4 - - - 101.3 0.14 49 LYD540 74182.4 - - - 84.0 0.18 23 LYD540 74183.3 - - - 91.9 0.23 35 LYD536 72529.5 - - - 90.3 0.03 33 LYD536 72532.2 4.8 0.06 26 - - LYD533 72721.1 5.0 0.23 30 97.7 0.19 43 LYD533 72721.2 4.7 0.20 23 95.2 0.02 40 LYD533 72722.1 - - - 89.2 0.09 31 LYD533 72723.1 5.8 0.29 51 117.9 0.07 73 LYD526 72164.4 4.7 0.11 24 96.3 0.12 41 CONT. - 3.8 - - 68.1 - LYD679 72650.6 8.6 0.03 56 151.9 0.09 33 LYD645 72339.2 10.2 0.01 85 192.3 0.02 68 LYD636 72200.3 9.2 0.02 68 160.6 0.05 40 LYD634 71998.2 9.9 0.03 80 197.9 0.05 73 LYD634 71999.3 7.5 0.24 36 137.0 0.30 20 LYD567 72496.3 8.8 0.21 59 - - LYD556 72904.3 9.1 0.06 65 184.3 0.09 61 LYD552 72983.2 9.5 0.01 73 170.6 0.02 49 CONT. - 5.5 - - 114.7 - LYD689 72712.3 5.5 0.24 37 - - LYD689 72713.1 9.6 0.05 141 174.7 L 118 LYD675 72643.1 7.3 0.08 82 142.2 0.08 77 LYD675 72644.3 8.7 0.01 119 174.8 L 118 LYD675 72646.1 9.6 L 140 165.4 0.01 106 LYD671 72877.1 - - - 100.3 0.12 25 LYD671 72878.2 6.8 0.02 69 119.2 0.16 49 WO 2013/128448 PCT/IL2013/050172 297 Gene Dry Weight [ng] Fresh Weight [mg] Name Event # r egt[g Name Ave. P-Val. % Incr. Ave. P-Val. % Incr. LYD671 72880.1 - - - 104.4 0.05 30 LYD654 73922.3 6.6 L 65 119.5 0.03 49 LYD654 73924.5 5.7 0.16 44 - - LYD652 72560.2 7.3 0.03 83 141.0 0.04 76 LYD652 72561.5 7.4 0.02 86 161.3 0.06 101 LYD652 72563.1 9.1 0.06 129 163.1 0.02 103 LYD648 72834.2 9.2 L 130 177.1 L 121 LYD641 72633.4 5.8 0.22 44 116.2 0.22 45 LYD641 72635.2 7.4 0.06 86 142.4 0.03 78 LYD636 72199.3 7.8 0.10 95 135.9 0.08 69 LYD636 72202.3 6.0 0.28 49 - - LYD602 72613.1 6.1 0.19 52 134.4 0.13 68 LYD602 72614.2 7.5 L 87 158.5 L 98 LYD599 72265.3 6.3 0.07 59 - - LYD599 72266.4 7.8 0.03 96 131.4 L 64 LYD599 72270.4 8.8 L 121 157.8 L 97 LYD555 74194.1 6.7 0.01 67 131.9 0.01 64 LYD555 74197.1 7.9 L 98 137.4 0.03 71 LYD555 74197.4 7.9 0.03 97 158.8 0.02 98 LYD555 74197.6 5.0 0.09 27 94.8 0.06 18 LYD548 72655.3 8.9 0.03 123 152.2 0.07 90 LYD548 72656.2 5.3 0.14 34 97.7 0.20 22 LYD541 72729.2 6.8 0.06 71 136.9 0.12 71 LYD541 72729.7 5.2 0.29 32 - - LYD541 72731.4 6.5 0.14 62 109.5 0.27 37 LYD540 74182.2 5.0 0.20 26 98.0 0.17 22 LYD540 74182.7 6.8 L 71 133.2 0.03 66 LYD524 72859.1 9.6 L 141 178.9 L 123 LYD524 72859.4 8.0 0.06 100 129.9 0.09 62 CONT. - 4.0 - - 80.2 - LYD683 72866.4 11.2 L 159 211.9 L 147 LYD683 72870.1 6.9 0.10 59 117.4 0.12 37 LYD683 72870.4 5.5 0.12 28 - - LYD654 73922.4 5.2 0.26 20 107.6 0.16 25 LYD654 73924.4 6.6 0.21 53 120.2 0.30 40 LYD654 73924.5 5.8 0.08 33 114.2 0.01 33 LYD654 73926.3 7.9 0.01 82 146.8 L 71 LYD628 73679.2 5.8 0.22 34 114.2 0.23 33 LYD628 73680.2 5.5 0.21 26 - - LYD628 73681.5 8.7 0.06 100 152.2 0.06 77 LYD624 73181.3 5.8 0.15 34 114.2 0.22 33 LYD624 73382.3 5.9 0.30 36 116.6 0.22 36 WO 2013/128448 PCT/IL2013/050172 298 Gene Dry Weight [ng] Fresh Weight [mg] Name Event # r egt[g Name Ave. P-Val. % Incr. Ave. P-Val. % Incr. LYD624 73383.1 6.3 L 45 124.5 0.01 45 LYD624 73385.3 5.6 0.22 29 117.8 0.11 37 LYD605 73642.3 6.2 L 44 114.7 0.09 33 LYD604 73045.1 6.9 0.17 60 125.7 0.22 46 LYD604 73045.4 6.5 L 49 120.0 0.04 40 LYD604 73048.2 6.6 0.26 51 119.3 0.28 39 LYD598 72421.1 6.2 0.26 42 - - LYD598 72445.1 6.0 0.01 39 112.0 0.07 30 LYD581 73107.1 5.9 0.03 37 108.6 0.10 27 LYD581 73107.5 5.5 0.27 27 - - LYD581 73109.2 7.7 0.04 78 144.2 L 68 LYD581 73109.3 8.5 L 95 142.1 0.04 65 LYD581 73110.1 7.8 L 81 135.5 L 58 LYD566 73480.4 7.7 0.03 78 143.1 0.07 67 LYD566 73482.4 7.2 L 65 123.7 L 44 LYD566 73483.6 5.0 0.26 15 - - LYD554 72171.1 9.1 0.01 109 153.4 0.01 79 LYD554 72174.4 7.2 0.17 65 126.6 0.20 47 LYD550 74186.3 6.5 0.14 50 - - LYD550 74187.1 6.2 L 44 110.1 0.11 28 LYD550 74187.2 6.3 0.12 45 121.3 0.13 41 LYD548 72655.3 6.1 0.03 41 109.7 0.10 28 LYD548 72673.3 5.2 0.28 20 106.8 0.26 24 LYD540 74181.2 8.7 L 101 157.3 L 83 LYD540 74182.2 7.2 L 67 134.2 L 56 LYD540 74182.4 7.0 0.05 61 129.8 0.01 51 LYD540 74182.7 5.9 0.27 35 117.9 0.10 37 LYD535 72850.5 6.8 0.07 57 116.6 0.14 36 LYD535 72851.4 6.1 0.15 40 - - LYD535 72852.2 5.2 0.25 21 - - LYD530 73052.3 9.5 L 120 153.3 L 79 LYD530 73053.3 9.0 L 107 152.0 L 77 LYD530 73053.5 7.1 0.03 64 127.7 0.07 49 LYD530 73054.3 5.3 0.22 22 108.0 0.21 26 CONT. - 4.3 - - 85.9 - LYD637 73685.1 9.0 0.15 42 173.7 0.13 53 LYD637 73685.2 8.0 0.18 26 142.9 0.25 26 LYD637 73685.3 9.8 0.03 54 183.6 0.05 62 LYD605 73642.3 - - - 149.8 0.17 32 LYD605 73644.2 8.2 0.14 29 142.8 0.22 26 LYD605 73645.2 10.2 0.03 60 168.6 0.12 49 LYD585 72986.1 8.5 0.13 34 167.2 0.08 48 WO 2013/128448 PCT/IL2013/050172 299 Gene Dry Weight [ng] Fresh Weight [mg] Name Ave. P-Val. % Incr. Ave. P-Val. % Incr. LYD585 72986.4 9.1 0.09 44 161.4 0.09 42 LYD573 72977.1 - - - 151.0 0.24 33 LYD573 72978.2 - - - 151.0 0.24 33 LYD559 73627.2 8.3 0.24 31 140.9 0.28 24 LYD537 73633.4 8.8 0.24 39 - - LYD537 73633.5 - - - 136.2 0.29 20 CONT. - 6.3 - - 113.3 - LYD683 72868.1 7.2 0.28 24 - - LYD647 72785.3 8.2 0.11 41 161.8 0.10 35 LYD611 71992.5 9.7 0.02 65 188.8 L 57 LYD611 71992.6 8.2 0.11 40 149.9 0.21 25 LYD585 72987.2 7.5 0.29 27 - - LYD573 72973.2 8.4 0.11 44 161.1 0.11 34 LYD550 74188.2 7.6 0.07 30 152.9 0.07 27 CONT. - 5.9 - - 120.2 - LYD686 72796.2 5.3 0.28 26 - - LYD673 72662.2 6.5 0.03 55 130.2 0.04 42 LYD663 72853.5 6.5 0.17 55 - - LYD655 72209.1 7.1 0.11 70 141.0 0.07 54 LYD638 72432.2 6.5 0.19 55 117.7 0.20 29 LYD638 72451.1 - - - 128.8 0.23 41 LYD615 72262.1 6.0 0.06 44 140.9 0.06 54 LYD613 72512.1 - - - 120.1 0.21 31 LYD608 72885.3 6.7 0.08 59 124.6 0.08 36 LYD608 72887.1 8.8 0.03 110 174.5 0.05 91 LYD608 72888.2 5.3 0.28 27 112.6 0.24 23 LYD607 71961.1 5.9 0.08 40 125.3 0.09 37 LYD607 71963.2 5.9 0.08 40 116.2 0.22 27 LYD597 72419.2 7.8 0.02 85 151.2 0.04 65 LYD597 72419.3 7.2 0.08 73 121.1 0.17 32 LYD597 72420.1 8.0 L 91 158.4 0.02 73 LYD583 71943.1 5.8 0.23 39 116.7 0.24 28 LYD583 71943.5 5.5 0.28 30 - - LYD579 72350.3 6.9 0.05 64 162.1 0.02 77 LYD579 72354.1 8.3 0.02 98 169.3 0.05 85 LYD563 72319.2 6.9 0.01 65 124.5 0.06 36 LYD563 72324.2 8.0 0.12 90 182.8 0.04 100 CONT. - 4.2 - - 91.5 - LYD592 74348.3 - - - 157.0 0.27 29 LYD592 74350.1 - - - 212.2 0.13 75 LYD592 74351.1 - - - 153.7 0.14 26 LYD592 74353.3 - - - 230.9 L 90 WO 2013/128448 PCT/IL2013/050172 300 Gene Dry Weight [ng] Fresh Weight [mg] Name Event # r egt[g Name Ave. P-Val. % Incr. Ave. P-Val. % Incr. CONT. - - - - 121.6 - LYD676 73881.2 5.8 0.15 16 131.1 0.29 51 LYD591 73905.1 5.9 0.13 16 97.4 0.24 12 CONT. - 5.0 - - 86.9 - LYD665 72211.2 6.8 L 97 127.0 L 82 LYD665 72216.4 5.0 0.11 45 97.7 0.14 40 LYD665 72216.5 6.3 0.13 84 120.8 0.17 74 LYD665 72216.6 5.3 0.13 54 100.8 0.25 45 LYD592 74348.3 6.6 0.02 93 122.9 0.02 77 LYD592 74348.4 8.3 0.02 143 149.5 0.02 115 LYD592 74349.2 6.2 0.06 80 112.5 0.07 62 LYD592 74350.1 9.6 L 179 175.3 L 152 LYD592 74351.1 9.8 0.10 185 196.6 0.09 183 LYD532 74343.2 5.6 L 64 108.0 L 55 LYD532 74344.2 4.8 0.20 40 84.0 0.26 21 LYD532 74345.1 4.7 0.08 36 89.0 0.05 28 LYD532 74345.3 6.5 0.01 90 135.9 0.01 95 LYD525 74229.2 6.4 0.04 87 117.9 0.02 69 LYD525 74230.2 7.8 0.09 128 141.5 0.09 103 LYD525 74233.1 4.3 0.16 25 81.1 0.28 17 CONT. - 3.4 - - 69.6 - LYD679 72652.3 6.7 0.03 55 153.5 0.11 41 LYD670 73346.2 4.9 0.20 13 - - LYD670 73348.1 5.7 0.04 33 - - LYD646 73040.3 6.5 0.19 52 143.2 0.26 32 LYD646 73040.4 5.6 L 31 134.8 0.17 24 LYD646 73042.4 5.1 0.23 19 - - LYD616 73057.4 5.1 0.20 19 - - LYD609 73124.2 8.7 0.04 101 200.8 0.07 85 LYD609 73128.5 5.4 0.23 26 - - LYD604 73047.3 5.8 0.08 34 - - LYD596 73634.2 5.4 0.09 26 127.1 0.26 17 LYD581 73107.1 7.2 L 67 164.9 0.07 52 LYD558 73112.3 5.5 0.01 28 137.2 0.12 26 LYD558 73113.1 5.1 0.13 18 - - LYD558 73114.3 6.5 0.21 51 163.2 0.26 50 LYD552 72981.3 6.9 L 60 168.9 L 56 LYD552 72981.4 5.9 0.17 37 145.5 0.05 34 LYD530 73052.3 5.2 0.06 21 - - LYD529 72899.7 6.4 L 48 135.5 0.08 25 CONT. - 4.3 - - 108.5 - - WO 2013/128448 PCT/IL2013/050172 301 Table 64. "CONT." - Control; "Ave." - Average; "% Incr." = % increment; "p-val." - p value, L- p<0.01. The transgenes were under the transcriptional regulation of the new At6669 promoter (SEQ ID NO: 4111). "-" = results are still unavailable. 5 The genes presented in Tables 65 and 66 show a significant improvement in plant performance since they produced a larger leaf biomass (leaf area) and root biomass (root length and root coverage) (Table 65) and a higher relative growth rate of leaf area, root coverage and root length (Table 66) when grown under normal growth conditions, as compared to control plants grown under identical growth conditions. 10 Plants producing larger root biomass have better possibilities to absorb larger amount of nitrogen from soil. Plants producing larger leaf biomass have better ability to produce assimilates. The genes were cloned under the regulation of a constitutive promoter (At6669). The evaluation of each gene was performed by testing the performance of different number of events. Some of the genes were evaluated in more than one tissue 15 culture assay. This second experiment confirmed the significant increment in leaf and root performance. Event with p-value < 0.1 was considered statistically significant. Table 65 Genes showing improved plant performance at Normal growth conditions under regulation 20 of At6669 promoter Leaf Area [cm 2 ] Roots Coverage [cm 2 ] Roots Length [cm] Gene Event # P- % P- % P- % Name Ave. Ave. Ave. Vl nr Val. Incr. Val. Incr. Val. Incr. LYD686 72796.2 0.5 L 56 10.9 0.03 48 7.8 0.23 6 LYD686 72798.1 0.5 L 59 - - - - - LYD685 72458.3 0.5 0.10 46 - - - - - LYD685 72458.5 0.5 L 58 12.4 0.02 67 8.4 L 15 LYD685 72459.1 0.4 0.08 33 8.8 0.18 19 - - LYD685 72462.4 0.5 0.08 45 - - - - - LYD685 72462.5 0.5 0.05 43 10.0 0.18 36 - - LYD673 72662.2 0.4 0.06 29 9.3 0.17 25 8.0 L 9 LYD673 72663.3 0.4 0.07 27 - - - - - LYD673 72664.1 0.4 0.15 26 - - - - - LYD673 72666.1 0.4 0.14 25 8.8 0.23 20 7.8 0.19 6 LYD663 72856.3 0.5 0.04 43 10.6 0.07 43 - - LYD663 72856.5 0.5 0.01 44 10.4 L 40 - - LYD663 72858.1 0.5 L 42 9.9 0.07 33 - - LYD663 72858.3 0.4 0.12 22 9.9 0.03 33 - - LYD655 72210.1 0.4 0.21 34 9.5 0.21 29 - - LYD640 72556.3 0.5 0.02 57 11.3 0.03 53 - - - WO 2013/128448 PCT/IL2013/050172 302 Leaf Area [cm 2 ] Roots Coverage [cm 2 ] Roots Length [cm] Gene Event # P- % P- % P- % Name Ave. Val. Incr. Ave. Val. Incr. Ave. Val. Incr. LYD640 72557.2 0.4 L 30 9.2 0.05 24 - - LYD640 72558.2 0.5 L 55 11.4 0.04 54 8.1 0.05 10 LYD638 72432.2 - - - 8.1 0.18 10 7.8 0.11 7 LYD638 72451.1 0.5 L 66 12.0 L 63 8.1 L 10 LYD615 72259.2 0.4 0.19 32 - - - - - LYD615 72260.1 0.5 0.05 58 11.1 0.01 50 8.3 L 13 LYD615 72264.2 0.4 0.02 32 - - - - - LYD613 72512.3 0.4 0.05 28 8.7 0.11 18 - - LYD613 72514.2 0.5 0.11 53 - - - - - LYD613 72515.4 0.4 0.01 24 - - - - - LYD608 72883.2 0.5 L 40 9.9 L 34 - - LYD608 72888.2 0.5 0.01 44 12.9 L 74 8.1 0.01 11 LYD607 71961.1 0.6 L 73 11.5 L 56 - - LYD607 71963.1 0.5 0.02 59 9.7 0.23 32 - - LYD607 71963.2 0.5 0.02 43 11.6 L 57 - - LYD607 71963.4 0.4 0.05 32 - - - - - LYD597 72419.3 0.5 L 37 8.6 0.19 16 - - LYD597 72420.1 0.4 0.16 11 - - - - - LYD583 71943.1 0.4 0.10 13 - - - - - LYD579 72350.2 0.4 0.03 18 8.0 0.15 8 - - LYD579 72350.3 0.5 L 37 10.9 0.06 47 7.8 0.19 6 LYD579 72354.1 0.5 0.02 43 11.2 0.01 51 8.0 0.03 9 LYD563 72319.2 0.4 0.02 20 8.8 0.19 19 - - LYD563 72319.4 0.5 0.04 54 11.4 0.01 54 7.8 0.17 6 LYD563 72321.2 0.4 0.24 25 - - - - - LYD563 72323.1 0.4 0.04 33 11.8 0.08 59 - - LYD563 72324.2 - - - - - - 7.8 0.15 7 CONT. - 0.3 - - 7.4 - - 7.3 - LYD676 73880.1 0.5 0.18 26 - - - - - LYD676 73884.1 - - - - - - 7.7 0.23 5 LYD660 73932.1 0.5 0.20 18 - - - - - LYD654 73924.4 0.5 0.11 21 7.5 0.24 25 7.7 0.15 6 LYD647 72784.3 0.6 0.13 45 10.3 0.08 71 8.2 0.01 12 LYD647 72785.2 0.5 0.04 28 7.5 0.19 25 - - LYD628 73678.3 0.5 0.27 20 - - - - - LYD628 73679.2 0.6 0.10 54 10.7 0.08 77 8.0 0.04 9 LYD628 73681.1 - - - - - - 7.8 0.12 7 LYD614 73917.1 0.5 0.09 35 - - - - - LYD614 73919.3 0.6 0.09 60 - - - - - LYD611 71988.3 - - - 7.4 0.22 23 7.8 0.18 7 LYD611 71992.3 - - - - - - 7.9 0.08 8 WO 2013/128448 PCT/IL2013/050172 303 Leaf Area [cm 2 ] Roots Coverage [cm 2 ] Roots Length [cm] Gene Event # P- % P- % P- % Name Ave. Val. Incr. Ave. Val. Incr. Ave. Val. Incr. LYD611 71992.5 0.5 0.05 33 - - - 7.8 0.18 7 LYD611 71992.6 0.6 0.03 43 9.0 0.12 49 8.0 0.07 9 LYD605 73643.1 0.5 0.17 26 - - - - - LYD605 73644.2 0.5 0.05 30 7.3 0.25 21 - - LYD598 72421.2 0.5 0.01 38 7.6 0.27 27 8.1 0.02 11 LYD598 72423.3 - - - 8.9 0.03 47 7.8 0.12 7 LYD591 73907.3 0.5 0.09 27 8.1 0.09 34 7.9 0.18 9 LYD591 73907.4 - - - - - - 7.8 0.13 7 LYD589 73898.1 0.6 0.01 43 8.3 0.09 37 7.7 0.19 6 LYD589 73903.3 0.5 0.08 35 - - - 7.8 0.11 7 LYD588 73854.1 0.6 0.01 52 8.5 0.12 40 8.5 L 16 LYD588 73855.3 0.5 0.03 37 8.6 0.08 42 7.6 0.28 5 LYD584 73910.2 0.4 0.26 14 - - - - - LYD584 73915.4 - - - - - - 7.8 0.11 8 LYD566 73480.4 - - - - - - 7.8 0.21 7 LYD566 73482.4 0.6 L 59 8.7 0.07 44 7.8 0.18 7 LYD566 73483.5 0.5 0.22 21 7.6 0.16 26 - - LYD535 72851.6 0.5 0.06 26 - - - 7.8 0.09 7 LYD535 72852.1 0.6 L 42 9.4 0.01 56 - - CONT. - 0.4 - - 6.0 - - 7.3 - LYD682 72566.1 0.5 0.12 13 - - - - - LYD665 72215.2 0.5 0.08 27 8.5 0.09 19 7.9 0.07 8 LYD665 72216.4 0.5 0.11 29 9.6 0.10 33 8.0 0.04 10 LYD650 72639.4 - - - - - - 8.1 L 10 LYD650 72641.2 0.5 0.19 17 8.7 0.06 21 7.7 0.17 5 LYD644 72775.1 0.5 L 27 9.3 0.11 29 - - LYD644 72778.1 - - - - - - 7.9 0.03 7 LYD644 72780.2 0.5 0.18 20 9.1 0.11 27 7.8 0.14 7 LYD639 72548.6 - - - - - - 7.7 0.18 5 LYD639 72549.3 - - - - - - 8.2 L 12 LYD639 72551.1 0.5 0.14 16 8.8 0.20 23 8.0 0.05 9 LYD626 72001.3 0.5 0.02 28 - - - - - LYD626 72002.1 0.6 L 37 11.1 L 54 8.3 0.03 13 LYD626 72004.4 - - - 8.5 0.15 19 8.0 0.07 9 LYD606 72500.3 - - - - - - 7.9 0.02 8 LYD555 74193.5 0.5 0.13 13 9.7 0.09 35 8.0 0.05 8 LYD555 74194.1 0.5 0.09 24 - - - 7.7 0.21 5 LYD555 74197.1 0.5 0.05 17 - - - - - LYD542 72733.1 0.5 0.08 24 - - - - - LYD542 72733.2 0.5 0.29 14 - - - - - LYD542 72736.1 - - - - - - 7.9 0.02 8 WO 2013/128448 PCT/IL2013/050172 304 Leaf Area [cm 2 ] Roots Coverage [cm 2 ] Roots Length [cm] Gene Event # P- % P- % P- % Name Ave. Val. Incr. Ave. Val. Incr. Ave. Val. Incr. LYD542 72736.4 0.5 0.16 26 8.9 0.15 24 7.9 0.15 8 LYD540 74182.2 0.5 0.10 26 - - - - - LYD540 74182.4 - - - 8.2 0.14 14 - - LYD536 72529.5 0.5 0.18 16 - - - - - LYD536 72532.2 0.5 0.06 21 8.6 0.20 20 8.0 0.09 8 LYD533 72721.1 0.5 0.06 27 9.5 0.08 33 8.4 L 14 LYD533 72721.2 0.5 0.05 21 9.0 0.03 25 - - LYD533 72722.1 0.5 0.17 15 - - - - - LYD533 72723.1 0.5 0.09 34 9.8 0.14 36 7.9 0.06 8 LYD526 72164.4 - - - 8.2 0.25 15 - - LYD526 72168.4 - - - - - - 7.6 0.29 4 CONT. - 0.4 - - 7.2 - - 7.3 - LYD679 72650.6 0.7 0.01 39 11.6 0.17 29 - - LYD679 72652.3 0.6 0.25 25 11.4 0.29 27 - - LYD645 72339.2 0.7 0.01 47 11.8 0.13 31 - - LYD636 72200.3 0.7 0.03 33 11.8 0.10 31 - - LYD634 71998.2 0.7 0.03 45 15.0 0.06 67 8.2 0.16 5 LYD634 71999.3 0.6 0.20 18 - - - - - LYD567 72496.3 0.7 0.15 37 - - - - - LYD556 72904.3 0.7 0.03 44 12.9 0.03 44 - - LYD552 72979.3 - - - - - - 8.1 0.15 4 LYD552 72983.2 0.6 0.03 32 12.2 0.04 36 - - LYD529 72898.2 0.6 0.21 27 - - - - - CONT. - 0.5 - - 9.0 - - 7.8 - LYD689 72711.2 - - - - - - 7.5 0.18 6 LYD689 72712.3 - - - 8.2 0.21 31 - - LYD689 72713.1 0.7 0.01 72 12.6 L 101 8.4 L 20 LYD675 72643.1 0.6 0.14 43 11.6 0.06 86 7.7 0.19 9 LYD675 72644.1 - - - - - - 7.7 0.13 10 LYD675 72644.3 0.7 L 86 13.3 L 113 8.3 L 18 LYD675 72646.1 0.7 L 68 12.5 0.02 100 7.7 0.15 10 LYD671 72877.1 0.5 0.06 29 9.1 0.09 46 8.0 L 14 LYD671 72878.2 0.6 0.05 50 11.4 0.09 82 8.1 0.02 16 LYD671 72880.1 0.5 0.19 28 9.8 0.12 58 8.1 0.03 15 LYD654 73922.3 0.6 L 54 9.8 L 56 7.9 L 13 LYD654 73924.4 - - - - - - 7.7 0.29 10 LYD654 73924.5 0.5 0.20 18 9.2 0.01 47 8.0 L 14 LYD652 72560.1 - - - - - - 7.8 0.06 12 LYD652 72560.2 0.6 0.04 48 12.2 L 96 8.4 L 19 LYD652 72561.5 0.6 0.02 52 9.7 0.03 56 7.8 0.06 11 LYD652 72563.1 0.6 0.02 64 12.4 0.04 98 8.5 L 21 WO 2013/128448 PCT/IL2013/050172 305 Leaf Area [cm 2 ] Roots Coverage [cm 2 ] Roots Length [cm] Gene Event # P- % P- % P- % Name Ave. Val. Incr. Ave. Val. Incr. Ave. Val. Incr. LYD648 72831.3 - - - - - - 7.3 0.28 4 LYD648 72834.1 - - - 8.6 0.16 38 8.1 L 15 LYD648 72834.2 0.7 L 73 14.8 L 136 8.0 0.09 14 LYD641 72632.2 - - - - - - 7.4 0.27 6 LYD641 72633.4 0.5 0.11 28 9.6 0.02 54 8.2 L 17 LYD641 72635.2 0.6 0.04 41 10.6 0.13 70 8.0 0.16 13 LYD636 72199.3 0.6 0.09 54 10.7 0.11 71 - - LYD636 72200.3 - - - - - - 7.6 0.11 9 LYD636 72202.3 - - - 8.6 0.15 38 7.4 0.18 6 LYD602 72613.1 0.5 0.19 34 8.6 0.19 37 - - LYD602 72614.2 0.6 L 51 11.3 0.04 81 7.9 0.01 13 LYD599 72265.3 0.5 0.24 23 - - - - - LYD599 72266.4 0.5 0.06 38 - - - - - LYD599 72270.4 0.7 L 72 8.0 0.05 29 - - LYD555 74193.1 0.5 0.28 15 - - - 7.7 0.15 10 LYD555 74194.1 0.6 L 56 13.0 L 109 8.4 L 20 LYD555 74197.1 0.7 L 80 9.6 0.04 54 7.6 0.12 9 LYD555 74197.4 0.7 L 66 11.8 0.01 89 7.9 0.01 12 LYD555 74197.6 0.5 0.08 28 8.5 0.02 36 7.9 0.10 12 LYD548 72655.3 0.7 0.01 84 11.6 0.02 85 8.2 0.03 17 LYD548 72656.2 0.5 0.27 17 8.9 0.04 42 7.8 0.04 11 LYD548 72673.3 - - - 7.8 0.10 24 7.6 0.06 8 LYD548 72677.1 - - - 7.1 0.24 14 7.5 0.06 8 LYD541 72729.2 0.6 0.07 55 10.4 0.12 67 7.6 0.26 9 LYD541 72729.7 0.5 0.16 28 - - - 8.0 0.02 14 LYD541 72731.4 0.6 0.03 45 7.9 0.26 26 - - LYD541 72732.1 0.4 0.15 9 - - - 7.7 0.06 9 LYD540 74182.2 0.5 0.17 30 - - - - - LYD540 74182.7 0.6 L 54 10.1 0.03 61 7.7 0.02 10 LYD524 72859.1 0.7 0.01 68 9.9 0.01 59 - - LYD524 72859.4 0.6 0.02 63 9.9 0.11 58 7.7 0.22 10 LYD524 72864.4 - - - - - - 7.7 0.05 10 CONT. - 0.4 - - 6.2 - - 7.0 - LYD683 72866.4 0.7 L 75 13.8 L 79 - - LYD683 72870.1 0.5 0.12 27 11.3 L 47 7.9 0.20 7 LYD683 72870.4 0.5 0.05 24 11.0 0.05 44 7.9 0.27 6 LYD654 73922.4 0.5 0.22 14 9.1 0.21 19 - - LYD654 73924.4 0.5 0.20 25 11.4 0.09 49 8.0 0.19 8 LYD654 73924.5 0.5 0.05 19 12.0 L 57 8.4 0.02 13 LYD654 73926.3 0.6 L 50 12.4 L 62 8.2 0.05 11 LYD628 73678.3 - - - 9.7 0.24 27 - - - WO 2013/128448 PCT/IL2013/050172 306 Leaf Area [cm 2 ] Roots Coverage [cm 2 ] Roots Length [cm] Gene Event # P- % P- % P- % Name Ave. Val. Incr. Ave. Val. Incr. Ave. Val. Incr. LYD628 73679.2 - - - 10.7 0.17 39 8.1 0.19 9 LYD628 73681.5 0.6 0.02 46 11.9 0.05 56 7.9 0.28 7 LYD624 73181.3 0.6 0.08 32 10.0 0.10 31 8.1 0.10 9 LYD624 73383.1 0.6 L 34 9.1 0.06 19 - - LYD624 73385.1 0.5 0.22 24 - - - - - LYD624 73385.3 0.5 0.07 29 11.0 L 43 8.1 0.12 9 LYD605 73642.3 0.5 0.06 28 8.7 0.19 14 - - LYD604 73045.1 0.6 0.23 31 10.2 0.22 33 8.1 0.10 9 LYD604 73045.4 0.6 L 31 9.4 L 22 - - LYD604 73048.2 - - - 9.9 0.11 29 7.9 0.28 6 LYD598 72421.2 - - - - - - 8.0 0.21 8 LYD598 72445.1 0.5 0.27 14 10.7 0.24 39 8.1 0.18 9 LYD581 73107.1 0.5 0.06 22 - - - - - LYD581 73109.2 0.5 0.07 30 11.2 0.03 46 8.1 0.10 8 LYD581 73109.3 0.6 0.02 49 10.2 0.08 33 - - LYD581 73110.1 0.6 L 51 12.7 L 66 8.0 0.22 7 LYD566 73480.4 0.7 0.02 56 9.0 0.14 17 - - LYD566 73482.4 0.7 L 56 10.5 0.03 37 8.0 0.17 8 LYD566 73483.6 - - - 9.2 0.14 20 8.0 0.10 8 LYD554 72171.1 0.6 0.02 51 12.1 0.09 57 8.2 0.15 11 LYD554 72174.4 - - - 11.7 0.12 52 8.0 0.26 8 LYD550 74186.3 0.6 0.16 36 - - - - - LYD550 74187.1 0.5 L 29 - - - - - LYD550 74187.2 0.6 0.09 42 10.7 0.10 39 8.0 0.26 7 LYD548 72655.3 0.5 0.05 20 10.3 0.04 35 - - LYD548 72673.3 0.5 0.25 11 9.2 0.28 20 8.3 0.04 12 LYD540 74181.2 0.7 L 58 13.0 L 69 8.5 0.02 14 LYD540 74182.2 0.6 L 36 10.6 L 38 - - LYD540 74182.4 0.5 0.06 20 10.8 0.03 41 8.3 0.05 11 LYD540 74182.7 0.5 0.25 25 10.0 0.20 30 - - LYD535 72850.5 0.6 0.02 33 9.3 0.14 22 - - LYD535 72851.4 0.5 0.18 23 - - - - - LYD535 72852.2 - - - - - - 7.9 0.28 7 LYD530 73052.3 0.7 L 63 13.5 L 76 8.2 0.04 11 LYD530 73053.3 0.7 L 61 13.1 L 71 8.1 0.11 9 LYD530 73053.4 - - - 10.1 0.16 32 8.1 0.12 9 LYD530 73053.5 0.6 0.05 40 12.5 L 63 8.2 0.05 11 LYD530 73054.3 - - - 9.1 0.21 19 8.1 0.09 9 CONT. - 0.4 - - 7.7 - - 7.4 - LYD677 72223.1 - - - 13.3 0.25 15 8.6 0.02 5 LYD677 72223.6 0.7 0.04 27 14.2 0.13 23 8.6 0.10 5 WO 2013/128448 PCT/IL2013/050172 307 Leaf Area [cm 2 ] Roots Coverage [cm 2 ] Roots Length [cm] Gene Event # P- % P- % P- % Name Ave. Val. Incr. Ave. Val. Incr. Ave. Val. Incr. LYD677 72223.7 - - - - - - 8.5 0.23 4 LYD637 73685.1 0.7 0.08 44 14.3 0.23 24 8.6 0.10 5 LYD637 73685.2 0.7 0.03 30 - - - - - LYD637 73685.3 0.8 0.02 47 13.9 0.25 21 - - LYD625 72756.1 0.6 0.16 23 - - - - - LYD605 73641.1 0.6 0.19 21 - - - - - LYD605 73642.3 0.7 0.15 34 - - - - - LYD605 73644.2 0.7 0.02 33 - - - - - LYD605 73645.2 0.8 L 62 14.8 0.08 28 - - LYD585 72986.1 0.7 0.04 38 14.5 0.06 26 8.8 0.03 7 LYD585 72986.4 0.7 0.01 45 13.9 0.11 21 8.7 0.14 6 LYD585 72988.3 0.7 0.10 38 - - - - - LYD573 72974.2 0.6 0.25 15 14.2 0.09 23 8.4 0.20 2 LYD573 72977.1 0.6 0.26 20 - - - - - LYD573 72978.2 0.7 0.12 35 - - - - - LYD566 73481.2 0.6 0.10 24 - - - - - LYD566 73483.6 - - - - - - 8.4 0.21 3 LYD559 73627.2 0.7 0.06 34 - - - 8.7 0.01 7 LYD537 73628.1 0.6 0.28 20 - - - - - LYD537 73633.1 0.6 0.12 26 - - - 8.7 0.13 6 LYD537 73633.4 0.7 0.13 36 15.3 0.10 33 8.6 0.08 5 LYD537 73633.5 0.7 0.05 28 13.1 0.24 14 - - CONT. - 0.5 - - 11.5 - - 8.2 - LYD683 72866.4 - - - - - - 7.9 0.15 6 LYD647 72784.3 - - - - - - 7.9 0.15 6 LYD647 72785.3 0.7 0.05 29 12.9 0.15 21 - - LYD647 72785.4 - - - - - - 8.0 0.23 7 LYD647 72786.1 - - - - - - 8.2 0.01 10 LYD611 71991.5 - - - - - - 7.9 0.05 7 LYD611 71992.5 0.8 L 55 13.0 0.17 22 - - LYD611 71992.6 0.7 0.02 29 - - - - - LYD585 72986.1 - - - - - - 7.9 0.11 7 LYD585 72986.4 - - - - - - 8.2 0.06 10 LYD585 72987.2 - - - - - - 7.9 0.22 6 LYD585 72988.1 0.7 L 29 14.3 L 34 7.9 0.10 6 LYD573 72973.2 0.6 0.06 26 13.0 0.19 22 7.9 0.17 7 LYD573 72974.2 - - - - - - 7.8 0.22 6 LYD573 72978.1 0.6 0.18 18 - - - 8.2 L 11 LYD550 74188.2 0.6 0.04 25 - - - - - CONT. - 0.5 - - 10.7 - - 7.4 - LYD686 72796.2 0.5 0.28 12 - - - - - - WO 2013/128448 PCT/IL2013/050172 308 Leaf Area [cm 2 ] Roots Coverage [cm 2 ] Roots Length [cm] Gene Event # P- % P- % P- % Name Ave. Val. Incr. Ave. Val. Incr. Ave. Val. Incr. LYD673 72662.2 0.6 0.03 29 10.5 0.13 25 - - LYD663 72858.1 0.6 0.25 29 - - - 7.9 0.27 4 LYD655 72209.1 0.6 0.08 41 10.3 0.11 23 7.8 0.14 4 LYD655 72210.1 0.6 0.17 40 11.5 0.02 36 - - LYD640 72557.2 0.6 L 40 11.8 0.07 40 7.9 0.27 4 LYD640 72558.3 0.5 0.10 20 10.0 0.19 19 - - LYD638 72432.2 0.6 0.12 28 - - - - - LYD638 72451.1 0.6 L 42 11.9 0.05 42 8.0 0.05 6 LYD615 72262.1 0.6 0.07 35 12.2 0.05 46 8.2 0.13 8 LYD613 72515.1 0.6 0.07 44 - - - - - LYD613 72516.1 0.6 0.06 26 - - - - - LYD608 72885.3 - - - - - - 8.1 0.02 7 LYD608 72887.1 0.7 0.04 60 12.4 0.02 47 - - LYD608 72888.1 - - - - - - 7.9 0.10 4 LYD608 72888.2 0.5 0.17 17 9.9 0.20 17 8.2 0.06 8 LYD607 71961.1 0.5 0.12 22 10.5 0.13 25 - - LYD607 71963.2 0.5 0.08 23 10.3 0.19 23 7.8 0.19 4 LYD607 71963.4 - - - - - - 7.8 0.20 3 LYD597 72419.2 0.6 0.06 28 - - - - - LYD597 72420.1 0.7 L 48 11.1 0.04 32 - - LYD583 71943.1 - - - - - - 7.8 0.25 3 LYD579 72350.3 0.6 0.05 42 11.4 0.04 35 8.1 L 7 LYD579 72354.1 0.7 0.03 62 12.1 0.05 44 8.2 0.01 8 LYD563 72319.2 0.6 0.01 37 11.5 0.02 37 8.1 0.05 7 LYD563 72319.4 - - - - - - 7.8 0.21 4 LYD563 72324.2 0.7 0.10 63 - - - 8.4 0.01 11 CONT. - 0.4 - - 8.4 - - 7.6 - LYD592 74348.3 0.7 0.15 29 - - - 8.6 0.12 8 LYD592 74349.2 0.7 0.29 15 - - - - - LYD592 74350.1 0.8 0.08 40 13.6 0.13 27 - - LYD592 74351.1 0.7 0.02 28 13.6 0.04 27 8.3 0.20 4 LYD592 74353.3 0.9 L 65 16.3 L 52 8.8 L 10 LYD525 74230.2 0.7 0.19 15 - - - 8.4 0.30 5 CONT. - 0.6 - - 10.7 - - 8.0 - LYD676 73881.2 0.6 0.14 22 10.4 0.19 32 - - LYD591 73905.1 - - - 10.3 L 29 8.2 L 11 CONT. - 0.5 - - 7.9 - - 7.4 - LYD665 72211.2 0.6 L 72 10.5 0.02 39 8.3 0.02 13 LYD665 72216.4 0.5 0.16 32 - - - 7.7 0.30 5 LYD665 72216.5 0.5 0.18 31 - - - - - LYD665 72216.6 0.4 0.27 24 9.1 0.30 20 7.9 0.21 8 WO 2013/128448 PCT/IL2013/050172 309 Leaf Area [cm 2 ] Roots Coverage [cm 2 ] Roots Length [cm] Gene Event # P- % P- % P- % Val. Incr. Val. Incr. Val. Incr. LYD592 74348.3 0.6 L 70 11.2 L 49 8.0 0.06 9 LYD592 74348.4 0.6 L 86 14.8 L 97 8.8 L 19 LYD592 74349.2 0.6 0.04 58 - - - - - LYD592 74350.1 0.7 L 109 14.3 L 90 8.3 0.03 13 LYD592 74351.1 0.7 0.07 96 13.3 0.09 76 8.2 0.05 12 LYD532 74343.2 0.5 L 51 9.5 0.05 25 - - LYD532 74345.1 0.4 0.06 23 9.2 0.12 22 - - LYD532 74345.3 0.6 L 78 11.7 L 55 8.0 0.09 8 LYD525 74229.2 0.5 0.01 56 - - - - - LYD525 74230.2 0.6 0.05 83 12.1 0.18 61 8.3 0.05 13 LYD525 74233.1 0.4 0.13 17 - - - - - CONT. - 0.3 - - 7.5 - - 7.3 - LYD679 72652.3 0.6 0.06 27 13.1 L 36 - - LYD670 73348.1 0.5 0.21 9 - - - - - LYD646 73040.3 0.6 0.17 29 - - - - - LYD646 73040.4 0.6 L 26 12.8 L 33 8.4 L 8 LYD624 73181.3 0.5 0.12 9 - - - - - LYD616 73057.4 0.5 0.26 9 - - - - - LYD616 73058.4 - - - - - - 8.3 0.09 7 LYD609 73124.2 0.7 0.06 50 12.1 0.19 26 - - LYD609 73128.5 0.6 0.16 18 - - - - - LYD604 73045.4 0.6 0.10 19 - - - - - LYD604 73047.3 0.6 L 24 10.7 0.24 11 - - LYD581 73107.1 0.6 L 29 13.3 L 38 - - LYD558 73112.3 0.6 0.23 18 - - - - - LYD558 73114.3 0.7 0.11 46 - - - 8.2 0.02 6 LYD552 72981.3 0.7 L 36 11.4 0.17 18 - - LYD552 72981.4 0.6 0.03 31 11.8 0.08 22 - - LYD552 72983.1 0.6 0.17 26 - - - - - LYD530 73052.3 0.6 0.11 21 - - - - - LYD529 72899.7 0.6 0.03 25 11.5 0.06 20 8.1 0.06 4 CONT. - 0.5 - - 9.6 - - 7.8 - Table 65. "CONT." - Control; "Ave." - Average; "% Incr." = % increment; "p-val." - p-value, L- p<0.01. The transgenes were under the transcriptional regulation of the new At6669 promoter (SEQ ID NO: 4111). "" = results are still unavailable.
WO 2013/128448 PCT/IL2013/050172 310 Table 66 Genes showing improved plant performance at Normal growth conditions under regulation of At6669 promoter RGR Of Leaf Area RGR Of Roots RGR Of Root Length Gene (cm 2 /day) Coverage (cm 2 lday) (cm/day) Nae Event # Name Ave. P- % AP- % .P- % Val. Incr. Val. Incr. Val. Incr. LYD686 72796.2 0.1 L 67 1.3 L 49 0.8 0.16 8 LYD686 72798.1 0.1 L 61 - - - - - LYD685 72458.3 0.0 0.02 45 - - - - - LYD685 72458.5 0.1 L 65 1.5 L 68 0.8 0.06 11 LYD685 72459.1 0.0 0.03 32 1.1 0.17 18 - - LYD685 72462.4 0.0 L 46 1.2 0.12 31 - - LYD685 72462.5 0.0 L 48 1.2 0.03 36 - - LYD673 72662.2 0.0 0.01 36 1.1 0.09 26 0.8 0.01 13 LYD673 72663.3 0.0 0.04 28 - - - - - LYD673 72664.1 0.0 0.06 28 - - - - - LYD673 72666.1 0.0 0.05 30 1.1 0.16 20 0.8 0.23 7 LYD663 72856.3 0.0 L 43 1.3 L 44 - - LYD663 72856.5 0.0 L 49 1.3 L 41 - - LYD663 72858.1 0.0 L 46 1.2 0.02 34 - - LYD663 72858.3 0.0 0.05 25 1.2 0.02 34 - - LYD655 72207.3 0.0 0.21 17 - - - - - LYD655 72210.1 0.0 0.05 37 1.2 0.08 30 - - LYD640 72556.3 0.1 L 60 1.4 L 54 - - LYD640 72557.2 0.0 L 32 1.1 0.06 25 - - LYD640 72557.4 0.0 0.30 20 - - - - - LYD640 72558.2 0.1 L 64 1.4 L 54 0.8 0.24 7 LYD640 72558.3 0.0 0.30 15 - - - - - LYD638 72432.2 - - - - - - 0.8 0.18 7 LYD638 72451.1 0.1 L 63 1.5 L 64 0.8 0.19 7 LYD615 72259.2 0.0 0.07 33 - - - - - LYD615 72260.1 0.1 L 66 1.4 L 51 0.8 0.02 14 LYD615 72264.2 0.0 0.01 31 - - - - - LYD613 72512.3 0.0 0.03 31 1.1 0.15 18 - - LYD613 72514.2 0.1 0.01 55 1.1 0.17 23 - - LYD613 72515.4 0.0 0.02 28 - - - - - LYD608 72883.2 0.0 L 46 1.2 L 35 - - LYD608 72888.2 0.0 L 48 1.6 L 75 0.8 0.19 7 LYD607 71961.1 0.1 L 80 1.4 L 54 - - LYD607 71963.1 0.1 L 64 1.2 0.07 31 - - LYD607 71963.2 0.0 L 46 1.4 L 57 - - LYD607 71963.4 0.0 L 37 - - - - - LYD597 72419.3 0.0 L 35 1.1 0.20 17 0.8 0.21 7 WO 2013/128448 PCT/IL2013/050172 311 RGR Of Leaf Area RGR Of Roots RGR Of Root Length Gene (cm 2 /day) Coverage (cm 2 /day) (cm/day) Name Event # NaeAve. p- % Ave. p- % Ave. Val %nr Val. Incr. Val. Incr. Val. Incr. LYD597 72420.1 0.0 0.27 13 - - - - - LYD597 72443.4 0.0 0.19 26 - - - - - LYD583 71943.1 0.0 0.29 12 - - - - - LYD579 72350.2 0.0 0.10 19 - - - - - LYD579 72350.3 0.0 L 41 1.3 L 48 - - LYD579 72354.1 0.0 L 42 1.4 L 52 0.8 0.19 7 LYD563 72319.2 0.0 0.29 12 1.1 0.16 19 - - LYD563 72319.4 0.1 L 62 1.4 L 55 - - LYD563 72321.2 0.0 0.15 24 1.1 0.18 21 - - LYD563 72323.1 0.0 L 40 1.4 L 60 - - CONT. - 0.0 - - 0.9 - - 0.7 - LYD676 73880.1 0.0 0.21 27 - - - 0.8 0.28 8 LYD676 73884.1 - - - - - - 0.8 0.12 12 LYD654 73924.4 0.0 0.18 25 0.9 0.23 28 0.8 0.05 15 LYD647 72784.3 0.1 0.05 49 1.3 0.01 74 0.8 0.12 13 LYD647 72785.2 0.1 0.09 33 0.9 0.24 26 - - LYD628 73679.2 0.1 0.01 68 1.3 L 79 - - LYD628 73681.1 - - - - - - 0.8 0.17 10 LYD614 73917.1 0.1 0.05 42 - - - - - LYD614 73919.3 0.1 0.04 55 - - - - - LYD611 71988.3 - - - 0.9 0.26 25 0.8 0.12 12 LYD611 71992.3 - - - - - - 0.8 0.03 16 LYD611 71992.5 0.1 0.10 32 - - - 0.8 0.28 8 LYD611 71992.6 0.1 0.04 44 1.1 0.05 51 0.8 0.08 14 LYD605 73643.1 0.1 0.14 31 - - - - - LYD605 73644.2 0.1 0.13 29 0.9 0.30 23 - - LYD598 72421.2 0.1 0.06 37 0.9 0.25 27 0.8 0.13 12 LYD598 72423.3 - - - 1.1 0.03 50 0.7 0.30 8 LYD591 73907.3 0.1 0.14 29 1.0 0.11 36 0.8 0.21 11 LYD591 73907.4 - - - - - - 0.8 0.04 15 LYD589 73898.1 0.1 0.04 45 1.0 0.09 40 0.8 0.18 11 LYD589 73903.3 0.1 0.08 38 - - - 0.8 0.19 11 LYD588 73851.2 - - - - - - 0.8 0.19 11 LYD588 73852.1 - - - - - - 0.8 0.10 13 LYD588 73852.2 0.0 0.28 25 - - - 0.8 0.20 12 LYD588 73854.1 0.1 0.02 51 1.0 0.08 42 0.8 0.01 20 LYD588 73855.3 0.1 0.04 40 1.0 0.06 44 0.8 0.25 9 LYD584 73915.4 - - - - - - 0.8 0.10 12 LYD566 73480.4 - - - - - - 0.8 0.02 20 LYD566 73481.2 - - - - - - 0.8 0.09 13 WO 2013/128448 PCT/IL2013/050172 312 RGR Of Leaf Area RGR Of Roots RGR Of Root Length Gene (cm 2 /day) Coverage (cm 2 /day) (cm/day) Name Event # NaeAve. p- % Ave. p- % Ave. Val %nr Val. Incr. Val. Incr. Val. Incr. LYD566 73482.4 0.1 L 59 1.1 0.05 47 0.8 0.28 9 LYD566 73483.5 0.0 0.28 22 0.9 0.20 28 - - LYD566 73483.6 - - - - - - 0.8 0.08 13 LYD535 72851.6 0.0 0.22 23 - - - 0.8 0.22 10 LYD535 72852.1 0.1 0.02 45 1.2 0.01 59 0.8 0.20 11 CONT. - 0.0 - - 0.7 - - 0.7 - LYD682 72566.1 0.0 0.30 15 - - - - - LYD665 72215.2 0.1 0.07 29 1.0 0.18 20 0.8 0.13 9 LYD665 72216.4 0.1 0.08 30 1.2 0.05 34 0.8 0.15 9 LYD650 72639.4 - - - - - - 0.8 0.06 11 LYD650 72641.2 0.0 0.16 22 1.1 0.14 22 0.8 0.10 10 LYD644 72775.1 0.1 0.03 32 1.1 0.07 29 - - LYD644 72778.1 - - - - - - 0.8 0.29 6 LYD644 72780.2 0.0 0.22 20 1.1 0.09 27 - - LYD639 72549.3 - - - - - - 0.8 0.21 7 LYD639 72551.1 0.1 0.13 22 1.1 0.15 24 0.9 0.02 15 LYD626 72001.1 - - - - - - 0.8 0.28 7 LYD626 72001.3 0.1 0.06 29 - - - - - LYD626 72002.1 0.1 0.03 35 1.4 L 55 - - LYD626 72004.4 - - - 1.0 0.22 19 0.8 0.18 8 LYD555 74193.5 - - - 1.2 0.04 35 - - LYD555 74194.1 0.1 0.08 27 - - - - - LYD555 74197.1 0.0 0.28 15 - - - - - LYD542 72733.1 0.0 0.17 21 - - - - - LYD542 72736.4 0.1 0.14 25 1.1 0.13 24 0.8 0.19 9 LYD540 74182.2 0.1 0.09 28 - - - - - LYD536 72532.2 0.0 0.16 21 1.1 0.19 21 0.8 0.05 13 LYD533 72721.1 0.1 0.06 31 1.2 0.05 32 0.8 0.06 11 LYD533 72721.2 0.1 0.10 24 1.1 0.09 25 - - LYD533 72722.1 0.0 0.28 15 - - - - - LYD533 72723.1 0.1 0.02 41 1.2 0.05 37 0.8 0.08 10 CONT. - 0.0 - - 0.9 - - 0.7 - LYD679 72650.6 0.1 0.06 38 1.4 0.17 29 - - LYD679 72652.3 0.1 0.18 30 1.4 0.23 27 - - LYD645 72339.2 0.1 L 55 1.4 0.14 31 - - LYD636 72200.3 0.1 0.06 37 1.4 0.13 30 - - LYD634 71998.2 0.1 0.01 55 1.8 L 67 - - LYD567 72496.3 0.1 0.10 39 - - - - - LYD556 72903.5 - - - 1.4 0.28 24 - - LYD556 72904.3 0.1 0.04 44 1.6 0.04 45 - - - WO 2013/128448 PCT/IL2013/050172 313 RGR Of Leaf Area RGR Of Roots RGR Of Root Length Gene (cm 2 /day) Coverage (cm 2 /day) (cm/day) Nae Event # Name AP- % P- % IP- % Val. Incr. Val. Incr. Val. Incr. LYD552 72979.3 - - - - - - 0.8 0.29 7 LYD552 72983.2 0.1 0.04 40 1.5 0.07 36 - - LYD529 72898.2 0.1 0.17 31 - - - - - CONT. - 0.1 - - 1.1 - - 0.7 - LYD689 72712.3 0.0 0.17 19 1.0 0.09 32 - - LYD689 72713.1 0.1 L 82 1.5 L 99 0.8 0.08 16 LYD675 72643.1 0.1 L 54 1.4 L 87 - - LYD675 72644.1 - - - - - - 0.7 0.27 10 LYD675 72644.3 0.1 L 99 1.6 L 114 - - LYD675 72646.1 0.1 L 82 1.5 L 102 - - LYD671 72877.1 0.1 L 34 1.1 0.01 48 0.8 0.03 19 LYD671 72878.2 0.1 L 62 1.3 L 80 0.7 0.20 12 LYD671 72880.1 0.1 0.02 34 1.2 0.01 59 0.8 0.15 14 LYD654 73922.3 0.1 L 65 1.2 L 54 0.8 0.10 14 LYD654 73924.4 0.0 0.13 29 1.0 0.14 40 - - LYD654 73924.5 0.0 0.07 22 1.1 0.01 44 - - LYD652 72560.1 - - - - - - 0.8 0.14 14 LYD652 72560.2 0.1 L 60 1.5 L 97 - - LYD652 72561.5 0.1 L 63 1.2 L 56 - - LYD652 72563.1 0.1 L 75 1.5 L 97 0.8 0.04 20 LYD648 72832.2 0.1 0.02 33 1.0 0.15 33 - - LYD648 72834.1 0.0 0.18 16 1.0 0.06 38 0.7 0.21 11 LYD648 72834.2 0.1 L 91 1.8 L 139 - - LYD641 72633.4 0.1 0.01 33 1.1 L 52 - - LYD641 72635.2 0.1 L 49 1.2 0.01 67 - - LYD636 72199.3 0.1 L 63 1.3 L 69 - - LYD636 72202.3 0.1 0.05 35 1.0 0.08 34 - - LYD602 72613.1 0.1 L 45 1.0 0.06 38 - - LYD602 72613.3 0.0 0.30 15 - - - - - LYD602 72614.2 0.1 L 66 1.4 L 82 - - LYD602 72617.3 0.0 0.11 22 - - - - - LYD599 72265.3 0.1 0.01 36 - - - 0.8 0.03 23 LYD599 72266.4 0.1 L 50 - - - - - LYD599 72270.4 0.1 L 91 1.0 0.07 29 - - LYD555 74193.1 0.0 0.27 12 - - - 0.7 0.24 11 LYD555 74194.1 0.1 L 72 1.5 L 107 0.7 0.23 11 LYD555 74197.1 0.1 L 86 1.1 L 53 - - LYD555 74197.4 0.1 L 70 1.4 L 89 - - LYD555 74197.6 0.1 L 34 1.0 0.04 33 - - LYD548 72655.3 0.1 L 101 1.4 L 81 - - - WO 2013/128448 PCT/IL2013/050172 314 RGR Of Leaf Area RGR Of Roots RGR Of Root Length Gene (cm 2 /day) Coverage (cm 2 /day) (cm/day) Nae Event # Name AP- % P- % IP- % Val. Incr. Val. Incr. Val. Incr. LYD548 72656.2 0.1 0.01 30 1.1 0.02 42 - - LYD548 72673.3 0.0 0.18 16 0.9 0.13 23 - - LYD541 72729.2 0.1 L 67 1.3 L 70 0.8 0.17 13 LYD541 72729.7 0.1 L 42 0.9 0.26 25 0.7 0.29 10 LYD541 72731.4 0.1 L 48 0.9 0.18 24 - - LYD541 72732.1 0.0 0.03 19 - - - - - LYD540 74182.2 0.1 0.03 32 - - - - - LYD540 74182.7 0.1 L 60 1.2 L 60 - - LYD524 72859.1 0.1 L 77 1.2 L 59 - - LYD524 72859.4 0.1 L 70 1.2 0.01 57 - - LYD524 72864.4 - - - - - - 0.7 0.20 11 CONT. - 0.0 - - 0.7 - - 0.7 - LYD683 72866.3 - - - 1.1 0.26 20 - - LYD683 72866.4 0.1 L 79 1.7 L 80 - - LYD683 72870.1 0.1 0.05 32 1.4 L 49 0.8 0.27 9 LYD683 72870.4 0.1 0.09 25 1.3 L 45 - - LYD654 73922.4 - - - 1.1 0.21 19 - - LYD654 73924.4 0.1 0.10 29 1.4 0.01 48 - - LYD654 73924.5 0.1 0.09 23 1.5 L 57 - - LYD654 73926.3 0.1 L 53 1.5 L 64 0.8 0.13 13 LYD628 73678.3 0.1 0.24 26 1.2 0.13 28 0.8 0.13 17 LYD628 73679.2 0.1 0.16 25 1.3 0.05 38 - - LYD628 73680.2 - - - 1.1 0.30 15 - - LYD628 73681.5 0.1 L 50 1.5 L 56 - - LYD624 73181.3 0.1 0.04 35 1.2 0.06 31 0.8 0.28 9 LYD624 73383.1 0.1 0.02 34 1.1 0.15 19 - - LYD624 73385.1 0.1 0.10 29 - - - - - LYD624 73385.3 0.1 0.06 30 1.3 L 45 0.8 0.16 12 LYD605 73642.3 0.1 0.08 27 1.1 0.29 15 - - LYD604 73045.1 0.1 0.08 36 1.2 0.08 32 - - LYD604 73045.4 0.1 0.06 29 1.1 0.10 23 0.8 0.22 11 LYD604 73048.2 0.1 0.23 24 1.2 0.07 29 - - LYD598 72421.2 - - - 1.1 0.29 17 - - LYD598 72445.1 0.1 0.18 20 1.3 0.08 37 - - LYD581 73107.1 0.1 0.09 24 - - - - - LYD581 73107.5 - - - 1.1 0.21 22 - - LYD581 73109.2 0.1 0.02 37 1.4 L 46 - - LYD581 73109.3 0.1 L 56 1.2 0.04 31 - - LYD581 73110.1 0.1 L 52 1.6 L 67 - - LYD566 73480.4 0.1 L 52 1.1 0.21 18 - - - WO 2013/128448 PCT/IL2013/050172 315 RGR Of Leaf Area RGR Of Roots RGR Of Root Length Gene (cm 2 /day) Coverage (cm 2 /day) (cm/day) Name Event # NaeAve. p- % Ave. p- % Ave. Val %nr Val. Incr. Val. Incr. Val. Incr. LYD566 73482.4 0.1 L 59 1.3 0.02 39 0.8 0.08 16 LYD566 73483.6 - - - 1.1 0.19 19 - - LYD554 72171.1 0.1 L 54 1.5 L 56 0.8 0.28 11 LYD554 72174.4 0.1 0.17 28 1.4 0.01 52 - - LYD550 74186.3 0.1 0.08 34 - - - - - LYD550 74187.1 0.1 0.02 34 - - - - - LYD550 74187.2 0.1 0.03 42 1.3 0.03 41 0.8 0.15 14 LYD548 72655.3 0.1 0.17 20 1.3 0.02 35 - - LYD548 72656.2 - - - - - - 0.8 0.11 15 LYD548 72673.3 - - - 1.1 0.20 20 0.8 0.06 16 LYD540 74181.2 0.1 L 57 1.6 L 69 0.8 0.11 15 LYD540 74182.2 0.1 L 42 1.3 0.01 37 - - LYD540 74182.4 0.1 0.10 23 1.3 L 42 - - LYD540 74182.7 0.1 0.21 23 1.2 0.08 31 - - LYD535 72850.5 0.1 0.03 33 1.1 0.12 23 - - LYD535 72851.4 0.1 0.13 24 - - - - - LYD530 73052.3 0.1 L 69 1.6 L 76 0.8 0.19 11 LYD530 73053.3 0.1 L 74 1.6 L 71 0.8 0.08 16 LYD530 73053.4 - - - 1.2 0.08 32 0.8 0.25 11 LYD530 73053.5 0.1 0.02 42 1.5 L 64 0.8 0.16 12 LYD530 73054.3 - - - 1.1 0.22 18 - - CONT. - 0.0 - - 0.9 - - 0.7 - LYD677 72223.1 - - - - - - 0.8 0.26 7 LYD677 72223.6 0.1 0.04 34 1.7 0.14 23 - - LYD637 73684.1 - - - - - - 0.8 0.26 8 LYD637 73685.1 0.1 0.05 40 1.7 0.18 24 - - LYD637 73685.2 0.1 0.06 31 - - - 0.8 0.26 7 LYD637 73685.3 0.1 0.02 47 1.7 0.22 21 - - LYD625 72756.1 0.1 0.16 25 - - - - - LYD605 73641.1 0.1 0.24 20 - - - 0.9 0.03 14 LYD605 73642.3 0.1 0.16 28 - - - - - LYD605 73644.2 0.1 0.06 32 - - - - - LYD605 73645.2 0.1 L 65 1.8 0.08 29 0.8 0.27 8 LYD585 72986.1 0.1 0.04 37 1.7 0.11 25 - - LYD585 72986.4 0.1 0.02 45 1.7 0.20 20 0.8 0.29 8 LYD585 72988.3 0.1 0.06 38 - - - - - LYD573 72974.2 0.1 0.29 18 1.7 0.15 22 - - LYD573 72977.1 0.1 0.24 21 - - - - - LYD573 72978.2 0.1 0.08 35 - - - - - LYD566 73481.2 0.1 0.20 22 - - - - - - WO 2013/128448 PCT/IL2013/050172 316 RGR Of Leaf Area RGR Of Roots RGR Of Root Length Gene (cm 2 /day) Coverage (cm 2 /day) (cm/day) Name Event # NaeAve. p- % Ave. p- % Ave. Val %nr Val. Incr. Val. Incr. Val. Incr. LYD559 73627.2 0.1 0.03 39 - - - 0.9 0.03 16 LYD537 73628.1 0.1 0.26 21 - - - - - LYD537 73633.1 0.1 0.12 28 - - - - - LYD537 73633.4 0.1 0.06 39 1.9 0.06 33 - - LYD537 73633.5 0.1 0.08 29 - - - - - CONT. - 0.1 - - 1.4 - - 0.7 - LYD683 72866.4 - - - - - - 0.8 0.07 15 LYD683 72867.4 - - - - - - 0.8 0.20 11 LYD683 72868.1 0.1 0.27 18 - - - - - LYD647 72784.3 - - - - - - 0.8 0.25 9 LYD647 72785.3 0.1 0.03 37 1.6 0.17 21 - - LYD647 72786.1 - - - - - - 0.8 0.12 12 LYD611 71991.5 - - - - - - 0.8 0.22 9 LYD611 71992.2 - - - - - - 0.8 0.19 11 LYD611 71992.5 0.1 L 66 1.6 0.14 23 0.8 0.11 12 LYD611 71992.6 0.1 0.02 36 - - - 0.8 0.27 9 LYD585 72986.4 0.1 0.26 17 - - - - - LYD585 72987.2 0.1 0.26 20 - - - - - LYD585 72988.1 0.1 0.02 33 1.7 0.02 34 - - LYD573 72973.2 0.1 0.04 33 1.6 0.17 21 0.8 0.07 14 LYD573 72974.2 - - - - - - 0.8 0.11 13 LYD573 72978.1 0.1 0.22 19 - - - 0.8 0.06 15 LYD550 74188.2 0.1 0.07 28 - - - - - CONT. - 0.1 - - 1.3 - - 0.7 - LYD686 72796.2 0.1 0.29 17 - - - - - LYD673 72662.2 0.1 0.08 29 1.3 0.16 25 - - LYD673 72663.3 0.1 0.27 20 - - - - - LYD663 72853.5 0.1 0.28 22 - - - - - LYD663 72858.1 0.1 0.15 32 - - - - - LYD655 72209.1 0.1 0.03 46 1.3 0.17 24 0.8 0.15 10 LYD655 72210.1 0.1 0.05 47 1.4 0.04 38 - - LYD640 72557.2 0.1 0.02 40 1.4 0.04 41 - - LYD640 72558.3 0.1 0.14 25 1.2 0.24 21 - - LYD638 72432.2 0.1 0.11 31 - - - - - LYD638 72451.1 0.1 0.01 45 1.4 0.04 40 - - LYD615 72260.1 0.1 0.29 20 - - - - - LYD615 72262.1 0.1 0.03 45 1.5 0.02 47 - - LYD613 72512.1 - - - - - - 0.8 0.13 12 LYD613 72515.1 0.1 0.02 52 - - - - - LYD613 72516.1 0.1 0.14 26 - - - - - - WO 2013/128448 PCT/IL2013/050172 317 RGR Of Leaf Area RGR Of Roots RGR Of Root Length Gene (cm 2 /day) Coverage (cm 2 /day) (cm/day) Nae Event # Name AP- % P- % IP- % Val. Incr. Val. Incr. Val. Incr. LYD608 72887.1 0.1 L 65 1.5 0.01 49 - - LYD608 72888.2 0.1 0.29 18 1.2 0.29 19 0.8 0.09 14 LYD607 71961.1 0.1 0.15 25 1.3 0.15 26 - - LYD607 71963.2 0.1 0.05 34 1.2 0.20 23 - - LYD597 72419.2 0.1 0.07 32 - - - - - LYD597 72420.1 0.1 L 60 1.4 0.06 34 - - LYD583 71943.2 0.1 0.29 21 1.3 0.22 25 - - LYD579 72350.3 0.1 0.02 48 1.4 0.05 36 - - LYD579 72354.1 0.1 L 72 1.5 0.03 45 - - LYD563 72319.2 0.1 0.02 42 1.4 0.04 37 - - LYD563 72324.2 0.1 0.04 56 1.3 0.20 33 - - CONT. - 0.0 - - 1.0 - - 0.7 - LYD592 74348.3 0.1 0.13 29 - - - - - LYD592 74350.1 0.1 0.04 42 1.6 0.17 25 - - LYD592 74351.1 0.1 0.08 29 1.6 0.13 25 - - LYD592 74353.3 0.1 L 66 2.0 L 51 - - CONT. - 0.1 - - 1.3 - - - - LYD676 73881.2 0.1 0.06 27 1.3 0.05 33 0.8 0.27 10 LYD591 73905.1 - - - 1.3 0.02 30 0.8 0.03 13 CONT. - 0.0 - - 1.0 - - 0.7 - LYD665 72211.2 0.1 L 78 1.3 0.02 38 0.9 0.15 10 LYD665 72216.4 0.0 0.03 39 1.1 0.28 19 - - LYD665 72216.5 0.1 0.02 43 1.1 0.25 23 - - LYD665 72216.6 0.0 0.08 31 1.1 0.24 20 0.9 0.23 9 LYD592 74348.3 0.1 L 79 1.4 L 47 0.9 0.21 8 LYD592 74348.4 0.1 L 95 1.8 L 96 0.9 0.16 10 LYD592 74349.2 0.1 L 59 1.1 0.26 20 - - LYD592 74350.1 0.1 L 116 1.7 L 86 - - LYD592 74351.1 0.1 L 103 1.6 L 72 - - LYD532 74343.2 0.1 L 51 1.2 0.11 26 - - LYD532 74345.1 0.0 0.04 28 1.1 0.21 20 - - LYD532 74345.3 0.1 L 84 1.4 L 51 - - LYD525 74229.2 0.1 L 53 - - - - - LYD525 74230.2 0.1 L 90 1.5 0.03 58 - - CONT. - 0.0 - - 0.9 - - 0.8 - LYD679 72652.3 0.1 L 32 1.6 L 37 - - LYD670 73347.4 0.1 0.21 14 - - - - - LYD670 73348.1 0.1 0.20 11 - - - - - LYD646 73040.3 0.1 0.04 31 1.3 0.26 14 - - LYD646 73040.4 0.1 L 29 1.5 L 33 0.8 0.18 10 WO 2013/128448 PCT/IL2013/050172 318 RGR Of Leaf Area RGR Of Roots RGR Of Root Length Gene (cm 2 /day) Coverage (cM 2 /day) (cm/day) Nae Event # Name Av. P- % Av. P- % Av. P- % Ave. Ave. Ave. Vl nr Val. Incr. Val. Incr. Val. Incr. LYD646 73042.3 0.1 0.22 14 - - - - - LYD624 73181.3 0.1 0.21 10 - - - - - LYD624 73382.4 0.1 0.22 17 - - - - - LYD609 73124.2 0.1 L 55 1.5 0.06 26 - - LYD609 73128.5 0.1 0.22 13 - - - - - LYD604 73045.4 0.1 0.05 20 - - - - - LYD604 73047.3 0.1 L 29 1.3 0.28 12 - - LYD581 73107.1 0.1 L 31 1.6 L 38 - - LYD581 73107.5 0.1 0.13 17 - - - - - LYD558 73112.3 0.1 0.13 18 - - - - - LYD558 73114.3 0.1 L 52 1.4 0.14 23 - - LYD552 72981.3 0.1 L 38 1.4 0.14 17 - - LYD552 72981.4 0.1 L 31 1.4 0.06 22 - - LYD552 72983.1 0.1 0.05 26 - - - - - LYD530 73052.3 0.1 0.02 27 - - - - - LYD529 72897.1 - - - - - - 0.8 0.15 9 LYD529 72899.7 0.1 L 30 1.4 0.08 20 - - LYD529 72900.2 - - - - - - 0.8 0.28 7 CONT. - 0.0 - - 1.2 - - 0.7 - Table 66. "CONT." - Control; "Ave." - Average; "% Incr." = % increment; "p-val." - p value, L- p< 0
.
0 1. The transgenes were under the transcriptional regulation of the new At6669 promoter (SEQ ID NO: 4111). "-" = results are still unavailable. 5 Results from Ti plants The genes presented in Tables 67-69 showed a significant improvement in plant biomass and root development since they produced a higher biomass (dry and fresh weight, Table 67), a larger leaf and root biomass (leaf area, root length and root coverage) (Table 68), and a higher relative growth rate of leaf area, root coverage and 10 root length (Table 69) when grown under normal growth conditions, as compared to control plants grown under identical growth conditions. Plants producing larger root biomass have better possibilities to absorb larger amount of nitrogen from soil. Plants producing larger leaf biomass has better ability to produce assimilates). The genes were cloned under the regulation of a constitutive promoter (At6669; SEQ ID NO:41 11). 15 The evaluation of each gene was performed by testing the performance of different number of events. Some of the genes were evaluated in more than one tissue culture WO 2013/128448 PCT/IL2013/050172 319 assay. This second experiment confirmed the significant increment in leaf and root performance. Event with p-value < 0.1 was considered statistically significant. Tables 67-69 summarize the observed phenotypes of transgenic plants expressing the gene constructs using the TC -TI Assays. 5 Table 67 Genes showing improved plant performance at Normal growth conditions under regulation of A6669 promoter Gene Name Dry Weight [mg] Fresh Weight [mg] Ave. P-Val. % Incr. Ave. P-Val. % Incr. LYD690 4.6 0.01 26 108.9 L 26 LYD550 4.8 L 30 121.0 L 40 LYD525 4.6 0.09 24 108.4 0.17 26 CONT. 3.7 - - 86.3 - LYD592 4.9 0.02 37 99.6 L 42 CONT. 3.6 - - 70.2 - LYD633 10.6 L 25 200.2 0.06 25 LYD619 10.8 0.03 28 194.8 0.03 21 LYD587 9.8 0.04 17 - - LYD565 10.2 0.19 21 - CONT. 8.4 - - 160.5 - LYD659 8.8 0.07 11 160.8 0.12 12 CONT. 8.0 - - 143.9 - LYD659 5.9 L 64 136.1 0.02 64 LYD578 4.3 0.27 20 96.3 0.18 16 LYD532 4.6 0.15 29 101.3 0.12 22 CONT. 3.6 - - 82.8 - LYD532 6.6 0.08 48 205.1 0.06 80 CONT. 4.4 - - 114.2 - LYD539_H11 7.8 0.20 25 - CONT. 6.2 - - - - LYD575 6.5 0.19 29 159.5 0.22 27 CONT. 5.0 - - 125.1 - Table 67. "CONT." - Control; "Ave." - Average; "% Incr." = % increment; "p-val." 10 value, L- p<0.01. The transgenes were under the transcriptional regulation of the new At6669 promoter (SEQ ID NO: 4111). "-" = results are still unavailable.
WO 2013/128448 PCT/IL2013/050172 320 Table 68 Genes showing improved plant performance at Normal growth conditions under regulation of At6669 promoter Leaf Area [cm 2 ] Roots Coverage [cm 2 ] Roots Length [cm] Gene Name P- % P- % P- % Val. Incr. Val. Incr. Ave. Val. Incr. LYD690 0.4 L 30 3.8 0.04 26 - - LYD550 0.4 L 31 - - - - - LYD525 0.4 0.15 21 - - - - - CONT. 0.3 - - 3.0 - - - - LYD592 0.5 0.05 41 4.2 0.17 26 - - LYD575 0.4 0.05 12 - - - - - LYD539_H11 0.4 0.18 21 4.5 0.23 34 4.9 0.26 12 CONT. 0.3 - - 3.4 - - 4.4 - LYD633 0.8 0.14 26 - - - 7.2 0.14 20 LYD619 0.7 0.01 21 - - - 6.7 0.14 12 LYD587 0.7 0.05 16 7.6 0.24 17 7.1 0.08 19 LYD565 0.7 0.23 18 - - - - - CONT. 0.6 - - 6.5 - - 6.0 - LYD659 0.8 0.17 11 - - - - - CONT. 0.7 - - - - - - - LYD659 0.5 L 34 4.5 0.12 37 - - LYD578 0.5 0.21 16 4.6 0.24 40 - - LYD532 0.4 0.28 11 - - - - - CONT. 0.4 - - 3.3 - - - - LYD576 0.5 0.12 22 - - - 6.7 0.09 11 LYD532 0.7 0.04 54 7.4 0.13 43 7.2 0.04 19 CONT. 0.4 - - 5.2 - - 6.0 - LYD539_H11 0.6 0.25 19 - - - - - CONT. 0.5 - - - - - - - LYD575 0.7 0.26 26 10.3 0.26 20 - - CONT. 0.5 - - 8.6 - - - - 5 Table 68. "CONT." - Control; "Ave." - Average; "% Incr." = % increment; "p-val." - p value, L- p< 0
.
0 1. The transgenes were under the transcriptional regulation of the new At6669 promoter (SEQ ID NO: 4111). "-" = results are still unavailable. Table 69 10 Genes showing improved plant performance at Normal growth conditions under regulation of At6669 promoter RGR Of Leaf Area RGR Of Roots RGR Of Root Length Gene Name (cm 2 /day) Coverage (cm 2 lday) (cm/day) Av. P- % Av. P- % P-e. % Val. Incr. Val. Incr. Ave. Val. Incr. LYD690 0.0 0.02 25 0.5 L 28 - - LYD550 0.0 L 28 - - - - - - WO 2013/128448 PCT/IL2013/050172 321 RGR Of Leaf Area RGR Of Roots RGR Of Root Length Gene Name (cm 2 /day) Coverage (cm 2 /day) (cm/day) Av. P- % Av. P- % Av. P- % Ave. Ave. Ave. Vl nr Val. Incr. Val. Incr. Val. Incr. LYD525 0.0 0.14 18 - - - - - CONT. 0.0 - - 0.4 - - - - LYD592 0.0 L 46 0.5 0.07 26 - - LYD539_H11 0.0 0.05 26 0.5 0.07 34 0.5 0.27 11 CONT. 0.0 - - 0.4 - - 0.5 - LYD633 0.1 0.13 26 - - - 0.8 0.15 22 LYD619 0.1 0.05 24 - - - 0.8 0.15 15 LYD587 0.1 0.15 18 0.9 0.28 18 0.8 0.07 20 LYD565 0.1 0.11 24 - - - - - CONT. 0.1 - - 0.8 - - 0.7 - LYD659 0.1 L 39 0.6 0.02 41 - - LYD578 0.0 0.13 18 0.6 0.04 41 - - LYD532 0.0 0.20 14 - - - - - CONT. 0.0 - - 0.4 - - - - LYD576 0.1 0.14 21 - - - 0.7 0.09 16 LYD532 0.1 L 56 0.9 0.03 45 0.8 0.02 25 CONT. 0.0 - - 0.6 - - 0.6 - LYD575 0.1 0.23 22 - - - - - LYD539_H11 0.1 0.20 21 - - - - - CONT. 0.1 - - - - - - - LYD575 0.1 0.08 31 1.3 0.21 20 - - CONT. 0.1 - - 1.1 - - - - Table 69. "CONT." - Control; "Ave." - Average; "% Incr." = % increment; "p-val." - p value, L- p<0.01. The transgenes were under the transcriptional regulation of the new At6669 promoter (SEQ ID NO: 4111). "-" = results are still unavailable. These results demonstrate that the polynucleotides of the invention are capable 5 of improving yield and additional valuable important agricultural traits such as increase of biomass, abiotic stress tolerance, nitrogen use efficiency, yield, vigor, fiber yield and/or quality. Thus, transformed plants showing improved fresh and dry weight demonstrate the gene capacity to improve biomass a key trait of crops for forage and plant productivity; transformed plants showing improvement of seed yield demonstrate 10 the genes capacity to improve plant productivity; transformed plants showing improvement of plot coverage and rosette diameter demonstrate the genes capacity to improve plant drought resistance as they reduce the loss of soil water by simple evaporation and reduce the competition with weeds; hence reduce the need to use herbicides to control weeds. Transformed plants showing improvement of relative WO 2013/128448 PCT/IL2013/050172 322 growth rate of various organs (leaf and root) demonstrate the gene capacity to promote plant growth and hence shortening the needed growth period and/or alternatively improving the utilization of available nutrients and water leading to increase of land productivity; Transformed plants showing improvement of organ number as 5 demonstrated by the leaf number parameter exhibit a potential to improve biomass yield important for forage crops and improve the plant productivity; Transformed plants showing increased root length and coverage demonstrate the gene capacity to improve drought resistance and better utilization of fertilizers as the roots can reach larger soil volume; Transformed plants showing improvement of leaf petiole relative area and leaf 10 blade area demonstrate the genes capacity to cope with limited light intensities results from increasing the plant population densities and hence improve land productivity. Although the invention has been described in conjunction with specific embodiments thereof, it is evident that many alternatives, modifications and variations will be apparent to those skilled in the art. Accordingly, it is intended to embrace all 15 such alternatives, modifications and variations that fall within the spirit and broad scope of the appended claims. All publications, patents and patent applications mentioned in this specification are herein incorporated in their entirety by reference into the specification, to the same extent as if each individual publication, patent or patent application was specifically and 20 individually indicated to be incorporated herein by reference. In addition, citation or identification of any reference in this application shall not be construed as an admission that such reference is available as prior art to the present invention. To the extent that section headings are used, they should not be construed as necessarily limiting.

权利要求:
Claims (30)
[1] 1. A method of increasing yield, growth rate, biomass, vigor, oil content, seed yield, fiber yield, fiber quality, nitrogen use efficiency, and/or abiotic stress of a plant, comprising expressing within the plant an exogenous polynucleotide comprising a nucleic acid sequence encoding a polypeptide at least 80 % identical to SEQ ID NO: 422, 362-421, 423-601, 2429-3646, 3648-4085 and 4086, thereby increasing the yield, growth rate, biomass, vigor, oil content, seed yield, fiber yield, fiber quality, nitrogen use efficiency, and/or abiotic stress of the plant.
[2] 2. A method of increasing yield, growth rate, biomass, vigor, oil content, seed yield, fiber yield, fiber quality, nitrogen use efficiency, and/or abiotic stress of a plant, comprising expressing within the plant an exogenous polynucleotide comprising a nucleic acid sequence encoding a polypeptide selected from the group consisting of SEQ ID NOs: 422, 362-421, 423-601, 2429-4085 and 4086, thereby increasing the yield, growth rate, biomass, vigor, oil content, seed yield, fiber yield, fiber quality, nitrogen use efficiency, and/or abiotic stress of the plant.
[3] 3. A method of producing a crop comprising growing a crop of a plant expressing an exogenous polynucleotide comprising a nucleic acid sequence encoding a polypeptide at least 80 % homologous to the amino acid sequence selected from the group consisting of SEQ ID NOs: 422, 362-421, 423-601, 2429-3646, 3648-4085 and 4086, wherein said plant is derived from a plant selected for increased yield, increased growth rate, increased biomass, increased vigor, increased oil content, increased seed yield, increased fiber yield, increased fiber quality, increased nitrogen use efficiency, and/or increased abiotic stress tolerance as compared to a control plant, thereby producing the crop.
[4] 4. A method of increasing yield, growth rate, biomass, vigor, oil content, seed yield, fiber yield, fiber quality, nitrogen use efficiency, and/or abiotic stress of a plant, comprising expressing within the plant an exogenous polynucleotide comprising a nucleic acid sequence at least 80 % identical to SEQ ID NO: 260, 1-259, 261-361, 602- WO 2013/128448 PCT/IL2013/050172 324 2427 and 2428, thereby increasing the yield, growth rate, biomass, vigor, oil content, seed yield, fiber yield, fiber quality, nitrogen use efficiency, and/or abiotic stress of the plant.
[5] 5. A method of increasing yield, growth rate, biomass, vigor, oil content, seed yield, fiber yield, fiber quality, nitrogen use efficiency, and/or abiotic stress of a plant, comprising expressing within the plant an exogenous polynucleotide comprising the nucleic acid sequence selected from the group consisting of SEQ ID NOs: 260, 1 259, 261-361, 602-2427 and 2428, thereby increasing the yield, growth rate, biomass, vigor, oil content, seed yield, fiber yield, fiber quality, nitrogen use efficiency, and/or abiotic stress of the plant.
[6] 6. A method of producing a crop comprising growing a crop of a plant expressing an exogenous polynucleotide which comprises a nucleic acid sequence which is at least 80 % identical to the nucleic acid sequence selected from the group consisting of SEQ ID NOs: 260, 1-259, 261-361, 602-2427 and 2428, wherein said plant is derived from a plant selected for increased yield, increased growth rate, increased biomass, increased vigor, increased oil content, increased seed yield, increased fiber yield, increased fiber quality, increased nitrogen use efficiency, and/or increased abiotic stress tolerance as compared to a control plant, thereby producing the crop.
[7] 7. An isolated polynucleotide comprising a nucleic acid sequence encoding a polypeptide which comprises an amino acid sequence at least 80 % homologous to the amino acid sequence set forth in SEQ ID NO: 422, 362-421, 423-601, 2429-3646, 3648 4085 and 4086, wherein said amino acid sequence is capable of increasing yield, growth rate, biomass, vigor, oil content, seed yield, fiber yield, fiber quality, nitrogen use efficiency, and/or abiotic stress of a plant.
[8] 8. An isolated polynucleotide comprising a nucleic acid sequence encoding a polypeptide which comprises the amino acid sequence selected from the group consisting of SEQ ID NOs: 422, 362-421, 423-601, 2429-4085 and 4086. WO 2013/128448 PCT/IL2013/050172 325
[9] 9. An isolated polynucleotide comprising a nucleic acid sequence at least 80 % identical to SEQ ID NOs: 260, 1-259, 261-361, 602-2427 and 2428, wherein said nucleic acid sequence is capable of increasing yield, growth rate, biomass, vigor, oil content, seed yield, fiber yield, fiber quality, nitrogen use efficiency, and/or abiotic stress of a plant.
[10] 10. An isolated polynucleotide comprising the nucleic acid sequence selected from the group consisting of SEQ ID NOs: 260, 1-259, 261-361, 602-2427 and 2428.
[11] 11. A nucleic acid construct comprising the isolated polynucleotide of claim 7, 8, 9 or 10, and a promoter for directing transcription of said nucleic acid sequence in a host cell.
[12] 12. An isolated polypeptide comprising an amino acid sequence at least 80% homologous to SEQ ID NO: 422, 362-421, 423-601, 2429-3646, 3648-4085 and 4086, wherein said amino acid sequence is capable of increasing yield, growth rate, biomass, vigor, oil content, seed yield, fiber yield, fiber quality, nitrogen use efficiency, and/or abiotic stress of a plant.
[13] 13. An isolated polypeptide comprising the amino acid sequence selected from the group consisting of SEQ ID NOs: 422, 362-421, 423-601, 2429-4085 and 4086.
[14] 14. A plant cell exogenously expressing the polynucleotide of claim 7, 8, 9 or 10, or the nucleic acid construct of claim 11.
[15] 15. A plant cell exogenously expressing the polypeptide of claim 12 or 13.
[16] 16. The method of claim 1, 3, 4 or 6, the isolated polynucleotide of claim 7, the nucleic acid construct of claim 11 or the plant cell of claim 14, wherein said nucleic acid sequence encodes an amino acid sequence selected from the group consisting of SEQ ID NOs: 422, 362-421, 423-601, 2429-4085 and 4086. WO 2013/128448 PCT/IL2013/050172 326
[17] 17. The method of claim 1, 2, 3, 4, 5 or 6, the isolated polynucleotide of claim 7, 8, 9, or 10, the nucleic acid construct of claim 11 or the plant cell of claim 14, wherein said nucleic acid sequence is selected from the group consisting of SEQ ID NOs: 260, 1-259, 261-361, 602-2427 and 2428.
[18] 18. The method of claim 1, 2, 3, 4, 5, or 6, the isolated polynucleotide of claim 7, 8, 9, or 10, the nucleic acid construct of claim 11 or the plant cell of claim 14, wherein said polynucleotide consists of the nucleic acid sequence selected from the group consisting of SEQ ID NOs: 260, 1-259, 261-361, 602-2427 and 2428.
[19] 19. The method of claim 1 or 3, the isolated polynucleotide of claim 7, the nucleic acid construct of claim 11, or the plant cell of claim 14, wherein said nucleic acid sequence encodes the amino acid sequence selected from the group consisting of SEQ ID NOs: 422, 362-421, 423-601, 2429-4085 and 4086.
[20] 20. The plant cell of claim 14 or 15, wherein said plant cell forms part of a plant.
[21] 21. The method of claim 1, 2, 3, 4, 5, 6, 16, 17, 18, or 19, further comprising growing the plant expressing said exogenous polynucleotide under the abiotic stress.
[22] 22. The method of any of claims 1, 2, 3, 4, 5, 6, 16, 17, 18, 19 and 21, the isolated polynucleotide of claim 7 or 9, the nucleic acid construct of claim 11, the isolated polypeptide of claim 12, or the plant cell of claim 14, 15 or 20, wherein said abiotic stress is selected from the group consisting of salinity, drought, osmotic stress, water deprivation, flood, etiolation, low temperature, high temperature, heavy metal toxicity, anaerobiosis, nutrient deficiency, nutrient excess, atmospheric pollution and UV irradiation.
[23] 23. The method of any of claims 1, 2, 3, 4, 5, 6, 16, 17, 18, 19 and 21, the isolated polynucleotide of claim 7 or 9, the nucleic acid construct of claim 11, the WO 2013/128448 PCT/IL2013/050172 327 isolated polypeptide of claim 12, or the plant cell of claim 14, 15 or 20, wherein the yield comprises seed yield or oil yield.
[24] 24. A transgenic plant comprising the nucleic acid construct of any of claims 11 and 16-19 or the plant cell of any of claims 14-20 and 22-23.
[25] 25. The method of claim 1, 2, 3, 4, 5, 6, 16, 17, 18, or 19, further comprising growing the plant expressing said exogenous polynucleotide under nitrogen-limiting conditions.
[26] 26. The nucleic acid construct of any of claims 11 and 16-19, the plant cell of any of claims 14-20 and 22-23, or the transgenic plant of claim 24, wherein said promoter is heterologous to said isolated polynucleotide and/or to said host cell.
[27] 27. A method of growing a crop, the method comprising seeding seeds and/or planting plantlets of a plant transformed with the isolated polynucleotide of 7, 8, 9, or 10, or with the nucleic acid construct of claim 11, wherein the plant is derived from plants selected for at least one trait selected from the group consisting of: increased nitrogen use efficiency, increased abiotic stress tolerance, increased biomass, increased growth rate, increased vigor, increased yield and increased fiber yield or quality, and increased oil content as compared to a non-transformed plant, thereby growing the crop.
[28] 28. The method of claim 27, wherein said non-transformed plant is a wild type plant of identical genetic background.
[29] 29. The method of claim 27, wherein said non-transformed plant is a wild type plant of the same species.
[30] 30. The method of claim 27, wherein said non-transformed plant is grown under identical growth conditions.

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法律状态:
2018-07-26| FGA| Letters patent sealed or granted (standard patent)|

优先权:

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申请号 | 申请日 | 专利标题

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US201261604588P| true| 2012-02-29|2012-02-29||

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US61/604,588||2012-02-29||

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US201261681252P| true| 2012-08-09|2012-08-09||

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US61/681,252||2012-08-09||

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PCT/IL2013/050172|WO2013128448A1|2012-02-29|2013-02-27|Isolated polynucleotides and polypeptides and methods of using same for increasing plant yield, biomass, growth rate, vigor, oil content, abiotic stress tolerance of plants and nitrogen use efficiency|AU2018204225A| AU2018204225B2|2012-02-29|2018-06-14|Isolated Polynucleotides and Polypeptides and Methods of Using Same for Increasing Plant Yield, Biomass, Growth Rate, Vigor, Oil Content, Abiotic Stress Tolerance of Plants and Nitrogen Use Efficiency|

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