# Patent

## Title
Methods of increasing biomass and/or growth rate of a plant under non-stress conditions

## Abstract

Provided are methods of increasing yield, biomass, growth rate, vigor, and/or abiotic stress tolerance of a plant by expressing within the plant an exogenous polynucleotide comprising a nucleic acid sequence at least 80% identical to SEQ ID NO: 908 or 71; or an exogenous polynucleotide encoding a polypeptide at least 80% identical to SEQ ID NO: 176.

## Background
RELATED APPLICATIONS
This application is a division of U.S. patent application Ser. No. 13/125,047 filed on Apr. 20, 2011, which is a National Phase of PCT Patent Application No. PCT/IB2009/054774 having International filing date of Oct. 28, 2009, which claims the benefit of priority from U.S. Provisional Patent Application No. 61/187,683 filed on Jun. 17, 2009 and 61/193,141 filed on Oct. 30, 2008. The content of the above document is incorporated by references as if fully set forth herein.
SEQUENCE LISTING STATEMENT
The ASCII file, entitled 60623SequenceListing.txt, created on Nov. 2, 2014, comprising 2,449,408 bytes, submitted concurrently with the filing of this application is incorporated herein by reference.


FIELD AND BACKGROUND OF THE INVENTION
The present invention, in some embodiments thereof, relates to polypeptides, polynucleotides encoding same, transgenic plants expressing same and methods of producing and using same, and, more particularly, but not exclusively, to methods of increasing plant yield, oil yield, seed yield, biomass, growth rate, vigor, oil content, abiotic stress tolerance and/or nitrogen use efficiency.
Abiotic stress conditions such 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 abiotic stress (ABS) 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.
The global shortage of water supply is one of the most severe agricultural problems affecting plant growth and crop yield and efforts are made to mitigate the harmful effects of desertificFation and salinization of the world's arable land. Thus, Agbiotech companies attempt to create new crop varieties which are tolerant to different abiotic stresses focusing mainly in developing new varieties that can tolerate water shortage for longer periods.
Suboptimal nutrient (macro and micro nutrient) affect plant growth and development through the whole plant life cycle. One of the essential macronutrients for the plant is Nitrogen. Nitrogen is responsible for biosynthesis of amino acids and nucleic acids, prosthetic groups, plant hormones, plant chemical defenses, and the like. Nitrogen is often the rate-limiting element in plant growth and all field crops have a fundamental dependence on inorganic nitrogenous fertilizer. Since fertilizer is rapidly depleted from most soil types, it must be supplied to growing crops two or three times during the growing season. Additional important macronutrients are Phosphorous (P) and Potassium (K), which have a direct correlation to yield and general plant tolerance.
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 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 oils as bio-fuel is the oil price, which is still higher than fossil fuel [Hypertext Transfer Protocol://World Wide Web(dot)eia(dot)doe(dot) gov/oiaf/analysispaper/biodiesel/; Hypertext Transfer Protocol://World Wide Web(dot) njbiz(dot)com/weekly article.asp?aID=19755147(dot) 6122555(dot) 957931(dot) 7393254(dot) 4337383(dot) 561&aID2=73678]. 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 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/), TAIR No. AT2G43710)], OleosinA (TAIR No. AT3G01570) or FAD3 (TAIR No. AT2G29980), and various transcription factors and activators such as Lec1 [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. 278(23): 21003-11] and Wri1 [TAIR No. AT3G54320, Cernac and Benning, 2004. Plant J. 40(4): 575-85].
Zabrouskov V., et al., 2002 (Physiol Plant. 116:172-185) describe an increase in the total lipid fraction by upregulation of endoplasmic reticulum (FAD3) and plastidal (FAD7) fatty acid desaturases in potato.
Wang H W et al., 2007 (Plant J. 52:716-29. Epub 2007 Sep. 18) describe an increase in the content of total fatty acids and lipids in plant seeds by over-expressing the GmDof4 and GmDof11 transcription factors.
Vigeolas H, et al. [Plant Biotechnol J. 2007, 5(3):431-41] and U.S. Pat. Appl. No. 20060168684 discloses an increase in seed oil content in oil-seed rape (Brassica napus L.) by over-expression of a yeast glycerol-3-phosphate dehydrogenase under the control of a seed-specific promoter.
Katavic V, et al., 2000 (Biochem Soc Trans. 28:935-7) describe the use of the Arabidopsis FAE1 and yeast SLC1-1 genes for improvements in erucic acid and oil content in rapeseed.
U.S. Pat. Appl. No. 20080076179 discloses an isolated moss nucleic acid encoding a lipid metabolism protein (LMP) and transgenic plants expressing same with increased lipid levels.
U.S. Pat. Appl. No. 20060206961 discloses a method of increasing oil content in plants (e.g., in plant seeds), by expressing in the plant the Ypr140w polypeptide.
U.S. Pat. Appl. No. 20060174373 discloses a method of increasing oil content in plants by expressing a nucleic acid encoding a triacylglycerols (TAG) synthesis enhancing protein (TEP) in the plant.
U.S. Pat. Appl. Nos. 20070169219, 20070006345, 20070006346 and 20060195943, disclose transgenic plants with improved nitrogen use efficiency which can be used for the conversion into fuel or chemical feedstocks.
WO2004/104162 teaches polynucleotide sequences and methods of utilizing same for increasing the tolerance of a plant to abiotic stresses and/or increasing the biomass of a plant.
WO2007/020638 teaches polynucleotide sequences and methods of utilizing same for increasing the tolerance of a plant to abiotic stresses and/or increasing the biomass, vigor and/or yield of a plant.
WO2008/122890 teaches polynucleotide sequences and methods of utilizing same for increasing oil content, growth rate, biomass, yield and/or vigor of a plant.
SUMMARY OF THE INVENTION
According to an aspect of some embodiments of the present invention there is provided a method of increasing yield, biomass, growth rate, vigor, oil content, abiotic stress tolerance and/or nitrogen use efficiency of a plant, comprising expressing within the plant an exogenous polynucleotide comprising a nucleic acid sequence at least 80% identical to SEQ ID NO: 905, 882, 1-12, 15-105, 203-297, 299-523, 845-881, 883-904, 906-925 or 933, thereby increasing the yield, biomass, growth rate, vigor, oil content, abiotic stress tolerance and/or nitrogen use efficiency of the plant.
According to an aspect of some embodiments of the present invention there is provided a method of increasing yield, biomass, growth rate, vigor, oil content, abiotic stress tolerance and/or nitrogen use efficiency 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: 905, 882, 1-13, 15-105, 203-523, 845-881, 883-904, 906-925 and 933, thereby increasing the yield, biomass, growth rate, vigor, oil content, abiotic stress tolerance and/or nitrogen use efficiency of the plant.
According to an aspect of some embodiments of the present invention there is provided a method of increasing yield, biomass, growth rate, vigor, oil content, abiotic stress tolerance and/or nitrogen use efficiency 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: 172, 146, 106-117, 120-145, 147-171, 173-202, 524-616, 621-844, 926-931 or 932, thereby increasing the yield, biomass, growth rate, vigor, oil content, abiotic stress tolerance and/or nitrogen use efficiency of the plant.
According to an aspect of some embodiments of the present invention there is provided a method of increasing yield, biomass, growth rate, vigor, oil content, abiotic stress tolerance and/or nitrogen use efficiency 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: 172, 146, 106-117, 120-145, 147-171, 173-202, 524-844 and 926-932, thereby increasing the yield, biomass, growth rate, vigor, oil content, abiotic stress tolerance and/or nitrogen use efficiency of the plant.
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% identical to SEQ ID NO: 905, 882, 1-12, 15-105, 203-297, 299-523, 845-881, 883-904, 906-925 or 933, wherein said nucleic acid sequence is capable of increasing yield, biomass, growth rate, vigor, oil content, abiotic stress tolerance and/or nitrogen use efficiency 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 the group consisting of SEQ ID NOs: 905, 882, 1-13, 15-105, 203-523, 845-881, 883-904, 906-925 and 933.
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 to the amino acid sequence set forth in SEQ ID NO: 172, 146, 106-117, 120-145, 147-171, 173-202, 524-616, 621-844, 926-931 or 932, wherein said amino acid sequence is capable of increasing yield, biomass, growth rate, vigor, oil content, abiotic stress tolerance and/or nitrogen use efficiency of a plant.
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 the amino acid sequence selected from the group consisting of SEQ ID NOs: 172, 146, 106-117, 120-145, 147-171, 173-202, 524-844 and 926-932.
According to an aspect of some embodiments of the present invention there is provided a nucleic acid construct comprising the isolated polynucleotide of the invention, and a promoter for directing transcription of said 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% homologous to SEQ ID NO: 172, 146, 106-117, 120-145, 147-171, 173-202, 524-616, 621-844, 926-931 or 932, wherein said amino acid sequence is capable of increasing yield, biomass, growth rate, vigor, oil content, abiotic stress tolerance and/or nitrogen use efficiency of a plant.
According to an aspect of some embodiments of the present invention there is provided an isolated polypeptide comprising the amino acid sequence selected from the group consisting of SEQ ID NOs: 172, 146, 106-117, 120-145, 147-171, 173-202, 524-844 and 926-932.
According to an aspect of some embodiments of the present invention there is provided a plant cell exogenously expressing the polynucleotide of the invention, or the nucleic acid construct of the invention.
According to an aspect of some embodiments of the present invention there is provided a plant cell exogenously expressing the polypeptide of the invention.
According to some embodiments of the invention, the nucleic acid sequence is as set forth in SEQ ID NO: 905, 882, 1-13, 15-105, 203-523, 845-881, 883-904, 906-925 or 933.
According to some embodiments of the invention, the polynucleotide consists of the nucleic acid sequence selected from the group consisting of SEQ ID NOs: 905, 882, 1-13, 15-105, 203-523, 845-881, 883-904, 906-925 and 933.
According to some embodiments of the invention, the nucleic acid sequence encodes an amino acid sequence at least 80% homologous to SEQ ID NO: 172, 146, 106-117, 120-145, 147-171, 173-202, 524-616, 621-844, 926-931 or 932.
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: 172, 146, 106-117, 120-145, 147-171, 173-202, 524-844 and 926-932.
According to some embodiments of the invention, the plant cell forms part of a plant.
According to some embodiments of the invention, the method further comprising growing the plant expressing said exogenous polynucleotide under the abiotic stress.
According to some embodiments of the invention, the abiotic stress is selected from the group consisting of salinity, drought, water deprivation, flood, etiolation, low temperature, high temperature, heavy metal toxicity, anaerobiosis, nutrient deficiency, nutrient excess, atmospheric pollution and UV irradiation.
According to some embodiments of the invention, the yield comprises seed yield or oil yield.
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 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 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 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:
FIG. 1 is a schematic illustration of the pGI binary plasmid used for expressing the isolated polynucleotide sequences of some embodiments of the invention. RB—T-DNA right border; LB—T-DNA left border; H—HindIII restriction enzyme; X—XbaI restriction enzyme; B—BamHI restriction enzyme; S—Sail restriction enzyme; Sm—SmaI restriction enzyme; R-I—EcoRI restriction enzyme; Sc—SacI/SstI/Ecl13611; (numbers)—Length in base-pairs; NOS pro=nopaline synthase promoter; NPT-II=neomycin 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 GUS intron reporter gene
FIG. 2 is a schematic illustration of the modified pGI binary plasmid 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; (numbers)—Length in base-pairs; NOS pro=nopaline synthase promoter; NPT-II=neomycin 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.
FIGS. 3A-F are images depicting visualization of root development of transgenic plants exogenously expressing the polynucleotide of some embodiments of the invention when grown in transparent agar plates under normal (FIGS. 3A-B), osmotic stress (15% PEG; FIGS. 3C-D) or nitrogen-limiting (FIGS. 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 at day 1 after transplanting. FIG. 3A—An image of a photograph of plants taken following 10 after transplanting days on agar plates when grown under normal (standard) conditions. FIG. 3B—An image of root analysis of the plants shown in FIG. 3A in which the lengths of the roots measured are represented by arrows. FIG. 3C—An image of a photograph of plants taken following 10 days after transplanting on agar plates, grown under high osmotic (PEG 15%) conditions. FIG. 3D—An image of root analysis of the plants shown in FIG. 3C in which the lengths of the roots measured are represented by arrows. FIG. 3E—An image of a photograph of plants taken following 10 days after transplanting on agar plates, grown under low nitrogen conditions. FIG. 3F—An image of root analysis of the plants shown in FIG. 3E in which the lengths of the roots measured are represented by arrows.



DESCRIPTION OF SPECIFIC EMBODIMENTS OF THE INVENTION
The present invention, in some embodiments thereof, relates to polypeptides, polynucleotides encoding same, nucleic acid constructs comprising same, transgenic plants expressing same and methods of producing and using same for increasing plant yield, oil yield, seed yield, biomass, growth rate, vigor, oil content, abiotic stress tolerance and/or nitrogen use efficiency.
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.
While reducing the present invention to practice, the present inventors have identified novel polypeptides and polynucleotides which can be used to increase yield, growth rate, biomass, oil content, vigor, abiotic stress tolerance and/or nitrogen use efficiency of a plant.
Thus, as shown in the Examples section which follows, the present inventors have utilized bioinformatics tools and microarray analyses to identify polynucleotides which enhance yield (e.g., seed yield, oil yield, oil content), growth rate, biomass, vigor, abiotic stress tolerance and/or nitrogen use efficiency of a plant. Genes which affect the trait-of-interest [Table 15; Example 5 of the Examples section which follows; SEQ ID NOs:1-105 (polynucleotides) and SEQ ID NOs:106-202 (polypeptides)] were identified based on correlation analyses between expression profiles of various genes in tissues, developmental stages, fertilizer limiting conditions, abiotic stress conditions or normal conditions across several Arabidopsis ecotypes, Sorghum Accessions and Tomato accessions and various parameters of yield, biomass, vigor, growth rate and/or oil content (Examples 1, 2, 3, 4, 10 and 11 of the Examples section which follows; Tables 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 28 and 29). Homologous polypeptides and polynucleotides having the same function (activity) were also identified [Table 16, Example 6 of the Examples section which follows; SEQ ID NOs:203-523 (polynucleotides), and SEQ ID NOs:524-844 (polypeptides)]. The identified genes were cloned in binary vectors (see for example, Tables 17, 18, 19 and 20; Example 7 of the Examples section which follows; SEQ ID NOs:47, 845-925 and 933) and transgenic plants over-expressing the identified genes of the invention were generated (see for example, Example 8 of the Examples section which follows). These plants which are transformed with the identified polynucleotides were found to exhibit increased yield, biomass, growth rate, vigor, seed yield, oil content, oil yield, flowering, harvest index and rosette area (Tables 21-27; Example 9 of the Examples section which follows). These results suggest the use of the novel polynucleotides and polypeptides of the invention for increasing yield (including oil yield, seed yield and oil content), growth rate, biomass, vigor, abiotic stress tolerance and/or nitrogen use efficiency of a plant.
Thus, according to an aspect of some embodiments of the invention, there is provided method of increasing yield, biomass, growth rate, vigor, oil content, abiotic stress tolerance and/or nitrogen use efficiency of a plant. The method is effected by expressing within the plant an exogenous polynucleotide comprising a nucleic acid sequence at least 80% identical to SEQ ID NO: 905, 882, 1-12, 15-105, 203-297, 299-523, 845-881, 883-904, 906-925, or 933, thereby increasing the yield, biomass, growth rate, vigor, oil content, abiotic stress tolerance and/or nitrogen use efficiency of the plant.
As used herein the phrase “plant yield” refers to the amount (as determined by weight or size) or quantity (numbers) of tissues or organs produced per plant or per 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 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 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 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 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 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 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).
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. 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 increase in plant biomass can be in the whole plant or in parts thereof such as aboveground (harvestable) parts, vegetative biomass, roots and seeds.
As used herein the phrase “growth rate” refers to the increase in plant organ/tissue size per time (can be measured in cm2 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 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.
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, 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 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.
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 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 plant to endure an abiotic stress without suffering a substantial alteration in metabolism, growth, productivity and/or viability.
As used herein the phrase “water use efficiency (WUE)” refers to the level of 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 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 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 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.
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.
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 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.
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, growth rate, biomass, vigor, oil content, abiotic stress tolerance and/or nitrogen use efficiency of a plant as compared to a native 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 growth conditions].
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 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 or which overexpression in the plant is desired. The exogenous polynucleotide may be introduced into the plant in a stable or 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 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 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 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: 905, 882, 1-12, 15-105, 203-297, 299-523, 845-881, 883-904, 906-925 and 933.
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 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 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: 905, 882, 1-12, 15-105, 203-297, 299-523, 845-881, 883-904, 906-925 and 933.
According to some embodiments of the invention the exogenous polynucleotide is set forth by SEQ ID NO: 905, 882, 1-12, 15-105, 203-297, 299-523, 845-881, 883-904, 906-925 or 933.
According to an aspect of some embodiments of the invention, there is provided a method of increasing yield, biomass, growth rate, vigor, oil content, abiotic stress tolerance and/or nitrogen use efficiency of a plant. The method is effected by expressing within the plant an exogenous polynucleotide comprising the nucleic acid sequence selected from the group consisting of SEQ ID NOs: 905, 882, 1-13, 15-105, 203-523, 845-881, 883-904, 906-925 and 933, thereby increasing the yield, biomass, growth rate, vigor, oil content, abiotic stress tolerance and/or nitrogen use efficiency of the plant.
According to some embodiments of the invention the exogenous polynucleotide is selected from the group consisting of SEQ ID NOs: 905, 882, 1-13, 15-105, 203-523, 845-881, 883-904, 906-925 and 933.
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 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.
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.
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 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.
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 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: 172, 146, 106-117, 120-145, 147-171, 173-202, 524-616, 621-844, 926-931 and 932.
Homology (e.g., percent homology) can be determined using any homology comparison software, including for example, the BlastP or TBLASTN software of the National Center of Biotechnology Information (NCBI) such as by using default parameters, when starting from a polypeptide sequence; or the tBLASTX algorithm (available via the NCBI) such as by using default parameters, which compares the six-frame conceptual translation products of a nucleotide query sequence (both strands) against a protein sequence database.
Homologous sequences include both orthologous and paralogous sequences. The term “paralogous” relates to gene-duplications within the genome of a species 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 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 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 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.
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: 172, 146, 106-117, 120-145, 147-171, 173-202, 524-616, 621-844, 926-931 or 932.
According to an aspect of some embodiments of the invention, the method of increasing yield, biomass, growth rate, vigor, oil content, abiotic stress tolerance and/or nitrogen use efficiency of a plant is effected by expressing within the plant an exogenous polynucleotide comprising the nucleic acid sequence encoding a polypeptide selected from the group consisting of SEQ ID NOs: 172, 146, 106-117, 120-145, 147-171, 173-202, 524-844 and 926-932, thereby increasing the yield, biomass, growth rate, vigor, oil content, abiotic stress tolerance and/or nitrogen use efficiency of the plant.
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.
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 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 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=1N[(Xn−Yn)/Yn]2/N, where Xn 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. (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 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 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-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.
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 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 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.
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 (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:72 (BDL90).
Thus, the invention encompasses nucleic acid sequences described hereinabove; fragments thereof, sequences hybridizable therewith, sequences homologous thereto, 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 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%, e.g., 100% identical to the polynucleotide selected from the group consisting of SEQ ID NOs: 905, 882, 1-12, 15-105, 203-297, 299-523, 845-881, 883-904, 906-925 and 933.
According to some embodiments of the invention the nucleic acid sequence is capable of increasing yield, growth rate, vigor, biomass, oil content, abiotic stress tolerance and/or nitrogen use efficiency of a plant.
According to some embodiments of the invention the isolated polynucleotide comprising the nucleic acid sequence selected from the group consisting of SEQ ID NOs: 905, 882, 1-13, 15-105, 203-523, 845-881, 883-904, 906-925 and 933.
According to some embodiments of the invention the isolated polynucleotide is set forth by SEQ ID NO: 905, 882, 1-13, 15-105, 203-523, 845-881, 883-904, 906-925 or 933.
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%, 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 NOs: 172, 146, 106-117, 120-145, 147-171, 173-202, 524-616, 621-844, 926-931 and 932.
According to some embodiments of the invention the amino acid sequence is capable of increasing yield, growth rate, vigor, biomass, oil content, abiotic stress tolerance and/or nitrogen use efficiency of a plant.
The invention provides 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: 172, 146, 106-117, 120-145, 147-171, 173-202, 524-844 and 926-932.
The invention provides an isolated polynucleotide comprising a nucleic acid sequence encoding a polypeptide selected from the group consisting of SEQ ID NOs: 172, 146, 106-117, 120-145, 147-171, 173-202, 524-844 and 926-932.
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 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 NOs: 172, 146, 106-117, 120-145, 147-171, 173-202, 524-616, 621-844, 926-931 and 932.
According to some embodiments of the invention, the polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NOs: 172, 146, 106-117, 120-145, 147-171, 173-202, 524-844 and 926-932.
According to some embodiments of the invention, the polypeptide is set forth by SEQ ID NO: 172, 146, 106-117, 120-145, 147-171, 173-202, 524-844, 926-931 or 932.
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.
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 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, 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, Cyclonia oblonga, Cryptomeria japonica, Cymbopogon spp., Cynthea dealbata, Cyclonia 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 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, 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 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 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, 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, 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 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, 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.
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.
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.
According to 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 of the isolated polynucleotide in a host cell.
According to some embodiments of the invention, the isolated polynucleotide is operably linked to the promoter sequence.
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 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.
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.
Suitable constitutive promoters include, for example, CaMV 35S promoter (SEQ ID NO:1184; Odell et al., Nature 313:810-812, 1985); Arabidopsis At6669 promoter (SEQ ID NO:1183; see PCT Publication No. WO04081173A2); maize Ubi 1 (Christensen et al., Plant Sol. Biol. 18:675-689, 1992); rice actin (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); GOS2 (de Pater et al, Plant J November; 2(6):837-44, 1992); ubiquitin (Christensen et al, Plant Mol. Biol. 18: 675-689, 1992); Rice cyclophilin (Bucholz et al, Plant Mol. 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.
Suitable tissue-specific promoters include, but not limited to, leaf-specific promoters [such as described, for example, by Yamamoto et al., Plant J. 12:255-265, 1997; Kwon et al., Plant Physiol. 105:357-67, 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], seed-preferred promoters [e.g., 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), 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, 143). 323-32 1990), napA (Stalberg, et al, Planta 199: 515-519, 1996), Wheat SPA (Albani et al, 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 and HMW, glutenin-1 (Mol Gen Genet. 216:81-90, 1989; NAR 17:461-2), wheat a, b and g gliadins (EMBO3:1409-15, 1984), Barley ltr1 promoter, barley B1, C, D 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), 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-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), sorghum gamma—kafirin (PMB 32:1029-35, 1996)], embryo specific promoters [e.g., rice OSH1 (Sato et al, Proc. Natl. Acad. Sci. USA, 93: 8117-8122), KNOX (Postma-Haarsma of 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), apetala-3].
Suitable abiotic stress-inducible promoters include, but not limited to, salt-inducible promoters such as RD29A (Yamaguchi-Shinozalei et al., Mol. Gen. Genet. 236:331-340, 1993); drought-inducible promoters such as maize rab17 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).
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 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.
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 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).
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, L. K., Academic Publishers, San Diego, Calif. (1989) p. 2-25; Gatenby, in Plant Biotechnology, eds. Kung, S, and Arntzen, 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., 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 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 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, 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 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 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 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 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 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 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 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 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, 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 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 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 (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.
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, 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 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 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 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. O. et al., Virology (1989) 172:285-292; Takamatsu et al. EMBO J. (1987) 6:307-311; French et al. Science (1986) 231:1294-1297; 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 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 the plasmid and translation of the viral genes to produce the coat protein(s) which encapsidate the viral RNA.
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 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 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-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 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 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 subgenomic promoters to produce the desired product.
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 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.
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; 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.
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 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 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 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.
Since processes which increase yield, growth rate, biomass, vigor, oil content, abiotic stress tolerance and/or nitrogen use efficiency 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 achieve superior effect on the yield, growth rate, biomass, vigor, oil content, abiotic stress tolerance and/or nitrogen use efficiency of the plant.
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 than be 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 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 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.
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.
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 yield, growth rate, biomass, vigor, oil content, abiotic stress tolerance and/or nitrogen use efficiency 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.
Non-limiting examples of abiotic stress conditions include, salinity, drought, water deprivation, excess of water (e.g., flood, waterlogging), etiolation, low temperature, high temperature, heavy metal toxicity, anaerobiosis, nutrient deficiency, nutrient excess, atmospheric pollution and UV irradiation.
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 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 blot analysis, reverse transcription polymerase chain reaction (RT-PCR) analysis (including quantitative, semi-quantitative or real-time RT-PCR) and RNA-in situ hybridization.
In addition, the endogenous homolog of the exogenous polynucleotide or polypeptide of the invention, or a fragment of the endogenous homolog (e.g. introns or untranslated regions) in the plant can be used as a marker for marker assisted selection (MAS), in which a marker is used for indirect selection of a genetic determinant or determinants of a trait of interest (e.g., biomass, growth rate, oil content, yield, abiotic stress tolerance). These genes (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 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 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 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 plant trait.
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.
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, 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 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, 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 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 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 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.
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 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 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 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 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 (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 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.
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 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 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:

RWC=[(FW−DW)/(TW−DW)]×100  Formula I

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 USA. 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 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 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.
Nitrogen Use Efficiency—
To analyze whether the transgenic Arabidopsis plants are more responsive to nitrogen, plant are grown in 0.75-1.5 mM (nitrogen deficient conditions) or 6-10 mM (optimal nitrogen concentration). Plants are allowed to grow for additional 20 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 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 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 Dof1 transcription factor in plants: Improved nitrogen assimilation and growth under low-nitrogen conditions” Proc. Natl. Acad. Sci. USA 101, 7833-7838). Briefly, transgenic plants which are grown for 7-10 days in 0.5×MS [Murashige-Skoog] supplemented with a selection agent are transferred to two nitrogen-limiting conditions: MS media in which the combined nitrogen concentration (NH4NO3 and KNO3) was 0.2 mM or 0.05 mM. Plants are allowed to grow for additional 30-40 days and then photographed, individually removed from the Agar (the shoot without the roots) and immediately weighed (fresh weight) for later statistical analysis. Constructs for which only T1 seeds are available are sown on selective media and at least 25 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 analyzed. Usually, 25 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 are used as control.
Nitrogen Determination—
The procedure for N (nitrogen) concentration determination in the structural parts of the plants involves the potassium persulfate 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 NO2− (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 standard curve of NaNO2. 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 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 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 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 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, rosette area, leaf size or root length per time (can be measured in cm2 per day of leaf area).
Relative growth rate area can be calculated using Formula II.

Relative growth area rate=Regression coefficient of area along time course.  Formula II:

Thus, the relative growth area rate is in units of 1/day and length growth rate is in units of 1/day.

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. 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 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:

1000 Seed Weight=number of seed in sample/sample weight×1000  Formula III:

The Harvest Index can be calculated using Formula IV

Harvest Index=Average seed yield per plant/Average dry weight  Formula IV:

Grain Protein Concentration—
Grain protein content (g grain protein m−2) is 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 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 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 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 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 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 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-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 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 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 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 example, Conway T F. and Earle F R., 1963, Journal of the American Oil Chemists'Society; Springer Berlin/Heidelberg, ISSN: 0003-021× (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 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).
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).
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 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, 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 portion oil.
According to some embodiments of the invention, the plant cell forms a part of a plant.
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 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 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 be considered to have specifically disclosed all the possible sub-ranges 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 sub-ranges such as from 1 to 3, from 1 to 4, from 1 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 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 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.
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.
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 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 hereinabove and as claimed in the claims section below find experimental support in the following examples.
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 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 examples are illustrative only and are not intended to be necessarily limiting.
EXAMPLES
Reference is now made to the following examples, which together with the 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 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, Baltimore, Md. (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); 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, Conn. (1994); Mishell and Shiigi (eds), “Selected Methods in Cellular 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 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 Applications”, Academic Press, San Diego, Calif. (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. All the information contained therein is incorporated herein by reference.
Example 1
Gene Identification and Gene Role Prediction Using Bioinformatics Tools
The present inventors have identified polynucleotides which can increase plant yield, seed yield, oil yield, oil content, biomass, growth rate, abiotic stress tolerance, nitrogen use efficiency and/or vigor of a plant, as follows.
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:
Genomes
Arabidopsis genome [TAIR genome version 6 (Hypertext Transfer Protocol://World Wide Web(dot)arabidopsis(dot)org/)];
Rice genome [IRGSP build 4.0 (Hypertext Transfer Protocol://rgp(dot)dna(dot)affrc(dot)go(dot)jp/IRGSP/)];
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/)];
Brachypodium [JGI 4× assembly, Hypertext Transfer Protocol://World Wide Web(dot)brachpodium(dot)org)];
Soybean [DOE-JGI SCP, version Glyma( ) (Hypertext Transfer Protocol://World Wide Web(dot)phytozome(dot)net/)];
Grape [French-Italian Public Consortium for Grapevine Genome Characterization grapevine genome (Hypertext Transfer Protocol://World Wide Web(dot)genoscope(dot)cns(dot)fr/)];
Castobean [TIGR/J Craig Venter Institute 4× assembly [(Hypertext Transfer Protocol://msc(dot)jcvi(dot)org/r communis];
Sorghum [DOE-JGI SCP, version Sbi1 [Hypertext Transfer Protocol://World 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:
GenBank versions 154, 157, 160, 161, 164, 165, 166 and 168 (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)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)org/biocyc/index(dot)jsp].
ENZYME [Hypertext Transfer Protocol://expasy(dot)org/enzyme/].
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 WO2008/122980 and Example 3 below).
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].
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, 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 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.
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 transcription.
For organisms with no available full genome sequence data, “expressed LEADS” clustering software was applied.
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 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 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.
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.
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.
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 tissue/organ in which the gene is expressed), developmental stage (the developmental stages at which a gene can be found) and profile of treatment (provides the physiological conditions under which a gene is expressed such as drought, 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) 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 (Analysis Of The Melon Fruit Transcriptome Based On 454 Pyrosequencing) in: Plant & Animal Genomes XVII Conference, San Diego, Calif. 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 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 sequencing and assembly. Expression patterns of selected genes fitted well their qRT-PCR data.
Example 2
Production of Arabidopsis Transcriptom and High Throughput Correlation Analysis of Yield, Biomass and/or Vigor Related Parameters Using 44K Arabidopsis 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 [Hypertext Transfer Protocol://World Wide Web(dot)chem.(dot)agilent(dot)com/Scripts/PDS(dot)asp?1Page=50879]. The array oligonucleotide represents about 40,000 A. thaliana genes and transcripts designed based on data from the TIGR ATH1 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 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
RNA Extraction—
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 using TRIzol Reagent from Invitrogen [Hypertext Transfer Protocol://World Wide Web(dot) invitrogen(dot)com/content(dot)cfm?pageid=469]. For convenience, each micro-array expression information tissue type has received a Set ID as summarized in Table 1 below.







TABLE 1







Tissues used for Arabidopsis transcriptom expression sets










Expression Set
Set ID







Root
A



Leaf
B



Flower
C



Seed 5 DAF
D



Seed 12 DAF
E







Table 1:



Provided are the identification (ID) letters of each of the Arabidopsis expression sets (A-E).



DAF = days after flowering.






Approximately 30-50 mg of tissue was taken from samples. The weighed tissues were ground using pestle and mortar in liquid nitrogen and resuspended in 500 μl of TRIzol Reagent. To the homogenized lysate, 100 μl of chloroform was added followed by precipitation using isopropanol and two washes with 75% ethanol. The RNA was eluted in 30 μl of RNase-free water. RNA samples were cleaned up using Qiagen's RNeasy minikit clean-up protocol as per the manufacturer's protocol.
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 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 plates. Most of chosen parameters were analyzed by digital imaging.
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 included 4 light units (4×150 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 greenhouse. The white tubs were square shape with measurements of 36×26.2 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 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 (3072×2048 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, 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 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 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 FIGS. 3A-F). The growth rate of roots was calculated according to Formula V.

Relative growth rate of root coverage=Regression coefficient of root coverage along time course.  Formula V:

Vegetative Growth Rate Analysis—
was calculated according to Formula VI. The analysis was ended with the appearance of overlapping plants.

Relative vegetative growth rate area=Regression coefficient of vegetative area along time course.  Formula VI

For comparison between ecotypes the calculated rate was normalized using plant 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 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 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 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 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.
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.
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 (gr).
Oil Yield—
The oil yield was calculated using Formula VII.

Seed Oil yield=Seed yield per plant(gr)*Oil % in seed  Formula VII:

Harvest Index—
The harvest index was calculated using Formula IV as 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). Data parameters are summarized in Table 2, below.







TABLE 2







Arabidopsis correlated parameters (vectors)








Correlated parameter with
Correlation ID











Root length day 13 (cm)
1


Root length day 7 (cm)
2


Relative root growth (cm/day) day 13
3


Fresh weight per plant (gr) at bolting stage
4


Dry matter per plant (gr)
5


Vegetative growth rate (cm2/day) till 8 true leaves
6


Blade circularity
7


Lamina width (cm)
8


Lamina length (cm)
9


Total leaf area per plant (cm)
10


1000 Seed weight (gr)
11


Oil % per seed
12


Seeds per silique
13


Silique length (cm)
14


Seed yield per plant (gr)
15


Oil yield per plant (mg)
16


Harvest Index
17


Leaf width/length
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 Tables 3 and 4 below.







TABLE 3







Measured parameters in Arabidopsis ecotypes





















Dry

Total





Seed yield
Oil yield
Oil %
1000 Seed
matter

leaf area
Seeds
Silique



per plant
per plant
per
weight
per plant
Harvest
per plant
per
length


Ecotype
(gr)
(mg)
seed
(gr)
(gr)
Index
(cm)
silique
(cm)



















An-1
0.34
118.63
34.42
0.0203
0.64
0.53
46.86
45.44
1.06


Col-0
0.44
138.73
31.19
0.0230
1.27
0.35
109.89
53.47
1.26


Ct-1
0.59
224.06
38.05
0.0252
1.05
0.56
58.36
58.47
1.31


Cvi
0.42
116.26
27.76
0.0344
1.28
0.33
56.80
35.27
1.47


(N8580)


Gr-6
0.61
218.27
35.49
0.0202
1.69
0.37
114.66
48.56
1.24


Kondara
0.43
142.11
32.91
0.0263
1.34
0.32
110.82
37.00
1.09


Ler-1
0.36
114.15
31.56
0.0205
0.81
0.45
88.49
39.38
1.18


Mt-0
0.62
190.06
30.79
0.0226
1.21
0.51
121.79
40.53
1.18


Shakdara
0.55
187.62
34.02
0.0235
1.35
0.41
93.04
25.53
1.00





Table 3. Provided are the values of each of the parameters measured in Arabidopsis ecotypes: Seed yield per plant (gram); oil yield per plant (mg); oil % per seed; 1000 seed weight (gr); dry matter per plant (gr); harvest index; total leaf area per plant (cm); seeds per silique; Silique length (cm).













TABLE 4







Additional measured parameters in Arabidopsis ecotypes


















Relat.
Root
Root
Fresh








root
length
length
weight
Lam.
Lam.
Leaf
Blade


Ecotype
Veg. GR
growth
day 7
day 13
per plant
Leng.
width
width/length
circularity



















An-1
0.313
0.631
0.937
4.419
1.510
2.767
1.385
0.353
0.509


Col-0
0.378
0.664
1.759
8.530
3.607
3.544
1.697
0.288
0.481


Ct-1
0.484
1.176
0.701
5.621
1.935
3.274
1.460
0.316
0.450


Cvi
0.474
1.089
0.728
4.834
2.082
3.785
1.374
0.258
0.370


(N8580)


Gr-6
0.425
0.907
0.991
5.957
3.556
3.690
1.828
0.356
0.501


Kondara
0.645
0.774
1.163
6.372
4.338
4.597
1.650
0.273
0.376


Ler-1
0.430
0.606
1.284
5.649
3.467
3.877
1.510
0.305
0.394


Mt-0
0.384
0.701
1.414
7.060
3.479
3.717
1.817
0.335
0.491


Shakdara
0.471
0.782
1.251
7.041
3.710
4.149
1.668
0.307
0.409





Table 4. Provided are the values of each of the parameters measured in Arabidopsis ecotypes: Veg. GR = vegetative growth rate (cm/day) until 8 true leaves; Relat. Root growth = relative root growth (cm/day); Root length day 7 (cm); Root length day 13 (cm); fresh weight per plant (gr) at bolting stage; Lam. Leng. = Lamima length (cm); Lam. Width = Lamina width (cm); Leaf width/length; Blade circularity.






Tables 5-7, below, provide the selected genes, the characterized parameters (which are used as x axis for correlation) and the correlated tissue transcriptom along with the correlation value (R, calculated using Pearson correlation). When the correlation coefficient (R) between the levels of a gene's expression in a certain tissue and a phenotypic performance across ecotypes is high in absolute value (between 0.5-1), there is an association between the gene (specifically the expression level of this gene) and the phenotypic character. A positive correlation indicates that the expression of the gene in a certain tissue or developmental stage and the correlation vector (phenotype performance) are positively associated (both, expression and phenotypic performance increase or decrease simultaneously) while a negative correlation indicates a negative association (while the one is increasing the other is decreasing and vice versa).







TABLE 5







Correlation between the expression level of selected genes in specific tissues or


developmental stages and the phenotypic performance across Arabidopsis ecotypes
















Gene

Exp.

Corr.
Exp.

Corr.
Exp.



Name
Corr. Vec.
Set
R
Vec.
Set
R
Vec.
Set
R



















BDL117
1
C
−0.907
1
A
−0.809
13
D
0.961


BDL118
13
A
0.817
6
A
0.805
5
D
−0.821


BDL118
17
D
0.958
17
D
0.834
8
D
−0.833


BDL118
8
D
−0.845
10
D
−0.912
10
D
−0.975


BDL118
4
D
−0.904


BDL126
5
B
0.942


BDL138
16
C
0.841
15
C
0.813
16
B
0.878


BDL138
15
B
0.896
13
A
0.94


BDL140
14
C
0.841
3
C
0.821
11
C
0.855


BDL140
14
B
0.836
11
B
0.855
7
E
−0.812


BDL140
6
E
0.889
13
D
0.826
14
D
0.862


BDL147
16
B
0.948
15
B
0.898


BDL149
14
B
0.83
3
B
0.891
14
A
0.951


BDL152
16
D
0.969
3
D
0.855
15
D
0.987


BDL153
14
C
0.836
11
C
0.823
14
A
−0.862


BDL153
11
A
0.88
8
D
−0.81


BDL154
11
C
0.874


BDL155
16
B
0.829
16
A
0.86


BDL156
3
C
0.923
14
B
0.901


BDL157
3
B
0.854
2
B
−0.825
5
D
−0.803


BDL157
17
D
0.923
9
D
−0.809
8
D
−0.834


BDL157
10
D
−0.915
4
D
−0.89


BDL158
8
B
0.953
10
B
0.945
4
B
0.899


BDL158
11
A
−0.833


BDL160
7
C
0.82
18
C
0.972
8
A
0.918


BDL160
8
A
0.839
8
A
0.834
10
A
0.93


BDL160
10
A
0.93
4
A
0.862
1
E
0.864


BDL160
1
E
0.841
2
E
0.861
2
E
0.839


BDL160
8
D
0.867
8
D
0.811
10
D
0.824


BDL162
5
B
0.89


BDL163
16
B
0.925
15
B
0.884
18
E
0.828


BDL165
8
B
0.952
10
B
0.902
4
B
0.821


BDL165
8
E
0.807
15
E
0.816
11
D
0.846


BDL167
16
B
0.899
15
B
0.946
17
D
0.859


BDL167
2
D
−0.806


BDL168
16
C
0.97
15
C
0.929
8
B
0.931


BDL168
10
B
0.88
13
A
−0.835
5
D
−0.911


BDL168
8
D
−0.946
10
D
−0.849


BDL169
14
B
−0.82
11
B
−0.848
12
A
0.901


BDL171
14
C
−0.842
2
B
−0.844
5
A
0.803


BDL171
1
A
−0.851
2
A
−0.821
5
D
−0.827


BDL171
17
D
0.958
17
D
0.853
17
D
0.825


BDL171
9
D
−0.82
8
D
−0.87
16
D
0.857


BDL171
10
D
−0.901
10
D
−0.948
4
D
−0.808


BDL171
4
D
−0.932
15
D
0.838


BDL173
7
B
0.892
9
B
−0.874
18
B
0.816


BDL173
17
D
0.948
8
D
−0.888
10
D
−0.974


BDL173
4
D
−0.871


BDL174
17
C
0.901
5
D
−0.917
8
D
−0.879


BDL174
10
D
−0.85


BDL176
5
D
−0.907
8
D
−0.913
13
D
0.93


BDL177
17
C
0.919
17
B
0.91
17
D
0.82


BDL181
16
C
0.893
15
C
0.838
8
B
0.816


BDL181
12
A
0.931
16
A
0.823
18
E
0.819


BDL181
16
D
0.865
15
D
0.856


BDL182
12
A
0.913
12
D
0.825


BDL183
16
B
0.915
15
B
0.898


BDL186
12
B
0.944
11
B
0.833
8
D
−0.807


BDL187
16
B
0.908
15
B
0.835
5
D
−0.803


BDL187
8
D
−0.892


BDL188
14
B
0.904
12
D
0.964
3
D
0.857


BDL188
2
D
−0.886


BDL189
16
B
0.951
15
B
0.907
6
E
−0.854


BDL189
8
D
−0.821
1
D
−0.938


BDL190
16
B
0.857
15
B
0.91
7
E
−0.865


BDL192
7
B
0.907
9
B
−0.806
17
D
0.91


BDL192
10
D
−0.907
4
D
−0.94
2
D
−0.82


BDL193
8
C
0.846
12
B
0.904
11
B
0.876


BDL193
11
A
0.885
11
E
0.923
5
D
−0.801


BDL193
8
D
−0.802
8
D
−0.844
10
D
−0.806


BDL194
12
B
0.933
18
D
0.877


BDL196
16
D
0.917
15
D
0.937


BDL197
13
A
0.91
8
D
0.837


BDL200
2
C
0.818
16
B
0.864
15
B
0.832


BDL200
14
A
0.917
1
E
0.815
3
D
0.851


BDL201
9
C
0.846
5
D
0.916
17
D
−0.906


BDL201
8
D
0.954
10
D
0.947
4
D
0.865


BDL203
10
B
0.926
4
B
0.893
14
A
−0.828


BDL219
1
A
0.879
2
A
0.821
9
E
−0.801


BDL220
8
B
0.822
10
B
0.844
4
B
0.839


BDL221
12
C
0.897
16
C
0.917
15
C
0.814


BDL221
3
B
0.936
9
D
−0.936
6
D
−0.897


BDL221
4
D
−0.808


BDL222
1
B
0.829
2
B
0.887
1
A
0.875


BDL222
2
A
0.849
2
D
0.925


BDL223
14
C
0.93
14
B
0.835
3
B
0.851


BDL223
14
A
0.831


BDL224
5
E
−0.826
9
E
−0.872


BDL225
7
C
0.833
15
B
−0.806
13
A
−0.836


BDL227
2
A
−0.931


BDL229
10
B
0.858
2
D
0.832


BDL231
16
B
0.911
15
B
0.869
11
D
0.88


BDL233
14
C
−0.885


BDL235
11
E
0.808
12
D
0.818
2
D
−0.887


BDL240
1
D
−0.808


BDL241
13
A
−0.88


BDL242
11
B
0.889


BDL243
11
B
0.929


BDL245
3
A
−0.863
11
A
−0.832
16
D
−0.806


BDL247
16
B
0.816


BDL248
13
A
−0.829


BDL249
8
C
−0.84
16
E
−0.808
15
E
−0.892


BDL250
9
A
−0.805
2
E
−0.85
17
D
0.815


BDL250
10
D
−0.809
4
D
−0.804
1
D
−0.9


BDL251
18
C
0.802
7
D
−0.861


BDL47
8
B
0.845


BDL49
7
E
0.805
9
E
−0.883
6
E
−0.809


BDL62
18
A
0.862
6
E
−0.869
13
D
0.829


BDL75
11
C
0.816
5
B
0.945
8
B
0.823


BDL79
7
B
0.876
18
B
0.841
12
D
0.884


BDL79
2
D
−0.938


BDL81
8
C
0.897
12
B
0.803
1
D
−0.81


BDL81
2
D
−0.86


BDL83
3
C
−0.861
2
C
0.905


BDL85
8
D
0.82





Table 5. Provided are the correlations between the expression level of selected genes in specific tissues or developmental stages (expression sets) and the phenotypic performance (correlation vector) across Arabidopsis ecotypes. The phenotypic characters [correlation (Corr.) vector (Vec.)] include yield (seed yield, oil yield, oil content), biomass, growth rate and/or vigor components as described in Tables 2, 3 and 4. Exp. Set = expression set according to Table 1 hereinabove.






Table 6 hereinbelow provides data about the homologous of selected genes, the characterized parameters (which are used as x axis for correlation) and the correlated tissue transcriptom along with the correlation value (R, calculated using Pearson correlation).







TABLE 6







Correlation between the expression level of homologous of the


selected genes in specific tissues or developmental stages and the


phenotypic performance across Arabidopsis ecotypes












Gene Name
Exp. Set
Corr. Vec.
R
















BDL155 H1
leaf
relative root growth
0.814



BDL155 H1
seed5daf
Silique length
−0.855



BDL171 H0
leaf
Leaf width/length
0.835



BDL171 H0
seed5daf
Dry matter per plant
−0.82



BDL171 H0
seed5daf
Lamina width
−0.813



BDL183 H0
seed12daf
Blade circularity
−0.878



BDL231 H0
flower
seed weight
0.825



BDL231 H0
leaf
Silique length
0.816



BDL231 H0
leaf
relative root growth
0.854



BDL231 H0
root
seed weight
0.92



BDL248 H0
seed5daf
relative root growth
0.851



BDL70 H0
seed12daf
Lamina length
−0.816



BDL70 H0
seed5daf
seed yield per plant
−0.82







Table 6. Provided are the correlations between the expression levels of homologues of selected Arabidopsis genes in various tissues or developmental stages (Expression sets) and the phenotypic performance in various yield (seed yield, oil yield, oil content), biomass, growth rate and/or vigor components [Correlation (Corr.) vector (Vec.)] Corr. Vec. = correlation vector specified in Tables 2, 3 and 4; Exp. Set = expression set specified in Table 1.






Example 3
Production of Arabidopsis Transcriptom and High Throughput Correlation Analysis of Normal and Nitrogen Limiting Conditions Using 44K Arabidopsis Oligonucleotide Micro-Array
In order to produce a high throughput correlation analysis, the present inventors utilized a Arabidopsis oligonucleotide micro-array, produced by Agilent Technologies [Hypertext Transfer Protocol://World Wide Web(dot)chem(dot)agilent(dot)com/Scripts/PDS(dot)asp?1Page=50879]. The array oligonucleotide represents about 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 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(dot)davidmlane(dot)com/hyperstat/A34739(dot)html].
Experimental Procedures
RNA Extraction—
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 using TRIzol Reagent from Invitrogen [Hypertext Transfer Protocol://World Wide Web(dot)invitrogen(dot)com/content(dot)cfm?pageid=469]. For convenience, each micro-array expression information tissue type has received a Set ID as summarized in Table 7 below.







TABLE 7







Tissues used for Arabidopsis transcriptom expression sets










Expression Set
Set ID







Leaves at 1.5 mM Nitrogen fertilization
A



Leaves at 6 mM Nitrogen fertilization
B



Stems at 1.5 mM Nitrogen fertilization
C



Stem at 6 mM Nitrogen fertilization
D







Table 7: Provided are the identification (ID) letters of each of the Arabidopsis expression sets.






Approximately 30-50 mg of tissue was taken from samples. The weighed tissues were ground using pestle and mortar in liquid nitrogen and resuspended in 500 μl of TRIzol Reagent. To the homogenized lysate, 100 μl of chloroform was added followed by precipitation using isopropanol and two washes with 75% ethanol. The RNA was eluted in 30 μl of RNase-free water. RNA samples were cleaned up using Qiagen's RNeasy minikit clean-up protocol as per the manufacturer's protocol (QIAGEN Inc, CA USA).
Assessment of Arabidopsis Yield Components and Vigor Related Parameters Under Different Nitrogen Fertilization Levels—
10 Arabidopsis accessions in 2 repetitive 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× 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 limiting conditions were achieved by irrigating the plants with a solution containing 1.5 mM inorganic nitrogen in the form of KNO3, supplemented with 2 mM CaCl2, 1.25 mM KH2PO4, 1.50 mM MgSO4, 5 mM KCl, 0.01 mM H3BO3 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 KNO3, supplemented with 2 mM CaCl2, 1.25 mM KH2PO4, 1.50 mM MgSO4, 0.01 mM H3BO3 and microelements. To follow plant growth, trays were photographed the day nitrogen limiting conditions 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 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 files and processed using the JMP statistical analysis software (SAS institute).
Data parameters collected are summarized in Table 8, hereinbelow.







TABLE 8







Arabidopsis correlated parameters (vectors)








Correlated parameter with
Correlation Id











N 1.5 mM; Rosette Area at day 8 [cm2]
1


N 1.5 mM; Rosette Area at day 10 [cm2]
2


N 1.5 mM; Plot Coverage at day 8 [%]
3


N 1.5 mM; Plot Coverage at day 10 [%]
4


N 1.5 mM; Leaf Number at day 10
5


N 1.5 mM; Leaf Blade Area at day 10 [cm2]
6


N 1.5 mM; RGR of Rosette Area at day 3 [cm2/day]
7


N 1.5 mM; t50 Flowering [day]
8


N 1.5 mM; Dry Weight [gr/plant]
9


N 1.5 mM; Seed Yield [gr/plant]
10


N 1.5 mM; Harvest Index
11


N 1.5 mM; 1000 Seeds weight [gr]
12


N 1.5 mM; seed yield/rosette area at day 10 [gr/cm2]
13


N 1.5 mM; seed yield/leaf blade [gr/cm2]
14


N 1.5 mM; % Seed yield reduction compared to N 6 mM
15


N 1.5 mM; % Biomass reduction compared to N 6 mM
16


N 1.5 mM; N level/DW [SPAD unit/gr]
17


N 1.5 mM; DW/N level [gr/SPAD unit]
18


N 1.5 mM; seed yield/N level [gr/SPAD unit]
19


N 6 mM; Rosette Area at day 8 [cm2]
20


N 6 mM; Rosette Area at day 10 [cm2]
21


N 6 mM; Plot Coverage at day 8 [%]
22


N 6 mM; Plot Coverage at day 10 [%]
23


N 6 mM; Leaf Number at day 10
24


N 6 mM; Leaf Blade Area at day 10
25


N 6 mM; RGR of Rosette Area at day 3 [cm2/gr]
26


N 6 mM; t50 Flowering [day]
27


N 6 mM; Dry Weight [gr/plant]
28


N 6 mM; Seed Yield [gr/plant]
29


N 6 mM; Harvest Index
30


N 6 mM; 1000 Seeds weight [gr]
31


N 6 mM; seed yield/rosette area day at day 10 [gr/cm2]
32


N 6 mM; seed yield/leaf blade [gr/cm2]
33


N 6 mM; N level/FW
34


N 6 mM; DW/N level [gr/SPAD unit]
35


N 6 mM; N level/DW (SPAD unit/gr plant)
36


N 6 mM; Seed yield/N unit [gr/SPAD unit]
37





Table 8. 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; “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 [cm2] (measured using digital analysis); RGR (relative growth rate) of Rosette Area at the indicated day [cm2/day] (calculated using Formula II); t50 Flowering [day] (the day in which 50% of plant flower); seed yield/rosette area at day 10 [gr/cm2] (calculated); seed yield/leaf blade [gr/cm2] (calculated); seed yield/N level [gr/SPAD unit] (calculated).






Assessment of NUE, Yield Components and Vigor-Related Parameters—
Ten 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.
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 is repeated every 2-3 days starting at day 9-12 till day 16-19 (respectively) from transplanting.
An 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 Protocol://rsbweb(dot)nih(dot)gov/. Images were captured in resolution of 10 Mega Pixels (3888×2592 pixels) and stored in a low compression JPEG (Joint Photographic Experts Group standard) format. Next, image processing output data was saved to text files and analyzed using the JMP statistical analysis software (SAS institute).
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 of the rosette and the leaves was calculated according to Formula II as described above.
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 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 vegetative portion above ground (excluding roots) after drying at 30° C. in a drying chamber.
Harvest Index—
The harvest index was calculated using Formula IV as described above [Harvest Index=Average seed yield per plant/Average dry weight].
T50 Days to Flowering—
Each of the repeats was monitored for flowering date. 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 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 nitrogen unit [DW/N level=plant biomass per plant [g]/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 plants when grown under nitrogen-limiting conditions compared to seed yield produced at normal nitrogen levels expressed in %.
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 calculated using the JMP software and values are summarized in Table 9 below. Subsequent correlation analysis between the various transcriptom sets (Table 7) was conducted. Following are the results integrated to the database.







TABLE 9







Correlation between the expression level of selected genes in tissues under limiting or


normal nitrogen fertilization and the phenotypic performance across Arabidopsis


ecotypes
















Gene

Corr.

Exp.
Corr.

Exp.
Corr.



Name
Exp. Set
Vec.
R
Set
Vec.
R
Set
Vec.
R



















BDL117
D
31
−0.748
A
12
−0.784





BDL118
C
11
−0.914
C
10
−0.723
C
14
−0.75


BDL118
C
8
0.74


BDL118
D
31
−0.766
B
30
−0.752
D
30
−0.794


BDL118
D
29
−0.715
B
27
0.791
A
11
−0.747


BDL126
A
1
−0.719


BDL126
D
25
0.801
A
6
−0.715
A
2
−0.711


BDL138
B
28
−0.797
B
27
−0.786
C
9
−0.754


BDL140
D
28
−0.761


BDL147
D
30
−0.703
C
11
−0.7


BDL149
C
9
−0.744
A
1
0.703


BDL152
A
14
−0.705


BDL117
D
31
−0.748
A
12
−0.784


BDL118
C
11
−0.914
C
10
−0.723
C
14
−0.75


BDL118
C
8
0.74


BDL154
B
26
0.896
B
32
0.76
B
33
0.861


BDL155
C
9
−0.719


BDL155_H0
B
28
0.768
D
28
0.757
D
29
0.751


BDL155_H0
C
7
0.743


BDL156
D
24
0.725
D
21
0.734


BDL157
B
29
0.714


BDL158
B
30
−0.722
B
27
0.708


BDL160
A
12
−0.807
C
9
−0.771
C
5
−0.797


BDL160
C
2
−0.816


BDL162
B
31
−0.792


BDL165
C
11
−0.755
C
8
0.748


BDL167
C
10
−0.898
C
14
−0.894
C
13
−0.874


BDL167
C
15
0.737


BDL167
D
30
−0.75
C
11
−0.709
C
7
−0.821


BDL168
A
9
0.703
A
11
−0.786


BDL168
B
30
−0.73
D
21
0.721
B
27
0.738


BDL169
A
11
−0.804
A
10
−0.746
A
14
−0.714


BDL169
A
13
−0.708
A
8
0.707


BDL171
B
33
0.865
A
9
−0.735


BDL171
D
25
0.879
B
26
0.891
D
21
0.765


BDL171
D
20
0.711
B
29
0.735
B
32
0.741


BDL171_H0
C
15
0.719
C
8
0.78


BDL173
B
26
0.723
B
33
0.72
A
15
0.751


BDL174
C
16
0.7
C
9
−0.73


BDL176
D
25
0.713
D
24
−0.713
D
26
0.765


BDL176
D
21
0.702
D
20
−0.719
D
32
0.806


BDL176
D
33
0.759
A
7
0.746


BDL177
B
27
−0.713
A
11
0.792


BDL181
C
10
−0.75
C
14
−0.795
C
13
−0.805


BDL181
C
15
0.72
A
8
0.794


BDL181
D
31
−0.704
B
27
0.723
C
11
−0.725


BDL182
A
6
0.728
A
2
0.717
A
1
0.763


BDL183
A
12
−0.764


BDL183_H0
A
2
−0.725


BDL186
A
10
−0.754
A
13
−0.713
A
15
0.805


BDL186
A
8
0.865


BDL117
D
31
−0.748
A
12
−0.784


BDL118
C
11
−0.914
C
10
−0.723
C
14
−0.75


BDL118
C
8
0.74


BDL186
B
31
−0.714
B
27
0.722
A
11
−0.816


BDL187
A
2
0.711
A
1
0.801
A
10
−0.775


BDL187
A
14
−0.843
A
13
−0.89
A
15
0.721


BDL189
A
13
−0.859
A
15
0.748
A
8
0.759


BDL189
B
30
−0.702
B
27
0.832
A
11
−0.71


BDL189
C
7
−0.714
A
10
−0.825
A
14
−0.82


BDL192
B
24
−0.788
B
21
−0.863
B
20
−0.857


BDL192
B
29
−0.701
B
32
0.769


BDL192
D
28
−0.764
B
30
−0.785
B
25
−0.802


BDL193
A
6
−0.754
A
2
−0.781
A
1
−0.875


BDL193
A
14
−0.732


BDL193
D
30
−0.721
D
29
−0.819
C
11
−0.7


BDL194
B
25
0.786
B
21
0.707


BDL196
D
25
−0.715
D
21
−0.71
D
20
−0.715


BDL197
A
6
−0.701
A
5
−0.843
A
2
−0.89


BDL197
A
1
−0.827


BDL201
A
10
−0.768
A
14
−0.84
A
13
−0.872


BDL201
A
15
0.746


BDL201
B
29
−0.815
A
2
0.747
A
1
0.784


BDL220
C
11
−0.81


BDL220
D
30
−0.707
B
29
−0.785
C
9
0.752


BDL221
A
2
0.768
C
2
0.763
A
1
0.817


BDL221
B
31
−0.81
D
25
−0.743
D
24
−0.896


BDL221
C
1
0.74


BDL221
D
21
−0.826
D
20
−0.776
A
5
0.825


BDL222
D
27
−0.716
A
11
0.77
A
14
0.731


BDL223
C
11
−0.757
C
15
0.786
C
8
0.821


BDL223_H0
C
11
−0.736


BDL223_H1
C
8
0.784


BDL223_H1
D
24
0.823
A
12
0.815
C
15
0.793


BDL229
C
11
−0.798
C
10
−0.723
C
14
−0.771


BDL229
C
13
−0.769
A
8
0.753
C
8
0.828


BDL229
D
30
−0.787
B
27
0.793
D
27
0.873


BDL231
A
11
−0.798
C
6
−0.704
A
10
−0.826


BDL231
A
14
−0.836
A
13
−0.843
A
15
0.823


BDL231
A
8
0.768


BDL231—
A
11
−0.779
A
10
−0.799
A
14
−0.841


BDL117
D
31
−0.748
A
12
−0.784


BDL118
C
11
−0.914
C
10
−0.723
C
14
−0.75


BDL118
C
8
0.74


H0


BDL231_H0
A
13
−0.835
A
15
0.706
A
8
0.721


BDL233
C
8
0.835


BDL233
D
28
0.755
C
11
−0.768
C
15
0.725


BDL235
C
11
−0.87
C
10
−0.749
A
14
−0.741


BDL235
C
14
−0.726
A
13
−0.702
C
8
0.802


BDL240
A
8
0.742


BDL240
D
24
0.794
B
27
0.737
A
11
−0.787


BDL241
B
27
0.752


BDL242
A
5
−0.719
A
15
−0.722


BDL245
D
31
−0.875


BDL247
D
31
0.851


BDL249
A
8
−0.707


BDL249
C
12
0.707
A
11
0.82
A
10
0.727


BDL250
A
10
0.717
A
14
0.797
A
13
0.81


BDL252
C
9
−0.707
C
7
−0.714


BDL49
B
30
0.866
B
26
0.85
B
29
0.933


BDL49
B
33
0.762


BDL58
B
26
0.763
D
26
0.755
B
29
0.897


BDL58
C
14
0.816
C
13
0.855
C
15
−0.784


BDL58
C
8
−0.843


BDL58
D
32
0.758
D
33
0.778
C
10
0.8


BDL62
C
11
−0.858
C
10
−0.739
C
14
−0.77


BDL62
C
13
−0.747
C
8
0.819


BDL63
C
16
−0.704


BDL64
B
31
−0.793
C
5
−0.739


BDL70_H0
C
8
0.757


BDL75
C
11
−0.716
C
8
0.713


BDL75
D
31
−0.776
D
28
0.75
D
30
−0.832


BDL79
B
31
−0.77


BDL85
C
10
0.824
C
14
0.754
C
13
0.721


BDL85
C
15
−0.705





Table 9. Provided are the correlations (R) between the expression levels of selected genes in tissues (leaves or stems) under limiting (1.5 mM Nitrogen) or normal (6 mM Nitrogen) conditions (Expression sets) and the phenotypic performance in various yield (seed yield, oil yield, oil content), biomass, growth rate and/or vigor components [Correlation (Corr.) vector (Vec.)] under limiting or normal Nitrogen conditions. Corr. Vec. = correlation vector according to Table 8 hereinabove; Exp. Set = expression set according to Table 7 hereinabove.






Example 4
Production of Sorghum Transcriptom and High Throughput Correlation Analysis with ABST Related Parameters Using 44K Sorghum Oligonucleotide Micro-Arrays
In order to produce a high throughput correlation analysis, the present inventors utilized a Sorghum oligonucleotide micro-array, produced by Agilent Technologies [Hypertext Transfer Protocol://World Wide Web(dot)chem.(dot)agilent(dot) com/Scripts/PDS(dot)asp?1 Page=50879]. The array oligonucleotide represents about 44,000 Sorghum genes and transcripts. In order to define correlations between the levels of RNA expression with ABST and yield components or vigor related parameters, various plant characteristics of 17 different sorghum 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 analyzed using Pearson correlation test [Hypertext Transfer Protocol://World Wide Web(dot)davidmlane(dot)com/hyperstat/A34739(dot)html].
Correlation of Sorghum Varieties Across Ecotype Grown Under Severe Drought Conditions
Experimental Procedures
17 Sorghum varieties were grown in 3 repetitive plots, in field. Briefly, the growing protocol was as follows: sorghum seeds were sown in soil and grown under normal condition until around 35 days from sowing, around V8 (Last leaf visible, but still rolled up, ear beginning to swell). At this point, irrigation was stopped, and severe drought stress was developed. In order to define correlations between the levels of RNA expression with drought, yield components or vigor related parameters, the 17 different sorghum 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 analyzed using Pearson correlation test [Hypertext Transfer Protocol://World Wide Web(dot)davidmlane(dot) com/hyperstat/A34739(dot)html].
RNA Extraction—
All 10 selected Sorghum varieties were sample per each treatment. Plant tissues [Flag leaf and Flower meristem] growing under severe drought stress and plants grown under Normal 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]. For convenience, each micro-array expression information tissue type has received a Set ID as summarized in Table 10 below.







TABLE 10







Sorghum transcriptom expression sets










Expression Set
Set ID







Drought Stress: Flag leaf
U



Normal conditions: Flag leaf
X



Normal conditions: Flower meristem
Y







Table 10: Provided are the sorghum transcriptom expression set U, X and Y. Flag leaf = the leaf below the flower; Flower meristem = Apical meristem following panicle initiation.






The collected data parameters were as follows:
Grain Per Plant (Gr.)—
At the end of the experiment (Inflorescence were dry) all spikes from plots within blocks A-C were collected. 5 Inflorescence were separately threshed and grains were weighted, all additional Inflorescence were threshed together and weighted as well. The average weight per Inflorescence was calculated by dividing the total grain weight by number of total Inflorescence per plot, or in case of 5 inflorescence, by weight by the total grain number by 5.
Plant Height—
Plants were characterized for height during growing period at 6 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.
Inflorescence Weight (Gr.)—
At the end of the experiment (when Inflorescence were dry) five Inflorescence from plots within blocks A-C were collected. The Inflorescence were weighted (gr.).
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 taken per plot.
Vegetative Dry Weight and Inflorescence—
At the end of the experiment (when Inflorescence were dry) all Inflorescence and vegetative material from plots within blocks A-C were collected. The biomass and Inflorescence weight of each plot was separated, measured and divided by the number of Inflorescence.
Dry weight=total weight of the vegetative portion above ground (excluding roots) after drying at 70° C. in oven for 48 hours;
Harvest Index (for Sorghum)—
The harvest index is calculated using Formula VIII.

Harvest Index=Average grain dry weight per Inflorescence/(Average vegetative dry weight per Inflorescence+Average Inflorescence dry weight)  Formula VIII:

Experimental Results
16 different sorghum varieties were grown and characterized for 7 parameters: “Seed/plant normal”=total seed weight per plant under normal conditions; “DW-5 Inflorescence Normal”—dry weight of five complete inflorescences (seeds and rachis) under normal conditions; “DW all Normal”=dry weight of per plot under normal conditions; “Weight of seeds (5 heads) gr Normal”=dry weight of seeds from five inflorescences under normal conditions; “Plant Height 4 Drought”=plant height in the 4th time point under drought conditions; “Plant Height 4 Normal”=plant height in the 4th time point under normal conditions; “Plant Height 6 Normal”=plant height in the 6th time point under normal conditions. The average for each of the measured parameter was calculated using the JMP software and values are summarized in Table 11 below. Subsequent correlation analysis between the various transcriptom sets (Table 10) and the average parameters, was conducted (Tables 12). Results were then integrated to the database.







TABLE 11







Measured parameters in Sorghum accessions


















Weight of







DW-5

seeds (5
Plant
Plant
Plant


Seed
Seed/Plant
Inflorescence
DW all
heads) gr
Height 4
Height 4
Height 6


ID
Normal
Normal
Normal
Normal
Drought
Normal
Normal

















20
0.031
0.039
5.408
0.237
38.000
37.313
37.313


21
0.026
0.062
3.091
0.225
30.833


22
0.019
0.033
21.341
0.142
110.833
47.750
47.750


24
0.038
0.030
5.329
0.352
42.833
40.083
40.083


25
0.027
0.074
20.600
0.161
49.583
45.938
45.938


26
0.046
0.049
21.685
0.332
49.750
41.438
41.438


27
0.048
0.046
11.205
0.317
46.875
44.875
44.875


28
0.031
0.033
9.045
0.222
41.917
42.125
42.125


29
0.040
0.048
10.293
0.283
46.125
41.000
41.000


30
0.038
0.038
9.139
0.300
50.167
42.500
42.063


31
0.032
0.023
9.549
0.227
43.583
41.875
41.875


32
0.033
0.039
10.424
0.277
50.833
43.375
43.375


33
0.033
0.049
10.150
0.353
42.417
39.813
39.813


34
0.052
0.050
8.783
0.351
45.500
40.625
40.625


35
0.036
0.038
10.259
0.270
50.375
44.375
44.375


36
0.038
0.042
12.005
0.299
48.833
43.250
43.250


37
0.042
0.063
15.681
0.263
49.833
41.000
41.000





Table 11: Provided are the values of each of the parameters (as described above) measured in Sorghum accessions (Seed ID) under normal and drought conditions. Growth conditions are specified in the experimental procedure section.













TABLE 12







Correlation between the expression level of homologues of selected


genes in various tissues and the phenotypic performance under normal


or abiotic stress conditions across Sorghum accessions










Gene Name
Exp. Set
Corr. Vec.
R













BDL102_H47
flower
DW all Normal
−0.721


BDL102_H47
flower
FW-Inflorescence/Plant
0.717




Normal


BDL102_H47
flower
Plant Height 4 Normal
−0.722


BDL102_H47
flower
Plant Height 6 Normal
−0.718


BDL83_H57
flag leaf
DW-5 Inflorescence
−0.712




Normal


BDL83_H57
flag leaf
Seed/Plant Normal
−0.708


BDL83_H57
flower
Plant Height 4 Normal
0.858


BDL83_H57
flower
Plant Height 6 Normal
0.853


BDL83_H58
flag leaf
Plant Height 4 Drought
0.763


BDL83_H58
flower
Seed/Plant Low-N
0.759


BDL83_H58
flower
Weight of seeds (5 heads)
−0.707




gr Normal


BDL83_H58
Flower meristem
Leaf_No 2 Normal
0.802


BDL88_H13
Flag leaf
Leaf_No 3 Drought
−0.893


BDL88_H13
Flag leaf
Leaf_TP 1 Drought
−0.929


BDL88_H13
Flag leaf
Plant Height 2 Drought
−0.796


BDL88_H13
Flag leaf
Plant Height 3 Drought
−0.837


BDL88_H13
Flag leaf
Seed/Plant_Normal
0.73





Table 12. Provided are the correlations (R) between the expression levels of homologues of selected genes in tissues (Flag leaf or Flower meristem; Expression sets) and the phenotypic performance in various yield, biomass, growth rate and/or vigor components [Correlation (Corr.) vector (Vec.)] under abiotic stress conditions (drought) or normal conditions across Sorghum accessions.






Sorghum Vigor Related Parameters Under 100 mM NaCl and Low Temperature (8-10° C.)—
Ten Sorghum varieties were grown in 3 repetitive plots, each containing 17 plants, at a net house under semi-hydroponics conditions. Briefly, the growing protocol was as follows: Sorghum seeds were sown in trays filled with a mix of vermiculite and peat in a 1:1 ratio. Following germination, the trays were transferred to the high salinity solution (100 mM NaCl in addition to the Full Hogland solution), low temperature (8-10° C. in the presence of Full Hogland solution) or at Normal growth solution [Full Hogland solution at 20-24° C.].
Full Hogland solution consists of: KNO3—0.808 grams/liter, MgSO4—0.12 grams/liter, KH2 PO4—0.172 grams/liter and 0.01% (volume/volume) of ‘Super coratin’ micro elements (Iron-EDDHA [ethylenediamine-N,N′-bis(2-hydroxyphenylacetic acid)]—40.5 grams/liter; Mn—20.2 grams/liter; Zn 10.1 grams/liter; Co 1.5 grams/liter; and Mo 1.1 grams/liter), solution's pH should be 6.5-6.8].
RNA Extraction—
All 10 selected Sorghum varieties were sampled per each treatment. Two tissues [leaves and roots] growing at 100 mM NaCl, low temperature (8-10° C.) or under Normal conditions (full Hogland at a temperature between 20-24° C.) 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].
Experimental Results
10 different Sorghum varieties were grown and characterized for the following parameters: “Leaf number Normal”=leaf number per plant under normal conditions (average of five plants); “Plant Height Normal”=plant height under normal conditions (average of five plants); “Root DW 100 mM NaCl”—root dry weight per plant under salinity conditions (average of five plants); The average for each of the measured parameter was calculated using the JMP software and values are summarized in Table 13 below. Subsequent correlation analysis between the various transcriptom sets and the average parameters was conducted (Table 14). Results were then integrated to the database.







TABLE 13







Measured parameters in Sorghum accessions














Plant


Leaf

DW


Seed
Height T1
Plant Height
Plant Height
number
Leaf number
Root/Plant


ID
NaCl
T1 + 8 NaCl
T1 + 15 NaCl
T1 NaCl
T1 + 8 Normal
NaCl
















20
7.900
14.200
21.800
3.000
4.167
0.05


22
9.500
16.267
23.167
3.133
4.500
0.10447479


26
10.933
20.367
30.367
3.400
4.800
0.12370635


27
7.933
13.333
22.833
3.067
4.600
0.06880519


28
9.700
15.900
23.700
3.333
4.533
0.07568254


29
8.533
16.533
23.300
3.067
4.967
0.07517045


30
8.900
15.467
22.467
3.067
4.600
0.13539542


31
10.367
18.933
26.833
3.267
4.933
0.09546434


34
7.000
13.680
20.280
3.000
4.500
0.16491667


37
7.833
15.767
23.567
3.067
4.567
0.13888278





Table 13: Provided are the measured parameters of the Sorghum Accessions under normal conditions or high salt conditions at the indicated time points. T1 (first day of measurements); T1 + 8 (8 days following the first day); T1 + 15 (15 days following the first day). The exact conditions are detailed above in the experiment description section.













TABLE 14







Correlation between the expression level of homologues of selected


genes in roots and the phenotypic performance under normal or abiotic


stress conditions across Sorghum accessions










Gene Name
Exp. Set
Corr. Vec.
R













BDL83_H58
root
DW Root/Plant NaCl
0.897


BDL83_H58
root
Leaf number T1 NaCl
−0.75


BDL83_H58
root
Plant Height T1 NaCl
−0.82


BDL83_H58
root
Plant Height T1 + 8 NaCl
−0.9


BDL83_H58
root
Plant Height T1 + 15 NaCl
−0.77


BDL83_H58
root
Leaf number T1 Normal
0.779





Table 14. Provided are the correlations (R) between the expression levels of homologues of selected genes in roots [Expression (Exp.) sets] and the phenotypic performance [yield, biomass, growth rate and/or vigor components (Correlation vector)] at the indicated time points under abiotic stress conditions (salinity) or normal conditions across Sorghum accessions. Corr. Vec. = correlation vector as described hereinabove (Table 13). T1 (first day of measurements); T1 + 8 (8 days following the first day); T1 + 15 (15 days following the first day).






Example 5
Identification of Genes which Increase Yield, Biomass, Growth Rate, Vigor, Oil Content, Abiotic Stress Tolerance of Plants and Nitrogen Use Efficieny
Based on the above described bioinformatics and experimental tools, the present inventors have identified 105 genes (89 distinct gene families) which have a major impact on yield, seed yield, oil yield, biomass, growth rate, vigor, oil content, abiotic stress tolerance, and/or nitrogen use efficiency when expression thereof is increased in plants. The identified genes, their curated polynucleotide and polypeptide sequences, as well as their updated sequences according to Genbank database are summarized in Table 15, hereinbelow.







TABLE 15







Identified polynucleotides which affect plant yield, seed yield,


oil yield, oil content, biomass, growth rate, vigor, abiotic


stress tolerance and/or nitrogen use efficiency of a plant












Serial
Gene


Polynucleotide
Polypeptide


No
Name
Cluster Name
Organism
SEQ ID NO:
SEQ ID NO:















1
BDL47
arabidopsis|gb165|AT4
arabidopsis
1
106




G38660


2
BDL47
arabidopsis|gb165|AT4
arabidopsis
1
194




G38660


3
BDL48
arabidopsis|gb165|AT2
arabidopsis
2
107




G25270


4
BDL62
arabidopsis|gb165|AT1
arabidopsis
3
108




G64390


5
BDL75
arabidopsis|gb165|AT3
arabidopsis
4
109




G55420


6
BDL79
arabidopsis|gb165|AT3
arabidopsis
5
110




G20010


7
BDL81
arabidopsis|gb165|AT1
arabidopsis
6
111




G13030


8
BDL83
arabidopsis|gb165|AT1
arabidopsis
7
112




G43670


9
BDL117
arabidopsis|gb165|AT4
arabidopsis
8
113




G33240


10
BDL118
arabidopsis|gb165|AT2
arabidopsis
9
114




G22125


11
BDL126
arabidopsis|gb165|AT3
arabidopsis
10
115




G59100


12
BDL138
arabidopsis|gb165|AT3
arabidopsis
11
116




G12180


13
BDL140
arabidopsis|gb165|AT5
arabidopsis
12
117




G02640


14
BDL147
arabidopsis|gb165|AT2
arabidopsis
13
118




G47930


15
BDL149
arabidopsis|gb165|AT5
arabidopsis
14
119




G15750


16
BDL152
arabidopsis|gb165|AT1
arabidopsis
15
120




G70420


17
BDL153
arabidopsis|gb165|AT5
arabidopsis
16
121




G47690


18
BDL154
arabidopsis|gb165|AT1
arabidopsis
17
122




G62940


19
BDL155
arabidopsis|gb165|AT4
arabidopsis
18
123




G11630


20
BDL156
arabidopsis|gb165|AT1
arabidopsis
19
124




G01570


21
BDL157
arabidopsis|gb165|AT1
arabidopsis
20
125




G14560


22
BDL158
arabidopsis|gb165|AT1
arabidopsis
21
126




G22030


23
BDL160
arabidopsis|gb165|AT1
arabidopsis
22
127




G28960


24
BDL162
arabidopsis|gb165|AT1
arabidopsis
23
128




G49360


25
BDL163
arabidopsis|gb165|AT1
arabidopsis
24
129




G51430


26
BDL165
arabidopsis|gb165|AT1
arabidopsis
25
130




G65010


27
BDL167
arabidopsis|gb165|AT1
arabidopsis
26
131




G79630


28
BDL168
arabidopsis|gb165|AT2
arabidopsis
27
132




G01910


29
BDL169
arabidopsis|gb165|AT2
arabidopsis
28
133




G19120


30
BDL171
arabidopsis|gb165|AT2
arabidopsis
29
134




G32320


31
BDL173
arabidopsis|gb165|AT2
arabidopsis
30
135




G36720


32
BDL174
arabidopsis|gb165|AT2
arabidopsis
31
136




G39580


33
BDL176
arabidopsis|gb165|AT3
arabidopsis
32
137




G10160


34
BDL177
arabidopsis|gb165|AT3
arabidopsis
33
138




G18610


35
BDL181
arabidopsis|gb165|AT4
arabidopsis
34
139




G12640


36
BDL182
arabidopsis|gb165|AT4
arabidopsis
35
140




G14605


37
BDL183
arabidopsis|gb165|AT4
arabidopsis
36
141




G15620


38
BDL186
arabidopsis|gb165|AT4
arabidopsis
37
142




G32560


39
BDL187
arabidopsis|gb165|AT4
arabidopsis
38
143




G35130


40
BDL188
arabidopsis|gb165|AT4
arabidopsis
39
144




G35560


41
BDL189
arabidopsis|gb165|AT5
arabidopsis
40
145




G05560


42
BDL190
arabidopsis|gb165|AT5
arabidopsis
41
146




G06690


43
BDL192
arabidopsis|gb165|AT5
arabidopsis
42
147




G09880


44
BDL193
arabidopsis|gb165|AT5
arabidopsis
43
148




G12950


45
BDL194
arabidopsis|gb165|AT5
arabidopsis
44
149




G16540


46
BDL196
arabidopsis|gb165|AT5
arabidopsis
45
150




G38180


47
BDL197
arabidopsis|gb165|AT5
arabidopsis
46
151




G39240


48
BDL200
arabidopsis|gb165|AT5
arabidopsis
47
152




G51470


49
BDL201
arabidopsis|gb165|AT5
arabidopsis
48
153




G58250


50
BDL203
arabidopsis|gb165|AT5
arabidopsis
49
154




G66440


51
BDL219
arabidopsis|gb165|AT1
arabidopsis
50
155




G36095


52
BDL220
arabidopsis|gb165|AT1
arabidopsis
51
156




G61170


53
BDL221
arabidopsis|gb165|AT1
arabidopsis
52
157




G75860


54
BDL222
arabidopsis|gb165|AT1
arabidopsis
53
158




G77885


55
BDL223
arabidopsis|gb165|AT2
arabidopsis
54
159




G37975


56
BDL229
arabidopsis|gb165|AT5
arabidopsis
55
160




G53830


57
BDL230
arabidopsis|gb154|ATH
arabidopsis
56
161




PEARA


58
BDL231
arabidopsis|gb165|AT1
arabidopsis
57
162




G16350


59
BDL235
arabidopsis|gb165|AT2
arabidopsis
58
163




G38970


60
BDL242
arabidopsis|gb165|AT3
arabidopsis
59
164




G22740


61
BDL243
arabidopsis|gb165|AT3
arabidopsis
60
165




G31430


62
BDL245
arabidopsis|gb165|AT4
arabidopsis
61
166




G12690


63
BDL247
arabidopsis|gb165|AT4
arabidopsis
62
167




G29510


64
BDL248
arabidopsis|gb165|AT4
arabidopsis
63
168




G37360


65
BDL250
arabidopsis|gb165|AT4
arabidopsis
64
169




G37400


66
BDL49
arabidopsis|gb165|AT3
arabidopsis
65
170




G06180


67
BDL58
arabidopsis|gb165|AT1
arabidopsis
66
171




G22160


68
BDL63
arabidopsis|gb165|AT2
arabidopsis
67
172




G40550


69
BDL64
arabidopsis|gb165|AT5
arabidopsis
68
173




G38020


70
BDL70
cotton|gb164|AF150730
cotton
69
174


71
BDL85
arabidopsis|gb165|AT1
arabidopsis
70
175




G05340


72
BDL88
rice|gb157.2|AA754446
rice
71
176


73
BDL90
rice|gb154|AK102950
rice
72


74
BDL94
rice|gb157.2|BE228242
rice
73
177


75
BDL102
maize|gb164|AI600933
maize
74
178


76
BDL224
arabidopsis|gb165|AT4
arabidopsis
75
179




G29780


77
BDL225
arabidopsis|gb165|AT5
arabidopsis
76
180




G39670


78
BDL226
arabidopsis|gb165|AT5
arabidopsis
77
181




G65470


79
BDL227
arabidopsis|gb165|AT3
arabidopsis
78
182




G56410


80
BDL228
castorbean|gb160|EE25
castorbean
79
183




6201


81
BDL232
arabidopsis|gb165|AT1
arabidopsis
80
184




G56100


82
BDL233
arabidopsis|gb165|AT1
arabidopsis
81
185




G66360


83
BDL234
arabidopsis|gb165|AT2
arabidopsis
82
186




G05400


84
BDL237
arabidopsis|gb165|AT2
arabidopsis
83
187




G45510


85
BDL238
arabidopsis|gb165|AT3
arabidopsis
84
188




G04540


86
BDL240
arabidopsis|gb165|AT3
arabidopsis
85
189




G18480


87
BDL241
arabidopsis|gb165|AT3
arabidopsis
86
190




G20020


88
BDL249
arabidopsis|gb165|AT4
arabidopsis
87
191




G37370


89
BDL251
arabidopsis|gb165|AT5
arabidopsis
88
192




G08250


90
BDL252
arabidopsis|gb165|AT5
arabidopsis
89
193




G18650


91
BDL79
arabidopsis|gb165|AT3
arabidopsis
90
110




G20010


92
BDL126
arabidopsis|gb165|AT3
arabidopsis
91
115




G59100


93
BDL153
arabidopsis|gb165|AT5
arabidopsis
92
195




G47690


94
BDL156
arabidopsis|gb165|AT1
arabidopsis
93
124




G01570


95
BDL167
arabidopsis|gb165|AT1
arabidopsis
94
196




G79630


96
BDL169
arabidopsis|gb165|AT2
arabidopsis
95
197




G19120


97
BDL171
arabidopsis|gb165|AT2
arabidopsis
96
134




G32320


98
BDL174
arabidopsis|gb165|AT2
arabidopsis
97
198




G39580


99
BDL187
arabidopsis|gb165|AT4
arabidopsis
98
143




G35130


100
BDL189
arabidopsis|gb165|AT5
arabidopsis
99
199




G05560


101
BDL197
arabidopsis|gb165|AT5
arabidopsis
100
200




G39240


102
BDL200
arabidopsis|gb165|AT5
arabidopsis
101
152




G51470


103
BDL231
arabidopsis|gb165|AT1
arabidopsis
102
162




G16350


104
BDL248
arabidopsis|gb165|AT4
arabidopsis
103
168




G37360


105
BDL70
cotton|gb164|AF150730
cotton
104
201


106
BDL238
arabidopsis|gb165|AT3
arabidopsis
105
202




G04540





Table 15: Provided are the identified genes, their annotation, organism and polynucleotide and polypeptide sequence identifiers.






Example 6
Identification of Homologous Sequences that Increase Seed Yield, Oil Yield, Growth Rate, Oil Content, Biomass, Vigor, ABST Resistance and/or Nue of a Plant
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 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 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.
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 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 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 function similarities between two homologous genes, similarities in the sequence level—identical amino acids in the protein domains and similarity in expression profiles.
Methods for searching and identifying homologues of yield and improved agronomic traits such as ABS tolerance and NUE related polypeptides or polynucleotides are well within the realm of the skilled artisan. The search and identification of homologous genes involves the screening of sequence information available, for example, in public databases such as the DNA 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 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 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.
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 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), Arabidopsis (Arabidopsis thaliana), maize (Zea mays), cotton (Gossypium), Oilseed rape (Brassica napus), Rice (Oryza sativa), Sugar cane (Saccharum officinarum), 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 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 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 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 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 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 acid from which they are derived.
Polynucleotides and polypeptides with significant homology to the identified genes described in Table 15 above have been identified from the databases using BLAST software using the Blastp and tBlastn algorithms. The query nucleotide sequences were SEQ ID NOs: 1-106 and the identified homologues are provided in Table 16, below. These genes are expected to increase plant yield, seed yield, oil yield, oil content, growth rate, biomass, vigor, ABST and/or NUE of a plant.







TABLE 16







Homologous polynucleotides and polypeptides













Polynuc.


Polypep.
Homol. to




SEQ ID


SEQ ID
SEQ ID
% Global


NO:
Gene Name
Organism/Cluster name
NO:
NO:
identity
Algor.
















203
BDL47_H0
radish|gb164|EW717854
524
194
85.15
tblastn


204
BDL48_H0
radish|gb164|EW735131
525
107
82.7
blastp


205
BDL62_H0
canola|gb161|CD835773
526
108
94.5
blastp


206
BDL62_H1
radish|gb164|EV543949
527
108
94.36
tblastn


207
BDL75_H0
canola|gb161|EE485008
528
109
84.1
blastp


208
BDL83_H0
apple|gb171|CN494551
529
112
86.8
blastp


209
BDL83_H1
aquilegia|gb157.3|DR916286
530
112
85.9
blastp


210
BDL83_H2
artemisia|gb164|EY037407
531
112
86.2
blastp


211
BDL83_H3
b_juncea|gb164|EVGN00808312601672
532
112
91.7
blastp


212
BDL83_H4
b_oleracea|gb161|AM387331
533
112
94.7
blastp


213
BDL83_H5
b_rapa|gb162|AY161288
534
112
94.4
blastp


214
BDL83_H6
banana|gb167|AF130251
535
112
85
blastp


215
BDL83_H7
barley|gb157.3|BE420760
536
112
83.4
blastp


216
BDL83_H8
barley|gb157.3|BG365169
537
112
82.1
blastp


217
BDL83_H9
bean|gb167|CA896765
538
112
87.1
blastp


218
BDL83_H10
bean|gb167|CB539815
539
112
87.4
blastp


219
BDL83_H11
beet|gb162|BE590341
540
112
85.9
blastp


220
BDL83_H12
brachypodium|gb169|BE213261
541
112
85.4
blastp


221
BDL83_H13
brachypodium|gb169|BE419504
542
112
82.7
blastp


222
BDL83_H14
canola|gb161|BNU20179
543
112
94.13
tblastn


223
BDL83_H15
canola|gb161|CD818253
544
112
94.4
blastp


224
BDL83_H16
cassava|gb164|DV445162
545
112
88
blastp


225
BDL83_H17
castorbean|gb160|EE256791
546
112
87.4
blastp


226
BDL83_H18
centaurea|gb166|EH734375
547
112
87.7
blastp


227
BDL83_H19
cichorium|gb171|EH680019
548
112
88
blastp


228
BDL83_H20
citrus|gb166|CV885954
549
112
89.15
tblastn


229
BDL83_H21
coffea|gb157.2|DV685589
550
112
87.1
tblastn


230
BDL83_H22
cotton|gb164|AI725778
551
112
86.8
blastp


231
BDL83_H23
cotton|gb164|CA993334
552
112
88.3
blastp


232
BDL83_H24
cowpea|gb166|FF537383
553
112
87.7
blastp


233
BDL83_H25
cynara|gb167|GE584395
554
112
84.16
tblastn


234
BDL83_H26
dandelion|gb161|DY806919
555
112
87.1
blastp


235
BDL83_H27
eucalyptus|gb166|CB967649
556
112
88
blastp


236
BDL83_H28
fescue|gb161|DT696580
557
112
82.8
blastp


237
BDL83_H29
ginger|gb164|DY345757
558
112
86.5
blastp


238
BDL83_H30
grape|gb160|CD008185
559
112
86.8
blastp


239
BDL83_H31
iceplant|gb164|CA833792
560
112
87.1
blastp


240
BDL83_H32
ipomoea|gb157.2|CJ755528
561
112
86.8
blastp


241
BDL83_H33
lettuce|gb157.2|AF162206
562
112
87.7
blastp


242
BDL83_H34
leymus|gb166|EG375854
563
112
84
blastp


243
BDL83_H35
lovegrass|gb167|DN481848
564
112
82.8
blastp


244
BDL83_H36
maize|gb170|BG355384
565
112
83
blastp


245
BDL83_H37
maize|gb170|LLAI603703
566
112
83.5
blastp


246
BDL83_H38
medicago|gb157.2|AL386990
567
112
80.5
blastp


247
BDL83_H39
medicago|gb157.2|AW695293
568
112
84.8
blastp


248
BDL83_H40
papaya|gb165|EX248440
569
112
84.5
blastp


249
BDL83_H41
peanut|gb171|EE126296
570
112
86.8
blastp


250
BDL83_H42
peanut|gb171|ES752783
571
112
85.9
blastp


251
BDL83_H43
pepper|gb171|CO907209
572
112
86.8
blastp


252
BDL83_H44
pepper|gb171|GD064098
573
112
87.4
blastp


253
BDL83_H45
physcomitrella|gb157|BJ157670
574
112
82.4
blastp


254
BDL83_H46
physcomitrella|gb157|BJ171093
575
112
83.63
tblastn


255
BDL83_H47
pine|gb157.2|AW010114
576
112
82.7
blastp


256
BDL83_H48
pine|gb157.2|CO169305
577
112
86.2
blastp


257
BDL83_H49
poplar|gb170|BI068614
578
112
88
blastp


258
BDL83_H50
poplar|gb170|BU878945
579
112
86.05
tblastn


259
BDL83_H51
potato|gb157.2|BF053889
580
112
86.2
blastp


260
BDL83_H52
prunus|gb167|DW341878
581
112
88.9
blastp


261
BDL83_H53
radish|gb164|EV537348
582
112
95
blastp


262
BDL83_H54
radish|gb164|EV565372
583
112
94.7
blastp


263
BDL83_H55
rice|gb170|OS01G64660
584
112
84.5
blastp


264
BDL83_H56
rice|gb170|OS05G36270
585
112
83.3
blastp


265
BDL83_H57
sorghum|gb161.crp|AW566083
586
112
84.8
blastp


266
BDL83_H58
sorghum|gb161.crp|AW671091
587
112
83.6
blastp


267
BDL83_H59
soybean|gb168|AL388391
588
112
81.3
blastp


268
BDL83_H60
soybean|gb168|BE941320
589
112
86.5
blastp


269
BDL83_H61
soybean|gb168|BF636881
590
112
87.1
blastp


270
BDL83_H62
soybean|gb168|CD394856
591
112
86.2
blastp


271
BDL83_H63
spikemoss|gb165|FE443631
592
112
83.9
blastp


272
BDL83_H64
spruce|gb162|CO227794
593
112
87.4
blastp


273
BDL83_H65
spruce|gb162|CO238226
594
112
83.3
blastp


274
BDL83_H66
spurge|gb161|DV121804
595
112
87.4
blastp


275
BDL83_H67
strawberry|gb164|DY671211
596
112
87.4
blastp


276
BDL83_H68
sugarcane|gb157.3|BQ533620
597
112
85.4
blastp


277
BDL83_H69
sunflower|gb162|BU672090
598
112
84.2
blastp


278
BDL83_H70
sunflower|gb162|CD847711
599
112
87.7
blastp


279
BDL83_H71
switchgrass|gb167|DN143181
600
112
84.8
blastp


280
BDL83_H72
switchgrass|gb167|DN148413
601
112
82.4
tblastn


281
BDL83_H73
tomato|gb164|AI486777
602
112
88.3
blastp


282
BDL83_H74
tomato|gb164|BG123415
603
112
85.9
blastp


283
BDL83_H75
triphysaria|gb164|EY166297
604
112
85.9
blastp


284
BDL83_H76
triphysaria|gb164|EY169717
605
112
87.4
blastp


285
BDL83_H77
wheat|gb164|BE213261
606
112
82.8
blastp


286
BDL83_H78
wheat|gb164|BE418868
607
112
82.8
blastp


287
BDL83_H79
wheat|gb164|BE500460
608
112
82.8
blastp


288
BDL118_H0
castorbean|gb160|MDL29877M000477
609
114
81.4
blastp


289
BDL118_H1
poplar|gb170|AI164922
610
114
81.3
blastp


290
BDL118_H2
poplar|gb170|BI138300
611
114
82
blastp


291
BDL118_H3
soybean|gb168|BE658051
612
114
80.1
blastp


292
BDL118_H4
soybean|gb168|CB540069
613
114
80
blastp


293
BDL138_H0
canola|gb161|CD817345
614
116
92.5
blastp


294
BDL138_H1
radish|gb164|EV536083
615
116
91.8
blastp


295
BDL138_H2
radish|gb164|EW725583
616
116
91.1
blastp


296
BDL147_H0
thellungiella|gb167|BY818222
617
118
81.6
blastp


297
BDL149_H0
b_rapa|gb162|DY009670
618
119
87.9
blastp


298
BDL149_H1
canola|gb161|CD818601
619
119
88.5
blastp


299
BDL149_H2
cowpea|gb166|FF400239
620
119
82.4
blastp


300
BDL154_H0
b_rapa|gb162|EX046206
621
122
90.77
tblastn


301
BDL154_H1
canola|gb161|CD841052
622
122
92.25
tblastn


302
BDL155_H0
arabidopsis|gb165|AT1G24240
623
123
92.9
blastp


303
BDL155_H1
arabidopsis|gb165|AT5G11750
624
123
91.7
blastp


304
BDL155_H2
canola|gb161|EE462449
625
123
81.3
blastp


305
BDL155_H3
radish|gb164|EV545009
626
123
80.34
tblastn


306
BDL155_H4
radish|gb164|EV569478
627
123
80.4
blastp


307
BDL158_H0
radish|gb164|EW715818
628
126
88.46
tblastn


308
BDL160_H0
canola|gb161|EE418738
629
127
83.9
blastp


309
BDL160_H1
radish|gb164|EV545765
630
127
85.1
blastp


310
BDL167_H0
radish|gb164|EV535056
631
196
82.7
tblastn


311
BDL168_H0
radish|gb164|EV525399
632
132
90.5
blastp


312
BDL171_H0
arabidopsis|gb165|AT2G31580
633
134
84
blastp


313
BDL182_H0
canola|gb161|CX188804
634
140
87.5
blastp


314
BDL183_H0
arabidopsis|gb165|AT4G15630
635
141
81.6
blastp


315
BDL183_H1
b_rapa|gb162|EE526726
636
141
83.7
blastp


316
BDL183_H2
canola|gb161|CD811977
637
141
80
blastp


317
BDL183_H3
canola|gb161|CN735162
638
141
83.7
blastp


318
BDL183_H4
canola|gb161|CN828640
639
141
83.7
blastp


319
BDL183_H5
radish|gb164|EW722612
640
141
83.2
blastp


320
BDL183_H6
radish|gb164|EX753993
641
141
81.6
blastp


321
BDL183_H7
thellungiella|gb167|BY824379
642
141
80
blastp


322
BDL190_H0
b_oleracea|gb161|AM395197
643
146
84.49
tblastn


323
BDL190_H1
canola|gb161|EE407003
644
146
87.2
blastp


324
BDL190_H2
radish|gb164|EV547395
645
146
86.6
blastp


325
BDL190_H3
thellungiella|gb167|BY827749
646
146
89.8
blastp


326
BDL192_H0
canola|gb161|CD827541
647
147
80.37
tblastn


327
BDL201_H0
b_juncea|gb164|EVGN00584109703185
648
153
81.8
blastp


328
BDL201_H1
b_oleracea|gb161|DY014784
649
153
80.4
blastp


329
BDL201_H2
b_oleracea|gb161|DY015288
650
153
82.2
blastp


330
BDL201_H3
b_rapa|gb162|BQ791239
651
153
83.2
blastp


331
BDL201_H4
canola|gb161|BQ704590
652
153
81.7
blastp


332
BDL201_H5
canola|gb161|CD822183
653
153
80.8
blastp


333
BDL201_H6
canola|gb161|CD838597
654
153
81.8
blastp


334
BDL201_H7
radish|gb164|EV527287
655
153
81.6
blastp


335
BDL201_H8
radish|gb164|EV534907
656
153
81.8
blastp


336
BDL201_H9
radish|gb164|EV543313
657
153
81.3
blastp


337
BDL201_H10
radish|gb164|EV565783
658
153
81.9
blastp


338
BDL201_H11
thellungiella|gb167|BY814893
659
153
83.89
tblastn


339
BDL223_H0
arabidopsis|gb165|AT3G54080
660
159
82.05
tblastn


340
BDL223_H1
arabidopsis|gb165|AT3G54085
661
159
82.1
blastp


341
BDL223_H2
b_juncea|gb164|EVGN01441114591370
662
159
96.15
tblastn


342
BDL223_H3
b_juncea|gb164|EVGN05602102561055
663
159
85
blastp


343
BDL223_H4
b_oleracea|gb161|EE534959
664
159
96.2
blastp


344
BDL223_H5
b_oleracea|gb161|ES947677
665
159
94.9
blastp


345
BDL223_H6
b_rapa|gb162|EE527700
666
159
96.2
blastp


346
BDL223_H7
canola|gb161|CD812251
667
159
96.2
blastp


347
BDL223_H8
canola|gb161|CN734091
668
159
96.15
tblastn


348
BDL223_H9
canola|gb161|DY007214
669
159
96.15
tblastn


349
BDL223_H10
canola|gb161|EG019597
670
159
97.4
blastp


350
BDL223_H11
canola|gb161|ES992154
671
159
97.4
blastp


351
BDL223_H12
canola|gb161|EV087632
672
159
97.4
blastp


352
BDL223_H13
radish|gb164|EV524950
673
159
96.15
tblastn


353
BDL223_H14
radish|gb164|EY899056
674
159
96.2
blastp


354
BDL229_H0
b_rapa|gb162|EX066757
675
160
83.5
blastp


355
BDL229_H1
radish|gb164|EW725388
676
160
82.59
tblastn


356
BDL231_H0
arabidopsis|gb165|AT1G79470
677
162
84.5
blastp


357
BDL231_H1
canola|gb161|CD826885
678
162
84.7
blastp


358
BDL231_H2
canola|gb161|CD827559
679
162
95.42
tblastn


359
BDL242_H0
radish|gb164|EV539529
680
164
85.9
blastp


360
BDL247_H0
b_oleracea|gb161|DY026136
681
167
90.82
tblastn


361
BDL247_H1
b_rapa|gb162|AY185359
682
167
91.1
blastp


362
BDL247_H2
canola|gb161|CD838112
683
167
89.1
blastp


363
BDL247_H3
canola|gb161|EE455228
684
167
91.1
blastp


364
BDL247_H4
maize|gb170|LLEU940833
685
167
92.8
blastp


365
BDL247_H5
radish|gb164|EV566311
686
167
92.6
blastp


366
BDL247_H6
thellungiella|gb167|DN773706
687
167
93.08
tblastn


367
BDL248_H0
arabidopsis|gb165|AT4G37340
688
168
80.6
blastp


368
BDL70_H0
arabidopsis|gb165|AT4G25960
689
201
80.6
blastp


369
BDL70_H1
poplar|gb170|CN192983
690
201
82.8
blastp


370
BDL70_H2
soybean|gb168|BE822547
691
201
81.9
blastp


371
BDL70_H3
soybean|gb168|CD415929
692
201
81.8
blastp


372
BDL85_H0
b_oleracea|gb161|AM385973
693
175
83.3
blastp


373
BDL85_H1
b_rapa|gb162|CV544456
694
175
83.3
blastp


374
BDL85_H2
b_rapa|gb162|EE523194
695
175
84.7
blastp


375
BDL85_H3
canola|gb161|CD813661
696
175
83.3
blastp


376
BDL85_H4
canola|gb161|CD822271
697
175
84.7
blastp


377
BDL85_H5
canola|gb161|CX280350
698
175
83.3
blastp


378
BDL85_H6
radish|gb164|EV527759
699
175
82.2
blastp


379
BDL85_H7
thellungiella|gb167|DN779034
700
175
83.6
blastp


380
BDL88_H0
barley|gb157.3|BI950587
701
176
82.3
blastp


381
BDL88_H1
barley|gb157.3|BI955547
702
176
88.6
blastp


382
BDL88_H2
brachypodium|gb169|BE425841
703
176
82.7
blastp


383
BDL88_H3
brachypodium|gb169|BM817094
704
176
90
blastp


384
BDL88_H4
fescue|gb161|CK802755
705
176
88.7
blastp


385
BDL88_H5
leymus|gb166|EG378145
706
176
83.2
blastp


386
BDL88_H6
maize|gb170|AI622555
707
176
89.9
blastp


387
BDL88_H7
maize|gb170|AI712236
708
176
89.2
blastp


388
BDL88_H8
maize|gb170|AI855432
709
176
80.7
blastp


389
BDL88_H9
pseudoroegneria|gb167|FF342352
710
176
88
blastp


390
BDL88_H10
pseudoroegneria|gb167|FF342444
711
176
82.3
blastp


391
BDL88_H11
rice|gb170|OS08G43320
712
176
84.5
blastp


392
BDL88_H12
sorghum|gb161.crp|AW562977
713
176
81.4
blastp


393
BDL88_H13
sorghum|gb161.crp|BE129901
714
176
91.1
blastp


394
BDL88_H14
sugarcane|gb157.3|SCFMEMPRO
715
176
91.4
blastp


395
BDL88_H15
switchgrass|gb167|DN144780
716
176
91.7
blastp


396
BDL88_H16
switchgrass|gb167|FE629824
717
176
92
blastp


397
BDL88_H17
wheat|gb164|BE406463
718
176
88
blastp


398
BDL88_H18
wheat|gb164|BE425841
719
176
82
blastp


399
BDL88_H19
wheat|gb164|BF474328
720
176
81.2
blastp


400
BDL88_H20
wheat|gb164|BQ484144
721
176
87.7
blastp


401
BDL88_H21
wheat|gb164|CA599299
722
176
88
blastp


402
BDL94_H0
rice|gb170|OS01G09220
723
177
96.7
blastp


403
BDL102_H0
avocado|gb164|CK767108
724
178
80.69
tblastn


404
BDL102_H1
banana|gb167|FL650176
725
178
82.8
blastp


405
BDL102_H2
banana|gb167|FL657720
726
178
80.4
blastp


406
BDL102_H3
banana|gb167|FL658383
727
178
83.4
blastp


407
BDL102_H4
barley|gb157.3|BE215743
728
178
84.83
tblastn


408
BDL102_H5
barley|gb157.3|BE411917
729
178
85.2
blastp


409
BDL102_H6
barley|gb157.3|BF627967
730
178
82.76
tblastn


410
BDL102_H7
brachypodium|gb169|BE398478
731
178
83.7
blastp


411
BDL102_H8
brachypodium|gb169|BE399017
732
178
87.6
blastp


412
BDL102_H9
brachypodium|gb169|BE423566
733
178
85.5
blastp


413
BDL102_H10
cenchrus|gb166|EB655509
734
178
89
blastp


414
BDL102_H11
cichorium|gb171|DT211967
735
178
80.1
blastp


415
BDL102_H12
cichorium|gb171|EH700664
736
178
80
blastp


416
BDL102_H13
citrus|gb166|BE208879
737
178
80
blastp


417
BDL102_H14
clover|gb162|BB906663
738
178
80
blastp


418
BDL102_H15
cowpea|gb166|FC462243
739
178
80.7
blastp


419
BDL102_H16
dandelion|gb161|DY813750
740
178
80.7
blastp


420
BDL102_H17
fescue|gb161|DT685902
741
178
85.6
blastp


421
BDL102_H18
ginger|gb164|DY369602
742
178
80.7
blastp


422
BDL102_H19
ipomoea|gb157.2|BJ557023
743
178
80
tblastn


423
BDL102_H20
ipomoea|gb157.2|BU690707
744
178
80
tblastn


424
BDL102_H21
lettuce|gb157.2|DW044786
745
178
80
blastp


425
BDL102_H22
lettuce|gb157.2|DW050757
746
178
80
tblastn


426
BDL102_H23
lettuce|gb157.2|DW108809
747
178
81.38
tblastn


427
BDL102_H24
lettuce|gb157.2|DW108810
748
178
80
tblastn


428
BDL102_H25
liquorice|gb171|FS238664
749
178
80.7
blastp


429
BDL102_H26
liquorice|gb171|FS241892
750
178
80
tblastn


430
BDL102_H27
liriodendron|gb166|CK766596
751
178
83.4
blastp


431
BDL102_H28
lotus|gb157.2|AW720301
752
178
82.1
blastp


432
BDL102_H29
lotus|gb157.2|CN825142
753
178
81.5
blastp


433
BDL102_H30
lovegrass|gb167|EH188388
754
178
88.97
tblastn


434
BDL102_H31
maize|gb170|AI391795
755
178
95.2
blastp


435
BDL102_H32
maize|gb170|LLBE510254
756
178
95.2
blastp


436
BDL102_H33
melon|gb165|DV632852
757
178
80
tblastn


437
BDL102_H34
millet|gb161|CD725312
758
178
85.7
blastp


438
BDL102_H35
nuphar|gb166|CV003178
759
178
81.4
blastp


439
BDL102_H36
oat|gb164|CN815719
760
178
91.03
tblastn


440
BDL102_H37
oil_palm|gb166|EL681098
761
178
86.21
tblastn


441
BDL102_H38
oil_palm|gb166|EL682630
762
178
84.1
blastp


442
BDL102_H39
oil_palm|gb166|EL684119
763
178
82.1
blastp


443
BDL102_H40
onion|gb162|CF446214
764
178
80.4
blastp


444
BDL102_H41
papaya|gb165|EX258155
765
178
80.7
blastp


445
BDL102_H42
pineapple|gb157.2|DT336701
766
178
84.8
blastp


446
BDL102_H43
pineapple|gb157.2|DT338401
767
178
84.8
blastp


447
BDL102_H44
poppy|gb166|FE964559
768
178
80
tblastn


448
BDL102_H45
rice|gb170|OS03G31090
769
178
93.8
blastp


449
BDL102_H46
rye|gb164|BE637001
770
178
85.2
blastp


450
BDL102_H47
sorghum|gb161.crp|AI673920
771
178
96.6
blastp


451
BDL102_H48
sorghum|gb161.crp|AW747023
772
178
83.3
blastp


452
BDL102_H49
soybean|gb168|AA661036
773
178
80
blastp


453
BDL102_H50
soybean|gb168|AW720301
774
178
80
tblastn


454
BDL102_H51
sugarcane|gb157.3|CA076952
775
178
96.6
blastp


455
BDL102_H52
sugarcane|gb157.3|CA087422
776
178
96.6
blastp


456
BDL102_H53
sugarcane|gb157.3|CA103720
777
178
97.2
blastp


457
BDL102_H54
sugarcane|gb157.3|CA113942
778
178
84.25
tblastn


458
BDL102_H55
sugarcane|gb157.3|CA114406
779
178
97.2
blastp


459
BDL102_H56
sugarcane|gb157.3|CA116867
780
178
87.6
blastp


460
BDL102_H57
sugarcane|gb157.3|CA119956
781
178
90.34
tblastn


461
BDL102_H58
sugarcane|gb157.3|CA128680
782
178
86.9
blastp


462
BDL102_H59
sugarcane|gb157.3|CA139681
783
178
84.3
blastp


463
BDL102_H60
sugarcane|gb157.3|CA151882
784
178
93.1
tblastn


464
BDL102_H61
sugarcane|gb157.3|CA153401
785
178
96.6
blastp


465
BDL102_H62
sugarcane|gb157.3|CA193794
786
178
97.2
blastp


466
BDL102_H63
sugarcane|gb157.3|CA215946
787
178
80
blastp


467
BDL102_H64
sugarcane|gb157.3|CA235573
788
178
80.3
blastp


468
BDL102_H65
sugarcane|gb157.3|CA241742
789
178
82.76
tblastn


469
BDL102_H66
sugarcane|gb157.3|CA289186
790
178
95.2
blastp


470
BDL102_H67
sugarcane|gb157.3|CF571967
791
178
93.79
tblastn


471
BDL102_H68
sugarcane|gb157.3|CF574520
792
178
97.2
blastp


472
BDL102_H69
sunflower|gb162|CD848588
793
178
80
blastp


473
BDL102_H70
sunflower|gb162|CD850971
794
178
80.7
blastp


474
BDL102_H71
switchgrass|gb167|DN142384
795
178
95.9
blastp


475
BDL102_H72
switchgrass|gb167|FE598349
796
178
96.6
blastp


476
BDL102_H73
switchgrass|gb167|FE608943
797
178
96.6
blastp


477
BDL102_H74
switchgrass|gb167|FE642870
798
178
96.6
blastp


478
BDL102_H75
switchgrass|gb167|FL710664
799
178
95.2
blastp


479
BDL102_H76
tea|gb171|FE861343
800
178
80.14
tblastn


480
BDL102_H77
walnuts|gb166|CV195103
801
178
80.7
blastp


481
BDL102_H78
walnuts|gb166|CV196374
802
178
80.7
blastp


482
BDL102_H79
wheat|gb164|BE398202
803
178
85.2
blastp


483
BDL102_H80
wheat|gb164|BE406254
804
178
85.2
blastp


484
BDL102_H81
wheat|gb164|BE414893
805
178
85.2
blastp


485
BDL102_H82
wheat|gb164|CA485952
806
178
96.6
blastp


486
BDL102_H83
wheat|gb164|CA486424
807
178
93.8
blastp


487
BDL226_H0
canola|gb161|CD835072
808
181
89.5
blastp


488
BDL226_H1
radish|gb164|EV568139
809
181
91.7
blastp


489
BDL233_H0
radish|gb164|EV549343
810
185
84.5
blastp


490
BDL237_H0
arabidopsis|gb165|AT2G44890
811
187
86.3
blastp


491
BDL238_H0
arabidopsis|gb165|AT1G32763
812
202
81.5
blastp


492
BDL240_H0
castorbean|gb160|MDL30174M008707
813
189
82.4
blastp


493
BDL240_H1
cotton|gb164|BG446934
814
189
81.4
blastp


494
BDL240_H2
soybean|gb168|AW329693
815
189
80.7
blastp


495
BDL240_H3
soybean|gb168|BE329627
816
189
80.1
blastp


496
BDL241_H0
canola|gb161|CN825973
817
190
85.3
blastp


497
BDL249_H0
radish|gb164|EW735252
818
191
86.7
blastp


498
BDL251_H0
arabidopsis|gb165|AT5G23190
819
192
80.07
tblastn


499
BDL252_H0
apple|gb171|CN489978
820
193
80.9
blastp


500
BDL252_H1
apple|gb171|CN883406
821
193
80.9
blastp


501
BDL252_H2
b_rapa|gb162|EX036871
822
193
91
blastp


502
BDL252_H3
cacao|gb167|CU476642
823
193
84.3
blastp


503
BDL252_H4
canola|gb161|CN732395
824
193
90.6
blastp


504
BDL252_H5
canola|gb161|ES900668
825
193
86.2
blastp


505
BDL252_H6
castorbean|gb160|MDL29726M003996
826
193
81.4
blastp


506
BDL252_H7
citrus|gb166|CB417408
827
193
82.8
blastp


507
BDL252_H8
cotton|gb164|AI725830
828
193
82.8
blastp


508
BDL252_H9
cotton|gb164|CO094656
829
193
82.5
blastp


509
BDL252_H10
cowpea|gb166|FC458375
830
193
80.5
blastp


510
BDL252_H11
grape|gb160|CB920145
831
193
80.5
blastp


511
BDL252_H12
ipomoea|gb157.2|AU223826
832
193
80.2
blastp


512
BDL252_H13
lettuce|gb157.2|DW116753
833
193
80.22
tblastn


513
BDL252_H14
medicago|gb157.2|AL371996
834
193
80.9
blastp


514
BDL252_H15
peach|gb157.2|BU039377
835
193
82.4
blastp


515
BDL252_H16
poplar|gb170|BU816161
836
193
80.7
blastp


516
BDL252_H17
prunus|gb167|BU039377
837
193
82.4
blastp


517
BDL252_H18
radish|gb164|EV535608
838
193
92.1
blastp


518
BDL252_H19
radish|gb164|EW723334
839
193
91.8
blastp


519
BDL252_H20
soybean|gb168|BF636462
840
193
80.1
blastp


520
BDL252_H21
soybean|gb168|BU546186
841
193
82.4
blastp


521
BDL252_H22
soybean|gb168|CD390334
842
193
82.4
blastp


522
BDL252_H23
strawberry|gb164|CX661379
843
193
82
blastp


523
BDL252_H24
thellungiella|gb167|BY812142
844
193
92.1
blastp





Table 16: Provided are polynucleotides and polypeptides which are homologous to the identified polynucleotides or polypeptides of Table 15. Homol. = homologue; Algor. = Algorithm;






Example 7
Gene Cloning and Generation of Binary Vectors for Plant Expression
To validate their role in improving oil content, plant yield, seed yield, biomass, growth rate, ABST, NUE and/or vigor, selected genes were over-expressed in plants, as follows.
Cloning Strategy
Genes listed in Examples 5 and 6 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 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 normal conditions. Total RNA was extracted as described in Example 2 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 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 Ambion, Clontech or Invitrogen (RACE=R apid A ccess to cDNA E nds) was used to access the full cDNA transcript of the gene from the RNA samples described above. The RACE procedure was performed for the genes BDL197 (SEQ ID NO:46), BDL156 (SEQ ID NO:19), BDL169 (SEQ ID NO:28), BDL189 (SEQ ID NO:40), BDL200 (SEQ ID NO:47), BDL79 (SEQ ID NO:5), BDL231 (SEQ ID NO:57), BDL238 (SEQ ID NO:84) and BDL248 (SEQ ID NO:103) using the primers sequences listed in Table 17, below. RACE products were cloned into high copy vector followed by sequencing or directly sequenced. RACE products were sequenced as described hereinbelow for the genes specified in Table 17.
The information from the RACE procedure was used for cloning of the full length ORF of the corresponding genes.







TABLE 17







RACE primers used for sequencing of the identified genes of the invention


Table 17. Provided are the PCR primers used for RACE sequencing.











High copy plasmid used for


Gene Name
Primers used for amplification
cloning of RACE products





BDL197_5′Race
BDL197_NGSP1_R2 (SEQ ID NO: 934)
TopoTA



(CGCCTGAAGCTTCTCCGAGAAC)



 


BDL156_5′Race
BDL156_NGSP1_R (SEQ ID NO: 937)




(ACGGTGTTTCCAGAATTTCGCAG)



 


BDL156_3′Race
BDL156_NGSP2_F (SEQ ID NO: 938)
TopoTA



(CTGAATGTGACTGGGATATGTCGG)



 


BDL169_5′Race
BDL169_NGSP1_R (SEQ ID NO: 939)




(TGCACTGGAGCGTGTAGGGACAG)



 


BDL169_3′Race
BDL169_NGSP1_F (SEQ ID NO: 940)




(GGCAGAAACTGTTTTATGGAAATGG)



 


BDL189_5′Race
BDL189_NGSP1_R (SEQ ID NO: 941)
TopoTA



(TTCTGTCCCTCGACCAAGGTTG)



 


BDL189_3′Race
BDL189_GSP2_F (SEQ ID NO: 942)




(CAGTCAATCTTCTTAGCATCGCTGAG)



 


BDL200_5′Race
BDL200_NGSP_Rb (SEQ ID NO: 943)
TopoTA



(CCAATGCCAATACGATGGTCGG)



 


BDL200_3′Race
BDL200_NGSP2_F (SEQ ID NO: 944)




(GAGCTTTGGAGATAAGATTGGTGCAG)



 


BDL79_5′Race
BDL79_GSP1_R (SEQ ID NO: 945)
TopoTA



(GTATCACTCGAGGCACCATTGGG)



 


BDL231_3′Race
BDL231 NGSP R (SEQ ID NO: 946)
TopoTA



(ATGTGGGATTCCGAGACAGTGTCC)



 


BDL238_5′Race
BDL238 NGSP R (SEQ ID NO: 947)




(TTTACCGTCCCCAAACGTTGCCG)



 


BDL238_3′Race
BDL238 NGSP F (SEQ ID NO: 948)




(CTCATCCGGACGATGTCTTACTTCTTCTCC)



 


BDL248_5′Race
BDL248 NGSP R (SEQ ID NO: 949)




(GAGGTGACCGATCACTGGTAACGC)



 


BDL215_5′Race
BDL215_NGSP1_R (SEQ ID NO: 950)




(TGGCTTTGAAAACGTAACATGCC)



 


BDL215_3′Race
BDL215_NGSP2_F (SEQ ID NO: 951)
TopoTA



(TATTGGGATTTTCGGATCGATGG)





Fwd = forward primer; Rev = reverse primer;






In case genomic DNA was cloned, as in the case of BDL90 and BDL94 the genes were amplified by direct PCR on 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 did not result in a satisfactory product for sequencing), an additional primer (or two) of the nested PCR primers were used. Table 18 below provides primers used for cloning of selected genes.







TABLE 18







The PCR primers used for cloning the genes of the invention


Table 18. Provided are the PCR primers used for cloning the genes of


some embodiments of the invention.










Restriction



Gene
Enzymes used for



Name
cloning
Primers used for amplification





BDL102
SalI, XbaI
BDL102_NF_SalI(SEQ ID NO: 952)




AATGTCGACTACCTGCCTTTCTCTCGTCC




BDL102_EF_SalI(SEQ ID NO: 953)




AAAGTCGACACTCTACCTGCCTTTCTCTCG




BDL102_NR_XbaI(SEQ ID NO: 954)




ATTCTAGACTATGTAGCCATCTCAACAATCAAAC




BDL102_ER_XbaI(SEQ ID NO: 955)




ATTCTAGAGGTTTTGATAAATAGGTACTCAGG


 


BDL117

BDL117_EF_SmaI(SEQ ID NO: 956)




CCCCGGGTCTCGGAGGTATCTTATTCCAG




BDL117_ER_SmaI(SEQ ID NO: 957)




CCCCGGGATGCCACACTTAAGGCCAAG


 


BDL118
SmaI, SmaI
BDL118_NF_SmaI(SEQ ID NO: 958)




TCCCGGGTCTGGGTCTACTTTTGATTTGAG




BDL118_NR_SmaI(SEQ ID NO: 959)




TCCCGGGTGAAGCAGAAGTTTCGATTTAAG


 


BDL138
SalI, XbaI
BDL138_NF_SalI(SEQ ID NO: 960)




AAAGTCGACCGAATCGTAATTGTTGAAGAGAG




BDL138_EF_SalI(SEQ ID NO: 961)




ATTGTCGACTTTAAGGAGAAGAGTCGCAGTC




BDL138_NR_XbaI(SEQ ID NO: 962)




ATTCTAGATTAGAGAGTGGTTGATAACGCAGAG




BDL138_ER_XbaI(SEQ ID NO: 963)




ACTCTAGACTACCTGTCACAATTTTCTAAAACAC


 


BDL140
XbaI, SacI
BDL140_NF_XbaI(SEQ ID NO: 964)




TATCTAGATTGAGAATGAACTCAGTGTGTATC




BDL140_EF_XbaI(SEQ ID NO: 965)




AATCTAGAAACTAAACATTGAGAATGAACTCAG




BDL140_NR_SacI(SEQ ID NO: 966)




TGAGCTCTTAAGTCATTTAGTTTGGATCAACAAC




BDL140_ER_SacI(SEQ ID NO: 967)




CGAGCTCAGACCATGCATTTAAGGATCAC


 


BDL147
SalI, XbaI
BDL147_NF_SalI(SEQ ID NO: 968)




TTAGTCGACCACAGTAACCATGTCCGTCTC




BDL147_NR_XbaI(SEQ ID NO: 969)




TATCTAGAGTGCTGCTTACTCGCTGTTTC


 


BDL149
SalI, XbaI
BDL149_NF_SalI(SEQ ID NO: 970)




AAAGTCGACCTCAAACCCAAGAACCTCATC




BDL149_NR_XbaI(SEQ ID NO: 971)




ATTCTAGATGCAATAGTAGTAGCAGTGAACC


 


BDL152
XbaI, SacI
BDL152_NF_XbaI(SEQ ID NO: 972)




TATCTAGATTCAGACAAAAACAGAGAGAAACT




BDL152_NR_SacI(SEQ ID NO: 973)




TGAGCTCCTAAGATCGGTTTAATCAATAGGG


 


BDL153
SalI, SmaI
BDL153_NF_SalI(SEQ ID NO: 974)




AAAGTCGACAACAGCTTCGGTTTAAGAGTTC




BDL153_NR_SmaI(SEQ ID NO: 975)




TCCCGGGTCTACATTACGGCATACGGC


 


BDL154
SalI, SacI
BDL154_NF_SalI(SEQ ID NO: 976)




TTAGTCGACTTAAAAATGGAGAGTCAAAAGC




BDL154_NR_SacI(SEQ ID NO: 977)




TGAGCTCCTACTACTTCTTGTTGATGCTGAGG


 


BDL155
SalI, XbaI
BDL155_NF_SalI(SEQ ID NO: 978)




AATGTCGACTCCTCTTGCGGAGAGATGC




BDL155_NR_XbaI(SEQ ID NO: 979)




ATTCTAGATCTCCTTTTGAGAGAGTGCAAC


 


BDL156
SalI, XbaI
BDL156_NF_SalI(SEQ ID NO: 980)




AATGTCGACTCGTCGTCTTCCTCATTTCG




BDL156_ER_XbaI(SEQ ID NO: 981)




ATTCTAGACTAATACGATTGGTAACAAGAAAACG


 


BDL157
SalI, XbaI
BDL157_NF_SalI(SEQ ID NO: 982)




ATTGTCGACTTTCAATAAGAAATCTGCGTCC




BDL157_EF_SalI(SEQ ID NO: 983)




AAAGTCGACGAATCTGCTTTTAAGCTTCTCG




BDL157_NR_XbaI(SEQ ID NO: 984)




ATTCTAGACTAAAGAGAGTGAAGGAACAAAGACC




BDL157_ER_XbaI(SEQ ID NO: 985)




ATTCTAGACTATTTTCTTCTGTCTTCTGTGTCTTC


 


BDL158

BDL158_EF_XbaI(SEQ ID NO: 986)




AATCTAGACCTCACTTCTCTCTCTCTCTCTTC




BDL158_ER_SmaI(SEQ ID NO: 987)




CCCCGGGAGCCTAAAGCCTAACCCAAC


 


BDL160
SalI, XbaI
BDL160_NF_SalI(SEQ ID NO: 988)




AAAGTCGACTGATCTACACAGAATCCATTTCC




BDL160_NR_XbaI(SEQ ID NO: 989)




AATCTAGATCATTCAGCCATTCACATTTTAGG


 


BDL162
SalI, XbaI
BDL162_NF_SalI(SEQ ID NO: 990)




TTAGTCGACCCTAATAATGGCTTGCAGAGC




BDL162_NR_XbaI(SEQ ID NO: 991)




TATCTAGAAAATCTTGAGACTAAATCAAGCTG


 


BDL167
SalI, XbaI
BDL167_NF_SalI(SEQ ID NO: 992)




AAAGTCGACGCAAGAAAGGGACTAACCAAG




BDL167_NR_XbaI(SEQ ID NO: 993)




ACTCTAGACTATGTCGGCATTAACTTAGAATCAC


 


BDL168
XbaI, SmaI
BDL168_NF_XbaI(SEQ ID NO: 994)




AATCTAGACTTGCTTCAAGATTCGAGTGAG




BDL168_EF_XbaI(SEQ ID NO: 995)




AATCTAGAATTAACCACCATTTCTGTGAAG




BDL168_NR_SmaI(SEQ ID NO: 996)




TCCCGGGCTACCTTCCTTCTTCTTCACTTCC




BDL168_ER_SmaI(SEQ ID NO: 997)




TCCCGGGTCCTAAAAGTCAGTCACCTTCTG


 


BDL169
SalI, XbaI
BDL169_NF_SalI(SEQ ID NO: 998)




AAAGTCGACGAAGGTGAAGTGATGGATTCTG




BDL169_EF_SalI(SEQ ID NO: 999)




AATGTCGACTGTTACCGATAAGAAGGTGAAG




BDL169_NR_XbaI(SEQ ID NO: 1000)




ATTCTAGACTAACAGCTTCAACGTAATTTGGTG




BDL169_ER_XbaI(SEQ ID NO: 1001)




ATTCTAGATCAACGTCATTTTGTGCATATC


 


BDL173
XbaI, SmaI
BDL173_EF_XbaI(SEQ ID NO: 1002)




ATTCTAGATTTTCCCGAATCTATTCATCAC




BDL173_ER_SmaI(SEQ ID NO: 1003)




CCCCGGGAACGCTTCACCCTTTAATCC


 


BDL174
SalI, SacI
BDL174_NF_SalI(SEQ ID NO: 1004)




AAAGTCGACCCGAGGAAGATGACGACAC




BDL174_NR_SacI(SEQ ID NO: 1005)




TGAGCTCCTAGTTTCAAGCAAGAGTGATTCC


 


BDL176
SmaI, SmaI
BDL176_NF_SmaI(SEQ ID NO: 1006)




TCCCGGGTATTGAGCAGCCGTGAAATC




BDL176_NR_SmaI(SEQ ID NO: 1007)




TCCCGGGTGGACCAAAGAATCAAATAGTAAC


 


BDL177
SalI, SacI
BDL177_NF_SalI(SEQ ID NO: 1008)




AATGTCGACTCAGGATCTATGGGCAAGTC




BDL177_EF_SalI(SEQ ID NO: 1009)




AAAGTCGACGCTTGTGATCAGGATCTATGG




BDL177_NR_SacI(SEQ ID NO: 1010)




TGAGCTCCTAAACAGCTTTCTTCTACTCTTCATC




BDL177_ER_SacI(SEQ ID NO: 1011)




CGAGCTCACAGAAAACAAAAGAAACTAGGC


 


BDL181
SalI, SacI
BDL181_NF_SalI(SEQ ID NO: 1012)




AAAGTCGACGCGATAGATCTGACGAATGC




BDL181_NR_SacI(SEQ ID NO: 1013)




TGAGCTCCTAGATTTCATACTCAGGAAGCCAC


 


BDL182
SalI, SacI
BDL182_NF_SalI(SEQ ID NO: 1014)




AACGTCGACTCTACCATCGACAACGAGAAAC




BDL182_NR_SacI_new(SEQ ID NO: 1015)




TGAGCTCCTACATTCACAACAAACCACCACTAC


 


BDL183
SalI, XbaI
BDL183_NF_SalI(SEQ ID NO: 1016)




AATGTCGACTTATTTTGATCTTCCTCACTTCTG




BDL183_EF_SalI(SEQ ID NO: 1017)




AAAGTCGACGATCAATCTTTGTTATCTCTCACTC




BDL183_NR_XbaI(SEQ ID NO: 1018)




ATTCTAGACTAATCACACAAAACGACAAGAACAG




BDL183_ER_XbaI(SEQ ID NO: 1019)




ACTCTAGAACGATGTGATAAAACATTAGAAGC


 


BDL186
SalI, XbaI
BDL186_NF_SalI(SEQ ID NO: 1020)




AAAGTCGACCGAAGTGAAAGTCGTGATGG




BDL186_EF_SalI(SEQ ID NO: 1021)




AAAGTCGACACGCAAACGTGATCCTAAAC




BDL186_NR_XbaI(SEQ ID NO: 1022)




ATTCTAGACTCAAGGGGACGAGATATCAG




BDL186_ER_XbaI(SEQ ID NO: 1023)




ACTCTAGAAGGTAGAGAGCATCAAGGAAGC


 


BDL187
SalI, SmaI
BDL187_NF_SalI(SEQ ID NO: 1024)




ATAGTCGACATTCTTTCAGTTTTCCGGTG




BDL187_EF_SalI(SEQ ID NO: 1025)




AAAGTCGACGCTTGAATTCTTTCAGTTTTCC




BDL187_NR_SmaI(SEQ ID NO: 1026)




TCCCGGGCTATTTTCACCAGTAATTTCCACAC




BDL187_ER_SmaI(SEQ ID NO: 1027)




TCCCGGGTTACTTTAGCCACAATCTGTGTTTTC


 


BDL188
XbaI, SmaI
BDL188_NF_XbaI(SEQ ID NO: 1028)




AATCTAGAATTTTCATTTGTTCGCTTCG




BDL188_NR_SmaI(SEQ ID NO: 1029)




TCCCGGGCTAACAGTAGGTAATTTTGACATCCAG


 


BDL189

BDL189_NF_SmaI(SEQ ID NO: 1030)




ACCCGGGCATTGCCTGTTGGCTTCG




BDL189_NR_SmaI(SEQ ID NO: 1031)




ACCCGGGTTACAATACAATTGTTTAATTCGAGG


 


BDL190
SalI, XbaI
BDL190_NF_SalI(SEQ ID NO: 1032)




TTAGTCGACAAAATAATGGCAGCTTTGGC




BDL190_EF_SalI(SEQ ID NO: 1033)




TTAGTCGACTCTCGTCACATATCTTCATCGAC




BDL190_NR_XbaI(SEQ ID NO: 1034)




TATCTAGACTACTAGACAAATTTGTTGATCAATTC




BDL190_ER_XbaI(SEQ ID NO: 1035)




TATCTAGACTAAAGAGAGAACTAGACAAATTTGTTG


 


BDL192
SalI, XbaI
BDL192_NF_SalI(SEQ ID NO: 1036)




ATTGTCGACTTTACGAAATACGCCGAATC




BDL192_EF_SalI(SEQ ID NO: 1037)




AATGTCGACTTCGAAACCCTAACAAAAGC




BDL192_NR_XbaI(SEQ ID NO: 1038)




ACTCTAGAATCTGCATAGCAGTTAGAACAAG




BDL192_ER_XbaI(SEQ ID NO: 1039)




ATTCTAGAGAAAGGTCCTCATTCATAATCC


 


BDL193
XbaI, SacI
BDL193_EF_XbaI(SEQ ID NO: 1040)




AATCTAGACTTCATATTCAAATCTCCTCTCC




BDL193_ER_SacI (SEQ ID NO: 1041)




CGAGCTCATCACAAACAAACCTAAGAGGC


 


BDL194
EcoRV, EcoRV
BDL194_NF_EcoRV(SEQ ID NO: 1042)




AAGATATCAGCCATTGTTCTTCATCATCTC




BDL194_NR_EcoRV(SEQ ID NO: 1043)




ACGATATCCTAACAGGGTTTTCAGTGCTGTG


 


BDL196
SalI, XbaI
BDL196_NF_salI(SEQ ID NO: 1044)




TTAGTCGACAAGACATGAAGTTCATGACACTAATG




BDL196_EF_SalI(SEQ ID NO: 1045)




TTAGTCGACAACTGAAACAAAAGAAGAGTCATC




BDL196_NR_XbaI(SEQ ID NO: 1046)




TATCTAGATTATGAGCTTTAACAACTAGTATAAGGAAC




BDL196_ER_XbaI(SEQ ID NO: 1047)




TATCTAGACACCACAATTTTAAGCTTCAAC


 


BDL197
SalI, XbaI
BDL197_NF_SalI(SEQ ID NO: 1048)




AAAGTCGACTGTTCTTGTTCTTCACGATGAG




BDL197_EF_SalI(SEQ ID NO: 1049)




AAAGTCGACTCTAAATCCTATGTTCTTGTTCTTC




BDL197_NR_XbaI(SEQ ID NO: 1050)




AATTCTAGAGGTTCAAAATACGTAACACATTG




BDL197_ER_XbaI(SEQ ID NO: 1051)




AACTCTAGAACCATATTAGGTTCAAAATACGTAAC


 


BDL201
SalI, XbaI
BDL201_NF_SalI(SEQ ID NO: 1052)




AAAGTCGACCGATCAACAGACTCTAATCAGC




BDL201_NR_XbaI(SEQ ID NO: 1053)




ATTCTAGATTAGTTCTATACTGCAGATTCTTGGG


 


BDL203
SalI, XbaI
BDL203_NF_SalI(SEQ ID NO: 1054)




AATGTCGACTTCTCTCTGTTCTTGCACTCG




BDL203_EF_SalI(SEQ ID NO: 1055)




AAAGTCGACCTTCTTCTTCTTTTCTCAATCTTTC




BDL203_NR_XbaI(SEQ ID NO: 1056)




ATTCTAGATCTGTATCATTAAAACTGAGGAAG




BDL203_ER_XbaI(SEQ ID NO: 1057)




ATTCTAGAGTGGCGAGACAACATTTCTAC


 


BDL220
SalI, XbaI
BDL220_NF_SalI(SEQ ID NO: 1058)




AAAGTCGACCTCTCTCTCTCTAATGGGTAATTG




BDL220_EF_SalI(SEQ ID NO: 1059)




AATGTCGACTCACCACACAACACAACCAAG




BDL220_NR_XbaI(SEQ ID NO: 1060)




ACTCTAGAAATCCAACGTCAAATGAGAAG




BDL220_NF_SalI(SEQ ID NO: 1061)




AAAGTCGACCTCTCTCTCTCTAATGGGTAATTG


 


BDL221
SalI, XbaI
BDL221_NF_SalI(SEQ ID NO: 1062)




AATGTCGACTTGGATCAGAGAAAATATGTCG




BDL221_EF_SalI(SEQ ID NO: 1063)




ATAGTCGACCTTGAATCTGAAGCTAATCTTGG




BDL221_NR_XbaI(SEQ ID NO: 1064)




ATTCTAGATTAGCATTAGAACGGGACAGTATAAG




BDL221_ER_XbaI(SEQ ID NO: 1065)




ACTCTAGATCAAAGAATCGAGCATTAGAACGG


 


BDL222
SalI, XbaI
BDL222_NF_SalI(SEQ ID NO: 1066)




AAAGTCGACCTAAACCGGTAAAAGATGTCG




BDL222_EF_SalI(SEQ ID NO: 1067)




AACGTCGACACTTTTGTTTTGCCTTTCCTC




BDL222_NR_XbaI(SEQ ID NO: 1068)




ATTCTAGATCTTCTTCATCACTCAATCGC




BDL222_ER_XbaI(SEQ ID NO: 1069)




ATTCTAGACTGTGGTATTTAGGGAATACATCC


 


BDL223
SalI, XbaI
BDL223_NF_SalI(SEQ ID NO: 1070)




AAAGTCGACCACAGAGAAATCATGGGGTTC




BDL223_EF_SalI(SEQ ID NO: 1071)




AACGTCGACAGATATCGTTGGCTTCGTCTC




BDL223_NR_XbaI(SEQ ID NO: 1072)




ATTCTAGATTAGGTTTGATCATTTTAACCAGAG




BDL223_ER_XbaI(SEQ ID NO: 1073)




ATTCTAGACTATGCAGAAATGTTTGGATTGAG


 


BDL224
XbaI, SmaI
BDL224_NF_XbaI(SEQ ID NO: 1074)




AATCTAGACCACAAAATTCGTCAAAGCTC




BDL224_EF_XbaI(SEQ ID NO: 1075)




ATTCTAGATTTTCAAACCACAAAATTCGTC




BDL224_NR_SmaI(SEQ ID NO: 1076)




CCCCGGGATCCAACCAATCCCTAAAATG




BDL224_ER_SmaI(SEQ ID NO: 1077)




CCCCGGGATCAGCCACTTCTACTCTCAATTC


 


BDL225
SalI, XbaI
BDL225_NF_SalI(SEQ ID NO: 1078)




AATGTCGACTCCTTGTGATTCATTATTTTGC




BDL225_EF_SalI(SEQ ID NO: 1079)




AAAGTCGACCAACATCTCCTCCAAAACATTC




BDL225_NR_XbaI(SEQ ID NO: 1080)




ACTCTAGATTAGCAAGAAGAAAAGAAGTGCAG




BDL225_ER_XbaI(SEQ ID NO: 1081)




ATTCTAGATTAGTAGTTTATACAAGGTGCGGAGAC


 


BDL226
EcoRV, EcoRV
BDL226_NF_EcoRV(SEQ ID NO: 1082)




AAGATATCGAAACTGGATCTGGGTTTATCC




BDL226_NR_EcoRV(SEQ ID NO: 1083)




ATGATATCCTAAACTAATCAAACATGGCACATAC


 


BDL227

BDL227_NF_SalI(SEQ ID NO: 1084)




AAAGTCGACAGAGTTAAGTCAATCACCAAACC




BDL227_NR_SmaI(SEQ ID NO: 1085)




TCCCGGGTTACCATCAAGTTTTCTTGCTGAAG


 


BDL228
SalI, XbaI
BDL228_NF_SalI(SEQ ID NO: 1086)




AAAGTCGACCCAACACTATATCATGGCTACTATC




BDL228_NR_XbaI(SEQ ID NO: 1087)




ATTCTAGACTAACCTCACTTGATGCTCTTGC


 


BDL229
SalI XbaI
BDL229_NR_XbaI(SEQ ID NO: 1088)




TATCTAGAGCTAAACAAAATCCGGAGATAG




BDL229_ER_XbaI(SEQ ID NO: 1089)




TATCTAGACAGTCACTCCATAACTATGATCAAAC




BDL229_F_SalI(SEQ ID NO: 1090)




TTAGTCGACCTCATTAATGGAAGTTTCAACATC




BDL229_F_SalI(SEQ ID NO: 1091)




TTAGTCGACCTCATTAATGGAAGTTTCAACATC


 


BDL230
SmaI, SmaI
BDL230_NF_SmaI(SEQ ID NO: 1092)




TCCCGGGTAAGTTTGTGAGATGGAATTAGTG




BDL230_NR_SmaI(SEQ ID NO: 1093)




TCCCGGGCTAATTGGTTGGTTACAAGATGC


 


BDL231
SalI, XbaI
BDL231_NF_SalI(SEQ ID NO: 1094)




AATGTCGACTGGACTGAAGATGTCAGGATTC




BDL231_EF_SalI(SEQ ID NO: 1095)




ATAGTCGACATTTCTCTCTATTGGCATCGAC




BDL231_NR_XbaI(SEQ ID NO: 1096)




AATTCTAGACTAAACTGGGGAAAGCTAAAACG




BDL231_ER_XbaI(SEQ ID NO: 1097)




AATTCTAGATCATAACATAAGAAAGTAAACTGGGG


 


BDL232
XbaI, SacI
BDL232_NF_XbaI(SEQ ID NO: 1098)




AATCTAGACACACCCCTCAAAGAAATATAAC




BDL232_EF_XbaI(SEQ ID NO: 1099)




AATCTAGAAAGAAATTCACACCCCTCAAAG




BDL232_NR_SacI(SEQ ID NO: 1100)




TGAGCTCCTAAAGGTGGAGTAATTAGAAGCG




BDL232_ER_SacI(SEQ ID NO: 1101)




TGAGCTCTGGTGAAGTGTTAAGTAATTGTCG


 


BDL233
SalI, SacI
BDL233_NF_SalI(SEQ ID NO: 1102)




AAAGTCGACGAAAGAGAGAAAATGGAGAATATG




BDL233_EF_SalI(SEQ ID NO: 1103)




AAAGTCGACCGATCTAAAGAAAGAGAGAAAATG




BDL233_NR_SacI(SEQ ID NO: 1104)




TGAGCTCCTAAGAGTCGATCTAGAAAGCAACATC




BDL233_ER_SacI(SEQ ID NO: 1105)




TGAGCTCGAATTAGTCCTTGTGGTTCTACTC


 


BDL234
SalI, SmaI
BDL234_NF_SalI(SEQ ID NO: 1106)




AATGTCGACTGATAAGAATGCTCCTGACTGG




BDL234_EF_SalI(SEQ ID NO: 1107)




AATGTCGACTCTTTCTCTGTATCTCGACGTTC




BDL234_NR_SmaI(SEQ ID NO: 1108)




TCCCGGGCTAAAATCCAAGTGCCCAAGAAC




BDL234_ER_SmaI(SEQ ID NO: 1109)




TCCCGGGCTAGCAAAACATAAATCCAAGTGC


 


BDL235
SalI, SmaI
BDL235_NF_SalI(SEQ ID NO: 1110)




AATGTCGACTCTTACTCAATCCGAAGAATGG




BDL235_NR_SmaI(SEQ ID NO: 1111)




CCCCGGGACTTCGATTCACATTTCTCCTC


 


BDL237
SalI, XbaI
BDL237_NF_SalI(SEQ ID NO: 1112)




AAAGTCGACCGAAGTAAGAAAAGAAAATGGAG




BDL237_EF_SalI(SEQ ID NO: 1113)




AAAGTCGACCTTCGAAGTAAGAAAAGAAAATG




BDL237_NR_XbaI(SEQ ID NO: 1114)




AATCTAGATCATACTCAAGTGCTTGTCCTCGG




BDL237_ER_XbaI(SEQ ID NO: 1115)




ATTCTAGAGTTATTGGTGTCTTGTTCCACC


 


BDL238
SalI, XbaI
BDL238_NF_SalI(SEQ ID NO: 1116)




AAAGTCGACCAACGAGCAAGAGAAAATGG




BDL238_EF_SalI(SEQ ID NO: 1117)




AAAGTCGACGATACAACGAGCAAGAGAAAATG




BDL238_NR_XbaI(SEQ ID NO: 1118)




AATTCTAGATGGTTCTAGCTATCACTAGGTGC




BDL238_ER_XbaI(SEQ ID NO: 1119)




AATTCTAGAGGCAATACAACAAGAGAAAACTC


 


BDL240
SalI, XbaI
BDL240_NF_SalI(SEQ ID NO: 1120)




AAAGTCGACCGAGTACAATGGAGGTTTCG




BDL240_NR_XbaI(SEQ ID NO: 1121)




ATTCTAGATCAAGCTTAAAGACCGTGAGGAAG


 


BDL241
XbaI, SmaI
BDL241_NF_XbaI(SEQ ID NO: 1122)




AATCTAGAACAGTCGTCGTCGTCAAGC




BDL241_NR_SmaI(SEQ ID NO: 1123)




TCCCGGGCTAAAGGTAAGGATGAATTGTCAGAG


 


BDL242
SalI, XbaI
BDL242_NF_SalI(SEQ ID NO: 1124)




AATGTCGACTCAAATCAATATGGGATCTTTC




BDL242_NR_XbaI(SEQ ID NO: 1125)




ATTCTAGATTATTGACAAGTCTATTGCCCG


 


BDL245
SalI, SmaI
BDL245_NF_SalI(SEQ ID NO: 1126)




AATGTCGACTTCGTTAAATTATGTCTTTGAGG




BDL245_EF_SalI(SEQ ID NO: 1127)




AAAGTCGACTGACTCAGAGATCAACAAAACC




BDL245_NR_SmaI(SEQ ID NO: 1128)




ACCCGGGTTAGACTTACTCCAATTTCCAAGC




BDL245_ER_SmaI(SEQ ID NO: 1129)




TCCCGGGTCAAGAGTCGGTCACACGC


 


BDL247
SmaI, SacI
BDL247_NF_SmaI(SEQ ID NO: 1130)




TCCCGGGTCCTTCTTGTGTGAGACCGAG




BDL247_NR_SacI(SEQ ID NO: 1131)




TGAGCTCCTAAGAACTTTAACGCATTTTGTAGTG


 


BDL248
SalI, XbaI
BDL248_NF_SalI(SEQ ID NO: 1132)




AAAGTCGACAACGTGATCAATATGGAAGCTC




BDL248_EF_SalI(SEQ ID NO: 1133)




AAAGTCGACACTCACCAAAATCCAACGTG




BDL248_NR_XbaI(SEQ ID NO: 1134)




AATTCTAGACTAAACTCAAGAGGAGTCGGGTAAG




BDL248_ER_XbaI(SEQ ID NO: 1135)




AATTCTAGATTAATTCGTTACCGTTGCTAAG


 


BDL249
SalI, XbaI
BDL249_NF_SalI(SEQ ID NO: 1136)




AAAGTCGACACCAAAATAGATCTAAAACATGG




BDL249_EF_SalI(SEQ ID NO: 1137)




AATGTCGACTTCACTCACCAAAATAGATCTAAAAC




BDL249_NR_XbaI(SEQ ID NO: 1138)




AATCTAGATCAACGTCAAACGGACTCGTTG




BDL249_ER_XbaI(SEQ ID NO: 1139)




AATCTAGATCACCAAAAGTCTAAACGTCAAACG


 


BDL250
SalI, XbaI
BDL250_NF_SalI(SEQ ID NO: 1140)




TTAGTCGACCAAAGATGTTTTACTATGTGATTGTC




BDL250_EF_SalI(SEQ ID NO: 1141)




TTAGTCGACAGGAAGAGAAAGGTCAAAGATG




BDL250_NR_XbaI(SEQ ID NO: 1142)




TATCTAGATCAAAATCTCACATCTCCATGCATAG




BDL250_ER_XbaI(SEQ ID NO: 1143)




TATCTAGATCATGTTCGCATTACACAAATATCC


 


BDL252
XbaI, SmaI
BDL252_NF_XbaI(SEQ ID NO: 1144)




ATTCTAGATTCTCTGTCTCTTTGGCTTTTC




BDL252_EF_XbaI(SEQ ID NO: 1145)




ATTCTAGATAAAACTCTCAGCTTCCCATTC




BDL252_NR_SmaI(SEQ ID NO: 1146)




TCCCGGGCTATTGTCATTGAGGAAGAACAGG




BDL252_ER_SmaI(SEQ ID NO: 1147)




TCCCGGGCTAAAAGTTCTTGCTTGCTTTCTG


 


BDL48
SalI, XbaI
BDL48_NF_SalI(SEQ ID NO: 1148)




AAAGTCGACAGATTGCGTCACTGTAGTAGTAGTAG




BDL48_EF_SalI(SEQ ID NO: 1149)




AAAGTCGACCTGCAACTCTTTCTCACTTTCAC




BDL48_NR_XbaI(SEQ ID NO: 1150)




AGTCTAGAAAACATTTTGCTTAAGATCTACAGAG




BDL48_ER_XbaI(SEQ ID NO: 1151)




ACTCTAGAAGACATGAAAGCACAAATCAAG


 


BDL49
SmaI, SacI
BDL49_NF_SmaI(SEQ ID NO: 1152)




ACCCGGGCTAACATGCTCCATCTCCTTC




BDL49_NR_SacI(SEQ ID NO: 1153)




TGAGCTCTCAACCTGATCAGCGATGGTCG


 


BDL58
SalI, XbaI
BDL58_NF_SalI(SEQ ID NO: 1154)




AAAGTCGACCACACAAGACTAACGATGTTGC




BDL58_NR_XbaI(SEQ ID NO: 1155)




ATTCTAGATTAAAAAGAGACCTACACGGCG


 


BDL62
SalI, SacI
BDL62_NF_SalI(SEQ ID NO: 1156)




AATGTCGACTCTCTGGTCTCCCTATATCAGC




BDL62_NR_SacI(SEQ ID NO: 1157)




TGAGCTCCTATTTGATGTTGTTGTTGTTGTCTG


 


BDL63
SalI, XbaI
BDL63_NF_SalI(SEQ ID NO: 1158)




ATAGTCGACGTTTTGAGATATGGGAGGACC




BDL63_EF_SalI(SEQ ID NO: 1159)




AAAGTCGACCTCTAGATTCTTGGCGATTCTC




BDL63_NR_XbaI(SEQ ID NO: 1160)




ATTCTAGATTAGTGGTTTTACTTGAGCCTCTCC




BDL63_ER_SacI(SEQ ID NO: 1161)




TGAGCTCCTATTGTTCGTTACGGTGGTTTTAC


 


BDL64

BDL64_NF_SalI(SEQ ID NO: 1162)




AATGTCGACGGACTTTAAACATGGGTGTTC




BDL64_NR_XbaI(SEQ ID NO: 1163)




ATTCTAGACTACTCATAGGTTTGTTACTTCCTTG


 


BDL75
SalI, XbaI
BDL75_NF_SalI(SEQ ID NO: 1164)




AAAGTCGACAAGAAGAAAGAAACAGAGAATCG




BDL75_NR_XbaI(SEQ ID NO: 1165)




ATTCTAGACTAATTGTTCAAAGTTCAGTGAGCC


 


BDL79
XbaI, SmaI
BDL79_NF_XbaI(SEQ ID NO: 1166)




ATTCTAGAGGAGATTTTGTAATGGATTCTGC




BDL79_EF_XbaI(SEQ ID NO: 1167)




ATTCTAGAGAAGGAGATTTTGTAATGGATTC




BDL79_NR_Sma(SEQ ID NO: 1168)




TCCCGGGTTACGCTTAGACCATACAACGAGTAG




BDL79_ER_Sma(SEQ ID NO: 1169)




TCCCGGGGTTATTTACTTATGGCCTGTTTC


 


BDL81
SalI, SacI
BDL81_EF_SalI(SEQ ID NO: 1170)




AAAGTCGACCAGGGGTTTAAGGATTTTCTC




BDL81_ER_SacI(SEQ ID NO: 1171)




CGAGCTCAAATGGCTTTCTCTACCCTTTG


 


BDL83
SalI, XbaI
BDL83_NF_SalI(SEQ ID NO: 1172)




AATGTCGACTGGTAGGCTGAGAGAAAGAAAG




BDL83_NR_XbaI(SEQ ID NO: 1173)




AGTCTAGATTAGAGAATAAAAGAAGAATGAGAAGC


 


BDL85
XbaI, SalI
BDL85_NF_SalI(SEQ ID NO: 1174)




AATGTCGACTTAATCGTTAGAAGATGAGCCAG




BDL85_NR_XbaI(SEQ ID NO: 1175)




ATTCTAGATCAGGCTTAGAAGCAAATGTCCAG


 


BDL88
SalI, XbaI
BDL88_NF_SalI(SEQ ID NO: 1176)




AATGTCGACGAGGAGATGGCGAGCAAC




BDL88_NR_XbaI(SEQ ID NO: 1177)




TATCTAGATTATTAGGTATTGCACTTCCACTTC


 


BDL90

BDL90_EF_SalI(SEQ ID NO: 1178)




AAAGTCGACCACCAGAAACAAAGAGAGAGTG




BDL90_ER_XbaI(SEQ ID NO: 1179)




ATTCTAGATATCATGCAACCACAAACAATAG


 


BDL94
XbaI, SmaI
BDL94_EF_XbaLnew(SEQ ID NO: 1180)




AATCTAGAAAGTCCAAGTGACCAACCATC




BDL94_ER_SmaLnew(SEQ ID NO: 1181)




TCCCGGGGGGATACAAGATTATGCAGGC





Fwd = forward primer; Rev = reverse primer; Nested = nested primer for PCR (internal primer); External = external primer for PCR.






To facilitate cloning of the cDNAs/genomic sequences, a 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 did not exist in the cDNA sequence; and (b). The restriction sites in the forward and reverse primers were designed such that the digested cDNA is inserted in the sense formation into the binary vector utilized for transformation.
Each digested PCR product was inserted into a high copy vector pBlue-script KS plasmid vector [pBlue-script KS plasmid vector, Hypertext Transfer Protocol://World Wide Web(dot)stratagene(dot)com/manuals/212205(dot)pdf] or into plasmids originating from this vector. In cases where the pGXN high copy vector (originated from pBlue-script KS) was used, the PCR product was inserted upstream to the NOS terminator (SEQ ID NO:1182) originated from pBI 101.3 binary vector (GenBank Accession No. U12640, nucleotides 4356 to 4693) and downstream to the 35S promoter (Table 20 below). The digested products and the linearized plasmid vector were ligated using T4 DNA ligase enzyme (Roche, Switzerland).
Sequencing of the amplified PCR products was performed, using ABI 377 sequencer (Amersham Biosciences Inc). In all cases, after confirmation of the sequence of the cloned genes, the cloned cDNA accompanied or not with the NOS terminator was introduced into the pGI binary vector [pBXYN or pQXYN containing the 35S CaMV promoter] according to Table 19 hereinabove, via digestion with appropriate restriction endonucleases. In any case the insert was followed by single copy of the NOS terminator (SEQ ID NO:1182×).
High copy plasmids containing the cloned genes were digested with the restriction endonucleases (New England BioLabs Inc) according to the sites designed in the primers (Table 18, above) and cloned into binary vectors according to Table 19, below.
Binary Vectors Used for Cloning:
The plasmid pPI was constructed by inserting a synthetic poly-(A) signal sequence, originating from pGL3 basic plasmid vector (Promega, Acc No U47295; by 4658-4811) into the HindIII restriction site of the binary vector pBI101.3 (Clontech, Acc. No. U12640). pGI (pBXYN) (FIG. 1) is 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:1182) (Vancanneyt. G, et al MGG 220, 245-50, 1990). pGI was used to clone the polynucleotide sequences, initially under the control of 35S promoter [Odell, J T, et al. Nature 313, 810-812 (28 Feb. 1985); SEQ ID NO:1184.
The modified pGI vector (pQXYN) is a modified version of the pGI vector in which the cassette is inverted between the left and right borders so the gene and its corresponding promoter are close to the right border and the NPTII gene is close to the left border.







TABLE 19







Restriction enzyme sites used to clone


the identified genes into binary vector













Restriction
Restriction





enzymes used
enzymes used
Restriction




for cloning
for cloning
enzymes used




into binary
into binary
for digesting


Gene
Binary
vector-
vector-
the binary


name
vector
FORWARD
REVERSE
vector





BDL62
pQXYN
SalI
SacI
SalI, SacI


BDL75
pQXYN
SalI
EcoRI
SalI, EcoRI


BDL79
pQXYN
XbaI
SmaI
XbaI, Ecl136II


BDL81
pQXYN
SalI
SacI
SalI, SacI


BDL83
pQXYN
SalI
EcoRI
SalI, EcoRI


BDL117
pQXYN
SmaI
SmaI
SmaI, Ecl136II


BDL118
pQXYN
SmaI
SmaI
SmaI, Ecl136II


BDL138
pQXYN
SalI
EcoRI
SalI, EcoRI


BDL140
pQXYN
XbaI
SacI
XbaI, SacI


BDL147
pQXYN
SalI
EcoRI
SalI, EcoRI


BDL149
pQXYN
SalI
EcoRI
SalI, EcoRI


BDL152
pQXYN
XbaI
SacI
XbaI, SacI


BDL153
pQXYN
SalI
SmaI
SalI, Ecl136II


BDL154
pQXYN
SalI
SacI
SalI, SacI


BDL155
pQXYN
SalI
EcoRI
SalI, EcoRI


BDL156
pQXYN
SalI
SacI
SacI, SalI


BDL157
pQXYN
SalI
SacI
SalI, SacI


BDL158
pQXYN
XbaI
SmaI
XbaI, Ecl136II


BDL160
pQXYN
SalI
EcoRI
SalI, EcoRI


BDL162
pQXYN
SalI
EcoRI
SalI, EcoRI


BDL167
pQXYN
SalI
EcoRI
SalI, EcoRI


BDL168
pQXYN
XbaI
SmaI
XbaI, Ecl136II


BDL169
pQXYN
SalI
EcoRI
SalI, EcoRI


BDL171
pQXYN
XbaI
SacI
XbaI, SacI


BDL173
pQXYN
XbaI
SmaI
XbaI, Ecl136II


BDL174
pQXYN
SalI
SacI
SalI, SacI


BDL176
pQXYN
SmaI
SmaI
SmaI, Ecl136II


BDL177
pQXYN
SalI
SacI
SalI, SacI


BDL181
pQXYN
SalI
SacI
SalI, SacI


BDL182
pQXYN
SalI
SacI
SalI, SacI


BDL183
pQXYN
SalI
EcoRI
SalI, EcoRI


BDL186
pQXYN
SalI
SacI
SalI, SacI


BDL187
pQXYN
SalI
SmaI
SalI, Ecl136II


BDL188
pQXYN
XbaI
SmaI
XbaI, Ecl136II


BDL189
pQXYN
SmaI
BamHI
SmaI, Ecl136II


BDL190
pQXYN
SalI
EcoRI
SalI, EcoRI


BDL192
pQXYN
SalI
EcoRI
SalI, EcoRI


BDL193
pQXYN
XbaI
SacI
XbaI, SacI


BDL194
pQXYN
EcoRV
EcoRV
SmaI, Ecl136II


BDL196
pQXYN
SalI
EcoRI
SalI, EcoRI


BDL197
pQXYN
SalI
EcoRI
SalI, EcoRI


BDL201
pQXYN
SalI
EcoRI
SalI, EcoRI


BDL203
pQXYN
SalI
EcoRI
SalI, EcoRI


BDL220
pQXYN
SalI
EcoRI
SalI, EcoRI


BDL221
pQXYN
SalI
EcoRI
SalI, EcoRI


BDL222
pQXYN
SalI
EcoRI
SalI, EcoRI


BDL223
pQXYN
SalI
EcoRI
SalI, EcoRI


BDL229
pQXYN
SalI
EcoRI
SalI, EcoRI


BDL230
pQXYN
SmaI
SmaI
SmaI, Ecl136II


BDL231
pQXYN
SalI
EcoRI
SalI, EcoRI


BDL235
pQXYN
SalI
SmaI
SalI, Ecl136II


BDL242
pQXYN
SalI
EcoRI
SalI, EcoRI


BDL245
pQXYN
SalI
SmaI
SalI, Ecl136II


BDL247
pQXYN
SmaI
SacI
SmaI, SacI


BDL248
pQXYN
SalI
EcoRI
SalI, EcoRI


BDL250
pQXYN
SalI
EcoRI
SalI, EcoRI


BDL49
pQXYN
EcoRV
SacI
SmaI, SacI


BDL58
pQXYN
SalI
EcoRI
SalI, EcoRI


BDL63
pQXYN
SalI
SacI
SalI, SacI


BDL64
pQXYN
SalI
XbaI
SalI, Ecl136II


BDL85
pQXYN
SalI
EcoRI
SalI, EcoRI


BDL88
pQXYN
SalI
EcoRI
SalI, EcoRI


BDL90
pQXYN
XbaI
SalI
SalI, Ecl136II


BDL94
pQXYN
XbaI
SmaI
xbaI, Ecl136II


BDL102
pQXYN
SalI
EcoRI
SalI, EcoRI


BDL224
pQXYN
XbaI
EcoRI
XbaI, EcoRI


BDL225
pQXYN
SalI
EcoRI
SalI, EcoRI


BDL226
pQXYN
EcoRV
EcoRV
SmaI, Ecl136II


BDL227
pQXYN
SalI
SmaI
SalI, Ecl136II


BDL228
pQXYN
SalI
EcoRI
SalI, EcoRI


BDL232
pQXYN
XbaI
EcoRI
XbaI, EcoRI


BDL233
pQXYN
SalI
EcoRI
SalI, EcoRI


BDL234
pQXYN
SalI
SmaI
SalI, Ecl136II


BDL237
pQXYN
SalI
SacI
SalI, SacI


BDL238
pQXYN
SalI
EcoRI
SalI, EcoRI


BDL240
pQXYN
SalI
SacI
SalI, SacI


BDL241
pQXYN
XbaI
SmaI
XbaI, Ecl136II


BDL249
pQXYN
SalI
EcoRI
SalI, EcoRI


BDL252
pQXYN
XbaI
SmaI
XbaI, Ecl136II


BDL47
pQXYN
XbaI
SmaI
XbaI, Ecl136II


BDL48
pQXYN
SalI
EcoRI
SalI, EcoRI





Table 19.













TABLE 20







Genes cloned from cDNA libraries or genomic DNA in a High copy number plasmid










Gene
Amplified from
Polynucleotide
Polypeptide












Name
High copy plasmid
Organism
Origin
SEQ ID NO:
SEQ ID NO:





BDL62
pGXN
Arabidopsis thaliana
RNA
847
108



(pKG + Nos + 35S)
ND


BDL75
pGXN
Arabidopsis thaliana
RNA
848
109



(pKG + Nos + 35S)
ND


BDL79
pKS(Pks_J)
Arabidopsis thaliana
RNA
849
110




ND


BDL81
pGXN
Arabidopsis thaliana
RNA
850
111



(pKG + Nos + 35S)
ND


BDL83
pGXN
Arabidopsis thaliana
RNA
851
112



(pKG + Nos + 35S)
ND


BDL117
Topo B
Arabidopsis thaliana
RNA
852
926




ND


BDL118
Topo B
Arabidopsis thaliana
RNA
853
114




ND


BDL138
pGXN
Arabidopsis thaliana
RNA
854
116



(pKG + Nos + 35S)
ND


BDL140
pGXN
Arabidopsis thaliana
RNA
855
117



(pKG + Nos + 35S)
ND


BDL147
pGXN
Arabidopsis thaliana
RNA
856
118



(pKG + Nos + 35S)
ND


BDL149
pGXN
Arabidopsis thaliana
RNA
857
119



(pKG + Nos + 35S)
ND


BDL152
pGXN
Arabidopsis thaliana
RNA
858
120



(pKG + Nos + 35S)
ND


BDL153
pKS(Pks_J)
Arabidopsis thaliana
RNA
859
121




ND


BDL154
pGXN
Arabidopsis thaliana
RNA
860
122



(pKG + Nos + 35S)
ND


BDL155
pGXN
Arabidopsis thaliana
RNA
861
123



(pKG + Nos + 35S)
ND


BDL156
pGXN
Arabidopsis thaliana
RNA
862
124



(pKG + Nos + 35S)
ND


BDL157
pGXN
Arabidopsis thaliana
RNA
863
125



(pKG + Nos + 35S)
ND


BDL158
pKS(Pks_J)
Arabidopsis thaliana
RNA
864
126




ND


BDL160
pGXN
Arabidopsis thaliana
RNA
865
127



(pKG + Nos + 35S)
ND


BDL162
pGXN
Arabidopsis thaliana
RNA
866
128



(pKG + Nos + 35S)
ND


BDL167
pGXN
Arabidopsis thaliana
RNA
867
196



(pKG + Nos + 35S)
ND


BDL168
pKS(Pks_J)
Arabidopsis thaliana
RNA
868
132




ND


BDL169
pGXN
Arabidopsis thaliana
RNA
869
133



(pKG + Nos + 35S)
ND


BDL171
pGXN
Arabidopsis thaliana
RNA
870
927



(pKG + Nos + 35S)
ND


BDL173
pKS(Pks_J)
Arabidopsis thaliana
RNA
871
135




ND


BDL174
pGXN
Arabidopsis thaliana
RNA
872
136



(pKG + Nos + 35S)
ND


BDL176
pKS(Pks_J)
Arabidopsis thaliana
RNA
873
137




ND


BDL177
pGXN
Arabidopsis thaliana
RNA
874
138



(pKG + Nos + 35S)
ND


BDL181
pGXN
Arabidopsis thaliana
RNA
875
139



(pKG + Nos + 35S)
ND


BDL182
pGXN
Arabidopsis thaliana
RNA
876
140



(pKG + Nos + 35S)
ND


BDL183
pGXN
Arabidopsis thaliana
RNA
877
141



(pKG + Nos + 35S)
ND


BDL186
pGXN
Arabidopsis thaliana
RNA
878
928



(pKG + Nos + 35S)
ND


BDL187
pKS(Pks_J)
Arabidopsis thaliana
RNA
879
929




ND


BDL188
pKS(Pks_J)
Arabidopsis thaliana
RNA
880
144




ND


BDL189
Topo B
Arabidopsis thaliana
RNA
881
145




ND


BDL190
pGXN
Arabidopsis thaliana
RNA
882
146



(pKG + Nos + 35S)
ND


BDL192
pGXN
Arabidopsis thaliana
RNA
883
147



(pKG + Nos + 35S)
ND


BDL193
pGXN
Arabidopsis thaliana
RNA
884
148



(pKG + Nos + 35S)
ND


BDL194
pKS(Pks_J)
Arabidopsis thaliana
RNA
885
149




ND


BDL196
pGXN
Arabidopsis thaliana
RNA
886
150



(pKG + Nos + 35S)
ND


BDL197
pGXN
Arabidopsis thaliana
RNA
887
151



(pKG + Nos + 35S)
ND


BDL201
pGXN
Arabidopsis thaliana
RNA
888
153



(pKG + Nos + 35S)
ND


BDL203
pGXN
Arabidopsis thaliana
RNA
889
154



(pKG + Nos + 35S)
ND


BDL220
pGXN
Arabidopsis thaliana
RNA
890
156



(pKG + Nos + 35S)
ND


BDL221
pGXN
Arabidopsis thaliana
RNA
891
157



(pKG + Nos + 35S)
ND


BDL222
pGXN
Arabidopsis thaliana
RNA
892
158



(pKG + Nos + 35S)
ND


BDL223
pGXN
Arabidopsis thaliana
RNA
893
159



(pKG + Nos + 35S)
ND


BDL229
pGXN
Arabidopsis thaliana
RNA
894
160



(pKG + Nos + 35S)
ND


BDL230
pKS(Pks_J)
Arabidopsis thaliana
RNA
895
161




ND


BDL231
pGXN
Arabidopsis thaliana
RNA
896
162



(pKG + Nos + 35S)
ND


BDL235
pKS(Pks_J)
Arabidopsis thaliana
RNA
897
163




ND


BDL242
pGXN
Arabidopsis thaliana
RNA
898
164



(pKG + Nos + 35S)
ND


BDL245
pKS(Pks_J)
Arabidopsis thaliana
RNA
899
166




ND


BDL247
pKS(Pks_J)
Arabidopsis thaliana
RNA
900
167




ND


BDL248
pGXN
Arabidopsis thaliana
RNA
901
168



(pKG + Nos + 35S)
ND


BDL250
pGXN
Arabidopsis thaliana
RNA
902
169



(pKG + Nos + 35S)
ND


BDL49
pKS(Pks_J)
Arabidopsis thaliana
RNA
903
170




ND


BDL58
pGXN
Arabidopsis thaliana
RNA
904
171



(pKG + Nos + 35S)
ND


BDL63
pGXN
Arabidopsis thaliana
RNA
905
172



(pKG + Nos + 35S)
ND


BDL64
Topo B
Arabidopsis thaliana
RNA
906
173




ND


BDL85
pGXN
Arabidopsis thaliana
RNA
907
175



(pKG + Nos + 35S)
ND


BDL88
pGXN
RICE Oryza sativa
RNA
908
176



(pKG + Nos + 35S)
L. Japonica ND


BDL90
Topo B
RICE Oryza sativa
gDNA
909
Non Coding




L. Japonica ND


polynucleotide


BDL94
pGXN
Rice Japonica ND
gDNA
910
930



(pKG + Nos + 35S)
leaves


BDL102
pGXN
MAIZE Zea mays L.
RNA
911
178



(pKG + Nos + 35S)
ND


BDL224
pGXN
Arabidopsis thaliana
RNA
912
179



(pKG + Nos + 35S)
ND


BDL225
pGXN
Arabidopsis thaliana
RNA
913
180



(pKG + Nos + 35S)
ND


BDL226
pKS(Pks_J)
Arabidopsis thaliana
RNA
914
181




ND


BDL227
Topo B
Arabidopsis thaliana
RNA
915
182




ND


BDL228
pGXN
CASTOR BEAN
RNA
916
931



(pKG + Nos + 35S)
Ricinus communis L.




ND


BDL232
pGXN
Arabidopsis thaliana
RNA
917
184



(pKG + Nos + 35S)
ND


BDL233
pGXN
Arabidopsis thaliana
RNA
918
932



(pKG + Nos + 35S)
ND


BDL234
pKS(Pks_J)
Arabidopsis thaliana
RNA
919
186




ND


BDL237
pGXN
Arabidopsis thaliana
RNA
920
187



(pKG + Nos + 35S)
ND


BDL238
pGXN
Arabidopsis thaliana
RNA
921
188



(pKG + Nos + 35S)
ND


BDL240
pGXN
Arabidopsis thaliana
RNA
922
189



(pKG + Nos + 35S)
ND


BDL241
pKS(Pks_J)
Arabidopsis thaliana
RNA
923
190




ND


BDL249
pGXN
Arabidopsis thaliana
RNA
924
191



(pKG + Nos + 35S)
ND


BDL252
pKS(Pks_J)
Arabidopsis thaliana
RNA
925
193




ND











BDL47
High copy plasmid
Synthetic DNA
845
106



pMA












BDL48
pGXN
Arabidopsis thaliana
RNA
846
107



(pKG + Nos + 35S)
ND











BDL200
High copy plasmid
Synthetic DNA
 47
152





Table 20: Cloned and synthetic genes are provided along with the sequence identifiers of their polynucleotides and polypeptides. Also provided are the source organism, tissue and the cloning vectors.


ND = not a determined ecotype.






Selected DNA sequences were synthesized by a commercial supplier GeneArt, GmbH [Hypertext Transfer Protocol://World Wide Web(dot)geneart(dot)com/)]. Synthetic DNA is designed in silico. Suitable restriction enzymes sites were added to the cloned sequences at the 5′ end and at the 3′ end to enabled later cloning into the pBXYN/pQXYN binary downstream of the CaMV 35S promoter (SEQ ID NO:1184). For example BDL47 (SEQ ID NO:1 was synthesized and the XbaI and SmaI restriction enzymes were added to the synthetic sequence in order to facilitate cloning.
For 7 genes, namely BDL117, BDL171, BDL186, BDL187, BDL94, BDL228 and BDL233, the protein translation of the amplified cDNA sequence did not match the initial bioinformatics prediction of the protein sequences. The polypeptide sequences encoded by the cloned sequence were predicted and are provided in SEQ ID NO: 926-932.
Example 8
Producing Transgenic Arabidopsis Plants Expressing the Identified Polynucleotides of the Invention
Materials and Experimental Methods
Plant Transformation—
The Arabidopsis thaliana var Columbia (T0 plants) were transformed according to the Floral Dip procedure [Clough S J, Bent A F. (1998) Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 16(6): 735-43; and Desfeux C, Clough S J, Bent A F. (2000) Female reproductive tissues are the primary targets of Agrobacterium-mediated transformation by the Arabidopsis floral-dip method. Plant Physiol. 123(3): 895-904] with minor modifications. Briefly, Arabidopsis thaliana Columbia (Col0) T0 plants were sown in 250 ml pots filled with wet peat-based growth mix. The pots were covered with aluminum foil and a plastic dome, kept at 4° C. for 3-4 days, then uncovered and incubated in a growth chamber at 18-24° C. under 16/8 hours light/dark cycles. The T0 plants were ready for transformation six days before anthesis.
Single colonies of Agrobacterium carrying the binary vectors harboring the seed oil genes were cultured in LB medium supplemented with kanamycin (50 mg/L) and gentamycin (50 mg/L). The cultures were incubated at 28° C. for 48 hours under vigorous shaking and centrifuged at 4000 rpm for 5 minutes. The pellets comprising Agrobacterium cells were resuspended in a transformation medium which contained half-strength (2.15 g/L) Murashige-Skoog (Duchefa); 0.044 μM benzylamino purine (Sigma); 112 μL B5 Gambourg vitamins (Sigma); 5% sucrose; and 0.2 ml/L Silwet L-77 (OSI Specialists, CT) in double-distilled water, at pH of 5.7.
Transformation of T0 plants was performed by inverting each plant into an Agrobacterium suspension such that the above ground plant tissue was submerged for 3-5 seconds. Each inoculated T0 plant was immediately placed in a plastic tray, then covered with clear plastic dome to maintain humidity and was kept in the dark at room temperature for 18 hours to facilitate infection and transformation. Transformed (transgenic) plants were then uncovered and transferred to a greenhouse for recovery and maturation. The transgenic T0 plants were grown in the greenhouse for 3-5 weeks until siliques were brown and dry, then seeds were harvested from plants and kept at room temperature until sowing.
For generating T1 and T2 transgenic plants harboring the genes, seeds collected from transgenic T0 plants were surface-sterilized by soaking in 70% ethanol for 1 minute, followed by soaking in 5% sodium hypochlorite and 0.05% triton for 5 minutes. The surface-sterilized seeds were thoroughly washed in sterile distilled water then placed on culture plates containing half-strength Murashig-Skoog (Duchefa); 2% sucrose; 0.8% plant agar; 50 mM kanamycin; and 200 mM carbenicylin (Duchefa). The culture plates were incubated at 4° C. for 48 hours then transferred to a growth room at 25° C. for an additional week of incubation. Vital T1 Arabidopsis plants were transferred to a fresh culture plates for another week of incubation. Following incubation the T1 plants were removed from culture plates and planted in growth mix contained in 250 ml pots. The transgenic plants were allowed to grow in a greenhouse to maturity. Seeds harvested from T1 plants were cultured and grown to maturity as T2 plants under the same conditions as used for culturing and growing the T1 plants.
Example 9
Improved Transgenic Plant Performance
To analyze the effect of expression of the isolated polynucleotides in plants, plants were grown in pots with an adequate amount of nutrients and water. The plants were analyzed for their overall size, growth rate, time to inflorescence emergence (bolting) and flowering, seed yield, weight of 1,000 seeds, 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 with an empty vector or expressing the uidA reporter gene (GUS-Intron) under the same promoter were used as control.
Parameters were measured as described in Examples 2, 3 and 4 above.
Statistical Analyses—
Plant growth rate, plant area, time to bolt, time to flower, weight of 1,000 seeds, seed yield, oil yield, dry matter, and harvest index area data were analyzed using t-test. To identify outperforming genes and constructs, results from mix of transformation events or independent events were analyzed. For gene versus control analysis t-test was applied, using significance of p<0.1. The JMP statistics software package was used (Version 5.2.1, SAS Institute Inc., Cary, N.C., USA).
Experimental Results
Plants expressing the polynucleotides of the invention were assayed for a number of commercially desired traits. Results are presented in Tables 21 and 22.
Analysis of Plants in Tissue Culture Assay—
Tables 21 and 22, hereinbelow, depict analyses of seed yield in plants overexpressing the polynucleotides of the invention under the regulation of the constitutive 35S (SEQ ID NO:1184) or At6669 (SEQ ID NO:1183) promoters. In cases where a certain event appears more than once, the event was tested in several independent experiments.







TABLE 21







Results obtained in a tissue culture assay



















Leaf
Leaf
Leaf
Roots
Roots
Roots
Roots





Area
Area
Area
Length
Length
Length
Coverage


Gene
Ev.
Par.
TP1
TP2
TP3
TP1
TP2
TP3
TP1



















BDL102
10471.1
P

0.24

0.01
0.02
0.13
0.05


BDL102
10471.1
Av

1.15

1.59
1.39
1.23
2.34


BDL102
10471.3
P

0.6

0.03
0.01
0.09
0.01


BDL102
10471.3
Av

1.1

1.43
1.37
1.24
1.72


BDL102
10472.1
P



0.04
0.15

0.03


BDL102
10472.1
Av



1.27
1.1

1.54


BDL102
10474.2
P
<0.01
<0.01
<0.01

0.23
0.13


BDL102
10474.2
Av
2.02
1.61
1.51

1.1
1.13


BDL102
10474.6
P

0.13
0.29


BDL102
10474.6
Av

1.21
1.14


BDL118
10481.2
P
<0.01
0.01
0.01


0.46


BDL118
10481.2
Av
2.02
1.91
2


1.1


BDL118
10481.5
P

0.2
0.01


BDL118
10481.5
Av

1.15
1.29


BDL118
10484.3
P
<0.01
<0.01
<0.01


BDL118
10484.3
Av
1.51
1.41
1.58


BDL140
10421.3
P
0.03
0.01
0.05



0.39


BDL140
10421.3
Av
1.61
1.72
1.68



1.18


BDL140
10423.1
P
0.21
0.09
0.28
0.01
0.11

0.19


BDL140
10423.1
Av
1.24
1.31
1.21
1.38
1.21

1.28


BDL140
10424.4
P
<0.01
<0.01
0.01


BDL140
10424.4
Av
1.43
1.48
1.62


BDL152
10431.4
P
0.15
0.12
0.12


BDL152
10431.4
Av
1.17
1.18
1.18


BDL152
10432.5
P
0.37
0.01

0.07
0.14

0.35


BDL152
10432.5
Av
1.16
1.28

1.22
1.13

1.25


BDL152
10434.1
P

0.43


BDL152
10434.1
Av

1.12


BDL152
10434.4
P

0.08

0.04
0.01
<0.01
0.08


BDL152
10434.4
Av

1.18

1.52
1.48
1.31
2.33


BDL153
10142.2
P



<0.01
<0.01

0.03


BDL153
10142.2
Av



1.83
1.43

1.99


BDL153
10144.1
P
<0.01
0.02
0.07

0.31
0.15
0.7


BDL153
10144.1
Av
1.3
1.31
1.38

1.13
1.12
1.1


BDL153
10144.4
P






0.03


BDL153
10144.4
Av






1.28


BDL154
10703.1
P



0.09
0.14
0.05
0.09


BDL154
10703.1
Av



1.36
1.14
1.2
1.77


BDL154
10703.11
P



0.01
0.17
0.3
0.5


BDL154
10703.11
Av



1.37
1.21
1.16
1.18


BDL154
10703.6
P






0.42


BDL154
10703.6
Av






1.23


BDL154
10703.1
P
<0.01
<0.01
<0.01

0.11
0.02


BDL154
10703.1
Av
1.34
1.5
1.61

1.14
1.18


BDL154
10703.5
P

0.46
0.36

0.02
0.02
0.21


BDL154
10703.5
Av

1.1
1.16

1.47
1.39
1.52


BDL154
10703.6
P



0.24
0.06
0.07
0.15


BDL154
10703.6
Av



1.19
1.33
1.24
1.59


BDL155
9994.3
P
0.22


BDL155
9994.3
Av
1.15


BDL156
10853.6
P


0.08


BDL156
10853.6
Av


1.12


BDL156
10852.6
P


0.15


BDL156
10852.6
Av


1.15


BDL156
10853.6
P

0.07
0.01


0.24


BDL156
10853.6
Av

1.34
1.71


1.22


BDL156
10854.4
P
0.11
0.11
<0.01


0.01


BDL156
10854.4
Av
1.13
1.26
1.66


1.24


BDL156
10855.3
P


0.01


0.1


BDL156
10855.3
Av


1.35


1.2


BDL158
9973.3
P



0.01
0.03
0.17
0.09


BDL158
9973.3
Av



1.21
1.27
1.1
1.21


BDL158
9971.3
P
0.42
0.32
0.27


BDL158
9971.3
Av
1.13
1.13
1.11


BDL158
9973.1
P



0.08
0.24
0.17
0.02


BDL158
9973.1
Av



1.27
1.16
1.13
1.37


BDL158
9973.3
P



<0.01
0.02
0.06
0.01


BDL158
9973.3
Av



1.66
1.39
1.17
2.06


BDL158
9974.2
P
<0.01
<0.01
0.09


BDL158
9974.2
Av
1.68
1.58
1.23


BDL158
9974.3
P
<0.01
<0.01
0.13


BDL158
9974.3
Av
1.76
1.62
1.58


BDL158
9971.3
P

0.07
0.15


0.02


BDL158
9971.3
Av

1.22
1.2


1.15


BDL158
9973.1
P
0.01
0.41
0.03
<0.01
<0.01
0.08
0.02


BDL158
9973.1
Av
1.28
1.11
1.35
1.49
1.35
1.26
1.8


BDL158
9973.3
P



<0.01
<0.01
<0.01
0.02


BDL158
9973.3
Av



1.36
1.52
1.39
1.51


BDL160
10011.5
P
0.01
0.22
0.15


BDL160
10011.5
Av
1.41
1.2
1.26


BDL160
10011.5
P






0.45


BDL160
10011.5
Av






1.25


BDL160
10011.7
P



0.04


0.01


BDL160
10011.7
Av



1.34


1.95


BDL160
10013.1
P


0.53


BDL160
10013.1
Av


1.11


BDL160
10014.9
P
0.2
0.39
0.61


BDL160
10014.9
Av
1.17
1.15
1.11


BDL160
10015.2
P

0.07
0.12


BDL160
10015.2
Av

1.19
1.22


BDL167
10042.3
P
<0.01


BDL167
10042.3
Av
1.3


BDL167
10043.1
P
<0.01
0.02
0.14


BDL167
10043.1
Av
1.37
1.18
1.2


BDL167
10043.2
P
0.06
0.13
0.03


BDL167
10043.2
Av
1.61
1.29
1.23


BDL167
10043.3
P
0.01
0.01
<0.01


0.01


BDL167
10043.3
Av
1.93
1.58
1.61


1.25


BDL167
10044.2
P
<0.01
0.01
0.02
0.05
0.04
0.03


BDL167
10044.2
Av
1.63
1.43
1.43
1.28
1.23
1.23


BDL167
10043.1
P
<0.01
<0.01
0.15

<0.01
0.12
0.47


BDL167
10043.1
Av
1.56
1.53
1.43

1.22
1.1
1.1


BDL167
10044.2
P



<0.01
<0.01

<0.01


BDL167
10044.2
Av



1.45
1.18

2.16


BDL168
9881.3
P



0.15


0.04


BDL168
9881.3
Av



1.23


1.67


BDL168
9881.4
P



<0.01
<0.01
<0.01
0.02


BDL168
9881.4
Av



1.89
1.72
1.38
2.28


BDL168
9882.1
P



0.01
0.01
0.04
<0.01


BDL168
9882.1
Av



1.9
1.68
1.29
2.57


BDL168
9883.3
P






0.2


BDL168
9883.3
Av






1.38


BDL168
9884.1
P



<0.01
<0.01
0.02
0.02


BDL168
9884.1
Av



2.05
1.73
1.38
2.61


BDL169
10744.2
P



0.08
0.02
0.08
0.29


BDL169
10744.2
Av



1.24
1.23
1.19
1.11


BDL169
10747.1
P



0.03
0.09
0.13


BDL169
10747.1
Av



1.15
1.12
1.11


BDL169
10747.5
P



0.06
0.01
<0.01
0.12


BDL169
10747.5
Av



1.62
1.59
1.4
1.73


BDL171
10661.2
P

0.25
0.28
<0.01
<0.01
<0.01
0.03


BDL171
10661.2
Av

1.19
1.23
1.62
1.65
1.39
1.8


BDL171
10661.5
P
0.02
0.04
0.12


BDL171
10661.5
Av
1.45
1.35
1.24


BDL171
10664.1
P
0.31
0.3
0.25
0.15
0.27
0.31
0.44


BDL171
10664.1
Av
1.17
1.18
1.23
1.23
1.15
1.14
1.17


BDL173
9951.2
P

0.18


0.42

0.3


BDL173
9951.2
Av

1.17


1.11

1.17


BDL173
9952.1
P



<0.01
<0.01
<0.01
<0.01


BDL173
9952.1
Av



2.17
1.99
1.45
3.32


BDL173
9952.2
P

0.35

<0.01
<0.01
0.01
0.02


BDL173
9952.2
Av

1.12

1.72
1.63
1.24
2.07


BDL174
11082.1
P




0.2
0.06
0.42


BDL174
11082.1
Av




1.14
1.17
1.18


BDL174
11083.1
P
<0.01
<0.01
0.07
<0.01
<0.01
0.01
0.01


BDL174
11083.1
Av
1.64
1.32
1.2
1.78
1.67
1.39
1.66


BDL174
11083.2
P
0.04
0.17
0.12

0.14
0.18


BDL174
11083.2
Av
1.2
1.16
1.25

1.34
1.32


BDL174
11084.1
P
<0.01
<0.01
<0.01

0.03
0.1
0.03


BDL174
11084.1
Av
2.56
2.29
2.1

1.31
1.31
1.68


BDL174
11085.1
P

0.41
0.07
<0.01
<0.01
<0.01
<0.01


BDL174
11085.1
Av

1.11
1.24
1.95
2.33
1.98
1.71


BDL174
11083.2
P
<0.01
<0.01
0.01
0.3


0.31


BDL174
11083.2
Av
1.41
1.35
1.21
1.16


1.27


BDL174
11084.1
P



0.15


<0.01


BDL174
11084.1
Av



1.22


2.13


BDL174
11085.1
P



<0.01
0.01
0.04
0.01


BDL174
11085.1
Av



2.04
1.36
1.16
2.33


BDL176
9891.4
P
0.1
0.05
0.06


BDL176
9891.4
Av
1.1
1.17
1.36


BDL176
9893.2
P
0.04
<0.01
0.27


BDL176
9893.2
Av
1.28
1.26
1.22


BDL176
9893.3
P



0.38


BDL176
9893.3
Av



1.13


BDL176
9893.2
P



0.15


BDL176
9893.2
Av



1.2


BDL176
9893.3
P
0.05
0.01

0.36


0.16


BDL176
9893.3
Av
1.42
1.34

1.16


1.42


BDL177
10521.3
P





0.23


BDL177
10521.3
Av





1.16


BDL177
10524.2
P



0.13


BDL177
10524.2
Av



1.16


BDL181
11293.6
P


0.32


BDL181
11293.6
Av


1.18


BDL181
11294.7
P


0.36


BDL181
11294.7
Av


1.13


BDL181
11293.1
P


0.6


BDL181
11293.1
Av


1.11


BDL181
11293.6
P

0.01
<0.01


BDL181
11293.6
Av

1.2
1.27


BDL181
11294.7
P




0.16
0.17


BDL181
11294.7
Av




1.1
1.1


BDL182
10691.8
P
0.03
0.07
0.16


BDL182
10691.8
Av
1.32
1.24
1.18


BDL182
10692.2
P
0.17
0.08
0.19


BDL182
10692.2
Av
1.19
1.27
1.2


BDL182
10693.3
P
0.01
0.07
0.1
0.17
0.1
0.11


BDL182
10693.3
Av
1.55
1.44
1.31
1.17
1.17
1.1


BDL182
10693.5
P
0.04
0.24
0.12
<0.01
<0.01
<0.01
0.48


BDL182
10693.5
Av
1.33
1.15
1.22
1.39
1.33
1.21
1.1


BDL183
9943.4
P



0.02
0.11

0.02


BDL183
9943.4
Av



1.26
1.17

1.61


BDL183
9944.4
P



0.01
<0.01
0.02
0.36


BDL183
9944.4
Av



1.24
1.36
1.21
1.26


BDL189
11351.2
P
0.05


BDL189
11351.2
Av
1.17


BDL189
11353.3
P
0.22
0.04
0.11


BDL189
11353.3
Av
1.19
1.2
1.17


BDL189
11353.5
P
0.26


BDL189
11353.5
Av
1.1


BDL189
11355.4
P
0.12
0.12
0.1


BDL189
11355.4
Av
1.12
1.11
1.11


BDL189
11356.7
P
0.27


BDL189
11356.7
Av
1.11


BDL196
10242.2
P
0.02
0.09

0.05
0.03
0.09


BDL196
10242.2
Av
1.18
1.13

1.29
1.28
1.16


BDL196
10243.4
P
0.09
0.25
0.24
0.13
0.05
0.17
<0.01


BDL196
10243.4
Av
1.16
1.23
1.24
1.11
1.25
1.15
1.74


BDL196
10244.1
P
<0.01
0.07


0.23

0.21


BDL196
10244.1
Av
1.21
1.19


1.22

1.33


BDL196
10243.3
P



0.02


0.68


BDL196
10243.3
Av



1.16


1.1


BDL196
10243.4
P

0.01
<0.01


0.23


BDL196
10243.4
Av

1.24
1.49


1.12


BDL197
11362.2
P


0.14


BDL197
11362.2
Av


1.17


BDL197
11363.1
P





0.04


BDL197
11363.1
Av





1.17


BDL197
11363.6
P


0.15


BDL197
11363.6
Av


1.17


BDL197
11364.1
P

0.08
0.01


0.09


BDL197
11364.1
Av

1.14
1.42


1.15


BDL197
11364.5
P

0.09
0.04


BDL197
11364.5
Av

1.12
1.25


BDL197
11363.6
P

0.2
0.07


BDL197
11363.6
Av

1.11
1.19


BDL201
9961.2
P
0.02
0.18
0.39


BDL201
9961.2
Av
1.41
1.18
1.18


BDL201
9961.3
P
0.08
0.13


BDL201
9961.3
Av
1.21
1.28


BDL201
9961.4
P



0.06
0.15
0.43
0.02


BDL201
9961.4
Av



1.37
1.25
1.11
1.76


BDL201
9964.3
P



<0.01
0.01

0.02


BDL201
9964.3
Av



1.34
1.24

1.84


BDL220
10331.2
P
<0.01
<0.01
0.15


BDL220
10331.2
Av
1.75
1.37
1.15


BDL220
10331.5
P
0.01
0.02
0.05


BDL220
10331.5
Av
1.48
1.64
1.75


BDL220
10334.2
P
<0.01
<0.01
0.04


BDL220
10334.2
Av
1.58
1.37
1.21


BDL221
10341.3
P
0.13
0.13
0.06


BDL221
10341.3
Av
1.26
1.19
1.44


BDL221
10341.4
P
<0.01
0.01
<0.01


BDL221
10341.4
Av
1.57
1.3
1.35


BDL221
10343.3
P

0.11
0.06
0.01
<0.01
<0.01
0.13


BDL221
10343.3
Av

1.1
1.16
1.37
1.4
1.4
1.55


BDL221
10341.1
P
0.26
0.45
0.19


BDL221
10341.1
Av
1.18
1.15
1.26


BDL221
10342.1
P
<0.01
<0.01
0.02
<0.01
<0.01
<0.01
<0.01


BDL221
10342.1
Av
1.9
1.46
1.32
2.02
2.08
1.68
4.31


BDL221
10343.1
P
0.18
0.05
0.07
0.26
<0.01
<0.01
<0.01


BDL221
10343.1
Av
1.3
1.51
1.58
1.12
1.35
1.32
1.67


BDL221
10343.3
P
<0.01
<0.01
<0.01
<0.01
<0.01
<0.01
<0.01


BDL221
10343.3
Av
2.7
1.8
1.59
1.75
2.12
1.87
2.4


BDL221
10343.4
P
0.05
0.11
0.19
0.01
<0.01
0.05
0.02


BDL221
10343.4
Av
1.88
1.56
1.57
1.46
1.65
1.49
2.07


BDL221
10344.3
P
0.02
0.01
0.05

0.1
0.18
<0.01


BDL221
10344.3
Av
1.9
1.61
1.56

1.14
1.12
1.63


BDL223
10793.5
P





0.11


BDL223
10793.5
Av





1.14


BDL223
10793.8
P



0.21
0.17
0.08


BDL223
10793.8
Av



1.18
1.17
1.18


BDL223
10796.2
P
<0.01
0.06


BDL223
10796.2
Av
1.22
1.14


BDL223
10791.1
P


0.07

0.12
0.03


BDL223
10791.1
Av


1.21

1.17
1.2


BDL223
10793.3
P
0.01
0.04
0.02


0.14


BDL223
10793.3
Av
1.33
1.3
1.55


1.18


BDL223
10793.5
P




0.07
0.04


BDL223
10793.5
Av




1.14
1.18


BDL223
10793.8
P

0.08
0.08
<0.01
<0.01
<0.01
<0.01


BDL223
10793.8
Av

1.17
1.19
1.54
1.65
1.5
1.64


BDL223
10796.1
P


0.11


BDL223
10796.1
Av


1.15


BDL224
10451.3
P

0.29


BDL224
10451.3
Av

1.11


BDL224
10451.5
P


0.1


BDL224
10451.5
Av


1.15


BDL224
10451.7
P
<0.01
<0.01
0.01
0.03
0.07
0.23
0.16


BDL224
10451.7
Av
1.58
1.69
1.8
1.39
1.26
1.19
1.41


BDL226
10861.2
P





0.4


BDL226
10861.2
Av





1.1


BDL227
11491.1
P



<0.01
<0.01
0.03
0.01


BDL227
11491.1
Av



1.5
1.46
1.21
1.95


BDL227
11491.3
P
<0.01
<0.01
<0.01
0.01
<0.01
0.02
0.04


BDL227
11491.3
Av
2.12
1.6
1.42
1.64
1.65
1.56
2.26


BDL227
11491.5
P
<0.01
<0.01
0.02
<0.01
<0.01
0.01
<0.01


BDL227
11491.5
Av
1.84
1.53
1.42
1.78
1.85
1.64
2.73


BDL227
11492.5
P
<0.01
<0.01
0.01
0.26
0.03
0.04
0.01


BDL227
11492.5
Av
2.13
1.91
1.72
1.17
1.48
1.32
1.58


BDL227
11493.5
P
<0.01
<0.01
0.02
0.33
<0.01
<0.01
0.02


BDL227
11493.5
Av
1.55
1.63
1.74
1.1
1.47
1.47
1.53


BDL230
10671.3
P
<0.01
0.06
0.01


BDL230
10671.3
Av
1.36
1.44
1.81


BDL230
10671.5
P



0.33
0.49
0.46


BDL230
10671.5
Av



1.22
1.16
1.11


BDL231
11111.1
P
<0.01
<0.01
<0.01


BDL231
11111.1
Av
1.55
1.53
1.51


BDL231
11111.2
P
0.11
0.15
0.04
0.19

0.04


BDL231
11111.2
Av
1.12
1.12
1.28
1.15

1.19


BDL231
11111.3
P
<0.01
0.04
0.05


BDL231
11111.3
Av
1.35
1.26
1.37


BDL231
11112.2
P
<0.01
0.01
0.03
<0.01
<0.01
<0.01
0.01


BDL231
11112.2
Av
1.72
1.43
1.38
2.08
1.68
1.48
2.34


BDL231
11116.5
P
<0.01
<0.01
<0.01
<0.01
0.01
0.03
<0.01


BDL231
11116.5
Av
1.82
1.77
1.76
1.67
1.38
1.31
1.92


BDL231
11111.1
P
<0.01
<0.01
<0.01

0.36

0.07


BDL231
11111.1
Av
1.88
1.78
1.49

1.11

1.43


BDL231
11111.2
P
0.01
0.03
0.01
0.01
0.1

0.05


BDL231
11111.2
Av
1.66
1.6
1.45
1.28
1.15

1.51


BDL231
11111.3
P



0.01
0.26

0.53


BDL231
11111.3
Av



1.31
1.1

1.1


BDL231
11112.2
P
0.24
0.17

<0.01
<0.01

<0.01


BDL231
11112.2
Av
1.12
1.12

1.51
1.3

1.97


BDL231
11116.5
P



0.11


0.24


BDL231
11116.5
Av



1.19


1.35


BDL232
10904.1
P

0.61
0.54

0.43
0.23


BDL232
10904.1
Av

1.17
1.2

1.1
1.14


BDL232
10905.1
P



0.02
<0.01
0.05
0.02


BDL232
10905.1
Av



1.5
1.46
1.25
1.4


BDL232
10906.3
P

0.25
0.14

0.59
0.25


BDL232
10906.3
Av

1.29
1.45

1.1
1.21


BDL232
10902.2
P



<0.01
<0.01
0.06
0.01


BDL232
10902.2
Av



1.7
1.47
1.24
2.1


BDL232
10905.1
P



<0.01
0.01
0.09
0.03


BDL232
10905.1
Av



1.59
1.42
1.2
2.17


BDL233
10825.4
P



<0.01
<0.01
<0.01
<0.01


BDL233
10825.4
Av



1.47
1.45
1.35
2.01


BDL233
10822.4
P


0.14


BDL233
10822.4
Av


1.23


BDL233
10824.2
P





0.05


BDL233
10824.2
Av





1.16


BDL233
10825.3
P






0.26


BDL233
10825.3
Av






1.27


BDL233
10825.4
P


0.24
<0.01
<0.01
<0.01
0.19


BDL233
10825.4
Av


1.17
1.56
1.59
1.51
1.3


BDL235
11413.2
P



<0.01
0.01
0.03
0.18


BDL235
11413.2
Av



1.63
1.3
1.19
1.43


BDL235
11413.2
P



<0.01
<0.01
0.05
0.01


BDL235
11413.2
Av



1.57
1.45
1.29
2.12


BDL237
10892.2
P
0.16



0.28
0.12
0.09


BDL237
10892.2
Av
1.21



1.1
1.12
1.4


BDL237
10893.1
P
<0.01
0.02
0.14

0.19
0.28


BDL237
10893.1
Av
1.96
1.39
1.24

1.13
1.14


BDL237
10895.3
P
<0.01
<0.01
0.01
0.01
<0.01
<0.01
0.02


BDL237
10895.3
Av
2.2
1.99
1.9
1.84
1.97
1.79
2.09


BDL237
10896.1
P
0.19

0.49


BDL237
10896.1
Av
1.29

1.1


BDL238
10951.4
P



0.08


0.01


BDL238
10951.4
Av



1.2


1.69


BDL238
10952.3
P
0.05


BDL238
10952.3
Av
1.2


BDL238
10953.3
P






0.32


BDL238
10953.3
Av






1.5


BDL238
10954.2
P



0.05


0.59


BDL238
10954.2
Av



1.24


1.13


BDL238
10954.3
P
0.09


0.03
0.17
0.26
0.17


BDL238
10954.3
Av
1.16


1.3
1.12
1.1
1.45


BDL238
10951.4
P



0.13
0.04
0.23
0.17


BDL238
10951.4
Av



1.22
1.24
1.11
1.39


BDL238
10952.3
P



0.02
0.01
0.02
0.11


BDL238
10952.3
Av



1.44
1.43
1.37
1.54


BDL238
10954.2
P



0.02
0.08
0.17
0.22


BDL238
10954.2
Av



1.26
1.2
1.17
1.2


BDL240
10802.2
P
<0.01
0.2
0.31

0.16
0.1
0.1


BDL240
10802.2
Av
1.57
1.23
1.17

1.17
1.19
1.25


BDL240
10803.5
P
0.11
0.4
0.31


BDL240
10803.5
Av
1.4
1.11
1.16


BDL240
10806.4
P
<0.01
0.18


BDL240
10806.4
Av
1.29
1.16


BDL240
10806.6
P
0.02
0.02
0.04
0.02
0.01
0.01
0.03


BDL240
10806.6
Av
2.29
1.87
1.52
1.59
1.63
1.49
3.75


BDL241
10873.1
P






0.51


BDL241
10873.1
Av






1.2


BDL241
10874.3
P






0.32


BDL241
10874.3
Av






1.42


BDL241
10875.1
P



0.04
0.01
0.13
<0.01


BDL241
10875.1
Av



1.4
1.34
1.21
2.29


BDL241
10874.3
P
<0.01
<0.01
0.02


0.1


BDL241
10874.3
Av
1.34
1.34
1.43


1.15


BDL241
10875.1
P



<0.01
0.03
0.3
0.03


BDL241
10875.1
Av



1.32
1.29
1.16
1.52


BDL242
10731.3
P

0.03


0.06
0.18
0.11


BDL242
10731.3
Av

1.12


1.14
1.13
1.36


BDL242
10731.5
P



0.4
0.11
0.18
0.32


BDL242
10731.5
Av



1.13
1.16
1.1
1.23


BDL242
10731.2
P
0.36


BDL242
10731.2
Av
1.2


BDL242
10731.3
P
<0.01
<0.01
<0.01

0.02
<0.01
0.03


BDL242
10731.3
Av
3.13
2.79
2.3

1.26
1.27
1.65


BDL242
10731.5
P
0.06


0.05
0.05

<0.01


BDL242
10731.5
Av
1.45


1.21
1.16

1.77


BDL242
10731.7
P
<0.01
<0.01
<0.01
0.04
<0.01
<0.01
0.14


BDL242
10731.7
Av
2.48
1.8
1.61
1.36
1.41
1.3
1.72


BDL242
10737.2
P
0.03
0.04
<0.01


0.47


BDL242
10737.2
Av
2.07
1.86
1.9


1.1


BDL247
10911.1
P



<0.01
0.08
0.23


BDL247
10911.1
Av



1.29
1.2
1.13


BDL247
10912.1
P





0.24


BDL247
10912.1
Av





1.13


BDL247
10912.6
P






0.19


BDL247
10912.6
Av






1.19


BDL247
10915.1
P


0.54


0.42


BDL247
10915.1
Av


1.11


1.12


BDL247
10911.1
P
0.01
0.05
0.02
0.02
0.06
0.05
0.05


BDL247
10911.1
Av
2.19
1.85
1.68
1.46
1.53
1.46
2.05


BDL247
10912.1
P
<0.01
<0.01
0.15

0.21
0.22


BDL247
10912.1
Av
1.48
1.28
1.24

1.11
1.12


BDL247
10912.2
P
0.02
0.01
0.01

0.04
<0.01


BDL247
10912.2
Av
1.66
1.57
1.41

1.28
1.38


BDL247
10912.6
P




0.45
0.38
0.37


BDL247
10912.6
Av




1.1
1.1
1.13


BDL247
10915.1
P
<0.01
0.01
<0.01


0.35
0.25


BDL247
10915.1
Av
2.22
2.04
1.88


1.15
1.29


BDL248
11051.2
P
0.15
0.1
0.01
0.01
0.01
<0.01
0.09


BDL248
11051.2
Av
1.21
1.26
1.34
1.29
1.44
1.38
1.66


BDL248
11052.2
P
<0.01
<0.01
<0.01

0.01
<0.01
0.01


BDL248
11052.2
Av
2.25
2.23
1.94

1.35
1.33
1.39


BDL248
11053.3
P
0.03
0.02
0.01
<0.01
0.01
0.02
<0.01


BDL248
11053.3
Av
1.56
1.5
1.33
1.38
1.44
1.35
2.29


BDL248
11054.3
P
0.38
0.4


0.21
0.09


BDL248
11054.3
Av
1.11
1.13


1.13
1.18


BDL248
11051.2
P




0.05


BDL248
11051.2
Av




1.1


BDL249
11401.2
P
<0.01
<0.01
<0.01
<0.01
<0.01
<0.01
0.01


BDL249
11401.2
Av
3.01
2.92
2.73
1.78
1.84
1.71
3.51


BDL249
11401.5
P
<0.01
<0.01
<0.01
<0.01
<0.01
<0.01
<0.01


BDL249
11401.5
Av
2.17
1.83
1.52
1.66
1.64
1.41
3.31


BDL249
11402.4
P
0.01
0.01
0.03
0.18
<0.01
<0.01
0.04


BDL249
11402.4
Av
1.49
1.44
1.39
1.14
1.64
1.49
1.54


BDL249
11403.2
P


0.48

0.19
0.26


BDL249
11403.2
Av


1.12

1.2
1.16


BDL249
11404.3
P



0.09
0.07
0.02
0.12


BDL249
11404.3
Av



1.41
1.4
1.26
1.57


BDL249
11401.2
P



0.29
0.2

0.17


BDL249
11401.2
Av



1.11
1.1

1.21


BDL249
11401.5
P



0.17


0.46


BDL249
11401.5
Av



1.2


1.21


BDL249
11403.2
P



0.04
0.15

0.35


BDL249
11403.2
Av



1.3
1.13

1.23


BDL249
11404.3
P



0.21
0.04
0.12
0.35


BDL249
11404.3
Av



1.11
1.27
1.19
1.14


BDL250
10841.3
P



0.01
0.12
0.17


BDL250
10841.3
Av



1.26
1.23
1.12


BDL250
10842.3
P

0.05
0.23
<0.01
<0.01
<0.01
0.03


BDL250
10842.3
Av

1.16
1.12
1.55
1.5
1.38
1.39


BDL250
10846.2
P



<0.01
<0.01
<0.01


BDL250
10846.2
Av



1.36
1.37
1.29


BDL250
10846.3
P



0.09
<0.01
<0.01
0.12


BDL250
10846.3
Av



1.33
1.39
1.29
1.44


BDL250
10841.3
P
0.01
0.1
0.09
<0.01
<0.01
<0.01
0.01


BDL250
10841.3
Av
1.23
1.21
1.22
1.82
1.89
1.68
2.37


BDL250
10842.3
P
0.05
0.15
0.26
<0.01
0.23
0.48
0.02


BDL250
10842.3
Av
1.73
1.59
1.5
1.4
1.26
1.14
2.03


BDL250
10843.2
P
0.01
0.02
0.04
<0.01
0.01
0.01
<0.01


BDL250
10843.2
Av
1.97
1.67
1.61
1.37
1.44
1.37
2.33


BDL250
10846.2
P
<0.01
0.01
<0.01
0.11
0.02
<0.01
0.08


BDL250
10846.2
Av
2.3
1.59
1.69
1.21
1.33
1.36
1.39


BDL250
10846.3
P
<0.01
<0.01
<0.01
0.01
<0.01
<0.01
0.01


BDL250
10846.3
Av
1.92
1.69
1.78
1.66
1.98
1.79
2.83


BDL252
10881.1
P
<0.01
<0.01
<0.01
0.13
0.01
<0.01
0.04


BDL252
10881.1
Av
1.96
1.94
1.72
1.29
1.48
1.42
1.52


BDL252
10882.1
P
<0.01
<0.01
<0.01
0.05
0.01
0.01
0.02


BDL252
10882.1
Av
2.97
2.36
2.12
1.65
1.88
1.77
3.43


BDL252
10882.2
P
<0.01
<0.01
<0.01
0.03
0.04
<0.01
0.03


BDL252
10882.2
Av
1.89
1.48
1.43
1.47
1.54
1.45
2.04


BDL252
10882.4
P
0.03
<0.01
0.11
<0.01
0.01
0.03
0.01


BDL252
10882.4
Av
1.64
1.4
1.3
1.7
1.48
1.31
2.99


BDL252
10884.1
P
<0.01
0.02
0.13


BDL252
10884.1
Av
1.55
1.31
1.17


BDL58
10281.5
P
0.23
0.48
0.16


BDL58
10281.5
Av
1.25
1.18
1.3


BDL58
10282.3
P
<0.01
<0.01
0.01
0.12
<0.01
<0.01
0.26


BDL58
10282.3
Av
1.79
1.72
1.77
1.27
1.62
1.62
1.43


BDL62
10682.1
P






0.53


BDL62
10682.1
Av






1.16


BDL62
10684.2
P



0.01


0.22


BDL62
10684.2
Av



1.43


1.3


BDL62
10682.1
P

0.37
0.56


BDL62
10682.1
Av

1.17
1.16


BDL62
10684.2
P





0.09


BDL62
10684.2
Av





1.13


BDL64
10651.5
P

0.08
0.27


BDL64
10651.5
Av

1.26
1.56


BDL64
10653.1
P
0.01
0.06
0.01


BDL64
10653.1
Av
1.24
1.23
1.53


BDL64
10654.3
P

0.32
0.3
0.2
0.04
0.09


BDL64
10654.3
Av

1.21
1.38
1.11
1.4
1.4


BDL64
10651.1
P

0.53


BDL64
10651.1
Av

1.11


BDL64
10653.1
P
0.11
0.02
0.05
0.01
<0.01
0.01
0.14


BDL64
10653.1
Av
1.34
1.57
1.61
1.34
1.42
1.28
1.34


BDL64
10654.3
P
0.01
<0.01
<0.01
<0.01
<0.01
0.01
0.29


BDL64
10654.3
Av
1.41
1.49
1.46
1.28
1.29
1.23
1.27


BDL64
10651.1
P
<0.01
<0.01

0.02
0.15

0.2


BDL64
10651.1
Av
1.5
1.31

1.41
1.13

1.44


BDL64
10651.3
P



<0.01
<0.01
0.13
<0.01


BDL64
10651.3
Av



1.96
1.41
1.15
3.02


BDL64
10653.1
P



0.03
0.3

0.08


BDL64
10653.1
Av



1.64
1.18

1.64


BDL64
10654.3
P



<0.01
0.22

0.04


BDL64
10654.3
Av



1.82
1.23

2.34


BDL79
11041.1
P






0.62


BDL79
11041.1
Av






1.12


BDL79
11042.1
P






0.61


BDL79
11042.1
Av






1.13


BDL79
11043.1
P






0.08


BDL79
11043.1
Av






1.64


BDL79
11042.3
P





0.33


BDL79
11042.3
Av





1.12


BDL79
11043.1
P


0.04
0.17
<0.01
0.01
0.37


BDL79
11043.1
Av


1.23
1.19
1.36
1.29
1.19


BDL81
10372.2
P
<0.01
0.35
0.43


BDL81
10372.2
Av
1.25
1.11
1.13


BDL81
10374.1
P






0.3


BDL81
10374.1
Av






1.24


BDL85
10411.3
P




0.08
0.03


BDL85
10411.3
Av




1.15
1.12


BDL85
10414.1
P
0.2

0.04


BDL85
10414.1
Av
1.16

1.26


BDL85
10414.2
P
0.19
0.02
<0.01


BDL85
10414.2
Av
1.1
1.2
1.35


BDL88
10291.2
P
0.01
0.03
0.03


0.07


BDL88
10291.2
Av
1.88
1.59
1.52


1.13


BDL88
10291.4
P
0.02
<0.01
<0.01

0.03
<0.01


BDL88
10291.4
Av
1.45
1.43
1.53

1.21
1.28


BDL88
10291.5
P
0.12
0.15
0.37



0.67


BDL88
10291.5
Av
1.43
1.35
1.17



1.11


BDL88
10293.3
P
<0.01
<0.01
<0.01



0.57


BDL88
10293.3
Av
2.76
2.34
2.24



1.12


BDL88
10291.2
P
<0.01
<0.01
<0.01


BDL88
10291.2
Av
1.64
1.57
1.58


BDL88
10291.4
P
<0.01
<0.01
<0.01


BDL88
10291.4
Av
1.67
1.5
1.53


BDL88
10291.5
P
<0.01
<0.01
<0.01


BDL88
10291.5
Av
1.8
1.7
1.84


BDL88
10293.3
P
0.03
0.05
0.06


BDL88
10293.3
Av
1.19
1.16
1.22


BDL88
10294.2
P
<0.01
0.01
0.02


BDL88
10294.2
Av
1.82
1.66
1.78


BDL90
10924.2
P



0.05
0.01
<0.01
0.16


BDL90
10924.2
Av



1.43
1.55
1.48
1.9


BDL90
10925.4
P



<0.01
<0.01
<0.01
0.07


BDL90
10925.4
Av



1.95
1.91
1.62
2.22


BDL90
10924.2
P
0.12
0.2
0.09
0.02
0.01
0.01
0.04


BDL90
10924.2
Av
1.32
1.23
1.22
1.31
1.31
1.31
1.93


BDL90
10925.4
P
0.04
0.12

<0.01
<0.01
<0.01
0.02


BDL90
10925.4
Av
1.25
1.15

1.68
1.61
1.51
2.25


BDL90
10921.6
P


0.1


BDL90
10921.6
Av


1.19


BDL90
10924.2
P


0.38
<0.01
<0.01
<0.01
0.03


BDL90
10924.2
Av


1.13
1.48
1.6
1.51
1.41


BDL90
10925.4
P
<0.01
<0.01
<0.01
<0.01
<0.01
<0.01
<0.01


BDL90
10925.4
Av
1.6
1.66
1.8
1.85
1.81
1.71
2.9


BDL94
11721.4
P
0.04
0.03
0.07


BDL94
11721.4
Av
1.41
1.39
1.16


BDL94
11725.2
P
0.04


BDL94
11725.2
Av
1.16


BDL94
11725.3
P
0.04


BDL94
11725.3
Av
1.21


BDL94
11725.5
P
0.14


BDL94
11725.5
Av
1.1


BDL94
11725.3
P
0.01


BDL94
11725.3
Av
1.29





Table 21. “P” = P-value; “Av” = ratio between the averages of event and control. Note that when the average ratio is higher than “1” the effect of exogenous expression of the gene is an increase of the desired trait; “Par” = Parameter according to the measured parameters; “Ev” = event. TP1 = Time point 1; TP2 = Time point 2; TP3 = Time point 3.













TABLE 22







Results obtained in a tissue culture assay



















Roots
Roots
RGR
RGR
RGR







Coverage
Coverage
Of Leaf
Of Root
Of Roots
Fresh
Dry


Gene
Ev.
Par.
TP2
TP3
Area
Coverage
Length
Weight
Weight



















BDL102
10471.1
P
0.08
0.05

0.11
0.36




BDL102
10471.1
Av
1.58
1.35

1.26
1.11


BDL102
10471.3
P
0.08
0.15

0.02
0.15


BDL102
10471.3
Av
1.72
1.58

1.57
1.18


BDL102
10472.1
P
0.19
0.28

0.25

0.29


BDL102
10472.1
Av
1.28
1.22

1.19

1.18


BDL102
10474.2
P
0.33
0.16
0.01
0.02
0.07
0.21
0.26


BDL102
10474.2
Av
1.22
1.38
1.4
1.44
1.19
1.53
1.5


BDL102
10474.6
P

0.2
0.31
0.14


BDL102
10474.6
Av

1.19
1.15
1.22


BDL118
10481.2
P
0.13
0.24
<0.01
0.14
0.28
0.03
0.01


BDL118
10481.2
Av
1.2
1.19
1.99
1.23
1.15
2.14
1.99


BDL118
10481.5
P


0.01


0.02
0.01


BDL118
10481.5
Av


1.36


2.03
1.97


BDL118
10483.4
P





0.07
0.03


BDL118
10483.4
Av





1.93
1.65


BDL118
10484.3
P


<0.01


<0.01
<0.01


BDL118
10484.3
Av


1.6


1.98
2.01


BDL140
10421.3
P
0.14
0.06
<0.01
<0.01

0.03
0.13


BDL140
10421.3
Av
1.45
1.64
1.7
1.68

1.81
1.57


BDL140
10423.1
P
0.21
0.28
0.22
0.16

0.41
0.33


BDL140
10423.1
Av
1.31
1.25
1.21
1.25

1.17
1.16


BDL140
10424.4
P

0.18
<0.01
0.2

0.08
0.45


BDL140
10424.4
Av

1.13
1.66
1.18

1.46
1.2


BDL152
10431.4
P

0.21
0.24
0.13

0.23
0.02


BDL152
10431.4
Av

1.23
1.18
1.27

1.18
1.27


BDL152
10432.5
P
0.1
0.04

0.03


BDL152
10432.5
Av
1.25
1.31

1.32


BDL152
10434.4
P
0.02
<0.01

<0.01
0.03


BDL152
10434.4
Av
1.76
1.51

1.44
1.23


BDL153
10142.2
P
0.04
0.58


BDL153
10142.2
Av
1.57
1.1


BDL153
10144.1
P
0.09
0.12
0.02
0.09
0.12
0.36


BDL153
10144.1
Av
1.51
1.32
1.42
1.35
1.18
1.18


BDL154
10703.1
P
0.38
0.47

0.52
0.44


BDL154
10703.1
Av
1.13
1.18

1.15
1.13


BDL154
10703.3
P




0.34


BDL154
10703.3
Av




1.17


BDL154
10703.5
P





0.38
0.16


BDL154
10703.5
Av





1.11
1.16


BDL154
10703.1
P
0.03
0.05
<0.01
0.01
0.01
0.01
0.01


BDL154
10703.1
Av
1.48
1.55
1.71
1.7
1.37
1.36
1.57


BDL154
10703.5
P
0.1
0.04
0.11
0.01
<0.01
0.34
0.11


BDL154
10703.5
Av
1.75
1.7
1.29
1.73
1.59
1.24
1.38


BDL154
10703.6
P
0.07
0.04

0.07
0.14


BDL154
10703.6
Av
1.63
1.47

1.45
1.28


BDL155
9991.2
P





0.22
0.45


BDL155
9991.2
Av





1.44
1.27


BDL155
9993.2
P





0.55


BDL155
9993.2
Av





1.45


BDL155
9994.4
P




0.19


BDL155
9994.4
Av




1.13


BDL156
10852.6
P
0.41
0.51

0.19
0.09


BDL156
10852.6
Av
1.1
1.12

1.21
1.22


BDL156
10852.7
P




0.35


BDL156
10852.7
Av




1.13


BDL156
10853.6
P
0.58
0.25
0.07
0.07
0.16
0.28
0.04


BDL156
10853.6
Av
1.13
1.24
1.21
1.33
1.19
1.2
1.26


BDL156
10852.6
P


0.05
0.59
0.33
0.35
0.21


BDL156
10852.6
Av


1.29
1.13
1.16
1.12
1.24


BDL156
10853.6
P
0.42
0.25
<0.01
0.05
0.06
<0.01
0.01


BDL156
10853.6
Av
1.29
1.69
1.97
1.83
1.43
1.78
2.26


BDL156
10854.4
P

0.03
<0.01
<0.01
<0.01
<0.01
<0.01


BDL156
10854.4
Av

1.59
1.87
1.76
1.53
1.61
1.94


BDL156
10855.3
P
0.32
<0.01
<0.01
<0.01
0.01
0.46
0.05


BDL156
10855.3
Av
1.17
1.78
1.49
1.99
1.44
1.18
1.42


BDL158
9973.3
P
0.26


BDL158
9973.3
Av
1.22


BDL158
9971.3
P

0.12
0.45
0.03
0.3


BDL158
9971.3
Av

1.27
1.11
1.34
1.11


BDL158
9973.1
P

0.04

0.1


BDL158
9973.1
Av

1.25

1.24


BDL158
9973.3
P
0.04
0.27

0.32


BDL158
9973.3
Av
1.43
1.23

1.16


BDL158
9974.2
P
0.01
0.03
0.34
<0.01


0.49


BDL158
9974.2
Av
1.48
1.41
1.14
1.45


1.1


BDL158
9974.3
P
0.08
0.05
0.02
<0.01

0.01
0.01


BDL158
9974.3
Av
1.5
1.49
1.54
1.54

1.5
1.54


BDL158
9971.3
P

0.33
0.06
0.13
<0.01


BDL158
9971.3
Av

1.13
1.25
1.24
1.46


BDL158
9973.1
P
0.09
0.25
0.02
0.45
0.29

0.16


BDL158
9973.1
Av
1.22
1.22
1.37
1.13
1.13

1.2


BDL158
9973.3
P
0.02
0.1

0.03
<0.01


BDL158
9973.3
Av
1.62
1.43

1.42
1.4


BDL158
9974.2
P
0.06
0.02

0.03


BDL158
9974.2
Av
1.21
1.24

1.32


BDL158
9974.3
P


0.51


BDL158
9974.3
Av


1.11


BDL160
10011.5
P


0.24


<0.01
0.53


BDL160
10011.5
Av


1.23


1.48
1.33


BDL160
10011.6
P





0.51
0.66


BDL160
10011.6
Av





1.18
1.1


BDL160
10011.7
P





0.56


BDL160
10011.7
Av





1.28


BDL160
10015.1
P





0.03
0.12


BDL160
10015.1
Av





1.57
1.25


BDL160
10011.5
P
0.61
0.38

0.42


BDL160
10011.5
Av
1.11
1.14

1.14


BDL160
10013.1
P


0.32


BDL160
10013.1
Av


1.16


BDL160
10014.9
P

0.52

0.37


BDL160
10014.9
Av

1.16

1.18


BDL160
10015.2
P


0.05


0.1
0.11


BDL160
10015.2
Av


1.28


1.29
1.42


BDL167
10042.3
P




0.12


BDL167
10042.3
Av




1.17


BDL167
10043.1
P

0.58
0.13
0.21
0.23


BDL167
10043.1
Av

1.17
1.16
1.25
1.18


BDL167
10043.2
P


0.18
0.34
0.09


BDL167
10043.2
Av


1.14
1.1
1.19


BDL167
10043.3
P
0.1
<0.01
<0.01
<0.01
<0.01


BDL167
10043.3
Av
1.27
1.67
1.54
1.79
1.46


BDL167
10044.2
P
0.05
<0.01
<0.01
<0.01
0.08

0.61


BDL167
10044.2
Av
1.26
1.48
1.38
1.55
1.2

1.12


BDL167
10043.1
P
<0.01
0.17
0.04
0.16
0.14
0.06


BDL167
10043.1
Av
1.63
1.27
1.4
1.3
1.17
1.6


BDL167
10044.2
P
0.01


BDL167
10044.2
Av
1.39


BDL168
9881.4
P
<0.01
0.14

0.08
0.05


BDL168
9881.4
Av
1.74
1.47

1.42
1.21


BDL168
9882.1
P
0.08
0.69


BDL168
9882.1
Av
1.85
1.11


BDL168
9884.1
P
<0.01
0.11

0.34
0.22


BDL168
9884.1
Av
1.84
1.29

1.2
1.15


BDL169
10744.2
P
0.02
0.17

0.13
0.24


BDL169
10744.2
Av
1.34
1.21

1.22
1.16


BDL169
10747.1
P
0.39


0.4


BDL169
10747.1
Av
1.1


1.11


BDL169
10747.5
P
0.04
0.02

0.02
0.07


BDL169
10747.5
Av
1.59
1.41

1.37
1.28


BDL171
10661.2
P
0.03
0.01
0.19
<0.01
0.01
0.06
0.02


BDL171
10661.2
Av
2.26
2.17
1.28
2.22
1.3
1.73
2.47


BDL171
10661.5
P

0.14
0.32
0.04

0.02
<0.01


BDL171
10661.5
Av

1.33
1.19
1.38

1.35
2.02


BDL171
10662.3
P

0.32

0.19


0.56


BDL171
10662.3
Av

1.12

1.18


1.13


BDL171
10663.3
P



0.45


0.39


BDL171
10663.3
Av



1.14


1.19


BDL171
10664.1
P

0.26
0.25
0.1
0.46
0.03
0.03


BDL171
10664.1
Av

1.33
1.24
1.35
1.1
1.39
1.89


BDL173
9951.2
P
0.37




0.27


BDL173
9951.2
Av
1.32




1.43


BDL173
9952.1
P
0.04
0.02

0.01
0.08


BDL173
9952.1
Av
2.68
1.72

1.61
1.21


BDL173
9952.2
P
0.15
0.56


BDL173
9952.2
Av
1.44
1.11


BDL173
9954.3
P





0.14


BDL173
9954.3
Av





1.46


BDL174
11082.1
P
0.29
0.39

0.43
0.05


BDL174
11082.1
Av
1.24
1.15

1.14
1.26


BDL174
11083.1
P
0.07
0.11
0.41
0.05
0.15
0.48
0.37


BDL174
11083.1
Av
1.76
1.43
1.13
1.42
1.21
1.1
1.2


BDL174
11083.2
P
0.17
0.25
0.13
0.09
0.04
0.2
0.4


BDL174
11083.2
Av
1.27
1.36
1.26
1.38
1.44
1.21
1.19


BDL174
11084.1
P
0.04
0.06
<0.01
<0.01
0.01
0.06
0.05


BDL174
11084.1
Av
2.13
1.94
2.01
1.96
1.42
2.06
2.27


BDL174
11085.1
P
<0.01
<0.01
0.1
<0.01
<0.01
0.2
0.24


BDL174
11085.1
Av
2.66
2.13
1.27
2.17
2
1.24
1.37


BDL174
11083.2
P


0.19


0.12
0.29


BDL174
11083.2
Av


1.15


1.2
1.14


BDL174
11084.1
P
0.6


BDL174
11084.1
Av
1.1


BDL174
11085.1
P
0.05
0.32


BDL174
11085.1
Av
1.42
1.14


BDL176
9891.4
P

0.67
0.01
0.47

0.06


BDL176
9891.4
Av

1.11
1.45
1.17

2.02


BDL176
9893.2
P
0.21
0.4
0.22
0.26

0.15


BDL176
9893.2
Av
1.37
1.22
1.21
1.25

1.38


BDL176
9893.3
P
0.47
0.23

0.12

0.14
0.48


BDL176
9893.3
Av
1.17
1.31

1.3

1.29
1.22


BDL177
10521.3
P
0.66
0.34

0.28
0.06


BDL177
10521.3
Av
1.1
1.15

1.17
1.3


BDL181
11293.6
P

0.59
0.1
0.37
0.45
0.39
0.37


BDL181
11293.6
Av

1.15
1.3
1.24
1.15
1.17
1.26


BDL181
11294.7
P


0.04

0.12
0.11
0.1


BDL181
11294.7
Av


1.36

1.28
1.26
1.38


BDL181
11293.1
P


0.25
0.4
0.02
0.05
0.02


BDL181
11293.1
Av


1.19
1.11
1.22
1.59
1.58


BDL181
11293.6
P
0.23
0.15
<0.01
0.09
0.03
<0.01
<0.01


BDL181
11293.6
Av
1.23
1.22
1.34
1.25
1.18
1.48
1.45


BDL181
11294.7
P
0.02
0.21
0.3
0.05
0.01

0.57


BDL181
11294.7
Av
1.55
1.26
1.11
1.3
1.23

1.1


BDL182
10691.8
P


0.42


0.06
0.01


BDL182
10691.8
Av


1.15


1.53
2.11


BDL182
10692.2
P
0.53
0.2
0.28
0.07

0.28
0.15


BDL182
10692.2
Av
1.12
1.21
1.21
1.28

1.47
1.93


BDL182
10692.3
P

0.63

0.3
0.43


BDL182
10692.3
Av

1.13

1.21
1.1


BDL182
10693.3
P
0.02
0.03
0.22
<0.01

0.17
0.01


BDL182
10693.3
Av
1.37
1.55
1.25
1.62

1.41
1.88


BDL182
10693.5
P
0.02
<0.01
0.32
<0.01
0.13
0.06
0.01


BDL182
10693.5
Av
1.47
1.72
1.19
1.8
1.13
1.38
1.91


BDL183
9943.4
P
0.19
0.3

0.48


BDL183
9943.4
Av
1.3
1.16

1.13


BDL183
9944.4
P
0.02
0.52

0.46
0.06
0.44


BDL183
9944.4
Av
1.37
1.15

1.15
1.2
1.16


BDL189
11353.3
P

0.17
0.18
0.18


0.46


BDL189
11353.3
Av

1.18
1.16
1.2


1.1


BDL189
11351.2
P


0.43



0.4


BDL189
11351.2
Av


1.1



1.17


BDL189
11353.3
P

0.24
0.22
0.11


0.33


BDL189
11353.3
Av

1.15
1.11
1.22


1.1


BDL189
11353.5
P





0.65


BDL189
11353.5
Av





1.1


BDL189
11355.4
P


0.22


0.28
0.32


BDL189
11355.4
Av


1.11


1.36
1.13


BDL196
10242.2
P




0.28
0.49


BDL196
10242.2
Av




1.13
1.15


BDL196
10243.4
P
<0.01
0.12
0.12
0.13
0.17
0.57


BDL196
10243.4
Av
1.45
1.36
1.27
1.34
1.17
1.11


BDL196
10244.1
P
0.16
0.43

0.28

0.02


BDL196
10244.1
Av
1.65
1.27

1.27

1.45


BDL196
10242.2
P


0.47


BDL196
10242.2
Av


1.1


BDL196
10243.3
P


0.6


0.43
0.23


BDL196
10243.3
Av


1.1


1.13
1.23


BDL196
10243.4
P
0.51
0.15
<0.01
0.11
0.16
0.13
0.03


BDL196
10243.4
Av
1.12
1.23
1.65
1.27
1.18
1.42
1.69


BDL197
11362.2
P

0.33
0.03
0.18
0.14

0.38


BDL197
11362.2
Av

1.18
1.35
1.32
1.24

1.19


BDL197
11363.1
P

0.23

0.12
<0.01


BDL197
11363.1
Av

1.25

1.38
1.53


BDL197
11363.6
P
0.39
0.01
0.05
<0.01
0.04
0.02
0.04


BDL197
11363.6
Av
1.19
1.59
1.31
1.77
1.36
1.41
1.61


BDL197
11364.1
P

0.04
<0.01
<0.01
<0.01
0.08
<0.01


BDL197
11364.1
Av

1.67
1.63
1.85
1.48
1.44
1.91


BDL197
11364.5
P


0.02
0.47

0.11
0.04


BDL197
11364.5
Av


1.37
1.16

1.18
1.42


BDL197
11363.1
P




0.1
0.53
0.17


BDL197
11363.1
Av




1.12
1.1
1.23


BDL197
11363.6
P
0.11
0.03
0.01
<0.01
<0.01
0.06
0.04


BDL197
11363.6
Av
1.39
1.49
1.3
1.58
1.24
1.45
1.55


BDL197
11364.1
P
0.3


0.53

0.62
0.07


BDL197
11364.1
Av
1.18


1.11

1.16
1.75


BDL197
11364.5
P




0.12

0.49


BDL197
11364.5
Av




1.12

1.13


BDL201
9961.2
P


0.47


0.57
0.47


BDL201
9961.2
Av


1.13


1.1
1.15


BDL201
9961.3
P





0.13


BDL201
9961.3
Av





1.39


BDL201
9961.4
P
0.19
0.41


BDL201
9961.4
Av
1.3
1.14


BDL201
9964.3
P
0.17
0.05

0.27


BDL201
9964.3
Av
1.25
1.21

1.15


BDL203
9831.14
P





0.62
0.42


BDL203
9831.14
Av





1.13
1.27


BDL203
9831.7
P




0.11


BDL203
9831.7
Av




1.22


BDL203
9833.6
P





0.71


BDL203
9833.6
Av





1.14


BDL203
9835.2
P




0.33


BDL203
9835.2
Av




1.14


BDL220
10331.2
P





<0.01
0.06


BDL220
10331.2
Av





1.51
1.25


BDL220
10331.5
P

0.22
<0.01
0.1
0.27
0.05
0.11


BDL220
10331.5
Av

1.22
1.81
1.28
1.11
1.97
1.6


BDL220
10333.5
P





0.47
0.41


BDL220
10333.5
Av





1.16
1.18


BDL220
10334.2
P


0.34


0.35


BDL220
10334.2
Av


1.13


1.14


BDL221
10341.1
P





0.19


BDL221
10341.1
Av





1.3


BDL221
10341.3
P


0.01


0.01
<0.01


BDL221
10341.3
Av


1.5


1.92
2.18


BDL221
10341.4
P


0.02


<0.01
0.01


BDL221
10341.4
Av


1.29


1.98
2.04


BDL221
10343.3
P
0.03
0.01
0.07
<0.01
<0.01


BDL221
10343.3
Av
1.55
1.6
1.21
1.6
1.41


BDL221
10344.3
P





0.41


BDL221
10344.3
Av





1.11


BDL221
10341.1
P


0.15



0.59


BDL221
10341.1
Av


1.27



1.16


BDL221
10342.1
P
<0.01
<0.01
0.17
<0.01
<0.01
0.25
0.42


BDL221
10342.1
Av
3.03
2.06
1.22
1.88
1.52
1.24
1.24


BDL221
10343.1
P
0.01
<0.01
0.01
<0.01
<0.01
0.15
0.33


BDL221
10343.1
Av
1.8
1.61
1.62
1.6
1.41
1.46
1.51


BDL221
10343.3
P
0.01
0.02
0.03
<0.01
<0.01


BDL221
10343.3
Av
3.03
2.69
1.4
2.71
1.92


BDL221
10343.4
P
0.03
0.08
0.07
<0.01
0.01
0.14
0.08


BDL221
10343.4
Av
2.15
2.07
1.51
2.07
1.49
1.44
1.53


BDL221
10344.3
P
0.01
0.07
0.02
0.02
0.09
0.17
0.12


BDL221
10344.3
Av
1.67
1.49
1.49
1.48
1.23
1.39
1.33


BDL223
10791.1
P




0.33


BDL223
10791.1
Av




1.13


BDL223
10793.5
P
0.1
0.01

0.01
0.02


BDL223
10793.5
Av
1.21
1.32

1.38
1.33


BDL223
10793.8
P




0.21


BDL223
10793.8
Av




1.18


BDL223
10796.1
P



0.58
0.41


BDL223
10796.1
Av



1.1
1.12


BDL223
10796.2
P
0.41



0.33
0.34
0.16


BDL223
10796.2
Av
1.11



1.13
1.14
1.4


BDL223
10791.1
P

0.03
0.02
0.05
0.06

0.3


BDL223
10791.1
Av

1.38
1.34
1.43
1.3

1.24


BDL223
10793.3
P

0.34
<0.01
0.08
0.01
0.24
0.16


BDL223
10793.3
Av

1.45
1.64
1.62
1.48
1.15
1.39


BDL223
10793.5
P
0.47
0.23
0.44
0.15
0.04


BDL223
10793.5
Av
1.13
1.29
1.11
1.34
1.31


BDL223
10793.8
P
<0.01
<0.01
0.07
<0.01
<0.01

0.21


BDL223
10793.8
Av
1.75
1.71
1.26
1.72
1.47

1.26


BDL223
10796.1
P

0.01
0.03
0.01
0.07

0.3


BDL223
10796.1
Av

1.47
1.31
1.61
1.29

1.2


BDL224
10451.5
P


0.17


0.21
0.2


BDL224
10451.5
Av


1.19


1.28
1.25


BDL224
10451.7
P
0.11
0.16
<0.01
0.01
0.35
0.11
0.19


BDL224
10451.7
Av
1.48
1.67
1.85
1.69
1.13
1.48
1.29


BDL224
10451.8
P



0.5


BDL224
10451.8
Av



1.13


BDL226
10861.2
P

0.41
0.41
0.15
0.08


BDL226
10861.2
Av

1.18
1.1
1.26
1.26


BDL226
10861.4
P

0.18

0.03
0.04

0.23


BDL226
10861.4
Av

1.27

1.37
1.28

1.2


BDL226
10862.2
P

0.56

0.23
0.19


BDL226
10862.2
Av

1.11

1.2
1.18


BDL227
11491.1
P
<0.01
0.12

0.25


BDL227
11491.1
Av
1.59
1.25

1.2


BDL227
11491.3
P
0.01
0.05
0.06
<0.01
<0.01
0.42
0.35


BDL227
11491.3
Av
1.87
1.71
1.29
1.66
1.52
1.12
1.23


BDL227
11491.5
P
0.01
0.03
0.04
<0.01
<0.01
0.36
0.15


BDL227
11491.5
Av
2.24
2
1.34
1.94
1.58
1.24
1.34


BDL227
11492.5
P
<0.01
0.03
<0.01
<0.01
0.02
0.13
0.12


BDL227
11492.5
Av
2.09
1.71
1.64
1.72
1.39
2.07
1.86


BDL227
11493.5
P
<0.01
0.01
<0.01
<0.01
<0.01
0.16
0.08


BDL227
11493.5
Av
2.13
2.02
1.78
2.05
1.64
1.55
1.73


BDL230
10671.3
P


<0.01


<0.01
<0.01


BDL230
10671.3
Av


1.95


1.84
2.02


BDL231
11111.1
P
0.58
0.12
<0.01
0.1
0.51
0.14
0.55


BDL231
11111.1
Av
1.1
1.24
1.5
1.27
1.1
1.24
1.1


BDL231
11111.2
P
0.24
0.09
<0.01
0.09
0.16


BDL231
11111.2
Av
1.18
1.24
1.31
1.27
1.2


BDL231
11111.3
P
0.33
0.08
<0.01
0.03

0.31
0.35


BDL231
11111.3
Av
1.13
1.36
1.38
1.39

1.15
1.2


BDL231
11112.2
P
<0.01
0.01
0.01
<0.01
0.05

0.52


BDL231
11112.2
Av
1.89
1.61
1.3
1.55
1.27

1.21


BDL231
11116.5
P
<0.01
<0.01
<0.01
<0.01
0.23
0.21
0.05


BDL231
11116.5
Av
1.97
1.79
1.74
1.78
1.18
1.28
1.45


BDL231
11111.1
P
0.09
0.31
<0.01
0.38
0.51
0.1
0.16


BDL231
11111.1
Av
1.25
1.18
1.41
1.16
1.1
1.23
1.2


BDL231
11111.2
P
0.02
0.2
0.01
0.32

0.07
0.28


BDL231
11111.2
Av
1.31
1.19
1.4
1.17

1.46
1.24


BDL231
11112.2
P
0.1


BDL231
11112.2
Av
1.42


BDL232
10904.1
P
0.6
0.26
0.33
0.16
0.11
0.71
0.5


BDL232
10904.1
Av
1.25
1.36
1.29
1.44
1.29
1.14
1.37


BDL232
10905.1
P
0.27
0.24

0.3


BDL232
10905.1
Av
1.18
1.26

1.23


BDL232
10906.3
P
0.48
0.24
0.02
0.07
0.06
0.14
0.13


BDL232
10906.3
Av
1.37
1.63
1.61
1.75
1.44
1.48
1.77


BDL232
10902.2
P
0.02
0.22

0.43


BDL232
10902.2
Av
1.65
1.24

1.12


BDL232
10905.1
P
0.18


BDL232
10905.1
Av
1.28


BDL232
10906.4
P




0.06


BDL232
10906.4
Av




1.15


BDL233
10822.4
P




0.28


BDL233
10822.4
Av




1.13


BDL233
10824.2
P




0.05


BDL233
10824.2
Av




1.25


BDL233
10825.3
P




0.1


BDL233
10825.3
Av




1.21


BDL233
10825.4
P
<0.01
0.01

<0.01
0.03


BDL233
10825.4
Av
1.78
1.49

1.43
1.29


BDL233
10822.4
P


0.04

0.19
0.26
0.37


BDL233
10822.4
Av


1.37

1.21
1.18
1.24


BDL233
10824.1
P


0.43

0.48


BDL233
10824.1
Av


1.11

1.1


BDL233
10824.2
P

0.38
0.3
0.19
<0.01


BDL233
10824.2
Av

1.16
1.16
1.29
1.5


BDL233
10825.4
P
0.22
0.02
0.18
0.04
0.01

0.42


BDL233
10825.4
Av
1.23
1.44
1.23
1.46
1.47

1.14


BDL235
11412.2
P

0.34

0.33
0.4


BDL235
11412.2
Av

1.14

1.17
1.11


BDL235
11413.2
P
0.07
0.06

0.03


BDL235
11413.2
Av
1.43
1.39

1.38


BDL235
11413.3
P





0.51
0.3


BDL235
11413.3
Av





1.15
1.18


BDL235
11411.2
P




0.08

0.62


BDL235
11411.2
Av




1.16

1.15


BDL235
11413.2
P
<0.01
0.08

0.12
0.15


BDL235
11413.2
Av
1.61
1.33

1.22
1.15


BDL235
11413.3
P




0.09


BDL235
11413.3
Av




1.16


BDL237
10892.1
P





0.05
0.14


BDL237
10892.1
Av





1.43
1.33


BDL237
10892.2
P
0.18
0.19

0.4
0.18


BDL237
10892.2
Av
1.23
1.16

1.14
1.18


BDL237
10893.1
P
0.23
0.29
0.51
0.28
0.09


BDL237
10893.1
Av
1.2
1.17
1.11
1.19
1.25


BDL237
10895.3
P
0.01
0.01
<0.01
<0.01
<0.01
0.09
0.05


BDL237
10895.3
Av
2.68
2.3
1.85
2.32
1.77
1.59
1.71


BDL237
10896.1
P

0.71

0.57
0.27


BDL237
10896.1
Av

1.11

1.13
1.21


BDL238
10951.4
P
0.51


BDL238
10951.4
Av
1.13


BDL238
10952.3
P
0.12
0.12

0.25
0.09


BDL238
10952.3
Av
1.3
1.29

1.25
1.32


BDL238
10953.1
P


0.37

0.37


BDL238
10953.1
Av


1.14

1.15


BDL238
10954.2
P

0.52

0.61
0.5


BDL238
10954.2
Av

1.13

1.11
1.12


BDL238
10954.3
P






0.67


BDL238
10954.3
Av






1.12


BDL240
10802.2
P




0.47


BDL240
10802.2
Av




1.1


BDL240
10806.6
P
0.33
0.43

0.27
0.19


BDL240
10806.6
Av
1.28
1.19

1.2
1.18


BDL240
10802.2
P
0.38



0.1


BDL240
10802.2
Av
1.17



1.24


BDL240
10803.5
P


0.48

0.17


BDL240
10803.5
Av


1.12

1.18


BDL240
10806.6
P
0.01
0.03
0.05
<0.01
0.01
0.15
0.26


BDL240
10806.6
Av
2.85
2.11
1.38
1.97
1.44
1.32
1.34


BDL241
10875.1
P
0.1



0.46


BDL241
10875.1
Av
1.25



1.13


BDL241
10873.1
P




0.22

0.61


BDL241
10873.1
Av




1.19

1.11


BDL241
10874.2
P




0.45


BDL241
10874.2
Av




1.11


BDL241
10874.3
P
0.54
0.05
0.01
0.03
0.05
0.08
0.01


BDL241
10874.3
Av
1.1
1.43
1.47
1.53
1.32
1.21
1.55


BDL241
10875.1
P
0.09
0.53


BDL241
10875.1
Av
1.36
1.13


BDL242
10731.3
P
<0.01
0.2

0.19
0.12

0.2


BDL242
10731.3
Av
1.38
1.21

1.19
1.21

1.22


BDL242
10731.5
P
0.1
0.31

0.32


BDL242
10731.5
Av
1.34
1.16

1.15


BDL242
10737.1
P




0.32


BDL242
10737.1
Av




1.14


BDL242
10731.3
P
<0.01
0.01
<0.01
<0.01
<0.01
0.05
0.04


BDL242
10731.3
Av
1.75
1.62
2.15
1.62
1.39
2.12
2.23


BDL242
10731.5
P
0.06


BDL242
10731.5
Av
1.29


BDL242
10731.7
P
<0.01
<0.01
0.01
0.01
0.03
0.01
0.04


BDL242
10731.7
Av
1.85
1.49
1.45
1.47
1.28
1.64
1.86


BDL242
10737.2
P
0.47
0.23
<0.01
0.07
0.05
<0.01
0.01


BDL242
10737.2
Av
1.26
1.38
1.86
1.43
1.32
1.91
2.05


BDL245
10811.2
P
0.54
0.17

0.08
0.21

0.3


BDL245
10811.2
Av
1.1
1.22

1.28
1.16

1.14


BDL245
10813.3
P




0.09


BDL245
10813.3
Av




1.22


BDL245
10816.3
P




0.14


BDL245
10816.3
Av




1.18


BDL247
10912.1
P

0.08

0.02
0.01


BDL247
10912.1
Av

1.31

1.4
1.37


BDL247
10912.2
P




0.08


BDL247
10912.2
Av




1.22


BDL247
10915.1
P

0.45
0.22
0.14
0.02

0.53


BDL247
10915.1
Av

1.19
1.2
1.28
1.4

1.12


BDL247
10911.1
P
0.15
0.1
0.01
0.01
0.02
0.3
0.23


BDL247
10911.1
Av
1.96
1.8
1.6
1.79
1.45
1.38
1.5


BDL247
10912.1
P
0.32
0.4
0.24
0.25
0.13
0.32
0.14


BDL247
10912.1
Av
1.15
1.22
1.2
1.24
1.21
1.27
1.56


BDL247
10912.2
P
0.04
0.01
0.03
<0.01
<0.01
0.09
0.3


BDL247
10912.2
Av
1.73
1.74
1.36
1.81
1.62
1.41
1.35


BDL247
10912.6
P

0.61

0.57
0.39
0.21
0.48


BDL247
10912.6
Av

1.11

1.11
1.13
1.37
1.3


BDL247
10915.1
P
0.23
0.14
<0.01
0.03
0.08
0.02
0.06


BDL247
10915.1
Av
1.47
1.52
1.81
1.54
1.3
1.74
1.58


BDL248
11051.2
P
<0.01
0.01
0.03
0.02
<0.01
0.21


BDL248
11051.2
Av
1.61
1.45
1.36
1.43
1.42
1.22


BDL248
11052.2
P
<0.01
<0.01
<0.01
<0.01
<0.01
0.04
0.01


BDL248
11052.2
Av
1.89
1.68
1.89
1.7
1.44
1.74
1.81


BDL248
11053.3
P
<0.01
<0.01
0.07
<0.01
0.03
0.46
0.65


BDL248
11053.3
Av
2.04
1.62
1.29
1.57
1.34
1.13
1.14


BDL248
11054.3
P
0.15
0.15

0.24
0.04


BDL248
11054.3
Av
1.18
1.18

1.19
1.29


BDL248
11051.2
P




0.18


BDL248
11051.2
Av




1.1


BDL248
11054.2
P




0.18


BDL248
11054.2
Av




1.1


BDL249
11401.2
P
<0.01
<0.01
<0.01
<0.01
<0.01
<0.01
<0.01


BDL249
11401.2
Av
3.19
2.43
2.68
2.35
1.67
2.55
3.02


BDL249
11401.5
P
<0.01
0.01
0.02
<0.01
0.02
0.39
0.44


BDL249
11401.5
Av
2.63
1.94
1.4
1.83
1.3
1.19
1.23


BDL249
11402.4
P
<0.01
<0.01
0.03
<0.01
<0.01
0.03
0.1


BDL249
11402.4
Av
2.42
1.99
1.38
2.02
1.65
1.37
1.43


BDL249
11403.2
P

0.46
0.34
0.27
0.2
0.56


BDL249
11403.2
Av

1.22
1.17
1.25
1.21
1.11


BDL249
11404.3
P
0.01
0.07

0.23
0.22


BDL249
11404.3
Av
1.43
1.22

1.19
1.19


BDL249
11401.5
P

0.31

0.45


BDL249
11401.5
Av

1.1

1.11


BDL249
11404.3
P
0.03
0.22

0.2
0.04


BDL249
11404.3
Av
1.33
1.18

1.18
1.23


BDL250
10842.3
P
<0.01
0.01
0.21
<0.01
0.02

0.34


BDL250
10842.3
Av
1.69
1.54
1.15
1.56
1.29

1.24


BDL250
10846.2
P
0.01
<0.01
0.29
<0.01
0.05
0.4
0.21


BDL250
10846.2
Av
1.43
1.41
1.12
1.45
1.25
1.19
1.33


BDL250
10846.3
P
0.02
0.36


0.05


BDL250
10846.3
Av
1.37
1.11


1.26


BDL250
10841.3
P
0.01
0.02
0.17
<0.01
<0.01


BDL250
10841.3
Av
1.99
1.66
1.22
1.61
1.62


BDL250
10842.3
P
0.23
0.52
0.12
0.44

0.41
0.59


BDL250
10842.3
Av
1.57
1.28
1.45
1.22

1.6
1.27


BDL250
10843.2
P
0.03
0.07
0.01
0.01
0.01
0.02
0.1


BDL250
10843.2
Av
1.85
1.67
1.55
1.62
1.37
1.53
1.6


BDL250
10846.2
P
0.04
<0.01
<0.01
<0.01
<0.01
0.45
0.67


BDL250
10846.2
Av
1.46
1.68
1.58
1.7
1.43
1.22
1.15


BDL250
10846.3
P
<0.01
<0.01
<0.01
<0.01
<0.01
0.05
0.03


BDL250
10846.3
Av
2.79
2.32
1.76
2.28
1.84
1.8
1.87


BDL252
10881.1
P
0.01
<0.01
<0.01
<0.01
<0.01
0.09
0.19


BDL252
10881.1
Av
2.1
1.87
1.68
1.9
1.48
1.43
1.68


BDL252
10882.1
P
0.01
0.01
<0.01
<0.01
<0.01
0.18
0.18


BDL252
10882.1
Av
3.11
2.51
1.97
2.43
1.82
1.4
1.51


BDL252
10882.2
P
0.05
<0.01
0.04
<0.01
0.01

0.62


BDL252
10882.2
Av
1.87
1.74
1.35
1.72
1.44

1.11


BDL252
10882.4
P
0.01
0.01
0.17
0.01
0.38


BDL252
10882.4
Av
2.06
1.62
1.24
1.52
1.13


BDL252
10884.1
P


0.5


0.24
0.24


BDL252
10884.1
Av


1.1


1.22
1.3


BDL58
10281.5
P


0.07
0.46
0.15
0.55
0.02


BDL58
10281.5
Av


1.32
1.15
1.18
1.14
1.37


BDL58
10282.3
P
<0.01
0.01
<0.01
<0.01
<0.01
<0.01
<0.01


BDL58
10282.3
Av
1.94
2.18
1.77
2.29
1.81
1.79
1.83


BDL58
10285.3
P




0.06


BDL58
10285.3
Av




1.21


BDL62
10682.1
P

0.31
0.43
0.12


0.4


BDL62
10682.1
Av

1.35
1.19
1.46


1.33


BDL62
10684.2
P

0.43

0.33
0.08

0.58


BDL62
10684.2
Av

1.17

1.23
1.26

1.11


BDL62
10684.5
P


0.41
0.64
0.31
0.67
0.64


BDL62
10684.5
Av


1.14
1.11
1.15
1.13
1.13


BDL64
10651.5
P


0.02
0.39
0.07
0.17
0.26


BDL64
10651.5
Av


1.77
1.14
1.19
1.54
1.52


BDL64
10653.1
P

0.14
<0.01
0.13

<0.01
0.03


BDL64
10653.1
Av

1.21
1.62
1.24

1.42
1.51


BDL64
10653.3
P




0.01


BDL64
10653.3
Av




1.25


BDL64
10654.3
P
0.15
0.23
0.06
0.02
<0.01
0.37
0.27


BDL64
10654.3
Av
1.53
1.6
1.5
1.71
1.55
1.45
1.44


BDL64
10651.1
P


0.5


0.31
0.16


BDL64
10651.1
Av


1.13


1.45
1.91


BDL64
10651.2
P






0.62


BDL64
10651.2
Av






1.13


BDL64
10651.5
P






0.48


BDL64
10651.5
Av






1.15


BDL64
10653.1
P
0.01
0.02
0.01
<0.01
0.02
0.05
0.03


BDL64
10653.1
Av
2.18
2.28
1.69
2.43
1.25
2.27
3.13


BDL64
10654.3
P
<0.01
<0.01
0.02
<0.01
0.03
0.01
<0.01


BDL64
10654.3
Av
1.78
1.9
1.46
1.97
1.2
1.7
2.53


BDL64
10651.1
P
0.11


BDL64
10651.1
Av
1.27


BDL64
10651.3
P
0.14
0.32

0.46


BDL64
10651.3
Av
1.43
1.22

1.14


BDL79
11042.3
P




0.5


BDL79
11042.3
Av




1.1


BDL79
11042.3
P

0.44

0.28
0.04


BDL79
11042.3
Av

1.18

1.26
1.36


BDL79
11042.7
P


0.4



0.55


BDL79
11042.7
Av


1.12



1.11


BDL79
11043.1
P

0.27
0.03
0.25
0.03
0.29
0.22


BDL79
11043.1
Av

1.28
1.35
1.3
1.35
1.18
1.22


BDL85
10411.1
P
0.74
0.55

0.42


BDL85
10411.1
Av
1.1
1.14

1.16


BDL85
10411.3
P
0.14
0.01

0.03
0.17


BDL85
10411.3
Av
1.24
1.28

1.32
1.13


BDL85
10412.2
P


0.44


0.06
0.15


BDL85
10412.2
Av


1.1


1.22
1.24


BDL85
10414.1
P

0.01
0.05
0.02
0.08
0.38
0.47


BDL85
10414.1
Av

1.3
1.29
1.39
1.18
1.17
1.11


BDL85
10414.2
P

0.27
<0.01
0.07
0.07
<0.01
0.08


BDL85
10414.2
Av

1.15
1.42
1.28
1.17
1.55
1.5


BDL88
10291.2
P
0.31
0.15
0.02
0.08
0.08
0.06
0.11


BDL88
10291.2
Av
1.26
1.33
1.45
1.36
1.24
1.35
1.36


BDL88
10291.4
P
0.01
0.02
<0.01
<0.01
<0.01
0.23
0.25


BDL88
10291.4
Av
1.72
1.57
1.54
1.62
1.42
1.44
1.35


BDL88
10291.5
P
0.59
0.44
0.48
0.38


BDL88
10291.5
Av
1.13
1.17
1.13
1.17


BDL88
10293.3
P
0.14
0.28
<0.01
0.11
0.26
0.16
0.08


BDL88
10293.3
Av
1.34
1.35
2.15
1.36
1.19
1.58
1.97


BDL88
10291.2
P
0.16
0.05
<0.01
0.01
0.21
0.33
0.47


BDL88
10291.2
Av
1.32
1.45
1.56
1.48
1.18
1.17
1.16


BDL88
10291.4
P


<0.01


BDL88
10291.4
Av


1.49


BDL88
10291.5
P


<0.01


0.15
0.38


BDL88
10291.5
Av


1.84


1.25
1.22


BDL88
10293.3
P


0.02



0.47


BDL88
10293.3
Av


1.23



1.15


BDL88
10294.2
P


<0.01


0.3
0.55


BDL88
10294.2
Av


1.76


1.23
1.16


BDL90
10921.3
P




0.22


BDL90
10921.3
Av




1.18


BDL90
10921.6
P




0.09


BDL90
10921.6
Av




1.28


BDL90
10924.2
P
0.06
0.04

<0.01
<0.01


BDL90
10924.2
Av
2
1.75

1.73
1.5


BDL90
10924.4
P




0.33


BDL90
10924.4
Av




1.12


BDL90
10925.4
P
0.02
0.03

<0.01
<0.01


BDL90
10925.4
Av
2.27
1.81

1.76
1.46


BDL90
10923.4
P




0.27


BDL90
10923.4
Av




1.17


BDL90
10924.2
P
0.06
0.28
0.22
0.33
0.06


BDL90
10924.2
Av
1.43
1.26
1.19
1.22
1.3


BDL90
10925.4
P
0.02
0.04

0.03
0.01


BDL90
10925.4
Av
1.7
1.58

1.54
1.43


BDL90
10921.6
P

0.75
0.04
0.42
0.02

0.13


BDL90
10921.6
Av

1.11
1.32
1.24
1.41

1.28


BDL90
10923.4
P



0.51
0.12

0.58


BDL90
10923.4
Av



1.15
1.25

1.15


BDL90
10924.2
P
0.16
0.01
0.28
0.01
<0.01


BDL90
10924.2
Av
1.4
1.65
1.18
1.7
1.54


BDL90
10925.4
P
<0.01
<0.01
<0.01
<0.01
<0.01
0.05
0.03


BDL90
10925.4
Av
2.34
2.48
1.88
2.4
1.61
1.55
1.78


BDL94
11721.4
P


0.45


0.09
0.26


BDL94
11721.4
Av


1.11


1.29
1.16


BDL94
11725.3
P





0.17


BDL94
11725.3
Av





1.2


BDL94
11725.3
P





0.31


BDL94
11725.3
Av





1.29





Table 22. “P” = P-value; “Av” = ratio between the averages of event and control. Note that when the average ratio is higher than “1” the effect of exogenous expression of the gene is an increase of the desired trait; “Par” = Parameter according to the measured parameters; “Ev” = event. TP1 = Time point 1; TP2 = Time point 2; TP3 = Time point 3; RGR = relative growth rate.






Greenhouse Assays—
Table 23 specifies the parameters that were measured in the greenhouse assays and which are presented in Tables 24, 25, 26 and 27. In cases where a certain event appears more than once, the event was tested in several independent experiments. The parameters were measured as follows:
The plants were analyzed for their overall size, growth rate, flowering, seed yield, weight of 1,000 seeds, 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 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 included 4 light units (4×150 Watts light bulb) is used for capturing images of plant samples.
The image capturing process was repeated every 2 days starting from day 1 after transplanting till day 16. 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 process, the tubs 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 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 (3888×2592 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 Growth Analysis—
Using the digital analysis leaves data was calculated, including leaf number, rosette area, rosette diameter, leaf blade area, plot coverage, leaf petiole length.
The Vegetative Growth Rate of the Plant was Defined by Formulas IX, X, XI and XII.

Relative growth rate of leaf blade area=Regression coefficient of leaf area along time course.  Formula IX:

Relative growth rate of rosette area=Regression coefficient of rosette area along time course.  Formula X:

Relative growth rate of rosette diameter=Regression coefficient of rosette diameter along time course.  Formula XI

Relative growth rate of plot coverage=Regression coefficient of plot coverage along time course.  Formula XII

Seeds Average Weight (Seed Weight or 1000 Seed 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.
Plant 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 seed weight (the weight of 1000 seeds) (gr.).
The harvest index was calculated using Formula IV (Harvest Index=Average seed yield per plant/Average dry weight) as described above.
Oil Percentage in Seeds—
At the end of the experiment all seeds from plots 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 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 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.
Oil Yield—
The oil yield was calculated using Formula VII (described above).
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.
Statistical Analyses—
To identify genes conferring significantly improved tolerance to abiotic stresses, 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 separately. Data was analyzed using Student's t-test and results were 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, N.C., USA).







TABLE 23







Parameters measured in greenhouse assays










Parameter
Number














Rosette Diameter TP2
1



Rosette Diameter TP3
2



Rosette Diameter TP4
3



Rosette Area TP2
4



Rosette Area TP3
5



Rosette Area TP4
6



Plot Coverage TP2
7



Plot Coverage TP3
8



Plot Coverage TP4
9



Leaf Number TP2
10



Leaf Number TP3
11



Leaf Number TP4
12



Leaf Blade Area TP2
13



Leaf Blade Area TP3
14



Leaf Blade Area TP4
15



Leaf Petiole Length TP2
16



Leaf Petiole Length TP3
17



Leaf Petiole Length TP4
18



Blade Relative Area TP2
19



Blade Relative Area TP3
20



Blade Relative Area TP4
21



Petiole Relative Area TP2
22



Petiole Relative Area TP3
23



Petiole Relative Area TP4
24



RGR Of Leaf Blade Area
25



RGR Of Leaf Number
26



RGR Of Rosette Area
27



RGR Of Rosette Diameter
28



RGR Of Plot Coverage
29



Dry Weight
30



Fresh Weight
31



Inflorescence Emergence
32



Flowering
33



Seed Yield
34



Harvest Index
35



Seeds Weight
36



Oil Content
37







Table 23. Provided are the parameters measured in greenhouse experiments which are presented in Tables 24-27 hereinbelow. TP1 = Time point 1; TP2 = Time point 2; TP3 = Time point 3; RGR = relative growth rate.













TABLE 24







Results from greenhouse experiments



















Gene
Ev.
Par:
1
2
3
4
5
6
7
8
9
10






















BDL102
10471.1
P
<0.01
<0.01

0.13
0.34
0.03
0.13
0.34
0.03



BDL102
10471.1
Av
1.24
1.14

1.31
1.21
1.15
1.31
1.21
1.15


BDL102
10472.1
P
0.13
0.11
0.33
0.25
0.02
0.32
0.25
0.02
0.32


BDL102
10472.1
Av
1.26
1.19
1.14
1.37
1.26
1.26
1.37
1.26
1.26


BDL102
10474.1
P
0.22
0.23
0.26
0.19
0.2
0.23
0.19
0.2
0.23
0.19


BDL102
10474.1
Av
1.35
1.33
1.2
1.65
1.87
1.49
1.65
1.87
1.49
1.1


BDL102
10474.2
P
0.17
0.02
0.01
0.1
0.05
<0.01
0.1
0.05
<0.01
<0.01


BDL102
10474.2
Av
1.3
1.23
1.11
1.59
1.53
1.27
1.59
1.53
1.27
1.11


BDL102
10474.6
P
0.02


0.23


0.23


BDL102
10474.6
Av
1.11


1.15


1.15


BDL117
10071.2
P



0.62


0.59


BDL117
10071.2
Av



1.14


1.16


BDL117
10074.1
P
0.28
0.22
0.16
0.29
0.3
0.3
0.28
0.29
0.29
0.34


BDL117
10074.1
Av
1.26
1.23
1.24
1.58
1.47
1.44
1.6
1.49
1.46
1.15


BDL117
10074.4
P
0.35
0.34
0.41
0.38
0.39
0.41
0.38
0.37
0.39
0.28


BDL117
10074.4
Av
1.21
1.14
1.15
1.41
1.29
1.26
1.43
1.3
1.28
1.13


BDL117
10073.1
P



0.57
0.58
0.64


BDL117
10073.1
Av



1.13
1.17
1.14


BDL117
10073.2
P


0.45
0.7
0.55
0.48
0.7
0.55
0.48


BDL117
10073.2
Av


1.14
1.1
1.21
1.22
1.1
1.21
1.22


BDL117
10074.1
P
0.41
0.4
0.39
0.44
0.37
0.38
0.44
0.37
0.38
0.13


BDL117
10074.1
Av
1.1
1.15
1.15
1.17
1.32
1.29
1.17
1.32
1.29
1.15


BDL117
10074.4
P


0.1

0.4
0.34

0.4
0.34


BDL117
10074.4
Av


1.09

1.1
1.13

1.1
1.13


BDL138
9812.1
P
0.04


BDL138
9812.1
Av
1.06


BDL138
9812.3
P



0.06


0.04


BDL138
9812.3
Av



1.18


1.19


BDL140
10423.1
P
0.02


0.01
0.22

0.01
0.22


BDL140
10423.1
Av
1.16


1.39
1.22

1.39
1.22


BDL140
10424.4
P



0.62


0.62


0.1


BDL140
10424.4
Av



1.18


1.18


1.08


BDL147
10301.5
P









0.1


BDL147
10301.5
Av









1.08


BDL147
10303.1
P
<0.01
0.01

0.06
0.04
0.08
0.06
0.04
0.08
0.05


BDL147
10303.1
Av
1.23
1.21

1.65
1.36
1.24
1.65
1.36
1.24
1.11


BDL147
10303.6
P



0.63
0.4

0.63
0.4


BDL147
10303.6
Av



1.14
1.11

1.14
1.11


BDL147
10304.2
P



0.33


0.33


BDL147
10304.2
Av



1.19


1.19


BDL147
10304.2
P




0.44
0.36

0.44
0.36


BDL147
10304.2
Av




1.17
1.11

1.17
1.11


BDL149
9823.3
P
0.22
0.08

0.33
0.13
0.29

0.03


BDL149
9823.3
Av
1.14
1.1

1.14
1.18
1.14

1.11


BDL149
9824.4
P
0.01
<0.01
<0.01
0.08
<0.01
0.04
0.09
<0.01
0.04
0.03


BDL149
9824.4
Av
1.16
1.13
1.13
1.35
1.26
1.29
1.37
1.28
1.31
1.05


BDL149
9823.3
P



0.65
0.67
0.63
0.65
0.67
0.63


BDL149
9823.3
Av



1.17
1.1
1.13
1.17
1.1
1.13


BDL152
10431.1
P



0.28


0.28


BDL152
10431.1
Av



1.13


1.13


BDL152
10431.4
P




0.2
0.45

0.2
0.45


BDL152
10431.4
Av




1.12
1.11

1.12
1.11


BDL152
10434.4
P


0.22
0.72

0.41
0.72

0.41
0.09


BDL152
10434.4
Av


1.12
1.12

1.2
1.12

1.2
1.07


BDL153
10141.3
P
<0.01
<0.01
<0.01
0.04
<0.01
<0.01
0.05
<0.01
<0.01


BDL153
10141.3
Av
1.21
1.17
1.17
1.41
1.33
1.34
1.43
1.34
1.36


BDL153
10142.2
P
0.21
0.41
0.38
0.33
0.38
0.38
0.32
0.37
0.38
0.49


BDL153
10142.2
Av
1.33
1.2
1.25
1.64
1.55
1.57
1.66
1.58
1.6
1.15


BDL153
10143.1
P
0.03


0.14
0.07
0.37
0.14
0.04
0.34


BDL153
10143.1
Av
1.07


1.22
1.12
1.14
1.23
1.13
1.16


BDL153
10144.1
P



0.08
0.08
0.1
0.03
0.03
0.04


BDL153
10144.1
Av



1.11
1.1
1.11
1.13
1.11
1.13


BDL153
10141.3
P
0.1
<0.01
0.01


0.01


0.01


BDL153
10141.3
Av
1.14
1.15
1.06


1.14


1.14


BDL153
10142.2
P
0.01
0.01
0.14
0.15
0.44
0.14
0.15
0.44
0.14


BDL153
10142.2
Av
1.17
1.16
1.16
1.18
1.19
1.31
1.18
1.19
1.31


BDL153
10142.3
P





0.4


0.4


BDL153
10142.3
Av





1.15


1.15


BDL153
10143.1
P









0.38


BDL153
10143.1
Av









1.12


BDL153
10143.2
P




0.25
0.11

0.25
0.11


BDL153
10143.2
Av




1.11
1.12

1.11
1.12


BDL153
10144.1
P

0.3
0.17

0.39
0.34

0.39
0.34


BDL153
10144.1
Av

1.23
1.1

1.44
1.13

1.44
1.13


BDL154
10703.8
P
<0.01
0.03

0.12
0.07
0.43
0.12
0.07
0.43


BDL154
10703.8
Av
1.29
1.2

1.53
1.37
1.13
1.53
1.37
1.13


BDL155
9991.5
P
0.22
0.07
0.1
0.31

0.31
0.31

0.31
0.03


BDL155
9991.5
Av
1.13
1.12
1.12
1.14

1.12
1.14

1.12
1.09


BDL155
9994.3
P
0.17
0.02
0.08
0.16
0.06
0.17
0.16
0.06
0.17
0.09


BDL155
9994.3
Av
1.15
1.17
1.12
1.17
1.27
1.21
1.17
1.27
1.21
1.07


BDL162
10492.2
P


0.32
0.16
0.25
0.11
0.16
0.25
0.11
0.59


BDL162
10492.2
Av


1.13
1.22
1.15
1.34
1.22
1.15
1.34
1.11


BDL167
10044.2
P




0.17


0.6


BDL167
10044.2
Av




1.17


1.1


BDL167
10043.3
P




0.39


0.39


BDL167
10043.3
Av




1.1


1.1


BDL167
10044.2
P



0.21
0.17
0.31
0.21
0.17
0.31
0.03


BDL167
10044.2
Av



1.14
1.15
1.2
1.14
1.15
1.2
1.09


BDL168
9881.3
P
0.1
0.11
0.09
0.18
0.14
0.09
0.18
0.14
0.1
0.22


BDL168
9881.3
Av
1.22
1.19
1.24
1.48
1.44
1.49
1.5
1.46
1.52
1.14


BDL168
9881.4
P
0.14
0.24
0.18
0.05
0.11
0.27
0.05
0.11
0.26
0.4


BDL168
9881.4
Av
1.23
1.17
1.19
1.43
1.38
1.34
1.45
1.4
1.35
1.1


BDL168
9882.1
P



0.04
0.05
0.12
0.01
0.02
0.05


BDL168
9882.1
Av



1.14
1.12
1.1
1.15
1.13
1.11


BDL168
9882.3
P
0.58
0.64
0.49
0.51
0.55
0.51
0.49
0.53
0.5
0.54


BDL168
9882.3
Av
1.1
1.11
1.17
1.3
1.24
1.33
1.32
1.26
1.35
1.1


BDL168
9884.4
P


0.72


0.76


0.74


BDL168
9884.4
Av


1.11


1.13


1.15


BDL168
9881.4
P

0.02



0.51


0.51


BDL168
9881.4
Av

1.09



1.15


1.15


BDL168
9882.1
P

0.04


0.15
0.22


BDL168
9882.1
Av

1.07


1.12
1.13


BDL168
9884.1
P


0.01


BDL168
9884.1
Av


1.1


BDL169
10743.4
P



0.43
0.55
0.56
0.54
0.7
0.72


BDL169
10743.4
Av



1.27
1.2
1.19
1.17
1.11
1.1


BDL169
10744.1
P
0.41


0.37
0.55

0.3
0.45
0.69
0.43


BDL169
10744.1
Av
1.1


1.27
1.18

1.35
1.25
1.1
1.13


BDL169
10747.1
P
0.29


0.47
0.64

0.42
0.54

<0.01


BDL169
10747.1
Av
1.15


1.34
1.15

1.42
1.22

1.17


BDL169
10747.5
P

0.08

0.01
0.02
0.24
0.01
0.01
0.13
<0.01


BDL169
10747.5
Av

1.09

1.4
1.28
1.11
1.49
1.36
1.18
1.16


BDL169
10741.3
P
0.58


0.43


0.43


BDL169
10741.3
Av
1.13


1.2


1.2


BDL169
10744.2
P
0.43
0.25
0.18
0.34
0.31
0.33
0.34
0.31
0.33
0.44


BDL169
10744.2
Av
1.24
1.26
1.21
1.6
1.61
1.42
1.6
1.61
1.42
1.12


BDL169
10747.1
P
0.01
0.14

0.33
0.09
0.53
0.33
0.09
0.53


BDL169
10747.1
Av
1.16
1.15

1.44
1.3
1.17
1.44
1.3
1.17


BDL169
10747.5
P
0.05
0.1
0.01
0.16
0.19
0.05
0.16
0.19
0.05


BDL169
10747.5
Av
1.13
1.08
1.09
1.28
1.24
1.12
1.28
1.24
1.12


BDL171
10661.2
P
0.7

0.44
0.59
0.7
0.56
0.59
0.7
0.56


BDL171
10661.2
Av
1.1

1.1
1.23
1.17
1.22
1.23
1.17
1.22


BDL171
10662.3
P
0.48
0.44

0.35
0.53

0.35
0.53


BDL171
10662.3
Av
1.12
1.13

1.26
1.19

1.26
1.19


BDL171
10664.1
P
0.01
<0.01
0.24
<0.01
0.01
0.42
<0.01
0.01
0.42
<0.01


BDL171
10664.1
Av
1.36
1.31
1.23
1.72
1.56
1.49
1.72
1.56
1.49
1.21


BDL171
10664.3
P
0.16
0.16
0.38
0.24
0.15
0.42
0.24
0.15
0.42
0.03


BDL171
10664.3
Av
1.26
1.22
1.14
1.49
1.44
1.36
1.49
1.44
1.36
1.19


BDL171
10661.5
P






0.29
0.38

0.42


BDL171
10661.5
Av






1.15
1.1

1.12


BDL171
10662.2
P
0.01
0.07

0.18


0.11


0.15


BDL171
10662.2
Av
1.16
1.1

1.2


1.28


1.18


BDL171
10662.3
P
0.02
<0.01
<0.01
<0.01
<0.01
0.01
<0.01
<0.01
<0.01
<0.01


BDL171
10662.3
Av
1.28
1.29
1.2
1.57
1.52
1.33
1.67
1.61
1.41
1.25


BDL171
10663.3
P
<0.01
<0.01

<0.01
0.04

<0.01
0.02

0.03


BDL171
10663.3
Av
1.26
1.18

1.32
1.21

1.4
1.28

1.18


BDL171
10664.1
P



0.76
0.81

0.69
0.75
0.85


BDL171
10664.1
Av



1.19
1.14

1.26
1.21
1.11


BDL171
10664.3
P
0.01
0.12

0.14
0.17
0.58
0.11
0.12
0.47
0.07


BDL171
10664.3
Av
1.23
1.15

1.44
1.3
1.16
1.52
1.37
1.23
1.25


BDL173
9952.1
P





0.67


0.64


BDL173
9952.1
Av





1.11


1.13


BDL177
10521.3
P



0.56


0.56


BDL177
10521.3
Av



1.15


1.15


BDL177
10524.2
P



0.09

0.44
0.09

0.44


BDL177
10524.2
Av



1.2

1.1
1.2

1.1


BDL182
10691.2
P




0.27


0.27

0.46


BDL182
10691.2
Av




1.12


1.12

1.11


BDL182
10692.3
P
0.44


0.43
0.37

0.43
0.37

0.05


BDL182
10692.3
Av
1.11


1.25
1.12

1.25
1.12

1.08


BDL182
10693.2
P




0.65


0.65


BDL182
10693.2
Av




1.1


1.1


BDL182
10693.3
P
0.03
0.08

0.16
0.06
0.38
0.16
0.06
0.38


BDL182
10693.3
Av
1.19
1.15

1.22
1.18
1.12
1.22
1.18
1.12


BDL182
10693.5
P



0.48


0.48


BDL182
10693.5
Av



1.1


1.1


BDL182
10691.4
P
0.51
0.43

0.39
0.44

0.47
0.6

0.32


BDL182
10691.4
Av
1.11
1.11

1.36
1.21

1.26
1.13

1.19


BDL182
10691.8
P






0.87


BDL182
10691.8
Av






1.1


BDL183
9941.1
P





0.21
0.16

0.16


BDL183
9941.1
Av





1.11
1.11

1.13


BDL183
9943.4
P





0.3


BDL183
9943.4
Av





1.1


BDL183
9944.1
P
0.09
0.03

0.1
0.15
0.22
0.1
0.15
0.21


BDL183
9944.1
Av
1.16
1.12

1.27
1.23
1.22
1.29
1.25
1.24


BDL183
9941.1
P





0.65


0.65


BDL183
9941.1
Av





1.11


1.11


BDL183
9942.1
P
0.02
0.02

0.16
0.33
0.38
0.16
0.33
0.38


BDL183
9942.1
Av
1.16
1.1

1.12
1.17
1.13
1.12
1.17
1.13


BDL186
10002.2
P


0.1

0.05
<0.01

0.02
<0.01


BDL186
10002.2
Av


1.07

1.13
1.25

1.14
1.27


BDL186
10004.3
P


0.6


0.69


0.66


BDL186
10004.3
Av


1.11


1.15


1.17


BDL186
10001.3
P









0.53


BDL186
10001.3
Av









1.11


BDL186
10004.6
P



0.43


0.43


0.1


BDL186
10004.6
Av



1.2


1.2


1.08


BDL187
10502.2
P



0.29


0.6


BDL187
10502.2
Av



1.2


1.13


BDL187
10503.1
P



0.09
0.27

0.09
0.27


BDL187
10503.1
Av



1.26
1.1

1.26
1.1


BDL187
10503.3
P



0.66


0.66


BDL187
10503.3
Av



1.16


1.16


BDL187
10503.5
P
0.26


BDL187
10503.5
Av
1.1


BDL188
10462.4
P



0.14
0.07

0.14
0.07

0.32


BDL188
10462.4
Av



1.13
1.09

1.13
1.09

1.13


BDL188
10462.1
P
0.02
0.11

0.04
0.11
0.4
0.04
0.11
0.4


BDL188
10462.1
Av
1.2
1.14

1.3
1.27
1.21
1.3
1.27
1.21


BDL188
10462.4
P
0.03
0.03
0.14

0.09
0.1

0.09
0.1


BDL188
10462.4
Av
1.16
1.16
1.1

1.24
1.23

1.24
1.23


BDL190
10232.2
P
0.01
0.01
<0.01
0.43
0.09
0.14
0.43
0.09
0.14


BDL190
10232.2
Av
1.18
1.15
1.13
1.17
1.25
1.24
1.17
1.25
1.24


BDL190
10233.2
P
0.03
<0.01
0.09
0.03
0.01
<0.01
0.03
0.01
<0.01


BDL190
10233.2
Av
1.14
1.16
1.18
1.19
1.35
1.29
1.19
1.35
1.29


BDL190
10233.4
P


0.11
0.18

<0.01
0.18

<0.01


BDL190
10233.4
Av


1.11
1.11

1.17
1.11

1.17


BDL190
10234.2
P

0.09


0.05


0.05


BDL190
10234.2
Av

1.06


1.18


1.18


BDL192
9921.6
P



0.26
0.4
0.48
0.23
0.37
0.44


BDL192
9921.6
Av



1.14
1.14
1.13
1.16
1.15
1.14


BDL192
9922.1
P
0.11


0.35
0.33
0.28
0.33
0.3
0.22


BDL192
9922.1
Av
1.1


1.21
1.14
1.1
1.23
1.15
1.12


BDL192
9921.6
P



0.21
0.14
0.41
0.21
0.14
0.41


BDL192
9921.6
Av



1.12
1.14
1.14
1.12
1.14
1.14


BDL192
9922.5
P



0.35
0.33
0.3
0.65
0.62


BDL192
9922.5
Av



1.18
1.2
1.13
1.11
1.13


BDL193
10152.2
P



0.08


0.06
0.17

0.01


BDL193
10152.2
Av



1.15


1.16
1.1

1.06


BDL193
10153.2
P






0.6


BDL193
10153.2
Av






1.11


BDL193
10153.4
P


0.04
0.4
0.37
0.21
0.38
0.34
0.18


BDL193
10153.4
Av


1.08
1.23
1.16
1.16
1.25
1.18
1.17


BDL193
10153.3
P
0.41
0.14

0.4
0.01
0.4
0.4
0.01
0.4
0.33


BDL193
10153.3
Av
1.12
1.15

1.21
1.31
1.14
1.21
1.31
1.14
1.13


BDL193
10153.4
P
0.33
0.25

0.51
0.27
0.17
0.51
0.27
0.17


BDL193
10153.4
Av
1.1
1.11

1.14
1.23
1.14
1.14
1.23
1.14


BDL196
10243.1
P
0.61
0.66

0.6
0.66
0.66
0.6
0.66
0.66


BDL196
10243.1
Av
1.14
1.1

1.2
1.16
1.15
1.2
1.16
1.15


BDL196
10243.1
P


0.02


BDL196
10243.1
Av


1.05


BDL201
9961.3
P
0.26
0.22
0.38
0.11
0.23
0.44
0.11
0.23
0.44
0.09


BDL201
9961.3
Av
1.13
1.11
1.16
1.33
1.23
1.35
1.33
1.23
1.35
1.07


BDL220
10333.5
P


0.48


BDL220
10333.5
Av


1.1


BDL223
10793.5
P
0.09
0.01
0.01
0.39
0.12
0.26
0.39
0.12
0.26
0.02


BDL223
10793.5
Av
1.15
1.12
1.1
1.12
1.25
1.13
1.12
1.25
1.13
1.06


BDL223
10793.8
P
<0.01
0.01

0.2
0.19

0.2
0.19


BDL223
10793.8
Av
1.17
1.1

1.31
1.18

1.31
1.18


BDL224
10451.7
P



0.59


0.59


0.05


BDL224
10451.7
Av



1.12


1.12


1.08


BDL226
10861.2
P
0.05
0.05

0.01
0.07

0.01
0.04

0.03


BDL226
10861.2
Av
1.12
1.12

1.26
1.17

1.34
1.24

1.21


BDL226
10861.4
P






0.65


0.31


BDL226
10861.4
Av






1.13


1.12


BDL226
10864.2
P
0.01
0.01
0.09
<0.01
<0.01
0.07
<0.01
<0.01
0.04
0.22


BDL226
10864.2
Av
1.2
1.15
1.09
1.49
1.34
1.21
1.59
1.42
1.29
1.13


BDL227
11491.3
P
0.21
0.01
0.08
0.27
0.07

0.27
0.07


BDL227
11491.3
Av
1.11
1.09
1.09
1.12
1.21

1.12
1.21


BDL227
11492.3
P
<0.01
<0.01


0.01
0.05

0.01
0.05


BDL227
11492.3
Av
1.17
1.12


1.23
1.12

1.23
1.12


BDL233
10822.1
P




0.63


0.63


BDL233
10822.1
Av




1.12


1.12


BDL233
10825.4
P
0.4
0.4
0.37
0.63
0.35
0.48
0.63
0.35
0.48


BDL233
10825.4
Av
1.16
1.16
1.16
1.14
1.39
1.25
1.14
1.39
1.25


BDL237
10893.1
P



0.09


0.09


BDL237
10893.1
Av



1.12


1.12


BDL237
10895.1
P
0.37
0.29

0.05
0.56
0.55
0.05
0.56
0.55


BDL237
10895.1
Av
1.13
1.1

1.13
1.15
1.11
1.13
1.15
1.11


BDL237
10895.2
P



0.29


0.29


BDL237
10895.2
Av



1.12


1.12


BDL237
10895.3
P
0.55


0.56


0.56


BDL237
10895.3
Av
1.13


1.12


1.12


BDL238
10951.4
P
0.35



0.1


0.1


BDL238
10951.4
Av
1.11



1.14


1.14


BDL238
10952.3
P




0.68


0.68


BDL238
10952.3
Av




1.1


1.1


BDL238
10954.2
P
0.04
<0.01
<0.01
0.08
<0.01
<0.01
0.08
<0.01
<0.01
<0.01


BDL238
10954.2
Av
1.33
1.28
1.23
1.73
1.76
1.52
1.73
1.76
1.52
1.13


BDL238
10954.3
P



0.74


0.74


BDL238
10954.3
Av



1.13


1.13


BDL240
10802.2
P
0.02
0.03
0.12
0.1
0.02
0.04
0.1
0.02
0.04


BDL240
10802.2
Av
1.22
1.26
1.18
1.34
1.54
1.35
1.34
1.54
1.35


BDL241
10873.1
P
0.02
0.13
0.11
<0.01
0.38
0.02
<0.01
0.38
0.02


BDL241
10873.1
Av
1.19
1.18
1.15
1.41
1.3
1.34
1.41
1.3
1.34


BDL242
10731.2
P
0.4
0.52

0.14
0.46
0.58
0.14
0.46
0.58


BDL242
10731.2
Av
1.13
1.12

1.22
1.28
1.14
1.22
1.28
1.14


BDL242
10731.5
P



0.1


0.1


BDL242
10731.5
Av



1.11


1.11


BDL242
10731.6
P
<0.01
<0.01
0.18
0.03
0.25
0.08
0.03
0.25
0.08


BDL242
10731.6
Av
1.21
1.22
1.19
1.48
1.45
1.36
1.48
1.45
1.36


BDL242
10731.7
P



0.06


0.06


BDL242
10731.7
Av



1.12


1.12


BDL245
10813.3
P

0.03


BDL245
10813.3
Av

1.08


BDL250
10841.3
P
0.02
0.18
0.26
0.06
0.22
0.32
0.06
0.22
0.32
0.05


BDL250
10841.3
Av
1.24
1.18
1.11
1.36
1.41
1.17
1.36
1.41
1.17
1.08


BDL250
10846.2
P
0.48


0.64
0.41

0.64
0.41


BDL250
10846.2
Av
1.1


1.12
1.16

1.12
1.16


BDL250
10846.3
P
0.38
0.36
0.48
0.58
0.46
0.62
0.58
0.46
0.62


BDL250
10846.3
Av
1.11
1.17
1.11
1.17
1.34
1.19
1.17
1.34
1.19


BDL252
10882.1
P
0.3
0.41
0.44
0.32
0.26
0.34
0.32
0.26
0.34
<0.01


BDL252
10882.1
Av
1.19
1.19
1.17
1.38
1.42
1.24
1.38
1.42
1.24
1.1


BDL48
10274.4
P
0.23
0.02
0.02
0.81
0.09
0.08
0.81
0.09
0.08


BDL48
10274.4
Av
1.14
1.15
1.2
1.1
1.23
1.36
1.1
1.23
1.36


BDL48
10271.1
P

0.06
<0.01
0.27
0.03
<0.01
0.27
0.03
<0.01


BDL48
10271.1
Av

1.08
1.16
1.11
1.22
1.27
1.11
1.22
1.27


BDL48
10274.3
P
0.07
0.01
<0.01
0.02
0.01
<0.01
0.02
0.01
<0.01


BDL48
10274.3
Av
1.21
1.19
1.09
1.25
1.35
1.22
1.25
1.35
1.22


BDL48
10274.4
P
0.29
0.2
0.13
0.22
0.03
0.22
0.22
0.03
0.22


BDL48
10274.4
Av
1.14
1.15
1.14
1.14
1.21
1.26
1.14
1.21
1.26


BDL48
10274.5
P
0.04
0.28
0.45
0.26
0.49
0.44
0.26
0.49
0.44


BDL48
10274.5
Av
1.11
1.13
1.11
1.14
1.22
1.22
1.14
1.22
1.22


BDL63
10381.1
P
0.12
0.02
<0.01
0.11
0.21
<0.01
0.11
0.21
<0.01


BDL63
10381.1
Av
1.2
1.18
1.17
1.2
1.39
1.37
1.2
1.39
1.37


BDL63
10381.2
P
0.03
0.25
0.37
0.31
0.6
0.42
0.31
0.6
0.42


BDL63
10381.2
Av
1.13
1.15
1.19
1.19
1.26
1.32
1.19
1.26
1.32


BDL63
10384.8
P

0.02
<0.01

0.06
<0.01

0.06
<0.01


BDL63
10384.8
Av

1.09
1.14

1.2
1.24

1.2
1.24


BDL79
11042.1
P

0.08


0.04
0.52

0.04
0.52


BDL79
11042.1
Av

1.06


1.16
1.1

1.16
1.1


BDL79
11044.3
P
<0.01
0.03


0.14


0.14


BDL79
11044.3
Av
1.17
1.11


1.14


1.14


BDL81
10371.8
P



0.34


0.34


BDL81
10371.8
Av



1.12


1.12


BDL81
10374.1
P



0.22


0.22


BDL81
10374.1
Av



1.16


1.16


BDL81
10371.5
P

0.02
0.17


0.21


0.21


BDL81
10371.5
Av

1.08
1.11


1.13


1.13


BDL81
10371.8
P


0.6

0.8
0.57

0.8
0.57


BDL81
10371.8
Av


1.13

1.13
1.22

1.13
1.22


BDL81
10374.1
P
0.26
0.31
0.44
0.16
0.19
0.32
0.16
0.19
0.32
0.26


BDL81
10374.1
Av
1.23
1.22
1.19
1.44
1.45
1.49
1.44
1.45
1.49
1.12


BDL85
10411.1
P
0.25
0.34
0.15
0.13
0.39
0.33
0.13
0.39
0.33
0.12


BDL85
10411.1
Av
1.2
1.16
1.14
1.39
1.29
1.28
1.39
1.29
1.28
1.16





Table 24. Results of the greenhouse experiments. Provided are the measured values of each parameter [parameters (Par.) 1-10 according to the parameters described in Table 23 above] in plants expressing the indicated polynucleotides. “Ev” = event; “P” = P-value; “Av” = ratio between the averages of event and control. Note that when the average ratio is higher than “1” the effect of exogenous expression of the gene is an increase of the desired trait;













TABLE 25







Results from greenhouse experiments



















Gene
Ev.
Par
11
12
13
14
15
16
17
18
19
20






















BDL102
10471.1
P


0.1
0.27
0.03
0.04
0.29





BDL102
10471.1
Av


1.35
1.23
1.18
1.27
1.1


BDL102
10472.1
P


0.17
0.35
0.25
0.21
0.22


BDL102
10472.1
Av


1.36
1.23
1.3
1.29
1.15


BDL102
10474.1
P


0.18
0.19
0.16
0.17
0.3


0.02


BDL102
10474.1
Av


1.56
1.82
1.54
1.4
1.3


1.03


BDL102
10474.2
P


0.04
<0.01
0.01
0.15
<0.01


BDL102
10474.2
Av


1.51
1.48
1.34
1.42
1.22


BDL102
10474.6
P


0.23


0.11


BDL102
10474.6
Av


1.19


1.12


BDL117
10071.2
P









0.1


BDL117
10071.2
Av









1.03


BDL117
10073.2
P





0.02
0.15


BDL117
10073.2
Av





1.1
1.1


BDL117
10074.1
P

0.21
0.27
0.29
0.26
0.18
0.12
0.04


BDL117
10074.1
Av

1.19
1.46
1.38
1.33
1.59
1.35
1.17


BDL117
10074.4
P
0.05
0.37
0.38
0.49
0.3
0.25
0.31


0.03


BDL117
10074.4
Av
1.06
1.12
1.28
1.16
1.19
1.43
1.28


1.02


BDL117
10073.1
P


0.62
0.52
0.63


BDL117
10073.1
Av


1.1
1.16
1.15


BDL117
10073.2
P



0.56
0.37
0.35
0.53
0.51


BDL117
10073.2
Av



1.19
1.25
1.14
1.13
1.15


BDL117
10074.1
P

0.01
0.53
0.37
0.36
0.33
0.42
0.43


BDL117
10074.1
Av

1.09
1.11
1.29
1.24
1.21
1.17
1.2


BDL117
10074.4
P



0.37
0.26

0.24
0.16


BDL117
10074.4
Av



1.1
1.12

1.13
1.11


BDL138
9811.4
P





0.06


BDL138
9811.4
Av





1.09


BDL138
9812.1
P





<0.01
0.02


BDL138
9812.1
Av





1.16
1.11


BDL138
9812.3
P
0.05

0.11


0.37
0.52

0.01


BDL138
9812.3
Av
1.04

1.13


1.14
1.1

1.03


BDL138
9811.1
P








0.02
<0.01


BDL138
9811.1
Av








1.04
1.04


BDL138
9813.4
P









<0.01


BDL138
9813.4
Av









1.04


BDL140
10423.1
P


0.01
0.22


BDL140
10423.1
Av


1.29
1.19


BDL140
10424.3
P









0.49


BDL140
10424.3
Av









1.27


BDL140
10424.4
P





0.64
0.68


BDL140
10424.4
Av





1.14
1.17


BDL140
10423.1
P








0.03


BDL140
10423.1
Av








1.04


BDL147
10303.1
P


0.11
0.07
0.11
0.12
0.01


BDL147
10303.1
Av


1.49
1.31
1.18
1.28
1.43


BDL147
10303.6
P





0.38
0.37


BDL147
10303.6
Av





1.11
1.12


BDL147
10304.2
P


0.33






0.05


BDL147
10304.2
Av


1.18






1.04


BDL147
10303.5
P



0.41


BDL147
10303.5
Av



1.1


BDL147
10304.2
P



0.48


BDL147
10304.2
Av



1.17


BDL149
9823.3
P


0.23


<0.01
0.01


BDL149
9823.3
Av


1.13


1.38
1.21


BDL149
9824.3
P

0.09


BDL149
9824.3
Av

1.04


BDL149
9824.4
P

0.02
0.12
0.03
0.17
<0.01
<0.01
0.02


BDL149
9824.4
Av

1.1
1.28
1.12
1.2
1.23
1.22
1.11


BDL149
9823.3
P


0.62
0.47
0.56


BDL149
9823.3
Av


1.13
1.16
1.12


BDL152
10431.1
P


0.31


BDL152
10431.1
Av


1.1


BDL152
10431.4
P



0.16
0.47
0.27

0.09

0.03


BDL152
10431.4
Av



1.1
1.1
1.18

1.18

1.02


BDL152
10432.5
P



0.18
0.62


BDL152
10432.5
Av



1.1
1.16


BDL152
10434.1
P






0.76


BDL152
10434.1
Av






1.11


BDL152
10434.4
P




0.32
0.25
0.04
0.16


BDL152
10434.4
Av




1.2
1.13
1.37
1.12


BDL152
10434.1
P








0.03


BDL152
10434.1
Av








1.04


BDL152
10434.4
P








0.05


BDL152
10434.4
Av








1.04


BDL153
10141.3
P


<0.01
<0.01
<0.01
0.25
0.05
<0.01


BDL153
10141.3
Av


1.32
1.24
1.27
1.33
1.26
1.15


BDL153
10142.2
P
0.03
0.33
0.28
0.54
0.41
0.2
0.33
0.55

0.07


BDL153
10142.2
Av
1.15
1.16
1.44
1.28
1.41
1.54
1.34
1.12

1.02


BDL153
10143.1
P
0.01

0.21

0.32

0.05

0.01
<0.01


BDL153
10143.1
Av
1.12

1.2

1.14

1.11

1.02
1.02


BDL153
10144.1
P

<0.01
0.05
0.08
0.07


BDL153
10144.1
Av

1.09
1.13
1.1
1.1


BDL153
10141.3
P



0.06
0.02
0.02
0.24


BDL153
10141.3
Av



1.14
1.1
1.26
1.19


BDL153
10142.2
P

0.1
0.17
0.35
0.06
0.02
0.05
0.04


BDL153
10142.2
Av

1.05
1.1
1.17
1.22
1.48
1.31
1.26


BDL153
10142.3
P




0.36
0.23


BDL153
10142.3
Av




1.14
1.1


BDL153
10143.1
P





0.15


BDL153
10143.1
Av





1.14


BDL153
10143.2
P

0.04

0.15

0.07

<0.01


BDL153
10143.2
Av

1.06

1.11

1.2

1.15


BDL153
10144.1
P



0.4
0.48

0.24
0.08


BDL153
10144.1
Av



1.43
1.11

1.34
1.13


BDL153
10144.4
P






0.54


BDL153
10144.4
Av






1.1


BDL154
10703.6
P





0.66


BDL154
10703.6
Av





1.1


BDL154
10703.8
P


0.08
0.09
0.54
<0.01
0.09


BDL154
10703.8
Av


1.47
1.41
1.13
1.47
1.22


BDL155
9991.5
P


0.36

0.09
0.31
0.41


BDL155
9991.5
Av


1.11

1.18
1.29
1.35


BDL155
9991.9
P






0.27


BDL155
9991.9
Av






1.17


BDL155
9993.2
P






0.64


BDL155
9993.2
Av






1.12


BDL155
9994.3
P
0.16

0.31
0.08
0.12
0.12
0.09
0.41


BDL155
9994.3
Av
1.14

1.1
1.16
1.17
1.43
1.44
1.12


BDL155
9993.2
P








0.06


BDL155
9993.2
Av








1.03


BDL155
9994.3
P








0.03


BDL155
9994.3
Av








1.04


BDL157
9911.4
P









0.09


BDL157
9911.4
Av









1.03


BDL157
9914.2
P






0.12
0.09


BDL157
9914.2
Av






1.11
1.06


BDL162
10492.2
P




0.12

0.44


BDL162
10492.2
Av




1.39

1.15


BDL162
10492.4
P






0.82


BDL162
10492.4
Av






1.13


BDL162
10494.1
P





0.1
0.13


BDL162
10494.1
Av





1.21
1.21


BDL167
10043.1
P








0.17


BDL167
10043.1
Av








1.21


BDL167
10043.2
P








<0.01
0.01


BDL167
10043.2
Av








1.04
1.03


BDL167
10044.2
P


0.05
0.07





0.03


BDL167
10044.2
Av


1.15
1.16





1.02


BDL167
10042.3
P

0.1





0.2


BDL167
10042.3
Av

1.05





1.12


BDL167
10043.3
P



0.35
0.19
0.38

0.41


BDL167
10043.3
Av



1.11
1.1
1.14

1.11


BDL167
10044.2
P


0.51
0.28
0.27
0.31
0.18


BDL167
10044.2
Av


1.1
1.14
1.15
1.17
1.17


BDL168
9881.3
P
0.08
<0.01
0.24
0.17
0.1
0.11
0.21
0.3

<0.01


BDL168
9881.3
Av
1.09
1.1
1.32
1.36
1.44
1.17
1.21
1.15

1.02


BDL168
9881.4
P

0.01
0.1
0.32
0.05
0.16
0.36
0.44


BDL168
9881.4
Av

1.15
1.3
1.23
1.32
1.45
1.25
1.14


BDL168
9882.3
P


0.61
0.54
0.49
0.66
0.71
0.66


BDL168
9882.3
Av


1.15
1.2
1.3
1.2
1.13
1.1


BDL168
9884.4
P




0.7


BDL168
9884.4
Av




1.15


BDL168
9881.4
P




0.57
0.57
0.37
0.4


BDL168
9881.4
Av




1.11
1.1
1.17
1.14


BDL168
9882.1
P



0.1
0.22
0.48

<0.01


BDL168
9882.1
Av



1.12
1.11
1.14

1.16


BDL168
9882.3
P





0.39
0.22


BDL168
9882.3
Av





1.12
1.11


BDL168
9884.1
P






0.11


BDL168
9884.1
Av






1.12


BDL169
10743.4
P


0.55
0.5
0.69
0.44


BDL169
10743.4
Av


1.16
1.19
1.12
1.17


BDL169
10744.1
P
0.41

0.38


0.29
0.31


BDL169
10744.1
Av
1.15

1.19


1.4
1.24


BDL169
10747.1
P
0.09

0.58


0.01


BDL169
10747.1
Av
1.11

1.22


1.42


BDL169
10747.5
P
<0.01

0.14
0.06


BDL169
10747.5
Av
1.11

1.29
1.15


BDL169
10741.3
P


0.42
0.68

0.53


BDL169
10741.3
Av


1.17
1.11

1.16


BDL169
10744.2
P
0.02

0.26
0.31
0.32
0.37
0.24
0.02

0.02


BDL169
10744.2
Av
1.04

1.48
1.56
1.44
1.37
1.26
1.23

1.03


BDL169
10747.1
P


0.34
<0.01
0.36
0.02
0.02


BDL169
10747.1
Av


1.39
1.32
1.2
1.16
1.17


BDL169
10747.3
P









0.45


BDL169
10747.3
Av









1.1


BDL169
10747.5
P


0.11
0.14
<0.01
<0.01


BDL169
10747.5
Av


1.2
1.26
1.27
1.22


BDL171
10661.2
P
0.6

0.63
0.74
0.35
0.84
0.55


BDL171
10661.2
Av
1.11

1.17
1.1
1.19
1.1
1.33


BDL171
10662.3
P


0.4
0.67

0.5
0.15


BDL171
10662.3
Av


1.21
1.11

1.18
1.46


BDL171
10664.1
P
0.09

<0.01
<0.01
0.48
0.03
<0.01
0.01


BDL171
10664.1
Av
1.15

1.56
1.44
1.42
1.57
1.6
1.29


BDL171
10664.3
P
0.34
0.47
0.24
0.04
0.46
0.08
0.38
0.48


BDL171
10664.3
Av
1.19
1.12
1.3
1.29
1.18
1.39
1.43
1.26


BDL171
10661.5
P
0.51




0.76
0.68


BDL171
10661.5
Av
1.1




1.11
1.12


BDL171
10662.2
P


0.39


0.06
0.42


BDL171
10662.2
Av


1.11


1.47
1.14


BDL171
10662.3
P
0.09

<0.01
0.02
<0.01
0.24
0.17
<0.01


BDL171
10662.3
Av
1.3

1.39
1.5
1.33
1.46
1.37
1.23


BDL171
10663.3
P
<0.01

0.04
0.07

<0.01
0.08


BDL171
10663.3
Av
1.2

1.2
1.17

1.54
1.24


BDL171
10664.1
P


0.71
0.79





0.01


BDL171
10664.1
Av


1.18
1.13





1.03


BDL171
10664.3
P
0.08

0.18
0.22

0.01
0.33

0.09


BDL171
10664.3
Av
1.18

1.29
1.22

1.54
1.23

1.03


BDL173
9951.2
P








<0.01


BDL173
9951.2
Av








1.03


BDL173
9952.1
P




0.61


BDL173
9952.1
Av




1.13


BDL173
9954.3
P








<0.01
0.02


BDL173
9954.3
Av








1.05
1.04


BDL173
9953.4
P









<0.01


BDL173
9953.4
Av









1.03


BDL177
10521.3
P


0.37

0.2


BDL177
10521.3
Av


1.22

1.16


BDL177
10522.2
P









<0.01


BDL177
10522.2
Av









1.05


BDL177
10524.2
P


0.16


0.21
0.28


BDL177
10524.2
Av


1.14


1.14
1.17


BDL182
10691.2
P



0.14
0.59
0.08


BDL182
10691.2
Av



1.11
1.12
1.2


BDL182
10692.3
P


0.53
0.2


0.73


BDL182
10692.3
Av


1.16
1.15


1.13


BDL182
10693.2
P



0.34

0.18

0.67


BDL182
10693.2
Av



1.13

1.24

1.11


BDL182
10693.3
P


0.25
0.07

0.05
0.25


BDL182
10693.3
Av


1.18
1.14

1.42
1.35


BDL182
10693.5
P





0.15
0.05


BDL182
10693.5
Av





1.18
1.29


BDL182
10691.2
P








0.02
0.01


BDL182
10691.2
Av








1.06
1.04


BDL182
10691.4
P
<0.01
0.2
0.56
0.65

<0.01
0.13


BDL182
10691.4
Av
1.25
1.15
1.19
1.12

1.48
1.29


BDL182
10691.8
P


0.79


0.84


BDL182
10691.8
Av


1.14


1.14


BDL182
10693.2
P








0.02


BDL182
10693.2
Av








1.05


BDL182
10693.3
P





0.85


BDL182
10693.3
Av





1.13


BDL183
9941.1
P

<0.01


0.26


BDL183
9941.1
Av

1.09


1.13


BDL183
9942.4
P





0.02
<0.01


BDL183
9942.4
Av





1.17
1.16


BDL183
9943.4
P



0.21
0.15


BDL183
9943.4
Av



1.11
1.14


BDL183
9944.1
P
0.05
<0.01
0.09
0.01
0.3
<0.01
0.02


BDL183
9944.1
Av
1.04
1.1
1.19
1.15
1.13
1.31
1.21


BDL183
9941.1
P




0.64


0.56


BDL183
9941.1
Av




1.11


1.16


BDL183
9942.1
P


0.12
0.31
0.46
0.02


BDL183
9942.1
Av


1.13
1.19
1.12
1.26


BDL186
10002.2
P



0.01
<0.01


0.1


BDL186
10002.2
Av



1.14
1.21


1.12


BDL186
10004.3
P



0.71
0.59



0.09
<0.01


BDL186
10004.3
Av



1.13
1.15



1.02
1.02


BDL186
10001.3
P





0.3


BDL186
10001.3
Av





1.25


BDL186
10004.6
P


0.54


BDL186
10004.6
Av


1.16


BDL187
10502.2
P


0.38


BDL187
10502.2
Av


1.12


BDL187
10502.4
P





0.59


BDL187
10502.4
Av





1.1


BDL187
10503.1
P


0.05



0.26


BDL187
10503.1
Av


1.26



1.15


BDL187
10503.3
P


0.29



0.3


BDL187
10503.3
Av


1.25



1.14


BDL187
10503.5
P





0.2
0.08


BDL187
10503.5
Av





1.36
1.25


BDL188
10462.4
P



0.09


BDL188
10462.4
Av



1.06


BDL188
10462.1
P


0.02
0.11
0.44
0.25
0.29


BDL188
10462.1
Av


1.28
1.32
1.19
1.15
1.14


BDL188
10462.4
P



0.02
0.09
0.01
0.25


BDL188
10462.4
Av



1.19
1.22
1.36
1.24


BDL188
10464.5
P





0.33


BDL188
10464.5
Av





1.19


BDL190
10234.1
P



0.5


BDL190
10234.1
Av



1.11


BDL190
10234.2
P



0.57




0.01


BDL190
10234.2
Av



1.1




1.03


BDL190
10231.1
P





0.21


BDL190
10231.1
Av





1.13


BDL190
10231.2
P





0.02


BDL190
10231.2
Av





1.24


BDL190
10232.2
P


0.44
0.08
0.16
0.1
0.39
0.25


BDL190
10232.2
Av


1.18
1.23
1.18
1.29
1.16
1.16


BDL190
10233.2
P


0.05
0.02
<0.01
0.02
0.05
0.05

0.04


BDL190
10233.2
Av


1.18
1.31
1.21
1.25
1.15
1.31

1.02


BDL190
10233.4
P




0.02
0.45
0.5
<0.01


BDL190
10233.4
Av




1.2
1.16
1.12
1.16


BDL190
10234.2
P



0.07

0.05


BDL190
10234.2
Av



1.17

1.19


BDL192
9921.3
P





0.38


BDL192
9921.3
Av





1.13


BDL192
9921.6
P


0.12
0.36
0.55


BDL192
9921.6
Av


1.15
1.13
1.11


BDL192
9922.1
P


0.11
0.12

0.57
0.56


BDL192
9922.1
Av


1.18
1.11

1.17
1.11


BDL192
9921.6
P

0.09
0.19

0.51


BDL192
9921.6
Av

1.07
1.1

1.13


BDL192
9922.5
P

0.01
0.35
0.29



0.5


BDL192
9922.5
Av

1.06
1.18
1.2



1.11


BDL193
10152.2
P
0.05
0.23



0.05
0.14


BDL193
10152.2
Av
1.04
1.1



1.17
1.11


BDL193
10152.3
P









0.02


BDL193
10152.3
Av









1.02


BDL193
10153.2
P





0.32


BDL193
10153.2
Av





1.1


BDL193
10153.4
P


0.37

0.29

0.46
0.09
<0.01


BDL193
10153.4
Av


1.14

1.15

1.1
1.09
1.02


BDL193
10153.2
P



0.42




0.07
<0.01


BDL193
10153.2
Av



1.12




1.02
1.03


BDL193
10153.3
P
0.07

0.37
0.01

0.2
0.22
0.09


BDL193
10153.3
Av
1.1

1.15
1.27

1.2
1.18
1.16


BDL193
10153.4
P


0.41
0.24
0.16
0.63


BDL193
10153.4
Av


1.13
1.16
1.1
1.11


BDL196
10243.1
P


0.65
0.77

0.63
0.71


BDL196
10243.1
Av


1.2
1.11

1.22
1.11


BDL201
9961.3
P
0.22
0.04
0.18
0.29
0.43

0.46
0.07

0.09


BDL201
9961.3
Av
1.1
1.06
1.28
1.16
1.33

1.12
1.25

1.02


BDL220
10331.5
P









<0.01


BDL220
10331.5
Av









1.05


BDL220
10331.7
P









0.39


BDL220
10331.7
Av









1.1


BDL220
10333.5
P




0.49


BDL220
10333.5
Av




1.18


BDL223
10793.3
P




0.1


BDL223
10793.3
Av




1.1


BDL223
10793.5
P
<0.01

0.47
0.01
0.02
0.1
0.21
0.12

0.08


BDL223
10793.5
Av
1.08

1.1
1.23
1.15
1.22
1.16
1.12

1.02


BDL223
10793.8
P
0.08

0.08
0.09
0.06
0.1
0.23


BDL223
10793.8
Av
1.03

1.28
1.2
1.11
1.21
1.1


BDL224
10451.7
P





0.57


BDL224
10451.7
Av





1.11


BDL224
10453.3
P









0.5


BDL224
10453.3
Av









1.12


BDL225
10401.4
P
0.07


BDL225
10401.4
Av
1.04


BDL226
10861.2
P
0.03

0.04
0.08

0.25
0.08
0.29
0.01


BDL226
10861.2
Av
1.19

1.17
1.14

1.37
1.31
1.12
1.06


BDL226
10864.2
P
<0.01
0.07
<0.01
0.01
0.11
0.06
<0.01


BDL226
10864.2
Av
1.17
1.08
1.38
1.24
1.13
1.43
1.36


BDL227
11491.3
P



<0.01

0.5
0.37


BDL227
11491.3
Av



1.23

1.12
1.12


BDL227
11492.3
P


0.04
<0.01
0.06
0.03
0.04
0.35


BDL227
11492.3
Av


1.16
1.25
1.14
1.21
1.19
1.14


BDL233
10822.1
P






<0.01


BDL233
10822.1
Av






1.21


BDL233
10825.4
P



0.39
0.47
0.32
0.5
0.02


BDL233
10825.4
Av



1.32
1.29
1.27
1.18
1.12


BDL237
10893.1
P


0.07


BDL237
10893.1
Av


1.17


BDL237
10895.1
P


0.09
0.44

0.16
0.26


BDL237
10895.1
Av


1.11
1.18

1.22
1.1


BDL237
10895.2
P


0.2
0.66


BDL237
10895.2
Av


1.13
1.12


BDL237
10895.3
P


0.51


0.36
0.64


BDL237
10895.3
Av


1.12


1.26
1.11


BDL237
10896.1
P



0.11



0.52


BDL237
10896.1
Av



1.13



1.1


BDL238
10951.4
P



0.09

0.22
0.18


BDL238
10951.4
Av



1.11

1.13
1.12


BDL238
10952.3
P



0.69



0.7


BDL238
10952.3
Av



1.1



1.1


BDL238
10954.2
P


0.08
<0.01
<0.01
0.11
<0.01


BDL238
10954.2
Av


1.59
1.7
1.46
1.34
1.29


BDL238
10954.3
P


0.67


0.58


BDL238
10954.3
Av


1.15


1.1


BDL240
10802.2
P


0.05
0.04
<0.01
<0.01
0.08
0.05


BDL240
10802.2
Av


1.34
1.61
1.3
1.22
1.27
1.17


BDL240
10806.2
P



0.3


BDL240
10806.2
Av



1.1


BDL240
10806.6
P
0.01








0.09


BDL240
10806.6
Av
1.06








1.04


BDL241
10873.1
P


<0.01
0.52
0.1
0.09
0.06


BDL241
10873.1
Av


1.41
1.24
1.33
1.23
1.23


BDL242
10731.2
P


0.05
0.45
0.62
0.49
0.45


BDL242
10731.2
Av


1.26
1.27
1.11
1.11
1.11


BDL242
10731.5
P


0.05


BDL242
10731.5
Av


1.13


BDL242
10731.6
P


0.01
0.19
0.02
<0.01
0.09

0.03


BDL242
10731.6
Av


1.46
1.43
1.37
1.29
1.21

1.02


BDL242
10731.7
P


0.04


0.25


BDL242
10731.7
Av


1.14


1.15


BDL245
10813.3
P
0.04
0.02



0.27
0.08
0.2


BDL245
10813.3
Av
1.07
1.08



1.14
1.2
1.15


BDL245
10816.3
P









0.02


BDL245
10816.3
Av









1.03


BDL245
10812.3
P







0.07


BDL245
10812.3
Av







1.09


BDL245
10813.3
P





0.12
0.03
0.01


BDL245
10813.3
Av





1.14
1.11
1.16


BDL247
10911.4
P









0.01


BDL247
10911.4
Av









1.03


BDL247
10912.6
P









0.02


BDL247
10912.6
Av









1.02


BDL248
11051.1
P








0.04


BDL248
11051.1
Av








1.03


BDL248
11054.1
P








0.06


BDL248
11054.1
Av








1.04


BDL250
10841.3
P


0.05
0.23
0.45
0.05
0.01
0.21


BDL250
10841.3
Av


1.31
1.31
1.12
1.38
1.32
1.1


BDL250
10842.3
P



0.17


BDL250
10842.3
Av



1.11


BDL250
10846.2
P



0.47

0.32
0.41


BDL250
10846.2
Av



1.13

1.2
1.11


BDL250
10846.3
P


0.54
0.46
0.51

0.14
0.26


BDL250
10846.3
Av


1.15
1.3
1.22

1.25
1.15


BDL252
10882.1
P


0.26
0.25
0.24
0.33
0.51
0.54
0.01


BDL252
10882.1
Av


1.35
1.36
1.22
1.35
1.28
1.21
1.02


BDL252
10882.4
P


0.49


BDL252
10882.4
Av


1.14


BDL48
10274.4
P
0.04



0.01
0.06
0.01
0.13


BDL48
10274.4
Av
1.11



1.33
1.4
1.49
1.14


BDL48
10271.1
P


0.18
0.02
<0.01
0.29

0.18
0.02
0.06


BDL48
10271.1
Av


1.13
1.21
1.24
1.11

1.22
1.02
1.02


BDL48
10271.5
P





0.51


BDL48
10271.5
Av





1.1


BDL48
10274.3
P


0.01
<0.01
<0.01
<0.01
<0.01
<0.01


BDL48
10274.3
Av


1.24
1.33
1.16
1.44
1.32
1.17


BDL48
10274.4
P


0.11
0.02
0.15
0.53
0.15
0.3


BDL48
10274.4
Av


1.21
1.23
1.2
1.18
1.25
1.21


BDL48
10274.5
P


0.41
0.48
0.59
0.27
0.02
0.21


BDL48
10274.5
Av


1.12
1.23
1.12
1.24
1.2
1.23


BDL63
10381.2
P





0.48


BDL63
10381.2
Av





1.29


BDL63
10381.1
P
0.04
0.1
0.21
0.23
0.04
0.19
0.01
<0.01


BDL63
10381.1
Av
1.1
1.05
1.22
1.34
1.29
1.34
1.26
1.25


BDL63
10381.2
P


0.21
0.5
0.48
0.17
0.01
0.23


BDL63
10381.2
Av


1.21
1.28
1.25
1.26
1.22
1.21


BDL63
10384.8
P

0.1

0.04
<0.01
0.33
0.14
<0.01


BDL63
10384.8
Av

1.05

1.2
1.2
1.15
1.1
1.25


BDL79
11042.1
P
<0.01


0.12

0.2
0.03


BDL79
11042.1
Av
1.08


1.1

1.14
1.11


BDL79
11044.3
P



0.12

<0.01
0.01
0.41


BDL79
11044.3
Av



1.12

1.24
1.15
1.18


BDL81
10371.8
P


0.18


BDL81
10371.8
Av


1.15


BDL81
10374.1
P


0.24


BDL81
10374.1
Av


1.13


BDL81
10371.5
P



0.2
0.32
0.06

0.02


BDL81
10371.5
Av



1.15
1.15
1.18

1.1


BDL81
10371.8
P



0.72
0.62
0.68
0.57
0.49


BDL81
10371.8
Av



1.16
1.19
1.15
1.11
1.23


BDL81
10374.1
P


0.18
0.17
0.35
0.1
0.15
0.41


BDL81
10374.1
Av


1.41
1.41
1.35
1.3
1.35
1.26


BDL85
10411.1
P


0.16
0.34
0.26
0.23
0.62
<0.01


BDL85
10411.1
Av


1.29
1.3
1.28
1.32
1.12
1.1


BDL85
10414.1
P









0.07


BDL85
10414.1
Av









1.02


BDL85
10414.2
P


0.71


BDL85
10414.2
Av


1.1





Table 25. Results of the greenhouse experiments. Provided are the measured values of each parameter [parameters (Par.) 11-20 according to the parameters described in Table 23 above] in plants expressing the indicated polynucleotides. “Ev” = event; “P” = P-value; “Av” = ratio between the averages of event and control. Note that when the average ratio is higher than “1” the effect of exogenous expression of the gene is an increase of the desired trait;













TABLE 26







Results from greenhouse experiments



















Gene
Ev.
Par
21
22
23
24
25
26
27
28
29
30






















BDL102
10471.1
P

0.18
0.42

0.39

0.46

0.46



BDL102
10471.1
Av

1.15
1.82

1.16

1.13

1.13


BDL102
10471.3
P


0.48


BDL102
10471.3
Av


1.38


BDL102
10472.1
P

0.01
0.54

0.17

0.22

0.22
0.43


BDL102
10472.1
Av

1.26
2.05

1.28

1.24

1.24
1.11


BDL102
10474.1
P

0.06

0.29
0.01

0.02
0.17
0.02
0.1


BDL102
10474.1
Av

1.15

1.43
1.54

1.48
1.14
1.48
1.29


BDL102
10474.2
P

0.03


0.1

0.18

0.18


BDL102
10474.2
Av

1.14


1.32

1.25

1.25


BDL102
10474.6
P
0.02

0.55


BDL102
10474.6
Av
1.02

1.76


BDL117
10071.2
P





0.24


BDL117
10071.2
Av





1.15


BDL117
10073.2
P

0.46
0.01
0.01


BDL117
10073.2
Av

1.19
1.2
1.14


BDL117
10074.1
P


0.53

0.08
0.08
0.03
0.11
0.02


BDL117
10074.1
Av


1.13

1.28
1.22
1.42
1.18
1.44


BDL117
10074.4
P




0.33

0.19

0.14


BDL117
10074.4
Av




1.16

1.24

1.26


BDL117
10071.2
P





0.21


BDL117
10071.2
Av





1.16


BDL117
10073.1
P




0.35

0.43


0.47


BDL117
10073.1
Av




1.17

1.14


1.16


BDL117
10073.2
P




0.09

0.16
0.08
0.16


BDL117
10073.2
Av




1.3

1.25
1.2
1.25


BDL117
10074.1
P




0.16
0.29
0.08
0.1
0.08


BDL117
10074.1
Av




1.24
1.12
1.31
1.17
1.31


BDL117
10074.4
P

0.71


0.54

0.43
0.27
0.43


BDL117
10074.4
Av

1.14


1.1

1.13
1.1
1.13


BDL138
9811.1
P



0.15


BDL138
9811.1
Av



1.13


BDL138
9811.4
P

0.41
0.03
<0.01


BDL138
9811.4
Av

1.21
1.07
1.26


BDL138
9812.1
P

<0.01
0.42
<0.01


BDL138
9812.1
Av

1.14
1.16
1.2


BDL138
9812.3
P
0.07


BDL138
9812.3
Av
1.02


BDL138
9813.1
P





0.28


BDL138
9813.1
Av





1.13


BDL138
9813.3
P

0.06
0.55


BDL138
9813.3
Av

1.3
1.12


BDL138
9811.1
P
0.04


BDL138
9811.1
Av
1.02


BDL138
9813.1
P

0.56



0.1


BDL138
9813.1
Av

1.19



1.18


BDL138
9813.4
P

0.75


BDL138
9813.4
Av

1.14


BDL138
9811.4
P

0.29


BDL138
9811.4
Av

1.1


BDL138
9812.1
P

0.39


BDL138
9812.1
Av

1.61


BDL138
9813.1
P

0.14



0.29


BDL138
9813.1
Av

1.33



1.12


BDL138
9813.3
P

0.36
0.09


BDL138
9813.3
Av

1.87
1.07


BDL140
10421.3
P

0.84

0.37


BDL140
10421.3
Av

1.16

1.18


BDL140
10424.3
P


0.47


BDL140
10424.3
Av


1.18


BDL140
10421.2
P

0.02
0.22


BDL140
10421.2
Av

1.14
1.12


BDL140
10423.1
P
0.08


BDL140
10423.1
Av
1.03


BDL147
10301.3
P

0.54


BDL147
10301.3
Av

1.17


BDL147
10303.1
P
0.01



0.53

0.32

0.32


BDL147
10303.1
Av
1.02



1.11

1.18

1.18


BDL147
10303.6
P
0.07


BDL147
10303.6
Av
1.02


BDL147
10304.2
P
<0.01




0.55


BDL147
10304.2
Av
1.04




1.1


BDL147
10301.5
P

0.36


BDL147
10301.5
Av

1.15


BDL147
10301.6
P

0.02


BDL147
10301.6
Av

1.14


BDL147
10303.1
P

0.01


BDL147
10303.1
Av

1.29


BDL147
10303.5
P

0.02

0.43

0.31



0.08


BDL147
10303.5
Av

1.17

1.17

1.12



1.09


BDL147
10304.2
P





0.04
0.36

0.36


BDL147
10304.2
Av





1.23
1.14

1.14


BDL149
9823.1
P

0.04
0.05
0.11


BDL149
9823.1
Av

1.17
1.19
1.17


BDL149
9823.3
P

<0.01
<0.01
0.23

0.34
0.42


BDL149
9823.3
Av

1.17
1.14
1.12

1.12
1.14


BDL149
9824.3
P





0.34


BDL149
9824.3
Av





1.11


BDL149
9824.4
P




0.28

0.11

0.08
<0.01


BDL149
9824.4
Av




1.17

1.28

1.3
1.15


BDL149
9823.3
P




0.48

0.48

0.48
0.1


BDL149
9823.3
Av




1.12

1.12

1.12
1.08


BDL149
9824.3
P





0.27


BDL149
9824.3
Av





1.14


BDL152
10431.1
P
0.01


BDL152
10431.1
Av
1.02


BDL152
10432.5
P




0.37


BDL152
10432.5
Av




1.17


BDL152
10434.1
P


0.05


BDL152
10434.1
Av


1.16


BDL152
10434.4
P

0.58
0.27

0.3

0.32
0.31
0.32
0.56


BDL152
10434.4
Av

1.14
1.17

1.19

1.19
1.15
1.19
1.1


BDL152
10431.1
P

0.43
0.58


BDL152
10431.1
Av

1.18
1.1


BDL152
10431.3
P



0.02


BDL152
10431.3
Av



1.18


BDL152
10434.1
P


0.42


BDL152
10434.1
Av


1.1


BDL152
10434.4
P
0.09


BDL152
10434.4
Av
1.03


BDL153
10141.3
P
0.09



0.12

0.07
0.23
0.05


BDL153
10141.3
Av
1.02



1.25

1.33
1.13
1.35


BDL153
10142.2
P




0.04
0.09
0.01
0.11
<0.01


BDL153
10142.2
Av




1.37
1.22
1.56
1.2
1.58


BDL153
10143.1
P




0.45

0.48

0.4


BDL153
10143.1
Av




1.12

1.12

1.14


BDL153
10144.1
P




0.52
0.25
0.53

0.45


BDL153
10144.1
Av




1.1
1.13
1.11

1.12


BDL153
10141.3
P

0.22
0.67

0.48

0.39

0.39


BDL153
10141.3
Av

1.28
1.12

1.11

1.14

1.14


BDL153
10142.2
P

0.05
<0.01
0.63
0.11

0.06
0.04
0.06


BDL153
10142.2
Av

1.36
1.2
1.1
1.26

1.33
1.18
1.33


BDL153
10142.3
P




0.26

0.29
0.2
0.29


BDL153
10142.3
Av




1.19

1.18
1.12
1.18


BDL153
10143.1
P

0.09







0.25


BDL153
10143.1
Av

1.09







1.11


BDL153
10143.2
P

0.05


0.47
0.22
0.36
0.23
0.36
0.23


BDL153
10143.2
Av

1.11


1.11
1.15
1.15
1.1
1.15
1.13


BDL153
10144.1
P




0.28

0.26
0.06
0.26


BDL153
10144.1
Av




1.17

1.18
1.17
1.18


BDL154
10703.1
P

0.11
0.64
0.67


BDL154
10703.1
Av

1.1
1.2
1.27


BDL154
10703.5
P

0.37
0.44
0.66


BDL154
10703.5
Av

1.18
1.26
1.13


BDL154
10703.6
P

0.25
0.59
0.59


BDL154
10703.6
Av

1.28
1.47
1.29


BDL154
10703.8
P

0.29


0.58

0.58

0.58


BDL154
10703.8
Av

1.17


1.1

1.1

1.1


BDL155
9991.3
P



0.65


BDL155
9991.3
Av



1.11


BDL155
9991.5
P


0.5

0.34

0.57
0.4
0.57
0.32


BDL155
9991.5
Av


1.23

1.17

1.11
1.12
1.11
1.22


BDL155
9991.9
P


0.39


BDL155
9991.9
Av


1.22


BDL155
9994.3
P


0.49
0.56
0.4

0.31
0.49
0.31


BDL155
9994.3
Av


1.1
1.14
1.15

1.19
1.1
1.19


BDL155
9994.5
P





0.41


BDL155
9994.5
Av





1.14


BDL157
9911.3
P

0.25
0.14


BDL157
9911.3
Av

1.54
1.11


BDL157
9911.4
P

<0.01


BDL157
9911.4
Av

1.26


BDL157
9914.2
P

0.37


BDL157
9914.2
Av

1.23


BDL157
9911.3
P

0.08
0.28


BDL157
9911.3
Av

1.15
1.25


BDL157
9911.4
P

0.46


BDL157
9911.4
Av

1.23


BDL157
9913.3
P

0.37


BDL157
9913.3
Av

1.21


BDL157
9914.2
P









0.45


BDL157
9914.2
Av









1.16


BDL160
10011.5
P

0.34

0.54

0.35


BDL160
10011.5
Av

1.59

1.26

1.15


BDL160
10011.6
P

0.03
0.61
0.67


BDL160
10011.6
Av

1.15
1.23
1.16


BDL160
10011.7
P

0.02


BDL160
10011.7
Av

1.16


BDL160
10013.1
P

0.01

0.41


BDL160
10013.1
Av

1.32

1.27


BDL160
10015.1
P

0.09

0.09


BDL160
10015.1
Av

1.1

1.14


BDL162
10491.1
P

0.42


BDL162
10491.1
Av

1.44


BDL162
10492.2
P




0.04

0.09
0.27
0.09
0.05


BDL162
10492.2
Av




1.4

1.34
1.17
1.34
1.44


BDL162
10492.4
P

0.37
0.39


0.55


BDL162
10492.4
Av

1.83
1.25


1.11


BDL162
10494.1
P


0.63


BDL162
10494.1
Av


1.13


BDL167
10042.3
P

0.19


BDL167
10042.3
Av

1.21


BDL167
10042.3
P





0.24


BDL167
10042.3
Av





1.15


BDL167
10043.2
P

0.13







0.6


BDL167
10043.2
Av

1.13







1.14


BDL167
10043.3
P




0.44




0.27


BDL167
10043.3
Av




1.12




1.12


BDL167
10043.4
P

0.05

0.33





0.14


BDL167
10043.4
Av

1.16

1.12





1.46


BDL167
10044.2
P

0.2


0.27

0.2

0.2
0.24


BDL167
10044.2
Av

1.18


1.18

1.21

1.21
1.19


BDL168
9881.3
P




0.01

0.01
0.04
0.01


BDL168
9881.3
Av




1.44

1.48
1.23
1.5


BDL168
9881.4
P


0.36

0.06
0.05
0.07
0.11
0.05


BDL168
9881.4
Av


1.14

1.31
1.24
1.33
1.18
1.35


BDL168
9882.1
P








0.51


BDL168
9882.1
Av








1.11


BDL168
9882.3
P




0.08

0.09
0.16
0.07


BDL168
9882.3
Av




1.31

1.33
1.17
1.35


BDL168
9884.4
P
<0.01



0.32

0.46
0.2
0.39


BDL168
9884.4
Av
1.03



1.17

1.14
1.16
1.16


BDL168
9881.3
P


0.66






<0.01


BDL168
9881.3
Av


1.1






1.19


BDL168
9881.4
P

0.12


0.44

0.34
0.14
0.34


BDL168
9881.4
Av

1.17


1.13

1.16
1.13
1.16


BDL168
9882.1
P




0.53

0.39


0.58


BDL168
9882.1
Av




1.1

1.14


1.13


BDL168
9882.3
P

0.01
0.42


0.35



0.18


BDL168
9882.3
Av

1.19
1.1


1.12



1.2


BDL168
9883.3
P


0.06


BDL168
9883.3
Av


1.09


BDL168
9884.1
P







0.07


BDL168
9884.1
Av







1.17


BDL169
10743.4
P




0.54

0.37

0.65


BDL169
10743.4
Av




1.11

1.18

1.1


BDL169
10744.1
P


0.28


0.3


BDL169
10744.1
Av


1.12


1.13


BDL169
10747.1
P

0.6
0.53


BDL169
10747.1
Av

1.12
1.17


BDL169
10747.5
P






0.61

0.44


BDL169
10747.5
Av






1.1

1.16


BDL169
10741.3
P

0.73


BDL169
10741.3
Av

1.1


BDL169
10744.2
P




0.04

0.05
0.07
0.05
0.84


BDL169
10744.2
Av




1.43

1.41
1.19
1.41
1.1


BDL169
10747.1
P


0.65
0.43
0.35

0.43

0.43


BDL169
10747.1
Av


1.21
1.24
1.18

1.15

1.15


BDL169
10747.3
P



0.4


BDL169
10747.3
Av



2.16


BDL169
10747.5
P




0.16

0.53

0.53


BDL169
10747.5
Av




1.27

1.11

1.11


BDL171
10661.2
P




0.3

0.31
0.54
0.31
0.34


BDL171
10661.2
Av




1.19

1.21
1.1
1.21
1.3


BDL171
10661.5
P


0.36


BDL171
10661.5
Av


1.13


BDL171
10664.1
P


0.02

0.07

0.03
0.28
0.03
0.67


BDL171
10664.1
Av


1.19

1.39

1.48
1.17
1.48
1.22


BDL171
10664.3
P




0.34

0.08
0.46
0.08
0.61


BDL171
10664.3
Av




1.17

1.36
1.11
1.36
1.25


BDL171
10662.2
P

0.09
0.07


BDL171
10662.2
Av

1.45
1.45


BDL171
10662.3
P


0.42

0.07

0.11
0.21
0.07
0.6


BDL171
10662.3
Av


1.2

1.33

1.32
1.16
1.4
1.15


BDL171
10663.3
P

0.22
0.01
0.56


BDL171
10663.3
Av

1.19
1.51
1.14


BDL171
10664.1
P








0.68


BDL171
10664.1
Av








1.1


BDL171
10664.3
P
0.09

0.07



0.48

0.34


BDL171
10664.3
Av
1.02

1.22



1.14

1.21


BDL173
9952.1
P


0.18

0.39
0.22
0.51

0.44


BDL173
9952.1
Av


1.13

1.14
1.15
1.12

1.13


BDL173
9954.2
P



0.09

0.35


BDL173
9954.2
Av



1.08

1.11


BDL173
9953.4
P
0.03








0.23


BDL173
9953.4
Av
1.02








1.3


BDL173
9954.2
P
0.02








0.1


BDL173
9954.2
Av
1.02








1.11


BDL176
9891.2
P

0.6
0.58


BDL176
9891.2
Av

1.24
1.19


BDL176
9892.3
P

0.38


BDL176
9892.3
Av

1.89


BDL176
9893.2
P

0.73


BDL176
9893.2
Av

1.11


BDL176
9893.3
P
0.01








0.37


BDL176
9893.3
Av
1.02








1.12


BDL177
10521.3
P




0.41


0.53


BDL177
10521.3
Av




1.15


1.1


BDL177
10522.2
P

0.44


BDL177
10522.2
Av

1.19


BDL182
10691.2
P


0.45

0.35

0.57
0.52
0.57


BDL182
10691.2
Av


1.11

1.17

1.11
1.1
1.11


BDL182
10693.2
P

0.12


BDL182
10693.2
Av

1.28


BDL182
10693.3
P






0.55

0.55


BDL182
10693.3
Av






1.11

1.11


BDL182
10693.5
P


0.01
0.07


BDL182
10693.5
Av


1.28
1.08


BDL182
10691.2
P



0.58


BDL182
10691.2
Av



1.12


BDL182
10691.4
P
0.09

0.29


0.11


BDL182
10691.4
Av
1.02

1.27


1.2


BDL182
10691.8
P


0.61


BDL182
10691.8
Av


1.11


BDL182
10693.2
P


0.38
0.57

0.37


BDL182
10693.2
Av


1.1
1.13

1.12


BDL182
10693.3
P

0.69
0.43
0.46


BDL182
10693.3
Av

1.25
1.59
1.25


BDL183
9941.1
P




0.37
0.25
0.5

0.42


BDL183
9941.1
Av




1.14
1.14
1.12

1.13


BDL183
9942.1
P









0.55


BDL183
9942.1
Av









1.12


BDL183
9942.4
P

0.22
0.09
0.01

0.07


0.53


BDL183
9942.4
Av

1.24
1.17
1.13

1.21


1.11


BDL183
9943.4
P




0.31

0.53
0.37


BDL183
9943.4
Av




1.16

1.11
1.1


BDL183
9944.1
P




0.46

0.23

0.18


BDL183
9944.1
Av




1.12

1.21

1.23


BDL183
9944.4
P
<0.01


BDL183
9944.4
Av
1.03


BDL183
9941.1
P




0.38

0.42
0.21
0.42


BDL183
9941.1
Av




1.15

1.13
1.13
1.13


BDL183
9942.1
P

0.17


0.48

0.42

0.42


BDL183
9942.1
Av

1.15


1.11

1.13

1.13


BDL183
9942.4
P

0.02
0.21


BDL183
9942.4
Av

1.16
1.13


BDL183
9943.4
P

0.35



0.33



0.12


BDL183
9943.4
Av

1.24



1.13



1.16


BDL183
9944.2
P

0.59
0.5


BDL183
9944.2
Av

1.12
1.14


BDL186
10002.2
P




0.15
0.23
0.14
0.24
0.1


BDL186
10002.2
Av




1.23
1.14
1.26
1.13
1.28


BDL186
10004.3
P




0.32

0.39
0.2
0.33


BDL186
10004.3
Av




1.16

1.16
1.16
1.18


BDL186
10001.3
P


0.46


BDL186
10001.3
Av


1.1


BDL186
10004.3
P

0.55


BDL186
10004.3
Av

1.15


BDL187
10502.2
P

0.43


BDL187
10502.2
Av

1.21


BDL187
10501.2
P
0.01
0.58


BDL187
10501.2
Av
1.02
1.38


BDL187
10502.4
P

0.66


BDL187
10502.4
Av

1.1


BDL187
10503.5
P

0.38
0.2
0.34


BDL187
10503.5
Av

1.13
1.24
1.12


BDL188
10462.1
P

0.46


BDL188
10462.1
Av

1.41


BDL188
10464.5
P





0.33


BDL188
10464.5
Av





1.12


BDL188
10462.1
P




0.38

0.35

0.35


BDL188
10462.1
Av




1.16

1.18

1.18


BDL188
10462.4
P
0.02
0.41


0.26

0.24

0.24


BDL188
10462.4
Av
1.02
1.32


1.2

1.22

1.22


BDL188
10464.3
P

0.66


BDL188
10464.3
Av

1.24


BDL188
10464.5
P

0.29
0.1


BDL188
10464.5
Av

1.38
1.12


BDL190
10232.2
P









0.6


BDL190
10232.2
Av









1.1


BDL190
10233.4
P









0.01


BDL190
10233.4
Av









1.2


BDL190
10234.1
P
0.01








0.4


BDL190
10234.1
Av
1.02








1.14


BDL190
10231.1
P

0.42
0.24


BDL190
10231.1
Av

1.18
1.21


BDL190
10231.2
P

0.64







0.5


BDL190
10231.2
Av

1.14







1.2


BDL190
10232.2
P

<0.01


0.26

0.14

0.14


BDL190
10232.2
Av

1.29


1.18

1.25

1.25


BDL190
10233.2
P




0.1
0.29
0.05
0.01
0.05


BDL190
10233.2
Av




1.25
1.13
1.32
1.24
1.32


BDL190
10233.4
P




0.16

0.29
0.29
0.29


BDL190
10233.4
Av




1.23

1.17
1.1
1.17


BDL190
10234.2
P

0.04







0.02


BDL190
10234.2
Av

1.11







1.09


BDL192
9921.3
P

0.54
0.56


0.16


BDL192
9921.3
Av

1.19
1.11


1.16


BDL192
9921.6
P




0.51

0.47

0.4


BDL192
9921.6
Av




1.1

1.12

1.14


BDL192
9922.1
P








0.52


BDL192
9922.1
Av








1.11


BDL192
9922.2
P
<0.01


BDL192
9922.2
Av
1.02


BDL192
9921.6
P




0.49
0.03
0.45

0.45


BDL192
9921.6
Av




1.15
1.25
1.16

1.16


BDL192
9922.5
P






0.54


0.51


BDL192
9922.5
Av






1.13


1.15


BDL193
10152.2
P





0.15


BDL193
10152.2
Av





1.17


BDL193
10152.3
P



0.3

0.1


BDL193
10152.3
Av



1.11

1.2


BDL193
10153.2
P





0.24


BDL193
10153.2
Av





1.14


BDL193
10153.4
P
0.04



0.39

0.4

0.33


BDL193
10153.4
Av
1.02



1.14

1.14

1.16


BDL193
10152.2
P


0.7


BDL193
10152.2
Av


1.12


BDL193
10152.3
P





0.14


BDL193
10152.3
Av





1.16


BDL193
10153.2
P
0.01


BDL193
10153.2
Av
1.02


BDL193
10153.3
P

0.35



0.4
0.48

0.48


BDL193
10153.3
Av

1.22



1.1
1.14

1.14


BDL193
10153.4
P




0.63

0.5

0.5


BDL193
10153.4
Av




1.1

1.14

1.14


BDL196
10241.3
P

0.5


BDL196
10241.3
Av

1.1


BDL196
10243.1
P


0.01



0.56

0.56


BDL196
10243.1
Av


1.08



1.14

1.14


BDL196
10243.2
P

0.37


BDL196
10243.2
Av

1.29


BDL196
10244.1
P

0.02
0.22
0.82





0.02


BDL196
10244.1
Av

1.21
1.11
1.1





1.13


BDL201
9961.3
P




0.12

0.12
0.31
0.12


BDL201
9961.3
Av




1.31

1.32
1.16
1.32


BDL201
9961.4
P


0.62


BDL201
9961.4
Av


1.14


BDL201
9961.6
P
0.01
0.01


BDL201
9961.6
Av
1.02
1.54


BDL201
9963.6
P

0.46
0.37
0.21


BDL201
9963.6
Av

1.29
1.13
1.15


BDL220
10331.5
P

0.76


BDL220
10331.5
Av

1.13


BDL220
10331.7
P


0.62
0.42

0.29


BDL220
10331.7
Av


1.21
1.17

1.18


BDL220
10333.2
P

0.62


BDL220
10333.2
Av

1.49


BDL220
10333.5
P



0.01
0.25


0.26

0.65


BDL220
10333.5
Av



1.13
1.22


1.18

1.14


BDL220
10334.1
P
<0.01

0.36
0.64


BDL220
10334.1
Av
1.04

1.31
1.11


BDL223
10791.1
P



0.51


BDL223
10791.1
Av



1.78


BDL223
10793.1
P

0.02
0.58


BDL223
10793.1
Av

1.16
1.34


BDL223
10793.3
P



0.7


BDL223
10793.3
Av



1.1


BDL223
10793.5
P

0.01

<0.01
0.42

0.48

0.48
0.18


BDL223
10793.5
Av

1.18

1.41
1.15

1.13

1.13
1.17


BDL223
10793.8
P


0.6


BDL223
10793.8
Av


1.36


BDL224
10451.3
P






0.61
0.5
0.61


BDL224
10451.3
Av






1.1
1.11
1.1


BDL224
10451.7
P









0.78


BDL224
10451.7
Av









1.11


BDL224
10451.8
P

0.03







0.54


BDL224
10451.8
Av

1.78







1.11


BDL224
10453.1
P









0.77


BDL224
10453.1
Av









1.11


BDL224
10453.3
P

0.62



0.39


BDL224
10453.3
Av

1.82



1.14


BDL225
10401.4
P





0.18


BDL225
10401.4
Av





1.17


BDL225
10402.2
P

0.29
0.74


BDL225
10402.2
Av

1.28
1.1


BDL225
10402.5
P



0.38


BDL225
10402.5
Av



1.13


BDL225
10401.4
P

0.5







0.65


BDL225
10401.4
Av

1.12







1.15


BDL225
10402.2
P



0.42





0.38


BDL225
10402.2
Av



1.1





1.15


BDL225
10402.6
P









0.38


BDL225
10402.6
Av









1.15


BDL225
10402.9
P


0.07
0.01


BDL225
10402.9
Av


1.14
1.15


BDL226
10861.2
P


0.53
0.54


BDL226
10861.2
Av


1.22
1.12


BDL226
10862.2
P
0.03


BDL226
10862.2
Av
1.03


BDL226
10864.2
P


0.44

0.58

0.32

0.21


BDL226
10864.2
Av


1.17

1.1

1.2

1.27


BDL226
10861.1
P


0.68
0.72


BDL226
10861.1
Av


1.27
1.21


BDL226
10861.4
P

0.04

0.41


BDL226
10861.4
Av

1.13

1.44


BDL226
10862.2
P



0.21


BDL226
10862.2
Av



1.51


BDL226
10863.4
P


0.53


BDL226
10863.4
Av


2.04


BDL227
11491.1
P

0.08

0.45


BDL227
11491.1
Av

1.17

2.04


BDL227
11491.3
P

0.13

0.34





0.08


BDL227
11491.3
Av

1.1

1.78





1.15


BDL227
11491.5
P

0.66


BDL227
11491.5
Av

1.15


BDL227
11492.3
P

0.04

0.71
0.48

0.49

0.49
0.02


BDL227
11492.3
Av

1.13

1.15
1.13

1.12

1.12
1.2


BDL227
11492.5
P



0.66


BDL227
11492.5
Av



1.29


BDL227
11493.5
P


0.65


BDL227
11493.5
Av


1.38


BDL230
10672.4
P

0.79


BDL230
10672.4
Av

1.1


BDL230
10673.2
P





0.42


BDL230
10673.2
Av





1.1


BDL233
10822.1
P



0.14


BDL233
10822.1
Av



1.37


BDL233
10822.2
P

0.02

0.46


BDL233
10822.2
Av

1.16

1.4


BDL233
10824.2
P



0.46


BDL233
10824.2
Av



1.69


BDL233
10825.4
P

0.03

0.16
0.15

0.19
0.12
0.19


BDL233
10825.4
Av

1.16

1.15
1.3

1.26
1.17
1.26


BDL237
10892.2
P

0.23


BDL237
10892.2
Av

1.15


BDL237
10893.1
P


0.48


BDL237
10893.1
Av


2.25


BDL237
10895.1
P

0.57
0.48
0.47


0.54

0.54


BDL237
10895.1
Av

1.11
1.28
1.35


1.11

1.11


BDL237
10895.2
P









0.61


BDL237
10895.2
Av









1.11


BDL237
10895.3
P

0.03
0.48


BDL237
10895.3
Av

1.18
2.07


BDL238
10951.4
P

0.03


BDL238
10951.4
Av

1.16


BDL238
10952.3
P



0.12

0.16


BDL238
10952.3
Av



1.15

1.16


BDL238
10953.1
P


0.43


BDL238
10953.1
Av


1.2


BDL238
10953.3
P

0.36


BDL238
10953.3
Av

1.18


BDL238
10954.2
P




0.02

0.01
0.05
0.01
0.04


BDL238
10954.2
Av




1.45

1.5
1.19
1.5
1.25


BDL238
10954.3
P


0.16


BDL238
10954.3
Av


1.77


BDL240
10802.2
P

0.24

0.44
0.1

0.07
0.06
0.07
0.25


BDL240
10802.2
Av

1.15

1.45
1.3

1.35
1.18
1.35
1.28


BDL240
10803.1
P



0.62


BDL240
10803.1
Av



1.45


BDL240
10803.5
P


0.63


BDL240
10803.5
Av


1.4


BDL240
10806.2
P

0.09







0.39


BDL240
10806.2
Av

1.1







1.11


BDL241
10873.1
P


0.55

0.11

0.09
0.17
0.09
0.34


BDL241
10873.1
Av


1.86

1.32

1.33
1.13
1.33
1.25


BDL241
10873.4
P



0.44


BDL241
10873.4
Av



1.73


BDL241
10874.2
P
<0.01


BDL241
10874.2
Av
1.03


BDL241
10875.1
P



0.33


BDL241
10875.1
Av



1.57


BDL241
10875.2
P


0.58
0.09


BDL241
10875.2
Av


1.48
1.19


BDL242
10731.2
P




0.59

0.46

0.46


BDL242
10731.2
Av




1.1

1.14

1.14


BDL242
10731.3
P


<0.01


BDL242
10731.3
Av


1.74


BDL242
10731.5
P


0.7


BDL242
10731.5
Av


1.18


BDL242
10731.6
P


0.63

0.07

0.07
0.09
0.07
0.04


BDL242
10731.6
Av


1.48

1.36

1.35
1.17
1.35
1.16


BDL242
10731.7
P


0.18


BDL242
10731.7
Av


2.28


BDL242
10737.2
P



0.07


BDL242
10737.2
Av



1.22


BDL245
10811.3
P

0.22
0.05
<0.01

0.2


BDL245
10811.3
Av

1.47
1.25
1.25

1.16


BDL245
10813.3
P


0.28
0.02

0.22


BDL245
10813.3
Av


1.17
1.33

1.15


BDL245
10811.2
P

0.37

0.3


BDL245
10811.2
Av

1.22

1.49


BDL245
10811.3
P

0.21
0.12
0.5


BDL245
10811.3
Av

1.18
1.44
1.79


BDL245
10812.3
P


0.55
0.11


BDL245
10812.3
Av


2.2
1.12


BDL245
10813.3
P

0.37

0.45

0.04


BDL245
10813.3
Av

1.19

1.1

1.26


BDL245
10816.3
P


0.52
0.23


BDL245
10816.3
Av


1.81
1.14


BDL247
10911.4
P

0.42


BDL247
10911.4
Av

1.1


BDL247
10912.1
P


0.48
0.58


BDL247
10912.1
Av


1.26
1.16


BDL247
10912.6
P



0.6


BDL247
10912.6
Av



1.33


BDL248
11051.2
P

0.45


BDL248
11051.2
Av

1.14


BDL250
10841.3
P

0.2

0.13
0.58

0.36

0.36


BDL250
10841.3
Av

1.14

1.16
1.1

1.17

1.17


BDL250
10842.1
P

0.45

0.37


BDL250
10842.1
Av

1.12

1.31


BDL250
10842.3
P

0.02

0.46


BDL250
10842.3
Av

1.15

1.14


BDL250
10843.2
P



0.42


BDL250
10843.2
Av



1.19


BDL250
10846.2
P

0.01

0.06


BDL250
10846.2
Av

1.17

1.22


BDL250
10846.3
P


0.48
0.22
0.26

0.34
0.25
0.34


BDL250
10846.3
Av


1.13
1.11
1.23

1.19
1.12
1.19


BDL252
10881.1
P


0.54


BDL252
10881.1
Av


2.4


BDL252
10882.1
P



0.59
0.24

0.2
0.14
0.2


BDL252
10882.1
Av



1.24
1.22

1.24
1.16
1.24


BDL252
10882.2
P


0.5
0.71


BDL252
10882.2
Av


1.52
1.27


BDL252
10882.4
P


0.52


BDL252
10882.4
Av


2.2


BDL252
10884.1
P

0.22

0.27


BDL252
10884.1
Av

1.16

1.28


BDL48
10271.1
P


0.01






0.34


BDL48
10271.1
Av


1.22






1.3


BDL48
10271.3
P



0.33

0.31


BDL48
10271.3
Av



1.23

1.17


BDL48
10271.5
P
<0.01


BDL48
10271.5
Av
1.03


BDL48
10274.4
P

0.5
0.02
0.01
0.07
0.52
0.06
0.15
0.06
0.01


BDL48
10274.4
Av

2.17
1.24
1.13
1.34
1.11
1.37
1.22
1.37
1.51


BDL48
10271.1
P




0.13
0.12
0.08
0.03
0.08


BDL48
10271.1
Av




1.25
1.17
1.29
1.2
1.29


BDL48
10271.3
P

0.21


BDL48
10271.3
Av

1.1


BDL48
10271.5
P

<0.01


BDL48
10271.5
Av

1.26


BDL48
10274.3
P

0.01


0.31

0.18

0.18


BDL48
10274.3
Av

1.18


1.15

1.21

1.21


BDL48
10274.4
P

0.57


0.22

0.12
0.18
0.12


BDL48
10274.4
Av

1.13


1.2

1.27
1.12
1.27


BDL48
10274.5
P


<0.01

0.45
0.35
0.2
0.3
0.2


BDL48
10274.5
Av


1.16

1.13
1.11
1.22
1.1
1.22


BDL58
10281.2
P



0.26

0.27


BDL58
10281.2
Av



1.11

1.19


BDL58
10281.3
P

0.65
0.64


BDL58
10281.3
Av

1.23
1.2


BDL58
10281.5
P



0.01


BDL58
10281.5
Av



1.12


BDL58
10282.3
P



0.02


BDL58
10282.3
Av



1.11


BDL63
10381.1
P

0.62
0.25
0.39


BDL63
10381.1
Av

1.35
1.28
1.11


BDL63
10381.2
P

0.1
0.19
0.39


BDL63
10381.2
Av

1.67
1.19
1.12


BDL63
10384.5
P

0.54

0.05





0.29


BDL63
10384.5
Av

1.95

1.09





1.19


BDL63
10381.1
P




0.06

0.02
0.04
0.02
<0.01


BDL63
10381.1
Av




1.31

1.4
1.18
1.4
1.16


BDL63
10381.2
P
0.06



0.19

0.1
0.07
0.1


BDL63
10381.2
Av
1.02



1.25

1.32
1.2
1.32


BDL63
10384.2
P


0.41
0.45





<0.01


BDL63
10384.2
Av


1.14
1.12





1.17


BDL63
10384.3
P









0.3


BDL63
10384.3
Av









1.14


BDL63
10384.7
P

0.04







<0.01


BDL63
10384.7
Av

1.12







1.16


BDL63
10384.8
P




0.12

0.11
0.06
0.11
0.31


BDL63
10384.8
Av




1.25

1.26
1.17
1.26
1.12


BDL79
11041.1
P

0.13
0.49
0.77


BDL79
11041.1
Av

1.11
2.06
1.1


BDL79
11042.1
P

0.09



0.2
0.54

0.54


BDL79
11042.1
Av

1.15



1.16
1.11

1.11


BDL79
11042.3
P


0.46


BDL79
11042.3
Av


1.37


BDL79
11043.1
P


0.47


BDL79
11043.1
Av


1.92


BDL79
11044.3
P

0.01

0.15


BDL79
11044.3
Av

1.21

1.23


BDL81
10371.5
P


0.6


BDL81
10371.5
Av


1.27


BDL81
10371.8
P


0.51


BDL81
10371.8
Av


2.2


BDL81
10372.1
P


0.54


BDL81
10372.1
Av


2.43


BDL81
10372.2
P

0.06
0.66


BDL81
10372.2
Av

1.12
1.28


BDL81
10374.1
P


0.42


BDL81
10374.1
Av


1.99


BDL81
10371.5
P



0.01
0.25

0.37
0.14
0.37
0.07


BDL81
10371.5
Av



1.13
1.18

1.14
1.13
1.14
1.11


BDL81
10371.8
P

0.2
0.05
0.02
0.33

0.23
0.19
0.23
0.04


BDL81
10371.8
Av

1.12
1.1
1.1
1.19

1.24
1.18
1.24
1.07


BDL81
10372.1
P

0.05


BDL81
10372.1
Av

1.1


BDL81
10372.2
P

0.33
0.4






0.59


BDL81
10372.2
Av

1.13
1.29






1.18


BDL81
10373.2
P

0.01


BDL81
10373.2
Av

1.19


BDL81
10374.1
P




0.06

0.02
0.23
0.02
0.04


BDL81
10374.1
Av




1.35

1.48
1.14
1.48
1.15


BDL85
10411.1
P



0.01
0.12

0.12
0.26
0.12
0.07


BDL85
10411.1
Av



1.09
1.29

1.28
1.12
1.28
1.16


BDL85
10411.3
P

0.59


BDL85
10411.3
Av

1.51


BDL85
10412.2
P

0.62


BDL85
10412.2
Av

1.6


BDL85
10414.1
P
0.1


BDL85
10414.1
Av
1.03


BDL85
10414.2
P









0.62


BDL85
10414.2
Av









1.19





Table 26. Results of the greenhouse experiments. Provided are the measured values of each parameter [parameters (Par.) 21-30 according to the parameters described in Table 23 above] in plants expressing the indicated polynucleotides. “Ev” = event; “P” = P-value; “Av” = ratio between the averages of event and control. Note that when the average ratio is higher than “1” the effect of exogenous expression of the gene is an increase of the desired trait;













TABLE 27







Results from greenhouse experiments
















Gene
Ev.
Par
31
32
33
34
35
36
37



















BDL102
10471.1
P
0.12








BDL102
10471.1
Av
1.12


BDL102
10474.1
P
0.26


BDL102
10474.1
Av
1.35


BDL117
10074.1
P



0.69


BDL117
10074.1
Av



1.1


BDL117
10074.4
P



0.45


BDL117
10074.4
Av



1.14


BDL138
9811.1
P

0.06
0.11

0.22


BDL138
9811.1
Av

1.18
1.11

1.1


BDL138
9811.4
P

<0.01
0.19

0.48


BDL138
9811.4
Av

1.21
1.11

1.2


BDL138
9813.1
P

0.1


0.02


BDL138
9813.1
Av

1.17


1.05


BDL138
9813.4
P





0.01


BDL138
9813.4
Av





1.08


BDL138
9811.1
P




0.26
0.58


BDL138
9811.1
Av




1.15
1.13


BDL138
9811.4
P

<0.01
0.02


BDL138
9811.4
Av

1.18
1.18


BDL138
9812.1
P

0.01
0.03

0.1


BDL138
9812.1
Av

1.13
1.1

1.07


BDL138
9813.1
P

0.02
0.09


BDL138
9813.1
Av

1.09
1.08


BDL138
9813.3
P

0.09
0.03


BDL138
9813.3
Av

1.17
1.16


BDL140
10423.1
P
0.71


BDL140
10423.1
Av
1.11


BDL147
10301.5
P

0.01


BDL147
10301.5
Av

1.1


BDL147
10301.6
P

0.06
0.02


BDL147
10301.6
Av

1.14
1.09


BDL147
10303.1
P

0.16



0.66


BDL147
10303.1
Av

1.11



1.14


BDL147
10303.5
P

0.01
0.01


BDL147
10303.5
Av

1.13
1.11


BDL147
10303.6
P





0.1


BDL147
10303.6
Av





1.13


BDL149
9824.4
P
0.01


BDL149
9824.4
Av
1.19


BDL152
10434.4
P
0.8


BDL152
10434.4
Av
1.13


BDL153
10143.1
P



0.65

0.52


BDL153
10143.1
Av



1.1

1.19


BDL153
10143.2
P



0.26


0.05


BDL153
10143.2
Av



1.1


1.02


BDL155
9991.5
P
0.56


BDL155
9991.5
Av
1.23


BDL155
9991.9
P
0.1


BDL155
9991.9
Av
1.31


BDL155
9993.2
P
0.62


BDL155
9993.2
Av
1.1


BDL155
9994.3
P
0.47


BDL155
9994.3
Av
1.14


BDL157
9911.3
P

0.02
0.33


BDL157
9911.3
Av

1.32
1.19


BDL157
9911.4
P



0.64


BDL157
9911.4
Av



1.14


BDL157
9913.1
P

0.01
<0.01


BDL157
9913.1
Av

1.19
1.08


BDL157
9913.3
P

0.11


BDL157
9913.3
Av

1.17


BDL157
9914.2
P

0.13


0.4


BDL157
9914.2
Av

1.18


1.1


BDL157
9911.3
P

0.15


BDL157
9911.3
Av

1.13


BDL157
9913.1
P





0.36


BDL157
9913.1
Av





1.15


BDL157
9913.3
P





0.03


BDL157
9913.3
Av





1.06


BDL157
9914.2
P



0.22


BDL157
9914.2
Av



1.18


BDL162
10492.2
P
0.1


BDL162
10492.2
Av
1.8


BDL167
10042.3
P

0.14


BDL167
10042.3
Av

1.15


BDL167
10042.4
P

0.01
0.01
0.19
0.01


BDL167
10042.4
Av

1.15
1.05
1.1
1.06


BDL167
10043.1
P

0.01
0.04

<0.01


BDL167
10043.1
Av

1.16
1.06

1.1


BDL167
10043.3
P

0.04
0.08

0.01


BDL167
10043.3
Av

1.15
1.05

1.06


BDL167
10044.2
P




0.52


BDL167
10044.2
Av




1.11


BDL167
10043.2
P



0.44
0.07


BDL167
10043.2
Av



1.22
1.08


BDL167
10043.3
P



<0.01


BDL167
10043.3
Av



1.2


BDL167
10043.4
P



0.22

0.2


BDL167
10043.4
Av



1.21

1.2


BDL167
10044.2
P



0.1


0.05


BDL167
10044.2
Av



1.22


1.03


BDL168
9881.3
P



<0.01


BDL168
9881.3
Av



1.27


BDL168
9881.4
P




0.4
0.42


BDL168
9881.4
Av




1.21
1.2


BDL168
9882.1
P





0.11


BDL168
9882.1
Av





1.39


BDL168
9882.3
P





0.18


BDL168
9882.3
Av





1.32


BDL169
10744.2
P
0.57


BDL169
10744.2
Av
1.16


BDL169
10747.1
P
0.46


BDL169
10747.1
Av
1.11


BDL169
10747.5
P
0.28


BDL169
10747.5
Av
1.16


BDL171
10661.2
P
0.7


BDL171
10661.2
Av
1.23


BDL171
10664.1
P
0.6


BDL171
10664.1
Av
1.39


BDL173
9951.2
P
0.66


BDL173
9951.2
Av
1.13


BDL173
9952.1
P



0.21
0.12


BDL173
9952.1
Av



1.23
1.14


BDL173
9952.2
P

0.14

0.64
0.34

0.04


BDL173
9952.2
Av

1.1

1.15
1.11

1.04


BDL173
9953.4
P

0.58

<0.01
0.47
0.06


BDL173
9953.4
Av

1.13

1.41
1.1
1.1


BDL173
9954.2
P

0.12
0.05
0.22


BDL173
9954.2
Av

1.17
1.08
1.1


BDL173
9954.5
P

<0.01
0.04
0.57


0.07


BDL173
9954.5
Av

1.21
1.09
1.13


1.03


BDL176
9891.2
P

0.01
<0.01
0.31
0.01

<0.01


BDL176
9891.2
Av

1.17
1.06
1.22
1.14

1.06


BDL176
9891.4
P

<0.01
0.05


BDL176
9891.4
Av

1.23
1.11


BDL176
9892.3
P

<0.01
<0.01



0.09


BDL176
9892.3
Av

1.34
1.17



1.03


BDL176
9893.2
P

0.08
0.16
0.25


BDL176
9893.2
Av

1.23
1.15
1.13


BDL176
9893.3
P

<0.01

0.01
0.12


BDL176
9893.3
Av

1.2

1.36
1.22


BDL177
10521.3
P
0.03


BDL177
10521.3
Av
1.43


BDL177
10524.2
P
0.22


BDL177
10524.2
Av
1.28


BDL183
9941.1
P




0.58


BDL183
9941.1
Av




1.1


BDL183
9942.1
P




0.08


BDL183
9942.1
Av




1.11


BDL183
9943.4
P



<0.01


BDL183
9943.4
Av



1.25


BDL183
9944.2
P





0.29


BDL183
9944.2
Av





1.24


BDL190
10232.2
P

0.27

0.54


BDL190
10232.2
Av

1.14

1.13


BDL190
10233.2
P

0.38




0.03


BDL190
10233.2
Av

1.13




1.04


BDL190
10233.4
P

0.03

<0.01
0.05


BDL190
10233.4
Av

1.13

1.34
1.12


BDL190
10234.1
P

0.21
0.03
0.53


BDL190
10234.1
Av

1.16
1.03
1.19


BDL190
10231.1
P



0.07
0.07
0.01


BDL190
10231.1
Av



1.06
1.09
1.15


BDL190
10231.2
P





0.33


BDL190
10231.2
Av





1.4


BDL190
10232.2
P



0.04


BDL190
10232.2
Av



1.08


BDL190
10233.2
P





0.25


BDL190
10233.2
Av





1.25


BDL192
9921.1
P

0.22
0.11



0.07


BDL192
9921.1
Av

1.18
1.1



1.03


BDL192
9922.1
P

0.01
0.04


BDL192
9922.1
Av

1.15
1.06


BDL192
9922.2
P

0.02
0.04


<0.01


BDL192
9922.2
Av

1.21
1.09


1.12


BDL192
9922.5
P



0.68


BDL192
9922.5
Av



1.1


BDL193
10152.2
P






0.08


BDL193
10152.2
Av






1.04


BDL196
10243.2
P





0.01


BDL196
10243.2
Av





1.14


BDL201
9963.6
P
0.15


BDL201
9963.6
Av
1.28


BDL201
9964.3
P
0.15


BDL201
9964.3
Av
1.36


BDL220
10333.5
P
0.35


BDL220
10333.5
Av
1.19


BDL223
10793.5
P
0.05


BDL223
10793.5
Av
1.15


BDL224
10451.8
P
0.02


BDL224
10451.8
Av
1.5


BDL225
10401.1
P
0.08


BDL225
10401.1
Av
1.32


BDL225
10401.4
P
0.01


BDL225
10401.4
Av
1.52


BDL225
10402.2
P
0.03


BDL225
10402.2
Av
1.43


BDL225
10402.5
P
0.26


BDL225
10402.5
Av
1.39


BDL225
10402.6
P
0.08


BDL225
10402.6
Av
1.57


BDL225
10402.9
P
0.12


BDL225
10402.9
Av
1.36


BDL226
10861.2
P
0.35


BDL226
10861.2
Av
1.1


BDL227
11492.3
P
0.05


BDL227
11492.3
Av
1.15


BDL233
10825.4
P
0.53


BDL233
10825.4
Av
1.13


BDL238
10954.2
P
<0.01


BDL238
10954.2
Av
1.34


BDL240
10802.2
P
0.23


BDL240
10802.2
Av
1.3


BDL241
10873.1
P
0.07


BDL241
10873.1
Av
1.29


BDL242
10731.2
P
0.62


BDL242
10731.2
Av
1.1


BDL242
10731.6
P
0.04


BDL242
10731.6
Av
1.21


BDL250
10846.3
P
0.53


BDL250
10846.3
Av
1.15


BDL48
10271.1
P
0.2


BDL48
10271.1
Av
1.23


BDL48
10271.3
P
0.08


BDL48
10271.3
Av
1.48


BDL48
10273.2
P
0.58


BDL48
10273.2
Av
1.12


BDL48
10274.4
P
0.01


BDL48
10274.4
Av
1.95


BDL48
10271.3
P

0.01
0.01


BDL48
10271.3
Av

1.12
1.1


BDL48
10271.5
P

0.06
0.1


BDL48
10271.5
Av

1.06
1.05


BDL48
10274.3
P





<0.01


BDL48
10274.3
Av





1.44


BDL48
10274.4
P





0.08


BDL48
10274.4
Av





1.05


BDL58
10282.3
P
0.63


BDL58
10282.3
Av
1.19


BDL63
10384.3
P
0.26


BDL63
10384.3
Av
1.27


BDL63
10381.1
P



<0.01
0.06


BDL63
10381.1
Av



1.26
1.08


BDL63
10381.2
P



0.56


BDL63
10381.2
Av



1.14


BDL63
10384.2
P



<0.01
0.04


BDL63
10384.2
Av



1.27
1.08


BDL63
10384.3
P

0.01
0.02
0.3


0.01


BDL63
10384.3
Av

1.12
1.09
1.15


1.04


BDL63
10384.7
P

0.05
0.06
0.08


BDL63
10384.7
Av

1.07
1.07
1.15


BDL63
10384.8
P



0.51


BDL63
10384.8
Av



1.13


BDL81
10371.5
P

<0.01
0.01
<0.01

0.23
0.04


BDL81
10371.5
Av

1.13
1.1
1.15

1.14
1.02


BDL81
10371.8
P



0.03


BDL81
10371.8
Av



1.08


BDL81
10372.1
P

<0.01
0.01


BDL81
10372.1
Av

1.17
1.1


BDL81
10372.2
P

0.22
0.1
0.59


BDL81
10372.2
Av

1.11
1.11
1.14


BDL81
10373.2
P

0.05


BDL81
10373.2
Av

1.07


BDL81
10374.1
P



0.05


BDL81
10374.1
Av



1.2


BDL85
10411.1
P
0.1


BDL85
10411.1
Av
1.21





Table 27. Results of the greenhouse experiments. Provided are the measured values of each parameter [parameters (Par.) 31-37 according to the parameters described in Table 23 above] in plants expressing the indicated polynucleotides. “Ev” = event; “P” = P-value; “Av” = ratio between the averages of event and control. Note that when the average ratio is higher than “1” the effect of exogenous expression of the gene is an increase of the desired trait;






Example 10
Production of Tomato Transcriptom and High Throughput Correlation Analysis of Yield and/or Vigor Related Parameters Using 44K Tomato Oligonucleotide Micro-Array: Tomato Field Experiments
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)com/Scripts/PDS(dot)asp?1 Page=50879]. The array oligonucleotide represents about 44,000 Toamto genes and transcripts. In order to define correlations between the levels of RNA expression with yield components, ABST 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 in field experiments was analyzed using Pearson correlation test [Hypertext Transfer Protocol://World Wide Web(dot)davidmlane(dot)com/hyperstat/A34739(dot)html].
Experimental Procedures
Growth Procedure in Tomato Field Experiments—
Tomato varieties were grown under normal conditions (4-6 Liters/m2 per day) until flower stage.
RNA Extraction—
Leaves at different developmental stages, representing different plant characteristics, 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].
Approximately 30-50 mg of tissue was taken from samples. The weighted tissues were ground using pestle and mortar in liquid nitrogen and resuspended in 500 μl of TRIzol Reagent. To the homogenized lysate, 100 μl of chloroform was added followed by precipitation using isopropanol and two washes with 75% ethanol. The RNA was eluted in 30 μl of RNase-free water. RNA samples were cleaned up using Qiagen's RNeasy minikit clean-up protocol as per the manufacturer's protocol (QIAGEN Inc, CA USA).
Ripe Fruit Average Weight (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 fruit weight by the number of fruits.
Experimental Results
10 different Tomato varieties were grown and characterized for ripe fruit average weight (grams) as described above and the measured parameter [Ripe fruit average weight (gr.) at Normal Irrigation] is presented in Table 28 below.







TABLE 28







Measured parameters Tomato accessions











Normal Irrigation; Ripe fruit



Variety
average weight (gr.)







612
0.05



613
0.01



617
0.01



618
0.05



622
0.01



623
0.01



626
0.03



629
0.00



630
0.00



631
0.01







Table 28: Provided are the measured yield components (Ripe fruit average weight under normal irrigation) for the tomato accessions (Varieties).






Subsequent correlation analysis between the leaf transcriptom set of BDL83_H74 Gene (SEQ ID NO:282) and the ripe fruit average weight under normal irrigation conditions was conducted and the correlation coefficient (R) was found to be 0.734.
Example 11
Production of Tomato Transcriptom and High Throughput Correlation Analysis of Vigor Related Parameters Using 44K Tomato Oligonucleotide Micro-Array
Experimental Procedures
Growth Conditions for Tomato Experiments
Correlation of Early Vigor Traits Across Collection of Tomato Ecotypes—
Ten Tomato varieties were grown in 3 repetitive plots, each containing 17 plants, at a net house under semi-hydroponics conditions. Briefly, the growing protocol was as follows: Tomato seeds were sown in trays filled with a mix of vermiculite and peat in a 1:1 ratio. Following germination, the trays were transferred to normal growth solution [full Hogland; KNO3—0.808 grams/liter, MgSO4—0.12 grams/liter, KH2 PO4—0.172 grams/liter and 0.01% (volume/volume) of ‘Super coratin’ micro elements (Iron-EDDHA [ethylenediamine-N,N′-bis(2-hydroxyphenylacetic acid)]-40.5 grams/liter; Mn—20.2 grams/liter; Zn 10.1 grams/liter; Co 1.5 grams/liter; and Mo 1.1 grams/liter), solution's pH should be 6.5-6.8] at a temperature of 20-24° C.
RNA Extraction—
All 10 selected Tomato varieties were sampled. Leaves from plant under Normal 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].
Tomato Vigor Related Parameters—
following 5 weeks of growing, plant were harvested and analyzed for leaf number. The analyzed data was saved to text files and processed using the JMP statistical analysis software (SAS institute).
Experimental Results
10 different Tomato varieties were grown and characterized for leaf number as described above. The average leaf number was calculated using the JMP software and values are summarized in Tables 29 below.







TABLE 29







Measured parameters Tomato accessions










Variety
Leaf number







1139
6.56



2078
6.89



2958
7.33



5077
6.22



5080
6.33



5084
6.44



5085
5.89



5088
5.56



5089
6.11



5092
5.67







Table 29. Provided are the measured vigor related parameter (leaf number) for the tomato accessions (Varieties).






Subsequent correlation analysis between the leaf transcriptom set of BDL83_H73 gene (SEQ ID NO:281) with the average leaf number was conducted, the correlation coefficient (R) was −0.794.
The genes identified herein improve plant yield in general, and more specifically oil yield, seed yield, oil content, plant growth rate, plant biomass, root measurements, and plant vigor. The output of the bioinformatics method described herein is a set of genes highly predicted to improve yield (seed yield, oil yield and content, biomass) and/or other agronomic important yields by modifying their expression. Although each gene is predicted to have its own impact, modifying the mode of expression of more than one gene is expected to provide an additive or synergistic effect on the plant yield, plant growth rate, root measurements, plant vigor and/or other agronomic important yields performance. Altering the expression of each gene described here alone or set of genes together increases the overall yield plant growth rate, root measurements, plant vigor and/or
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 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 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.

## Claims

1. A method of increasing leaf area, relative growth rate of leaf area, relative growth rate of root length, root coverage, and/or relative growth rate of root coverage of a plant, comprising:
(a) expressing within the plant an exogenous polynucleotide comprising a nucleic acid sequence encoding a polypeptide comprising an amino acid sequence as set forth by SEQ ID NO: 176, wherein said polypeptide is capable of increasing leaf area, relative growth rate of leaf area, relative growth rate of root length, root coverage, and/or relative growth rate of root coverage of a plant under non-stress conditions, and
(b) selecting said plant expressing said exogenous polynucleotide for an increased leaf area, an increased relative growth rate of leaf area, an increased relative growth rate of root length, an increased root coverage, and/or an increased relative growth rate of root coverage under non-stress growth conditions as compared to a non-transformed plant which is grown under the same growth conditions,
thereby increasing the leaf area, relative growth rate of leaf area, relative growth rate of root length, root coverage, and/or relative growth rate of root coverage of the plant.

2. A method of producing seeds of a crop comprising:
(a) selecting a parent plant being transformed with an exogenous polynucleotide encoding a polypeptide comprising an amino acid sequence as set forth by SEQ ID NO: 176 for an increased trait selected from the group consisting of: an increased leaf area, an increased relative growth rate of leaf area, an increased relative growth rate of root length, an increased root coverage, and an increased relative growth rate of root coverage under non-stress growth conditions as compared to a non-transformed plant which is grown under the same growth conditions,
(b) growing a seed producing plant from said parent plant resultant of step (a), wherein said seed producing plant which comprises said exogenous polynucleotide has said increased trait and
(c) producing seeds from said seed producing plant resultant of step (b), wherein said seeds comprise said exogenous polynucleotide,
thereby producing seeds of the crop.

3. The method of claim 1, wherein said exogenous polynucleotide is set forth by SEQ ID NO: 908.

4. The method of claim 1, wherein said exogenous polynucleotide is set forth by SEQ ID NO: 71.

5. The method of claim 2, wherein said exogenous polynucleotide is set forth by SEQ ID NO: 908.

6. The method of claim 2, wherein said exogenous polynucleotide is set forth by SEQ ID NO: 71.