INCORPORATION OF SEQUENCE LISTING
Two copies of the sequence listing (Copy 1 and Copy 2) and a computer readable form (CRF) of the sequence listing, all on CD-ROMs, each containing the file named “pa—01184—53452B.rpt”, which is 67,108,864 bytes (measured in MS-WINDOWS, MEDIUM TYPE: CD-ROM (ASC11 TEXT) COMPUTER: IBM PC/XT/AT, IBM PS/2 OR COMPATIBLES. OPERATING SYSTEM: DOS/WINDOWS 2000/NT) and was created on Jul. 18, 2005, are herein incorporated by reference.
FIELD OF THE INVENTION
Disclosed herein are inventions in the field of plant genetics and developmental biology. More specifically, this invention provides transgenic seeds for crops, wherein the genome of said seed comprises recombinant DNA, the expression of which results in the production of transgenic plants that have improved trait(s).
BACKGROUND OF THE INVENTION
Transgenic plants with improved traits such as improved yield, environmental stress tolerance, pest resistance, herbicide tolerance, modified seed compositions, and the like are desired by both farmers and consumers. Although considerable efforts in plant breeding have provided significant gains in desired traits, the ability to introduce specific DNA into plant genomes provides further opportunities for generation of plants with improved and/or unique traits. The ability to develop transgenic plants with improved traits depends in part on the identification of genes that are useful in recombinant DNA constructs for production of transformed plants with improved properties.
SUMMARY OF THE INVENTION
This invention provides transgenic seeds, transgenic plants and DNA constructs with trait-improving recombinant DNA from a gene for a protein having an amino acid sequence with at least 90% identity to a consensus amino acid sequence in the group consisting of SEQ ID NO: 270 and its homologs through SEQ ID NO: 538, where the respective homolog proteins have amino acid sequences SEQ ID NO: 539 through SEQ ID NO: 22568, as indicated in Table 17. In some cases of trait improvement, the recombinant DNA encodes a protein; in other cases, the recombinant DNA suppresses endogenous protein expression. In a broad aspect this invention provides transgenic seeds for growing crop plants with improved traits, such crop plants with improved traits and the plant parts including transgenic seed produced by such crop plants. The improved traits provided by the recombinant DNA in the transgenic crop plant of this invention are identified by comparison to a control plant, i.e., a plant without the trait-improving recombinant DNA. In one aspect of the invention, transgenic crop plant grown from the transgenic seed has improved yield, as compared to the yield of a control plant, e.g., a plant without the recombinant DNA that produces the increased yield. Some plants of this invention exhibit increased yield by producing a yield increase under non-stress conditions. Other plants of this invention exhibit increased yield by producing a yield increase under one or more environmental stress conditions including, but not limited to, water deficit stress, cold stress, heat stress, high salinity stress, shade stress, and low nitrogen availability stress. Still other plants of this invention have other improved phenotypes, such as improved plant development, plant morphology, plant physiology or seed composition as compared to a corresponding trait of a control plant. The various aspects of this invention are especially useful for transgenic seed and transgenic plants having improved traits in corn (maize), soybean, cotton, canola (rape), wheat, sunflower, sorghum, alfalfa, barley, millet, rice, tobacco, fruit and vegetable crops, and turfgrass.
The invention also comprises recombinant DNA constructs. In one aspect, such recombinant DNA constructs useful for the transgenic seed and transgenic plants of this invention comprise a promoter functional in a plant cell operably linked to a DNA segment for expressing a protein associated with a trait in a model plant or a homologue. In another aspect the recombinant DNA constructs useful for the transgenic seed and transgenic plants of this invention comprise a promoter functional in a plant cell operably linked to a DNA segment for suppressing the level of an endogenous plant protein which is a homologue to a model-plant protein, the suppression of which is associated with an improved trait. Suppression can be effected by any of a variety of methods known in the art, e.g., post transcriptional suppression by anti-sense, sense, dsRNA and the like or by transcriptional suppression.
This invention also provides a method of producing a transgenic crop plant having at least one improved trait, wherein the method comprises providing to a grower of transgenic seeds comprising recombinant DNA for expression or suppression of a trait-improving gene provided herein, and growing transgenic plant from said transgenic seed. Such methods are used to generate transgenic crop plants having at least one improved trait under one or more environmental stress conditions including, but not limited to, water deficit stress, cold stress, heat stress, high salinity stress, shade stress, and low nitrogen availability stress. In another aspect, such methods are used to generate transgenic crop plants having improved plant development, plant morphology, plant physiology or seed component phenotype as compared to a corresponding phenotype of a control plant. Of particular interest are uses of such methods to generate transgenic crop plants having increased yield under non-stress condition, or under one or more stress conditions.
DETAILED DESCRIPTION OF THE INVENTION
This invention provides transgenic plant seed having in its genome trait-improving recombinant DNA and transgenic plants grown from such seed which exhibit an improved trait as compared a control plant. In one aspect, the invention provides transgenic plants where the improved trait is one or more of improved drought stress tolerance, improved heat stress tolerance, improved cold stress tolerance, improved high salinity stress tolerance, improved low nitrogen availability stress tolerance, improved shade stress tolerance, improved plant growth and development at the stages of seed imbibition through early vegetative phase, and improved plant growth and development at the stages of leaf development, flower production and seed maturity. Particular transgenic plants grown from transgenic seeds of this invention exhibit increased seed yield. Recombinant DNA constructs used in this invention comprise recombinant DNA disclosed herein which produces mRNA to modulate gene expression imparting improved traits to plants.
“Gene” means all or part of the DNA that encodes a protein or mRNA, e.g., chromosomal DNA, plasmid DNA, cDNA, or synthetic DNA, and includes DNA regions flanking the coding sequences, e.g., introns, 5′UTR, 3′UTR, promoters and other DNA involved in the regulation of expression.
“Transgenic seed” means plant seed having a genome altered by the incorporation of recombinant DNA, e.g., by transformation. “Transgenic plant” means a plant produced from an original transformation event, or progeny from later generations or crosses of a plant to a transformed plant, so long as the progeny contains the recombinant DNA in its genome. “Recombinant DNA” means a DNA molecule having a genetically engineered modification introduced through a combination of endogenous and/or exogenous DNA elements in a transcription unit, manipulation via mutagenesis, restriction enzymes, and the like or simply by inserting multiple copies of a native transcription unit. Recombinant DNA may comprise DNA segments obtained from different sources, or DNA segments obtained from the same source, but which have been manipulated to join DNA segments which do not naturally exist in the joined form. Recombinant DNA can exist outside of a cell, e.g., as a PCR fragment or in a plasmid, or can be integrated into a genome such as a plant genome.
“Trait” means a physiological, morphological, biochemical, or physical characteristic of a plant or particular plant material or cell. In some instances the characteristic is visible to the human eye, e.g., seed or plant size, or can be measured by biochemical techniques, e.g., detecting the protein, starch, or oil content of seed or leaves, or by observation of a metabolic or physiological process, e.g., by measuring uptake of carbon dioxide, or by the observation of the expression level of a gene or genes, e.g., by employing Northern analysis, RT-PCR, microarray gene expression assays, or reporter gene expression systems, or by agricultural observations such as stress tolerance, yield, or pathogen tolerance.
“Control plant” is a plant without trait-improving recombinant DNA. A control plant is used to measure and compare trait improvement in a transgenic plant with such trait-improving recombinant DNA. One suitable control plant is a non-transgenic plant of the parental line that was used to generate a transgenic plant. Another suitable control plant is a transgenic plant that comprises recombinant DNA without the specific trait producing DNA, e.g., simply a marker gene. Another suitable control plant is a negative segregant progeny of hemizygous transgenic plant. In certain demonstrations of trait improvement, e.g., in field conditions, the use of a limited number of control plants can cause a wide variation in the control dataset. To minimize the effect of the variation within the control dataset, a “reference” is used, i.e., a trimmed mean of all data from both transgenic and control plants grown under the same conditions and at the same developmental stage. The trimmed mean is calculated by eliminating a specific percentage, i.e., 20%, of the smallest and largest observation from the data set and then calculating the average of the remaining observation.
“Trait improvement” means a detectable and desirable difference in a characteristic in a transgenic plant relative to a control plant or a reference. In some cases, the trait improvement is measured quantitatively. For example, the trait improvement can entail at least a 2% desirable difference in an observed trait, at least a 5% desirable difference, at least about a 10% desirable difference, at least about a 20% desirable difference, at least about a 30% desirable difference, at least about a 50% desirable difference, at least about a 70% desirable difference, or at least about a 100% difference, or an even greater desirable difference. In other cases, the trait improvement is only measured qualitatively. It is known that there are natural variations in a trait. Therefore, the trait improvement observed entails a change of the normal distribution of the trait in the transgenic plant compared with the trait distribution observed in a control plant or a reference, which is evaluated by statistical methods provided herein. Trait improvement includes, but not limited to, yield increase, including increased yield under non-stress conditions and increased yield under environmental stress conditions. Stress conditions may include, for example, drought, shade, fungal disease, viral disease, bacterial disease, insect infestation, nematode infestation, cold temperature exposure, heat exposure, osmotic stress, reduced nitrogen nutrient availability, reduced phosphorus nutrient availability and high plant density. Many agronomic traits can affect “yield”, including without limitation, plant height, pod number, pod position on the plant, number of internodes, incidence of pod shatter, grain size, efficiency of nodulation and nitrogen fixation, efficiency of nutrient assimilation, resistance to biotic and abiotic stress, carbon assimilation, plant architecture, resistance to lodging, percent seed germination, seedling vigor, and juvenile traits. Other traits that can affect yield include, efficiency of germination (including germination in stressed conditions), growth rate (including growth rate in stressed conditions), ear number, seed number per ear, seed size, composition of seed (starch, oil, protein) and characteristics of seed fill. Also of interest is the generation of transgenic plants that demonstrate desirable phenotypic properties that may or may not confer an increase in overall plant yield. Such properties include improved plant morphology, plant physiology or improved components of the mature seed harvested from the transgenic plant.
“Yield-limiting environment” means a condition under which a plant would have the limitation on yield including environmental stress conditions.
“Stress condition” means a condition unfavorable for a plant, which adversely affects plant metabolism, growth and/or development. A plant under the stress condition typically shows reduced germination rate, retarded growth and development, reduced photosynthesis rate, and eventually leading to reduction in yield. Specifically, “water deficit stress” means sub-optimal conditions for water and humidity needed for normal growth of natural plants. Relative water content (RWC) is one physiological measure of plant water deficit. RWC measures the effect of osmotic adjustment in plant water status, when a plant is under stressed conditions. RWC can result from heat, drought, high salinity and induced osmotic stress.
“Cold stress” means exposure of a plant to temperatures below, e.g., at least two or more degrees Celsius below, those temperatures that are normal for a particular species or particular strain of plant.
“Sufficient nitrogen growth condition” means a growth condition where the soil or growth medium contains or receives enough amounts of nitrogen nutrient to sustain a healthy plant growth and/or for a plant to reach its typical yield for a particular plant species or a particular strain. “Nitrogen nutrient” means any one or any mix of the nitrate salts commonly used as plant nitrogen fertilizer, including, but not limited to, potassium nitrate, calcium nitrate, sodium nitrate, ammonium nitrate. “Ammonium” means any one or any mix of the ammonium salts commonly used as plant nitrogen fertilizer, e.g., ammonium nitrate, ammonium chloride, ammonium sulfate, etc. Those skilled in the art know what constitutes such soil, media and fertilizer inputs for most plant species. “Low nitrogen availability stress” means a plant growth condition that does not contain sufficient nitrogen nutrient to maintain a healthy plant growth and/or for a plant to reach its typical yield under a sufficient nitrogen growth condition; a useful low nitrogen availability stress is a growth condition with 50% or less of the conventional nitrogen inputs.
“Shade stress” means a limited light availability that triggers the shade avoidance response in plant. Plants are subject to shade stress when localized at lower part of the canopy, or in close proximity of neighboring vegetation. Shade stress is exacerbated when the planting density exceeds the average prevailing density for a particular plant species. The average prevailing densities per acre of a few other examples of crop plants in the USA in the year 2000 were: wheat 1,000,000-1,500,000; rice 650,000-900,000; soybean 150,000-200,000, canola 260,000-350,000, sunflower 17,000-23,000 and cotton 28,000-55,000 plants per acre.
“Increased yield” of a transgenic plant of this invention is evidenced and measured in a number of ways, including test weight, seed number per plant, seed weight, seed number per unit area (i.e., seeds, or weight of seeds, per acre), bushels per acre, tons per acre, tons per acre, kilo per hectare. For example, corn yield is measured as production of shelled corn kernels per unit of production area, e.g., in bushels per acre or metric tons per hectare, often reported on a moisture adjusted basis, e.g., at 15.5% moisture. Increased yield is often achieved from improved utilization of key biochemical compounds, such as nitrogen, phosphorous and carbohydrate, or from improved responses to environmental stresses, such as cold, heat, drought, salt, and attack by pests or pathogens. Trait-improving recombinant DNA is used to provide transgenic plants having improved growth and development, and ultimately increased yield, as the result of modified expression of plant growth regulators or modification of cell cycle or photosynthesis pathways.
“Expression” means transcription of DNA to produce RNA. The resulting RNA includes mRNA encoding a protein, antisense RNA that is complementary to an mRNA encoding a protein, or an RNA transcript comprising a combination of sense and antisense gene regions, such as for use in RNAi gene suppression. Expression also means production of encoded protein from mRNA.
“Promoter” means a region of DNA upstream from the start of transcription and involved in recognition and binding of RNA polymerase and other proteins to initiate transcription. A “plant promoter” is a promoter capable of initiating transcription in plant cells whether or not its origin is a plant cell. Exemplary plant promoters include, but are not limited to, those that are obtained from plants, plant viruses, and bacteria which comprise genes expressed in plant cells such as Agrobacterium or Rhizobium. “Tissue preferred” promoters preferentially regulate expression in certain tissues, such as leaves, roots, or seeds. “Tissue specific” promoters predominately regulate expression only in certain tissues. “Cell type” specific promoter primarily regulate expression in certain cell types in one or more organs, for example, vascular cells in roots or leaves. “Inducible” and “repressible” promoters regulate expression under environmental influences, under the effect of anaerobic conditions, certain chemicals, or the presence of light. Tissue specific, tissue preferred, cell type specific, and inducible promoters constitute a class of “non-constitutive” promoters. “Constitutive” promoters are promoters which are active under most conditions. “Anti-sense orientation” refers to a DNA sequence that is operably linked to a promoter in an orientation where the anti-sense strand is transcribed. “Operably linked” refers to an association of two or more DNA elements in a single construct so that the function of one is affected by the other. For example, a promoter is operably linked with transcribable DNA when it is capable of affecting the expression of that DNA; that is, the coding DNA is under the transcriptional control of the promoter.
“Consensus sequence” means an artificial, amino acid sequence of conserved parts of the proteins encoded by homologous genes, e.g., as determined by a CLUSTALW alignment of amino acid sequence of homolog proteins.
“Homologs” means genes that produce functionally similar proteins, e.g., in the same organism or in different organisms. A gene can be related to a homolog gene by descent from a common ancestral DNA. Homologs include genes where the relationship is by speciation, e.g., often called orthologs, or by genetic duplication, e.g., often called paralogs. More specifically, “orthologs” include homologs in different species that evolved from a common ancestral gene by specification. Normally orthologs retain the same function in the course of evolution. “Paralogs” include homologs in the same species that have diverged from each other as a consequence of genetic duplication.
“Percent identity” means the extent to which two optimally aligned DNA or protein segments are invariant throughout a window of alignment of components, e.g., nucleotide sequence or amino acid sequence. An “identity fraction” for aligned segments of sequences is the number of identical components which are shared divided by the total number of sequence components in the segment used as a reference over a window of alignment which is the smaller of the sequences. “Percent identity” (“% identity”) is the identity fraction times 100. “% identity” to a consensus amino acid sequence” is 100 times the identity fraction in a window of alignment of an amino acid sequence of a test protein optimally aligned to consensus amino acid sequence of this invention.
“Arabidopsis” means plants of Arabidopsis thaliana.
Recombinant DNA Constructs
This invention provides recombinant DNA constructs comprising DNA elements for imparting one or more improved traits to transgenic plant. Such constructs typically comprise a promoter operatively linked to DNA to provide for expression of a protein or RNA for gene suppression in a target plant. Recombinant DNA constructs can also include additional regulatory elements, such as 5′ or 3′ untranslated regions (UTRs) such as polyadenylation sites, introns, and transit or signal peptides. Such recombinant DNA constructs are assembled using methods known to those of ordinary skill in the art.
In certain embodiments, recombinant DNA constructs comprise sense-oriented, trait-imparting DNA operably linked to a promoter that is functional in a plant to provide for expression of the trait-imparting DNA in the sense orientation such that a desired protein is produced. In other embodiments at least a part of the trait-imparting DNA is in an anti-sense orientation for gene suppression activity.
Recombinant DNA constructs, especially for expressing proteins are typically prepared with a 3′ UTR that a polyadenylation site and signal. Recombinant DNA constructs can also include a transit peptide for targeting of a gene target to a plant organelle, particularly to a chloroplast, leucoplast or other plastid organelle. For descriptions of the use of chloroplast transit peptides, see U.S. Pat. No. 5,188,642 and U.S. Pat. No. 5,728,925, incorporated herein by reference.
Table 1 provides a list of genes that can provide trait-imparting DNA for recombinant DNA constructs. DNA from each gene was used in a model plant (Arabidopsis) to discover associations with improved traits. The DNA was also used to identify homologs from which a consensus amino acid sequence is defined for characterizing the aspects of the invention where recombinant DNA is incorporated in the transgenic seeds, transgenic plants, DNA constructs and methods of this invention. With reference to Table 1:
“NUC SEQ ID NO” refers to a SEQ ID NO. for particular DNA sequence in the Sequence Listing.
“PEP SEQ ID NO” refers to a SEQ ID NO. in the Sequence Listing for the amino acid sequence of a protein cognate to a particular DNA
“construct_id” refers to arbitrary number used to identify a particular recombinant DNA construct comprising the particular DNA.
“gene” refers to an arbitrary name used to identify the particular DNA.
“orientation” refers to the orientation of the particular DNA in a recombinant DNA construct relative to the promoter.
“species” refers to the organism from which the particular DNA was derived.
TABLE 1
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Nuc SEQ IDPep SEQ IDconstruct_idGeneorientationSpecies
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127014324CGPG1560SENSEArabidopsis thaliana
227117484CGPG2630SENSEArabidopsis thaliana
327219109CGPG1381ANTI-SENSEArabidopsis thaliana
427370423CGPG3165SENSEArabidopsis thaliana
527470424CGPG3180SENSEArabidopsis thaliana
627570480CGPG3833SENSEArabidopsis thaliana
727670509CGPG2420SENSEArabidopsis thaliana
827770647CGPG4334SENSEArabidopsis thaliana
927870675CGPG4519SENSEArabidopsis thaliana
1027970829CGPG518SENSEArabidopsis thaliana
1128070849CGPG596SENSEArabidopsis thaliana
1228171627CGPG1270SENSEArabidopsis thaliana
1328271934CGPG2294SENSEArabidopsis thaliana
1428372615CGPG4829SENSEArabidopsis thaliana
1528472927CGPG1477SENSEArabidopsis thaliana
1628573014CGPG5692SENSEXenorhabdus nematophilus 85816
1728673559CGPG6535SENSEBacillus subtilis 168
1828774251CGPG5489SENSEArabidopsis thaliana
1928819631CGPG3627SENSEArabidopsis thaliana
2028970121CGPG2380SENSESaccharomyces cerevisiae
2129070654CGPG4352SENSEArabidopsis thaliana
2229170696CGPG4590SENSEArabidopsis thaliana
2329270713CGPG1462ANTI-SENSEArabidopsis thaliana
2429370740CGPG3700SENSEArabidopsis thaliana
2529471321CGPG4418SENSEArabidopsis thaliana
2629571835CGPG4634SENSEArabidopsis thaliana
2729672934CGPG5798SENSESaccharomyces cerevisiae
2829772945CGPG5787SENSESaccharomyces cerevisiae
2929872980CGPG5773SENSESaccharomyces cerevisiae
3029973504CGPG6480SENSESynechocystis sp. PCC 6803
3130073507CGPG6504SENSEBacillus subtilis 168
3230173573CGPG6462SENSEAgrobacterium tumefacians C58
3330273586CGPG6471SENSEBacillus subtilis 168
3430373770CGPG5435SENSEArabidopsis thaliana
3530474105CGPG6574SENSEXenorhabdus nematophilus 86068
3630574111CGPG6622SENSEEscherichia coli K-12
3730674136CGPG6632SENSESynechocystis
3830774139CGPG6561SENSEEscherichia coli K-12
3930874267CGPG5364SENSEArabidopsis thaliana
4030974291CGPG5363SENSEArabidopsis thaliana
4131074318CGPG5826SENSEArabidopsis thaliana
4231174319CGPG5831SENSEArabidopsis thaliana
4331274324CGPG5885SENSEArabidopsis thaliana
4431374512CGPG32SENSEArabidopsis thaliana
4531474583CGPG6649SENSERalstonia metallidurans CH34
4631570427CGPG3067SENSEArabidopsis thaliana
4731671811CGPG4426SENSEArabidopsis thaliana
4831773463CGPG6384SENSERalstonia metallidurans CH34
4931872081CGPG5279SENSEGlycine max
5031910139CGPG101ANTI-SENSEArabidopsis thaliana
5132011410CGPG103SENSEArabidopsis thaliana
5232111604CGPG48ANTI-SENSEArabidopsis thaliana
5332212368CGPG1006SENSEArabidopsis thaliana
5432313502CGPG1354SENSEArabidopsis thaliana
5532413745CGPG1576ANTI-SENSEArabidopsis thaliana
5632513821CGPG1569SENSEArabidopsis thaliana
5732614240CGPG1697SENSEArabidopsis thaliana
5832714718CGPG1082SENSEArabidopsis thaliana
5932817022CGPG1774SENSEArabidopsis thaliana
6032917924CGPG2882SENSEArabidopsis thaliana
6133018259CGPG3368SENSEArabidopsis thaliana
6233119171CGPG2952SENSESaccharomyces cerevisiae
6333219201CGPG2332SENSEArabidopsis thaliana
6433319317CGPG3662SENSEXanthomonas
6533470417CGPG3427SENSEArabidopsis thaliana
6633570467CGPG3785SENSEArabidopsis thaliana
6733670806CGPG712SENSEArabidopsis thaliana
6833770818CGPG479SENSEArabidopsis thaliana
6933870820CGPG655SENSEArabidopsis thaliana
7033970919CGPG4029SENSEGlycine max
7134071623CGPG4696SENSEArabidopsis thaliana
7234171662CGPG4679SENSEGlycine max
7334271693CGPG4652SENSEGlycine max
7434372384CGPG4639SENSESaccharomyces cerevisiae
7534472439CGPG5075SENSEArabidopsis thaliana
7634572619CGPG4835SENSEArabidopsis thaliana
7734672624CGPG4842SENSEArabidopsis thaliana
7834772715CGPG5521SENSESaccharomyces cerevisiae
7934872754CGPG5548SENSESaccharomyces cerevisiae
8034972819CGPG4989SENSEArabidopsis thaliana
8135075516CGPG7689SENSEGlycine max
8235175701CGPG7856SENSEGlycine max
8335273515CGPG6473SENSEBacillus subtilis 168
8435374684CGPG6360SENSEArabidopsis thaliana
8535419542CGPG3069SENSEArabidopsis thaliana
8635519618CGPG3574SENSEArabidopsis thaliana
8735619649CGPG3140SENSEArabidopsis thaliana
8835719745CGPG3973SENSEGlycine max
8935819768CGPG4096SENSEGlycine max
9035919772CGPG3939SENSEGlycine max
9136019779CGPG4113SENSEGlycine max
9236119833CGPG4074SENSEGlycine max
9336219862CGPG3961SENSEGlycine max
9436319879CGPG4009SENSEGlycine max
9536470445CGPG3728SENSEArabidopsis thaliana
9636570738CGPG3195SENSEArabidopsis thaliana
9736671437CGPG4043SENSEGlycine max
9836771572CGPG4520SENSEArabidopsis thaliana
9936871617CGPG1227SENSEArabidopsis thaliana
10036972532CGPG4780SENSEArabidopsis thaliana
10137072757CGPG5572SENSEArabidopsis thaliana
10237173412CGPG6448SENSEPseudomonas syringae var tomato DC3000
10337274102CGPG6550SENSEBacillus halodurans C-125
10437372633CGPG4853SENSEArabidopsis thaliana
10537472456CGPG4745SENSEArabidopsis thaliana
10637572963CGPG1746SENSEArabidopsis thaliana
10737670426CGPG3199SENSEArabidopsis thaliana
10837770772CGPG4627SENSEArabidopsis thaliana
10937871137CGPG125SENSEArabidopsis thaliana
11037971529CGPG2808SENSEArabidopsis thaliana
11138071601CGPG1858SENSEArabidopsis thaliana
11238172362CGPG983SENSEArabidopsis thaliana
11338272466CGPG4767SENSEArabidopsis thaliana
11438372524CGPG4770SENSEArabidopsis thaliana
11538473085CGPG5689SENSESynechocystis sp. PCC 6803
11638574241CGPG5457SENSEArabidopsis thaliana
11738674247CGPG5475SENSEArabidopsis thaliana
11838774284CGPG5413SENSEArabidopsis thaliana
11938874652CGPG6168SENSEArabidopsis thaliana
12038970437CGPG3706SENSEArabidopsis thaliana
12139071633CGPG857SENSEArabidopsis thaliana
12239172948CGPG5617SENSEArabidopsis thaliana
12339272519CGPG4749SENSEArabidopsis thaliana
12439310475CGPG399SENSEArabidopsis thaliana
12539411120CGPG459ANTI-SENSEArabidopsis thaliana
12639519736CGPG4129SENSEGlycine max
12739671606CGPG4715SENSEArabidopsis thaliana
12839771840CGPG4353SENSEArabidopsis thaliana
12939874240CGPG5454SENSEArabidopsis thaliana
13039974331CGPG5834SENSEArabidopsis thaliana
13140074610CGPG6048SENSEArabidopsis thaliana
13240175527CGPG7682SENSEGlycine max
13340270681CGPG4584SENSEArabidopsis thaliana
13440371663CGPG4638SENSEXanthomonas
13540472769CGPG5573SENSEArabidopsis thaliana
13640571508CGPG1541SENSEArabidopsis thaliana
13740674248CGPG5476SENSEArabidopsis thaliana
13840772771CGPG2166SENSEArabidopsis thaliana
13940872085CGPG5228SENSEArabidopsis thaliana
14040972744CGPG5563SENSESaccharomyces cerevisiae
14141073039CGPG810SENSEArabidopsis thaliana
14241173054CGPG5754SENSESaccharomyces cerevisiae
14341273501CGPG6456SENSEAgrobacterium tumefacians C58
14441319707CGPG4179SENSEGlycine max
14541419951CGPG3941SENSEGlycine max
14641519967CGPG4032SENSEGlycine max
14741670543CGPG3815SENSEArabidopsis thaliana
14841770707CGPG1273ANTI-SENSEArabidopsis thaliana
14941870719CGPG1712ANTI-SENSEArabidopsis thaliana
15041971134CGPG817SENSEArabidopsis thaliana
15142071146CGPG2928SENSEArabidopsis thaliana
15242171660CGPG4690SENSEArabidopsis thaliana
15342272086CGPG5236SENSEArabidopsis thaliana
15442372632CGPG4852SENSEArabidopsis thaliana
15542472716CGPG5529SENSESaccharomyces cerevisiae
15642572723CGPG1848SENSEArabidopsis thaliana
15742672987CGPG1787SENSEArabidopsis thaliana
15842774109CGPG6606SENSEXenorhabdus nematophilus 86068
15942874140CGPG6569SENSEBacillus halodurans C-125
16042974191CGPG6597SENSERhodobacter sphaeroides 2.4.1
16143074265CGPG5356SENSEArabidopsis thaliana
16243174369CGPG6076SENSEArabidopsis thaliana
16343270217CGPG6SENSEArabidopsis thaliana
16443372711CGPG1846SENSEArabidopsis thaliana
16543470932CGPG4089SENSEGlycine max
16643573518CGPG6497SENSEPseudomonas fluorescens PfO-1
16743619771CGPG4011SENSEGlycine max
16843773549CGPG6460SENSEXenorhabdus nematophilus 85816
16943872994CGPG5803SENSESaccharomyces cerevisiae
17043971928CGPG1617SENSEArabidopsis thaliana
17144072903CGPG5584SENSEArabidopsis thaliana
17244173017CGPG5733SENSESaccharomyces cerevisiae
17344274587CGPG6774SENSEAgrobacterium tumefacians C58
17444372453CGPG4735SENSEArabidopsis thaliana
17544472967CGPG5742SENSESaccharomyces cerevisiae
17644572961CGPG5591SENSEArabidopsis thaliana
17744673070CGPG5627SENSEArabidopsis thaliana
17844773475CGPG6385SENSERhodopseudomonas palustris CGA009
17944872916CGPG1814SENSEArabidopsis thaliana
18044972969CGPG5789SENSESaccharomyces cerevisiae
18145074449CGPG6659SENSEAgrobacterium tumefaciens
18245116615CGPG2539SENSEAgrobacterium
18345219187CGPG3310SENSEArabidopsis thaliana
18445319648CGPG3134SENSEArabidopsis thaliana
18545470354CGPG3995SENSEGlycine max
18645570421CGPG2942SENSEArabidopsis thaliana
18745670459CGPG3758SENSEArabidopsis thaliana
18845770465CGPG3775SENSEArabidopsis thaliana
18945870683CGPG4587SENSEArabidopsis thaliana
19045970725CGPG2097ANTI-SENSEArabidopsis thaliana
19146070852CGPG1465SENSEArabidopsis thaliana
19246171112CGPG934SENSEArabidopsis thaliana
19346271127CGPG945SENSEArabidopsis thaliana
19446371132CGPG1561SENSEArabidopsis thaliana
19546471217CGPG95SENSEArabidopsis thaliana
19646571645CGPG4688SENSEArabidopsis thaliana
19746671726CGPG3894SENSEArabidopsis thaliana
19846772432CGPG4562SENSEArabidopsis thaliana
19946872450CGPG4732SENSEArabidopsis thaliana
20046972455CGPG4742SENSEArabidopsis thaliana
20147072727CGPG5522SENSESaccharomyces cerevisiae
20247172817CGPG4987SENSEArabidopsis thaliana
20347272992CGPG5777SENSESaccharomyces cerevisiae
20447373007CGPG5760SENSESaccharomyces cerevisiae
20547473073CGPG5688SENSESynechocystis sp. PCC 6803
20647573506CGPG6496SENSEPseudomonas fluorescens PfO-1
20747674107CGPG6590SENSESinorhizobium meliloti 1021
20847774117CGPG6575SENSEXenorhabdus nematophilus 86068
20947874131CGPG6592SENSESynechocystis sp. PCC 6803
21047974344CGPG5929SENSEArabidopsis thaliana
21148014320CGPG1229SENSEArabidopsis thaliana
21248116756CGPG2117SENSEArabidopsis thaliana
21348217448CGPG2673SENSEArabidopsis thaliana
21448317633CGPG2839SENSEArabidopsis thaliana
21548418876CGPG3096SENSEArabidopsis thaliana
21648519120CGPG1976ANTI-SENSEArabidopsis thaliana
21748619221CGPG2958SENSEArabidopsis thaliana
21848770206CGPG4116SENSEGlycine max
21948870223CGPG53SENSEArabidopsis thaliana
22048970347CGPG3147SENSEArabidopsis thaliana
22149070406CGPG1687SENSEArabidopsis thaliana
22249170469CGPG3791SENSEArabidopsis thaliana
22349270564CGPG1864SENSEArabidopsis thaliana
22449370601CGPG2917SENSEArabidopsis thaliana
22549470612CGPG3721SENSEArabidopsis thaliana
22649570720CGPG1358ANTI-SENSEArabidopsis thaliana
22749670735CGPG2661SENSEArabidopsis thaliana
22849770846CGPG377SENSEArabidopsis thaliana
22949870923CGPG4020SENSEGlycine max
23049971149CGPG3457SENSEArabidopsis thaliana
23150071608CGPG4687SENSEArabidopsis thaliana
23250171739CGPG4345SENSEArabidopsis thaliana
23350272014CGPG5230SENSEArabidopsis thaliana
23450372051CGPG5241SENSEArabidopsis thaliana
23550474259CGPG5343SENSEArabidopsis thaliana
23650572463CGPG4760SENSEArabidopsis thaliana
23750672902CGPG5597SENSEArabidopsis thaliana
23850774572CGPG6640SENSESynechocystis
23950873055CGPG5768SENSESaccharomyces cerevisiae
24050974103CGPG6558SENSEEscherichia coli K-12
24151072921CGPG5781SENSESaccharomyces cerevisiae
24251172968CGPG5772SENSESaccharomyces cerevisiae
24351219703CGPG4172SENSEGlycine max
24451319946CGPG4097SENSEGlycine max
24551419980CGPG3914SENSEGlycine max
24651570435CGPG3701SENSEArabidopsis thaliana
24751671114CGPG1657SENSEArabidopsis thaliana
24851772451CGPG4733SENSEArabidopsis thaliana
24951872947CGPG5607SENSEGlycine max
25051973012CGPG5786SENSESaccharomyces cerevisiae
25152073022CGPG5622SENSEArabidopsis thaliana
25252173488CGPG6394SENSEBacillus subtilis 168
25352273901CGPG5237SENSEArabidopsis thaliana
25452373964CGPG5804SENSESaccharomyces cerevisiae
25552474019CGPG5706SENSEBacillus subtilis 168
25652574022CGPG5724SENSEArabidopsis thaliana
25752674114CGPG6551SENSEAgrobacterium tumefacians C58
25852774262CGPG5353SENSEArabidopsis thaliana
25952874292CGPG5367SENSEArabidopsis thaliana
26052974302CGPG5384SENSEArabidopsis thaliana
26153074325CGPG5898SENSEArabidopsis thaliana
26253174429CGPG6689SENSEBacillus subtilis 168
26353274440CGPG6682SENSEBacillus halodurans C-125
26453374462CGPG6668SENSESynechocystis
26553474465CGPG6692SENSEBacillus subtilis 168
26653574474CGPG6669SENSESynechocystis
26753674505CGPG6783SENSEEscherichia coli K-12
26853774507CGPG6799SENSEXenorhabdus nematophilus 85816
26953874562CGPG6764SENSEBacillus subtilis 168
|
Recombinant DNA
Trait-imparting DNA for use in this invention for improved traits in plants is disclosed herein as having a DNA sequence of SEQ ID NO:1 through SEQ ID NO:269 and any of the respective homologs. A subset of the trait-imparting DNA includes fragments with less than the full DNA sequence, e.g., consisting of oligonucleotides of at least about 15 to 20 or more consecutive nucleotides from one of the disclosed sequences. Such oligonucleotides are fragments of the larger molecules having a sequence selected from the group consisting of SEQ ID NO: 1 through SEQ ID NO: 269, and find use, for example as probes and primers for detection of the polynucleotides of the invention or for cloning DNA for use in this invention.
Useful DNA includes variants of the disclosed DNA. Such variants include naturally occurring, including homologous DNA from genes of the same or a different species, or non-natural variants, for example DNA synthesized using chemical synthesis methods, or generated using recombinant DNA techniques. Degeneracy of the genetic code provides the possibility to substitute at least one nucleotide of a disclosed DNA without causing the amino acid sequence of the protein produced to be changed. Hence, useful DNA can have any base sequence that has been changed from the sequences provided herein by substitution in accordance with degeneracy of the genetic code.
Homologs of the trait-imparting DNA generally demonstrate significant identity with the DNA provided herein. Homologous DNA is substantially identical to a trait-imparting DNA if, when the nucleotide sequences are optimally aligned there is at least about 60% nucleotide identity, or higher, e.g., at least 70% or 80% or 85% or even 90% identity or higher, such as 95% or 98% identity over a comparison window of at least 50 to 100 nucleotides, and up to the entire length of the trait-imparting DNA. Optimal alignment of sequences for aligning a comparison window can be conducted by algorithms including computerized implementations of the algorithms (for example, the Wisconsin Genetics Software Package Release 7.0-10.0, Genetics Computer Group, 575 Science Dr., Madison, Wis.). The reference DNA sequence can represent a full-length coding sequence or a portion.
Proteins useful for imparting improved traits are entire proteins or at least a sufficient portion of the entire protein to impart the relevant biological activity of the protein. Proteins useful for generation of transgenic plants having improved traits include the proteins with an amino acid sequence provided herein as SEQ ID NO: 270 through SEQ ID NO: 538, as well as homologs of such proteins.
One method to identify homologs of the proteins useful in this invention is by comparison of the amino acid sequence of the trait-imparting protein to amino acid sequences of proteins from the same or different organisms, e.g., manually or by using known homology-based search algorithms such as those commonly known and referred to as BLAST, FASTA, and Smith-Waterman. In one method a local sequence alignment program, e.g., BLAST, is used to search a database of sequences to find similar sequences, and the summary Expectation value (E-value) is used to measure the sequence base similarity. As a protein hit with the best E-value for a particular organism may not necessarily be an ortholog or the only ortholog, a reciprocal BLAST search is used to filter hit sequences with significant E-values for ortholog identification. The reciprocal BLAST entails search of the significant hits against a database of amino acid sequences from the base organism that are similar to the sequence of the query protein. A hit is a likely ortholog, when the reciprocal BLAST's best hit is the query protein itself or a protein encoded by a duplicated gene after speciation. Thus, homolog is used herein to described proteins that are assumed to have functional similarity by inference from sequence base similarity. The relationship of homologs with amino acid sequences of SEQ ID NO: 539 through SEQ ID NO: 22568 to the proteins with amino acid sequences of SEQ ID NO: 270 through SEQ ID NO: 538 is found is found in Table 17.
Aspects of the invention also use DNA encoding functional homolog proteins which differ in one or more amino acids from those of protein encoded by disclosed trait-imparting DNA as the result of one or more of the well-known conservative amino acid substitutions, e.g., valine is a conservative substitute for alanine and threonine is a conservative substitute for serine. Conservative substitutions for an amino acid within the native sequence are selected from other members of a class to which the naturally occurring amino acid belongs. Representative amino acids within these various classes include, but are not limited to: (1) acidic (negatively charged) amino acids such as aspartic acid and glutamic acid; (2) basic (positively charged) amino acids such as arginine, histidine, and lysine; (3) neutral polar amino acids such as glycine, serine, threonine, cysteine, tyrosine, asparagine, and glutamine; and (4) neutral nonpolar (hydrophobic) amino acids such as alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan, and methionine. Conserved substitutes for an amino acid within a native amino acid sequence are selected from other members of the group to which the naturally occurring amino acid belongs. For example, a group of amino acids having aliphatic side chains is glycine, alanine, valine, leucine, and isoleucine; a group of amino acids having aliphatic-hydroxyl side chains is serine and threonine; a group of amino acids having amide-containing side chains is asparagine and glutamine; a group of amino acids having aromatic side chains is phenylalanine, tyrosine, and tryptophan; a group of amino acids having basic side chains is lysine, arginine, and histidine; and a group of amino acids having sulfur-containing side chains is cysteine and methionine. Naturally conservative amino acids substitution groups are: valine-leucine, valine-isoleucine, phenylalanine-tyrosine, lysine-arginine, alanine-valine, aspartic acid-glutamic acid, and asparagine-glutamine. A further aspect of the invention uses DNA encoding proteins that differ in one or more amino acids from those of protein encoded from a described trait-imparting DNA as the result of deletion or insertion of one or more amino acids in a native sequence.
Homologs of the proteins encoded by disclosed trait-improving DNA will generally demonstrate significant sequence identity, e.g., at least 50% amino acid sequence identity or higher such as at least 70% identity or at least 80% or at least 90% identity with an amino acid sequence of SEQ ID NO:270 through SEQ ID NO:538. Identity of protein homologs is determined by optimally aligning the amino acid sequence of a putative protein homolog with a defined amino acid sequence of a protein encoded by a disclosed trait-imparting DNA and by calculating the percentage of identical and conservatively substituted amino acids over the window of comparison. The window of comparison for determining identity can be the entire amino acid sequence disclosed herein, e.g., the full sequence of any of SEQ ID NO:270 through SEQ ID NO:538.
Genes that are homologs to each other can be grouped into families and included in multiple sequence alignments to allow a consensus sequence to be derived. This analysis enables the derivation of conserved and class- (family) specific residues or motifs that are functionally important. These conserved residues and motifs can be further validated with 3D protein structure if available. A consensus sequence is used to define the full scope of the invention, e.g., to identify proteins with a homolog relationship and the corresponding trait-imparting DNA. Thus, this invention contemplates that protein homologs include proteins with an amino acid sequence that has at least 90% identity to such a consensus amino acid sequence.
Promoters
Numerous promoters that are active in plant cells have been described in the literature. These include promoters present in plant genomes as well as promoters from other sources, including nopaline synthase (NOS) promoter and octopine synthase (OCS) promoters carried on tumor-inducing plasmids of Agrobacterium tumefaciens, caulimovirus promoters such as the cauliflower mosaic virus or figwort mosaic virus promoters. For instance, see U.S. Pat. Nos. 5,858,742 and 5,322,938 which disclose versions of the constitutive promoter derived from cauliflower mosaic virus (CaMV35S), U.S. Pat. No. 5,378,619 which discloses a Figwort Mosaic Virus (FMV) 35S promoter, U.S. Pat. No. 6,437,217 which discloses a maize RS81 promoter, U.S. Pat. No. 5,641,876 which discloses a rice actin promoter, U.S. Pat. No. 6,426,446 which discloses a maize RS324 promoter, U.S. Pat. No. 6,429,362 which discloses a maize PR-1 promoter, U.S. Pat. No. 6,232,526 which discloses a maize A3 promoter, U.S. Pat. No. 6,177,611 which discloses constitutive maize promoters, U.S. Pat. No. 6,433,252 which discloses a maize L3 oleosin promoter, U.S. Pat. No. 6,429,357 which discloses a rice actin 2 promoter and intron, U.S. Pat. No. 5,837,848 which discloses a root specific promoter, U.S. Pat. No. 6,084,089 which discloses cold inducible promoters, U.S. Pat. No. 6,294,714 which discloses light inducible promoters, U.S. Pat. No. 6,140,078 which discloses salt inducible promoters, U.S. Pat. No. 6,252,138 which discloses pathogen inducible promoters, U.S. Pat. No. 6,175,060 which discloses phosphorus deficiency inducible promoters, U.S. Patent Application Publication 2002/0192813A1 which discloses 5′, 3′ and intron elements useful in the design of effective plant expression vectors, U.S. patent application Ser. No. 09/078,972 which discloses a coixin promoter, U.S. patent application Ser. No. 09/757,089 which discloses a maize chloroplast aldolase promoter, and U.S. patent application Ser. No. 10/739,565 which discloses water-deficit inducible promoters, all of which are incorporated herein by reference. These and numerous other promoters that function in plant cells are known to those skilled in the art and available for use in recombinant DNA to provide for expression of desired genes in transgenic plant cells.
It is well known in the art that promoters are usefully altered to contain multiple “enhancer sequences” to assist in elevating gene expression. By including an enhancer sequence with such constructs, expression is generally enhanced. These enhancers often are found 5′ to the start of transcription in a promoter that functions in eukaryotic cells, and can also be inserted in the forward or reverse orientation 5′ or 3′ to the coding sequence. In some instances, 5′ enhancing elements are introns. Particularly useful enhancers are the 5′ introns of the rice actin 1 gene and the rice actin 2 gene. Other enhancers include elements from the CaMV 35S promoter, octopine synthase genes, the maize alcohol dehydrogenase gene, the maize shrunken 1 gene and promoters from non-plant eukaryotes.
In some aspects of the invention it is preferred that the promoter element in the DNA construct be capable of causing sufficient expression in water deficit conditions. Such promoters can be identified and isolated from the regulatory region of plant genes that are over expressed in water deficit conditions. Specific water-deficit-inducible promoters for use in this invention are derived from the 5′ regulatory region of genes identified as a heat shock protein 17.5 gene (HSP17.5), an HVA22 gene (HVA22), a Rab17 gene and a cinnamic acid 4-hydroxylase (CA4H) gene (CA 4H) of Zea maize. Such water-deficit-inducible promoters are disclosed in U.S. 2004-0123347 A1, incorporated herein by reference.
In other aspects of the invention, sufficient expression in plant seed tissues is desired to effect improvements in seed composition. Exemplary promoters for use for seed composition modification include promoters from seed genes such as napin (U.S. Pat. No. 5,420,034), maize L3 oleosin (U.S. Pat. No. 6,433,252), zein Z27 (Russell, et al., (1997) Transgenic Res. 6(2):157-166), globulin 1 (Belanger, et al., (1991) Genetics 129:863-872), glutelin 1 (Russell (1997) supra), and peroxiredoxin antioxidant (Per1) (Stacy, et al., (1996) Plant Mol. Biol. 31(6):1205-1216).
In still other aspects of the invention, preferential expression in plant green tissues is desired. Promoters of interest for such uses include those from genes such as SSU (Fischhoff, et al., (1992) Plant Mol. Biol. 20:81-93), aldolase and pyruvate orthophosphate dikinase (PPDK) (Taniguchi, et al., (2000) Plant Cell Physiol. 41(1):42-48).
Gene Overexpression
“Gene overexpression” means expression, e.g., of a gene at a level in its native host that exceeds levels of expression in a non-trans genic host. In many embodiments of the invention, a recombinant DNA construct provides gene overexpression, e.g., as identified in Table 1.
Gene Suppression
Gene suppression includes any of the well-known methods for suppressing expression, typically indicated by reduced levels of protein. Posttranscriptional gene suppression is mediated by transcription of integrated recombinant DNA to form double-stranded RNA (dsRNA) having homology to a gene targeted for suppression. This formation of dsRNA most commonly results from transcription of an integrated inverted repeat of an element of a target gene, and is a common feature of gene suppression methods known as anti-sense suppression, co-suppression and RNA interference (RNAi). Transcriptional suppression can be mediated by a transcribed dsRNA having homology to a promoter DNA sequence to effect what is called promoter trans suppression.
More particularly, posttranscriptional gene suppression by inserting a recombinant DNA construct with one or more copies of anti-sense oriented DNA to regulate gene expression in plant cells is disclosed in U.S. Pat. No. 5,107,065 (Shewmaker, et al.,) and U.S. Pat. No. 5,759,829 (Shewmaker, et al.,). Transgenic plants transformed using such anti-sense oriented DNA constructs for gene suppression can comprise integrated DNA arranged as an inverted repeats that result from insertion of the DNA construct into plants by Agrobacterium-mediated transformation, as disclosed by Redenbaugh, et al., in “Safety Assessment of Genetically Engineered Flavr Savr™ Tomato, CRC Press, Inc. (1992). Inverted repeat insertions can comprises a part or all of the T-DNA construct, e.g., an inverted repeat of a complete transcription unit or an inverted repeat of transcription terminator sequence. Screening for inserted DNA comprising inverted repeat elements can improve the efficiency of identifying transformation events effective for gene silencing whether the transformation construct is a simple anti-sense DNA construct which must be inserted in multiple copies or a complex inverted repeat DNA construct (e.g., an RNAi construct) which can be inserted as a single copy.
Posttranscriptional gene suppression by inserting a recombinant DNA construct with sense-oriented DNA to regulate gene expression in plants is disclosed in U.S. Pat. No. 5,283,184 (Jorgensen, et al.) and U.S. Pat. No. 5,231,020 (Jorgensen, et al.). Inserted T-DNA providing gene suppression in plants transformed with such sense constructs by Agrobacterium is organized predominately in inverted repeat structures, as disclosed by Jorgensen, et al., Mol. Gen. Genet., 207:471-477 (1987). See also Stam, et al., The Plant Journal, 12(1), 63-82 (1997) who used segregation studies to support Jorgensen's finding that gene silencing is mediated by multimeric transgene T-DNA loci in which the T-DNAs are arranged in inverted repeats. Screening for inserted DNA comprising inverted repeat elements can improve the gene silencing efficiency when transforming with simple sense-orientated DNA constructs. Gene silencing efficiency can also be improved by screening for single insertion events when transforming with an RNAi construct containing inverted repeat elements
As disclosed by Redenbaugh, et al., gene suppression can be achieved by inserting into a plant genome recombinant DNA that transcribes dsRNA. Such a DNA insert can be transcribed to an RNA element having the 3′ region as a double stranded RNA. RNAi constructs are also disclosed in EP 0426195 A1 (Goldbach, et al.,—1991) where recombinant DNA constructs for transcription into hairpin dsRNA for providing transgenic plants with resistance to tobacco spotted wilt virus. Double-stranded RNAs were also disclosed in WO 94/01550 (Agrawal, et al.,) where anti-sense RNA was stabilized with a self-complementary 3′ segment. Agrawal, et al., referred to U.S. Pat. No. 5,107,065 for using such self-stabilized anti-sense RNAs for regulating gene expression in plant cells; see International Publication No. 94/01550. Other double-stranded hairpin-forming elements in transcribed RNA are disclosed in International Publication No. 98/05770 (Werner, et al.,) where the anti-sense RNA is stabilized by hairpin forming repeats of poly(CG) nucleotides. See also U.S. Patent Application Publication No. 2003/0175965 A1 (Lowe, et al.,) which discloses gene suppression using and RNAi construct comprising a gene coding sequence preceded by inverted repeats of 5′UTR. See also U.S. Patent Application Publication No. 2002/0048814 A1 (Oeller) where RNAi constructs are transcribed to sense or anti-sense RNA which is stabilized by a poly(T)-poly(A) tail. See also U.S. Patent Application Publication No. 2003/0018993 A1 (Gutterson, et al.,) where sense or anti-sense RNA is stabilized by an inverted repeat of the 3′ untranslated region of the NOS gene. See also U.S. Patent Application Publication No. 2003/0036197 A1 (Glassman, et al.,) where RNA having homology to a target is stabilized by two complementary RNA regions.
Gene silencing can also be affected by transcribing RNA from both a sense and an anti-sense oriented DNA, e.g., as disclosed by Shewmaker, et al., in U.S. Pat. No. 5,107,065 where in Example 1 a binary vector was prepared with both sense and anti-sense aroA genes. See also U.S. Pat. No. 6,326,193 where gene targeted DNA is operably linked to opposing promoters.
Gene silencing can also be affected by transcribing from contiguous sense and anti-sense DNA. In this regard see Sijen, et al., The Plant Cell, Vol. 8, 2277-2294 (1996) discloses the use of constructs carrying inverted repeats of a cowpea mosaic virus gene in transgenic plants to mediate virus resistance. Such constructs for posttranscriptional gene suppression in plants by double-stranded RNA are also disclosed in International Publication No. WO 99/53050 (Waterhouse, et al.,), International Publication No. WO 99/49029 (Graham, et al.), U.S. 2004-0029283 A1 (Fillatti), U.S. Pat. No. 6,506,559 (Fire, et al.,). See also U.S. 2004-0006792 A1 (Shewmaker, et al.,) that discloses constructs and methods for simultaneously expressing one or more recombinant genes while simultaneously suppressing one or more native genes in a transgenic plant. See also U.S. Pat. No. 6,448,473 (Mitsky, et al.,) that discloses multi-gene suppression vectors for use in plants. All of the above-described patents, applications and international publications disclosing materials and methods for posttranscriptional gene suppression in plants are incorporated herein by reference. Transcriptional suppression such as promoter trans suppression can be affected by a expressing a DNA construct comprising a promoter operably linked to inverted repeats of promoter DNA for a target gene. Constructs useful for such gene suppression mediated by promoter trans suppression are disclosed by Mette, et al., The EMBO Journal, Vol. 18, No. 1, pp. 241-148, 1999 and by Mette, et al., The EMBO Journal, Vol. 19, No. 19, pp. 5194-5201-148, 2000, both of which are incorporated herein by reference.
Suppression can also be achieved by insertion mutations created by transposable elements may also prevent gene function. For example, in many dicot plants, transformations with the T-DNA of Agrobacterium are readily achieved and large numbers of transformants can be rapidly obtained. Also, some species have lines with active transposable elements that are efficiently be used for the generation of large numbers of insertion mutations, while some other species lack such options. Mutant plants produced by Agrobacterium or transposon mutagenesis and having altered expression of a polypeptide of interest are identified using the polynucleotides of this invention. For example, a large population of mutated plants are screened to detect mutated plants having an insertion in the gene encoding the polypeptide of interest.
Gene Stacking
This invention also contemplates that the trait-improving recombinant DNA is used in combination with other recombinant DNA to create plants with a multiple desired traits. The combinations generated include multiple copies of any one or more of the recombinant DNA constructs. These stacked combinations are created by any method, including but not limited to cross breeding of transgenic plants, or multiple genetic transformation.
Plant Transformation Methods
Numerous methods for transforming plant cells with recombinant DNA are known in the art and are useful in producing the transgenic seeds of this invention. Two commonly used methods for plant transformation are Agrobacterium-mediated transformation and microprojectile bombardment. Microprojectile bombardment methods are illustrated in U.S. Pat. Nos. 5,015,580 (soybean); 5,550,318 (corn); 5,538,880 (corn); 5,914,451 (soybean); 6,160,208 (corn); 6,399,861 (corn) and 6,153,812 (wheat) and Agrobacterium-mediated transformation is described in U.S. Pat. Nos. 5,159,135 (cotton); 5,824,877 (soybean); 5,591,616 (corn); and 6,384,301 (soybean), all of which are incorporated herein by reference. For Agrobacterium tumefaciens based plant transformation system, additional elements present on transformation constructs include T-DNA left and right border sequences to facilitate incorporation of the recombinant polynucleotide into the plant genome.
In general it is preferred to introduce heterologous DNA randomly, i.e., at a non-specific location, in the genome of a target plant line. In special cases it is useful to target heterologous DNA insertion in order to achieve site-specific integration, e.g., to replace an existing gene in the genome, to use an existing promoter in the plant genome, or to insert a recombinant polynucleotide at a predetermined site known to be active for gene expression. Several site specific recombination systems exist which are known to function implants include cre-lox as disclosed in U.S. Pat. No. 4,959,317 and FLP-FRT as disclosed in U.S. Pat. No. 5,527,695, both incorporated herein by reference.
Transformation methods of this invention are preferably practiced in tissue culture on media and in a controlled environment. “Media” means any of the numerous nutrient mixtures that are used to grow cells in vitro, that is, outside of the intact living organism. Recipient cell targets include, but are not limited to, meristem cells, callus, immature embryos and gametic cells such as microspores, pollen, sperm and egg cells. It is contemplated that any cell from which a fertile plant is regenerated is useful as a recipient cell. Callus is initiated from tissue sources including, but not limited to, immature embryos, seedling apical meristems, microspores and the like. Cells capable of proliferating as callus are also recipient cells for genetic transformation. Practical transformation methods and materials for making transgenic plants of this invention, e.g., various media and recipient target cells, transformation of immature embryos and subsequent regeneration of fertile transgenic plants are disclosed in U.S. Pat. Nos. 6,194,636 and 6,232,526 and U.S. 2004-0216189 A1, which are incorporated herein by reference.
In practice DNA is introduced into only a small percentage of target cells in any one experiment. Marker genes are used to provide an efficient system for identification of those cells that are stably transformed by receiving and integrating a transgenic DNA construct into their genomes. Preferred marker genes provide selective markers that confer resistance to a selective agent, such as an antibiotic or herbicide. Potentially transformed cells are exposed to the selective agent. In the population of surviving cells are those cells where, generally, the resistance-conferring gene has been integrated and expressed at sufficient levels to permit cell survival. Cells are tested further to confirm stable integration of the exogenous DNA. Useful selective marker genes include those conferring resistance to antibiotics such as kanamycin (nptII), hygromycin B (aph IV) and gentamycin (aac3 and aacC4) or resistance to herbicides such as glufosinate (bar or pat) and glyphosate (EPSPS). Examples of such selectable are illustrated in U.S. Pat. Nos. 5,550,318; 5,633,435; 5,780,708 and 6,118,047, all of which are incorporated herein by reference. Screenable markers which provide an ability to visually identify transformants are also often employed, e.g., a gene expressing a colored or fluorescent protein such as a luciferase or green fluorescent protein (GFP) or a gene expressing a beta-glucuronidase or uidA gene (GUS) for which various chromogenic substrates are known. It is also contemplated that combinations of screenable and selectable markers will be useful for identification of transformed cells. See PCT publication WO 99/61129 which discloses use of a gene fusion between a selectable marker gene and a screenable marker gene, e.g., an NPTII gene and a GFP gene.
Cells that survive exposure to the selective agent, or cells that have been scored positive in a screening assay, are cultured in regeneration media and allowed to mature into plants. Developing plantlets are transferred to soil less plant growth mix, and hardened off, e.g., in an environmentally controlled chamber at about 85% relative humidity, 600 ppm CO2, and 25-250 microeinsteins m−2s−1 of light, prior to transfer to a greenhouse or growth chamber for maturation. Plants are preferably matured either in a growth chamber or greenhouse. Plants are regenerated from about 6 wk to 10 months after a transformant is identified, depending on the initial tissue. During regeneration, cells are grown to plants on solid media at about 19 to 28 degrees C. After regenerating plants have reached the stage of shoot and root development, they are transferred to a greenhouse for further growth and testing. Plants are pollinated using conventional plant breeding methods known to those of skill in the art and seed produced.
Progeny are recovered from transformed plants and tested for expression of the exogenous recombinant polynucleotide. Useful assays include, for example, “molecular biological” assays, such as Southern and Northern blotting and PCR; “biochemical” assays, such as detecting the presence of RNA, e.g., double stranded RNA, or a protein product, e.g., by immunological means (ELISAs and Western blots) or by enzymatic function; plant part assays, such as leaf or root assays; and also, by analyzing the phenotype of the whole regenerated plant.
Discovery of Trait-Improving Recombinant DNA
To identify recombinant DNA that confer improved traits to plants, Arabidopsis plants were transformed with a large population of recombinant DNA constructs for expressing a large variety of distinct DNA. Transgenic plants were produced and screened to identify those plants having recombinant DNA constructs expressing trait-imparting DNA. A two-step screening process was employed which comprised two passes of trait characterization to ensure that the trait modification was dependent on expression of the recombinant DNA, but not due to the chromosomal location of the integration of the transgene. Twelve independent transgenic lines for each recombinant DNA construct were established and assayed for the transgene expression levels. Five transgenic lines with high transgene expression levels were used in the first pass screen to evaluate the transgene's function in T2 transgenic plants. Subsequently, three transgenic events, which had been shown to have one or more improved traits, were further evaluated in the second pass screen to confirm the transgene's ability to impart an improved trait. The following Table 2 summarizes the improved traits that have been confirmed as provided by a recombinant DNA construct.
In particular, Table 2 reports
“PEP Seq ID” which is the amino acid sequence of the protein cognate to the DNA in the recombinant DNA construct corresponding to a protein sequence of a SEQ ID NO. in the Sequence Listing.
“construct_id” is an arbitrary name for the recombinant DNA describe more particularly in Table 1.
“annotation” refers to a description of the top hit protein obtained from an amino acid sequence query of each PEP SEQ ID NO to GenBank database of the National Center for Biotechnology Information (ncbi). More particularly, “gi” is the GenBank ID number for the top BLAST hit.
“description” refers to the description of the top BLAST hit.
“e-value” provides the expectation value for the BLAST hit.
“identity” refers to the percentage of identically matched amino acid residues along the length of the portion of the sequences which is aligned by BLAST between the sequence of interest provided herein and the hit sequence in GenBank.
“traits” identified by two letters codes the confirmed improvement in a transgenic plant provided by the recombinant DNA. The codes for improved traits are:
“CK” which indicates cold tolerance improvement identified under a cold shock tolerance screen;
“CS” which indicates cold tolerance improvement identified by a cold germination tolerance screen;
“DS” which indicates drought tolerance improvement identified by a PEG induced osmotic stress tolerance screen;
“PEG” which idicates osmotic stress tolerance improvement identified by a PEG induced osmotic stress tolerance screen;
“HS”which indicates heat stress tolerance improvement identified by a heat stress tolerance screen;
“SS” which indicates high salinity stress tolerance improvement identified by a salt stress tolerance screen;
“LN” which indicates nitrogen use efficiency improvement identified by a limited nitrogen tolerance screen;
“LL” which indicates attenuated shade avoidance response identified by a shade tolerance screen under a low light condition;
“PP” which indicates improved growth and development at early stages identified by an early plant growth and development screen;
“SP” which indicates improved growth and development at late stages identified by a late plant growth and development screen provided herein.
TABLE 2
|
|
Pepannotation
SEQconstructe%
Ididgenevalueidentityncbi iddescriptiontraits
|
27014324CGPG15601.00E−12786gi|15232185|ref|NP_191546.1|expressedCKSS
protein [Arabidopsis
thaliana]]
27117484CGPG2630093gi|15220912|ref|NP_173239.1|zinc fingerCK
(C3HC4-type RING finger)
family protein [Arabidopsis
thaliana]
27219109CGPG13819.00E−3181gi|18404521|ref|NP_565870.1|expressedCK
protein [Arabidopsis
thaliana]
27370423CGPG31651.00E−13496gi|30688808|ref|NP_850953.1|MADS-CKCSCKHSPP
box protein (AGL9)
[Arabidopsis thaliana]
gb|AAM65812.1| putative
floral homeotic protein,
AGL9 [Arabidopsis
thaliana]
27470424CGPG31801.00E−14281gi|25405039|pir||H96827proteinCK
F20B17.12 [imported]-
Arabidopsis thaliana
gb|AAF68121.1| F20B17.12
[Arabidopsis thaliana]
27570480CGPG38331.00E−12299gi|18411867|ref|NP_565174.1|14-3-3CK
protein GF14 pi (GRF13)
[Arabidopsis thaliana]
27670509CGPG24201.00E−11382gi|15225186|ref|NP_180770.1|ovateCK
protein-related [Arabidopsis
thaliana]
27770647CGPG43341.00E−17194gi|15237269|ref|NP_200093.1|ornithineCK
cyclodeaminase/mu-
crystallin family protein
[Arabidopsis thaliana]
dbj|BAB10429.1]
27870675CGPG45190100gi|15224730|ref|NP_180115.1|2-CK
oxoglutarate-dependent
dioxygenase, putative
[Arabidopsis thaliana]
pir||E84648 probable
dioxygenase]
27970829CGPG518092gi|15232841|ref|NP_186854.1|potassiumCK
transporter (KUP3)
[Arabidopsis thaliana]
28070849CGPG5961.00E−16696gi|15224801|ref|NP_179547.1|cytidineCK
deaminase (CDD)/cytidine
aminohydrolase
[Arabidopsis thaliana]
28171627CGPG1270099gi|18398032|ref|NP_566315.1|ABC1CK
family protein [Arabidopsis
thaliana]
28271934CGPG22941.00E−15479gi|15233973|ref|NP_195575.1|26SCK
proteasome regulatory
subunit S5A (RPN10)
[Arabidopsis thaliana]
sp|P55034|PSD4_ARATH
26S proteasome non-
ATPase regulatory subunit
4 (26S proteasome
regulatory
28372615CGPG48292.00E−4988gi|18422886|ref|NP_568693.1|expressedCK
protein [Arabidopsis
thaliana]
28472927CGPG14771.00E−11481gi|15234815|ref|NP_194797.1|MA3CK
domain-containing protein
[Arabidopsis thaliana]
pir||A85359 translation
initiation factor-like protein
28573014CGPG56921.00E−18093gi|37528369|ref|NP_931714.1|Fructose-CKPP
1,6-bisphosphatase (D-
fructose-1,6-bisphosphate
1-phosphohydrolase)
(FBPase) [Photorhabdus
luminescens subsp.
laumondii TTO1]
28673559CGPG6535093gi|16078422|ref|NP_389241.1|similar toCK
aspartate aminotransferase
[Bacillus subtilis]
sp|O31665|MTNE_BACSU
Transaminase mtnE
pir||F69863 probable
transaminase (EC 2.6.1.—)
ykrV
28774251CGPG54891.00E−17187gi|15238437|ref|NP_200760.1|zincCKSP
transporter (ZIP2)
[Arabidopsis thaliana]
sp|Q9LTH9|ZIP2_ARATH
Zinc transporter 2 precursor
(ZRT/IRT-like protein 2)
28819631CGPG36271.00E−9490gi|18410249|ref|NP_565053.1|SNF7CS
family protein [Arabidopsis
thaliana] pir||G96755
developmental protein
homolog DG1118
[imported]-Arabidopsis
thaliana
28970121CGPG23801.00E−111100gi|6323765|ref|NP_013836.1|HypotheticalCS
ORF; Ymr118cp
[Saccharomyces
cerevisiae]
sp|Q04487|YM07_YEAST
Putative succinate
dehydrogenase cytochrome
B subunit, mitochondrial
precursor
29070654CGPG43522.00E−6388gi|18400941|ref|NP_566531.1|expressedCS
protein [Arabidopsis
thaliana]
29170696CGPG45908.00E−9287gi|25408379|pir||E84768hypotheticalCSPP
protein At2g35430
29270713CGPG1462095gi|30678679|ref|NP_191966.2|malateCS
oxidoreductase, putative
29370740CGPG3700094gi|18402759|ref|NP_566667.1|transcriptionCSLLPP
factor jumonji (jmjC)
domain-containing protein
29471321CGPG4418091gi|13878402|sp|Q9STL0|C71N_ARATHCS
Cytochrome P450 71A23
pir||T06712 probable
cytochrome P450
T29H11.180
29571835CGPG46340100gi|15234361|ref|NP_192100.1|DC1CSSP
domain-containing protein
[Arabidopsis thaliana]
pir||E85024 probable CHP-
rich zinc finger protein
29672934CGPG5798098gi|6323512|ref|NP_013583.1|High-CS
affinity inorganic phosphate
(Pi) transporter and low-
affinity manganese
transporter; regulated by
Pho4p and Spt7p; mutation
confers resistance to
arsenate; exit from the ER
during maturation requires
Pho86p; Pho84p
[Saccharomyces
cerevisiae]
29772945CGPG5787094gi|6319991|ref|NP_010071.1|GABA-CS
specific transport protein;
Uga4p [Saccharomyces
cerevisiae]
sp|P32837|UGA4_YEAST
GABA-specific permease
(GABA-specific transport
protein)
29872980CGPG5773089gi|6321960|ref|NP_012036.1|Subunit ofCS
the anaphase-promoting
complex/cyclosome
(APC/C), which is a
ubiquitin-protein ligase
required for degradation of
anaphase inhibitors,
including mitotic cyclins,
during the
metaphase/anaphase
transition; Cdc23p
29973504CGPG64801.00E−178100gi|16330153|ref|NP_440881.1|fructokinaseCSPP
[Synechocystis sp. PCC
6803] pir||S77227
fructokinase (EC 2.7.1.4)-
Synechocystis sp. (strain
PCC 6803)
30073507CGPG65041.00E−173100gi|16078547|ref|NP_389366.1|similar toCSLLPPPEG
glutaminase [Bacillus
subtilis]
30173573CGPG64620100gi|15890038|ref|NP_355719.1|AGR_C_5067pCSPP
[Agrobacterium
tumefaciens str. C58]
ref|NP_533456.1|3-
isopropylmalate
dehydrogenase
30273586CGPG64711.00E−177100gi|160776841ref|NP_388498.1|similar toCSDSPP
fructokinase [Bacillus
subtilis]
30373770CGPG54352.00E−3468gi|15235771|ref|NP_193383.1|cysteineCSPP
protease inhibitor family
protein/cystatin family
protein [Arabidopsis
thaliana]
30474105CGPG6574073gi|23059330|ref|ZP_00084307.1|COG1012:CS
NAD-dependent
aldehyde dehydrogenases
[Pseudomonas fluorescens
PfO-1]
30574111CGPG6622099gi|16131442|ref|NP_418028.1|alpha-CS
amylase [Escherichia coli
K12]
30674136CGPG66329.00E−8199gi|16330993|ref|NP_441721.1|unknownCSCKHS
protein [Synechocystis sp.
PCC 6803]
30774139CGPG65611.00E−18095gi|24112825|ref|NP_707335.1|glyceraldehyde-CSLL
3-phosphate
dehydrogenase A [Shigella
flexneri 2a str. 301]
30874267CGPG5364097gi|18399375|ref|NP_566402.1|U-boxCS
domain-containing protein
[Arabidopsis thaliana]
30974291CGPG5363094gi|18401867|ref|NP_565676.1|armadillo/CS
beta-catenin repeat family
protein/U-box domain-
containing protein
[Arabidopsis thaliana]
31074318CGPG58260100gi|15219730|ref|NP_176847.1|cellCSHS
division protein kinase,
putative [Arabidopsis
thaliana]
31174319CGPG5831096gi|15224359|ref|NP_181907.1|mitogen-CS
activated protein kinase,
putative/MAPK, putative
(MPK6) [Arabidopsis
thaliana]
31274324CGPG58851.00E−17495gi|42569304|ref|NP_180094.2|proteinCS
kinase family protein
[Arabidopsis thaliana]
31374512CGPG32096gi|15217945|ref|NP_176132.1|aminoCSHSSP
acid permease I (AAP1)
[Arabidopsis thaliana]
31474583CGPG66491.00E−15183gi|22978283|ref|ZP_00024043.1|COG0252:CSPP
L-
asparaginase/archaeal Glu-
tRNAGln amidotransferase
subunit D [Ralstonia
metallidurans]
31570427CGPG30670100gi|42572771|ref|NP_974481.1|kelchCSDS
repeat-containing F-box
family protein [Arabidopsis
thaliana]
31671811CGPG4426097gi|15223341|ref|NP_171627.1|cytochromeCSDSLLLN
P450, putative
[Arabidopsis thaliana]
31773463CGPG63840100gi|22977164|ref|ZP_00022985.1|COG0538:DS
Isocitrate
dehydrogenases [Ralstonia
metallidurans]
31872081CGPG52797.00E−6677gi|42570373|ref|NP_850277.2|CCAAT-DSPEG
box binding transcription
factor, putative [Arabidopsis
thaliana]
31910139CGPG101089gi|15229877|ref|NP_187154.1|sodiumDS
proton exchanger, putative
(NHX2) [Arabidopsis
thaliana]
32011410CGPG103082gi|15236418|ref|NP_192555.1|homeoboxDS
protein knotted-1 like 1
(KNAT1) [Arabidopsis
thaliana]
32111604CGPG48092gi|15233457|ref|NP_194642.1|hexokinaseDS
1 (HXK1) [Arabidopsis
thaliana]
32212368CGPG10061.00E−14685gi|15231451|ref|NP_190238.1|epsin N-DS
terminal homology (ENTH)
domain-containing protein/
clathrin assembly protein-
related [Arabidopsis
thaliana]
32313502CGPG1354095gi|15224557|ref|NP_180632.1|serine/threonineDSPP
protein kinase,
putative [Arabidopsis
thaliana]
32413745CGPG15761.00E−11284gi|15222987|ref|NP_177749.1|hypotheticalDS
protein [Arabidopsis
thaliana] gb|AAF17642.1|
T23E18.15 [Arabidopsis
thaliana]
32513821CGPG15691.00E−15585gi|18416499|ref|NP_567716.1|expressedDS
protein [Arabidopsis
thaliana]
32614240CGPG1697094gi|15241302|ref|NP_197527.1|expressedDS
protein [Arabidopsis
thaliana]
32714718CGPG1082086gi|18407200|ref|NP_566090.1|expressedDS
protein [Arabidopsis
thaliana]
32817022CGPG17741.00E−159100gi|15237803|ref|NP_197755.1|nodulinDS
MtN3 family protein
[Arabidopsis thaliana]
32917924CGPG28823.00E−92100gi|15233350|ref|NP_192875.1|zinc fingerDS
(C3HC4-type RING finger)
family protein (RHA1b)
[Arabidopsis thaliana]
33018259CGPG33682.00E−9488gi|30685085|ref|NP_849549.1|zinc fingerDSPP
protein (LSD1) [Arabidopsis
thaliana]
33119171CGPG2952091gi|6320063|ref|NP_010143.1|plasmaDS
membrane glucose sensor;
Rgt2p [Saccharomyces
cerevisiae]
33219201CGPG2332096gi|15233948|ref|NP_194205.1|proteinDS
kinase (AFC2) [Arabidopsis
thaliana]
sp|P51567|AFC2_ARATH
Protein kinase
33319317CGPG36621.00E−15191gi|21232858|ref|NP_638775.1|conservedDS
hypothetical protein
[Xanthomonas campestris
pv. campestris str. ATCC
33913]
33470417CGPG3427081gi|18396278|ref|NP_566180.1|integralDSPPSP
membrane family protein
[Arabidopsis thaliana]
33570467CGPG37850100gi|15241416|ref|NP_196953.1|no apicalDS
meristem (NAM) family
protein [Arabidopsis
thaliana]
33670806CGPG7120100gi|15218225|ref|NP_173010.1|cyclin,DS
putative [Arabidopsis
thaliana]
33770818CGPG4791.00E−15792gi|30691978|ref|NP_568508.2|bZIPDS
transcription factor family
protein [Arabidopsis
thaliana]
33870820CGPG655093gi|15224342|ref|NP_181899.1|acyl-[acyl-DS
carrier-protein] desaturase/
stearoyl-ACP desaturase
(SSI2) [Arabidopsis
thaliana]
33970919CGPG40291.00E−16973gi|6996560|emb|CAB75429.1|oligouridylateDS
binding protein
[Nicotiana plumbaginifolia]
34071623CGPG46961.00E−15095gi|15236511|ref|NP_192588.1|mitogen-DS
activated protein kinase,
putative [Arabidopsis
thaliana] pir||T01835
serine/threonine-specific
protein kinase ARA.KIN
homolog T15F16.3-
Arabidopsis thaliana
34171662CGPG46791.00E−17391gi|5929964|gb|AAD56659.1|malateDS
dehydrogenase [Glycine
max]
34271693CGPG46526.00E−8656gi|21553460|gb|AAM62553.1|snap25aDS
[Arabidopsis thaliana]
34372384CGPG4639098gi|1169548|sp|P38604|DS
ERG7_YEASTLanosterol
synthase
(Oxidosqualene--lanosterol
cyclase) (2,3-
epoxysqualene--lanosterol
cyclase) (OSC)
gb|AAA64377.1|2,3-
oxidosqualene-lanosterol
cyclase
34472439CGPG50758.00E−5790gi|22331337|ref|NP_683594.1|NPR1/NIM1-DS
interacting protein 2
(NIMIN-2)
34572619CGPG48356.00E−8388gi|15237317|ref|NP_200108.1|expressedDS
protein [Arabidopsis
thaliana]
34672624CGPG48420100gi|15242148|ref|NP_200558.1|expressedDS
protein [Arabidopsis
thaliana]
34772715CGPG5521091gi|6323933|ref|NP_014004.1|Carboxy-DSSS
terminal domain (CTD)
phosphatase, essential for
dephosphorylation of the
repeated C-terminal
domain of the RNA
polymerase II large subunit
(Rpo21p); Fcp1p
[Saccharomyces
cerevisiae]
34872754CGPG55481.00E−169100gi|728961|sp|Q00618|DS
BET4_YEASTGeranylgeranyl
transferase
type II alpha subunit (Type
II protein geranyl-
34972819CGPG49890100gi|18417026|ref|NP_567780.1|pfkB-typeDS
carbohydrate kinase family
protein [Arabidopsis
thaliana]
35075516CGPG76891.00E−13870gi|42568081|ref|NP_197938.2|zinc fingerDS
(C3HC4-type RING finger)
family protein [Arabidopsis
thaliana]
35175701CGPG78568.00E−4137gi|15225413|ref|NP_182037.1|zinc fingerDSLN
(C2H2 type) family protein
[Arabidopsis thaliana]
35273515CGPG64731.00E−162100gi|16079626|ref|NP_390450.1|similar toHSCSPEG
6-phosphogluconate
dehydrogenase (pentose
phosphate) [Bacillus
subtilis]
35374684CGPG63601.00E−64100gi|18390735|ref|NP_563782.1|expressedCSHS
protein [Arabidopsis
thaliana]
35419542CGPG3069090gi|18403574|ref|NP_564592.1|F-boxHS
family protein [Arabidopsis
thaliana]
35519618CGPG35741.00E−121100gi|15218423|ref|NP_177373.1|trypsinHS
and protease inhibitor
family protein/Kunitz
family protein [Arabidopsis
thaliana] pir||F96746
probable drought induced
protein
35619649CGPG31401.00E−14187gi|18412787|ref|NP_567287.1|vesicle-HS
associated membrane
family protein/VAMP
family protein
35719745CGPG39732.00E−6046gi|15239303|ref|NP_201424.1|expressedHS
protein [Arabidopsis
thaliana]
35819768CGPG40961.00E−17981gi|25052804|gb|AAN65180.1|mitogen-HSSS
activated protein kinase 4
[Petroselinum crispum]
35919772CGPG39393.00E−8279gi|7488744|pir||T09700MADS-boxHS
protein —alfalfa (fragment)
gb|AAB51377.1| MADS-box
protein [Medicago sativa]
36019779CGPG41131.00E−15389gi|30681126|ref|NP_196201.2|phosphateCSHS
translocator-related
[Arabidopsis thaliana]
36119833CGPG40741.00E−10779gi|6683777|gb|AAF23363.1|CAGL2CSHSPP
[Cucumis sativus]
36219862CGPG39612.00E−8956gi|15229637|ref|NP_188469.1|no apicalHS
meristem (NAM) family
protein [Arabidopsis
thaliana] dbj|BAB01106.1|
unnamed protein product
[Arabidopsis thaliana]
36319879CGPG4009075gi|18401703|ref|NP_564504.1|proteinHSCSSS
phosphatase 2C-related/
PP2C-related [Arabidopsis
thaliana]
36470445CGPG37282.00E−5188gi|30696602|ref|NP_200357.2|proteaseHS
inhibitor/seed storage/lipid
transfer protein (LTP)
family protein [Arabidopsis
thaliana]
36570738CGPG31951.00E−96100gi|15234797|ref|NP_194791.1|expressedHSPP
protein [Arabidopsis
thaliana]
36671437CGPG40431.00E−16481gi|15241535|ref|NP_196433.1|serine/threonineHS
protein kinase,
putative [Arabidopsis
thaliana]
36771572CGPG45203.00E−8392gi|18403850|ref|NP_565804.1|expressedHS
protein [Arabidopsis
thaliana]
36871617CGPG12270100gi|15236219|ref|NP_195218.1|1-HSCK
phosphatidylinositol
phosphodiesterase-related
[Arabidopsis thaliana]
36972532CGPG47801.00E−11890gi|15236659|ref|NP_194120.1|expressedHS
protein [Arabidopsis
thaliana]
37072757CGPG5572089gi|15242402|ref|NP_197088.1|zinc fingerHSLLPEG
protein CONSTANS (CO)
[Arabidopsis thaliana]
37173412CGPG6448099gi|28867589|ref|NP_790208.1|glutamineHS
synthetase, type I
[Pseudomonas syringae pv.
tomato str. DC3000]
37274102CGPG65501.00E−16794gi|15614187|ref|NP_242490.1|L-HS
asparaginase [Bacillus
halodurans C-125]
37372633CGPG48531.00E−14586gi|15238013|ref|NP_199519.1|caseinCSLLPEG
kinase II beta chain,
putative [Arabidopsis
thaliana]
37472456CGPG47451.00E−7592gi|15239846|ref|NP_196763.1|17.6 kDaDSLL
class II heat shock protein
(HSP17.6-CII) [Arabidopsis
thaliana]
37572963CGPG17461.00E−15187gi|15222239|ref|NP_172174.1|ovateLLLN
family protein [Arabidopsis
thaliana]
37670426CGPG31998.00E−5488gi|18397268|ref|NP_564336.1|double-LL
stranded DNA-binding
family protein [Arabidopsis
thaliana]
37770772CGPG46271.00E−9280gi|15220084|ref|NP_173175.1|MADS-LL
box protein (AGL100)
[Arabidopsis thaliana] P
37871137CGPG1251.00E−11190gi|15218957|ref|NP_176202.1|two-LL
component responsive
regulator/response
regulator 3 (ARR3)
[Arabidopsis thaliana]
37971529CGPG28081.00E−13172gi|42562375|ref|NP_174152.3|Dof-typeLL
zinc finger domain-
containing protein
[Arabidopsis thaliana]
38071601CGPG18581.00E−16892gi|15231425|ref|NP_187378.1|transcriptionalLL
activator, putative
[Arabidopsis thaliana]
38172362CGPG9831.00E−16395gi|15242779|ref|NP_200562.1|xyloglucaLL
n: xyloglucosyl transferase,
putative/xyloglucan
endotransglycosylase,
putative/endo-xyloglucan
transferase, putative
[Arabidopsis thaliana]
38272466CGPG47673.00E−6083gi|15234046|ref|NP_195030.1|glutaredoCKLLPEG
xin family protein
[Arabidopsis thaliana]
38372524CGPG47701.00E−13491gi|18412649|ref|NP_567140.1|expressedCKLL
protein [Arabidopsis
thaliana]
38473085CGPG56891.00E−134100gi|16331347|ref|NP_442075.1|triosephosphateLL
isomerase
[Synechocystis sp. PCC
6803]
38574241CGPG5457089gi|444790|prf||1908224AnucleotideLL
translocator
38674247CGPG54751.00E−159100gi|18411863|ref|NP_565172.1|proteinLL
phosphatase 2C, putative/
PP2C, putative
[Arabidopsis thaliana]
38774284CGPG5413097gi|15230577|ref|NP_190087.1|serineLL
carboxypeptidase III,
putative [Arabidopsis
thaliana]
38874652CGPG61681.00E−9080gi|15235970|ref|NP_194879.1|expressedLLDS
protein [Arabidopsis
thaliana]
38970437CGPG37061.00E−172100gi|30678824|ref|NP_186983.2|short-CKLN
chain
dehydrogenase/reductase
(SDR) family protein
[Arabidopsis thaliana]
39071633CGPG8571.00E−10086gi|6690274|gb|AAF24061.1|v-SNAREDSLN
AtVTI1a [Arabidopsis
thaliana]
39172948CGPG5617094gi|15225456|ref|NP_182059.1|leucine-LNPEG
rich repeat transmembrane
protein kinase, putative
[Arabidopsis thaliana]
39272519CGPG4749LNSS
39310475CGPG3991.00E−16496gi|15240972|ref|NP_195761.1|stress-LN
responsive protein, putative
[Arabidopsis thaliana]
39411120CGPG4590100gi|15227169|ref|NP_179812.1|inositol-3-LN
phosphate synthase
isozyme 2/myo-inositol-1-
phosphate synthase 2/MI-
1-P synthase 2/IPS 2
[Arabidopsis thaliana]
39519736CGPG41292.00E−9467gi|13346194|gb|AAK19619.1|GHMYB9LN
[Gossypium hirsutum]
39671606CGPG4715091gi|15218674|ref|NP_171800.1|phototropic-LN
responsive NPH3 family
protein [Arabidopsis
thaliana]
39771840CGPG4353096gi|18401087|ref|NP_566542.1|mitoticDSLLLN
phosphoprotein N′ end
(MPPN) family protein
[Arabidopsis thaliana]
39874240CGPG54541.00E−15590gi|15233884|ref|NP_194188.1|mitochondrialCKLN
substrate carrier family
protein [Arabidopsis
thaliana] pir||T05577
uncoupling protein homolog
F22K18.230-Arabidopsis
thaliana
39974331CGPG5834094gi|15220416|ref|NP_172003.1|proteinLN
kinase family protein
[Arabidopsis thaliana]
40074610CGPG60481.00E−117100gi|15217568|ref|NP_172434.1|Ras-LLLN
related GTP-binding
protein, putative
[Arabidopsis thaliana]
sp|O04486|RB1C_ARATH
Ras-related protein
Rab11C
40175527CGPG76821.00E−5565gi|15240946|ref|NP_195750.1|phosphatiLN
dylethanolamine-binding
family protein [Arabidopsis
thaliana]
40270681CGPG45849.00E−6493gi|18411465|ref|NP_567196.1|auxin-CKPEG
responsive family protein
[Arabidopsis thaliana]
40371663CGPG4638093gi|21230153|ref|NP_636070.1|conservedCKPEG
hypothetical protein
[Xanthomonas campestris
pv. campestris str. ATCC
33913]
40472769CGPG55730100gi|15225499|ref|NP_182075.1|cytochromeCKPEG
P450, putative
[Arabidopsis thaliana]
40571508CGPG15412.00E−24100gi|15241504|sp|Q9SD80|OM05_ARATHPEGCSSPPEG
Mitochondrial import
receptor subunit TOM5
homolog (Translocase of
outer membrane 5 kDa
subunit homolog)
40674248CGPG54760100gi|15226152|ref|NP_180926.1|proteinPEGCS
phosphatase 2C, putative/
PP2C, putative
[Arabidopsis thaliana] p
40772771CGPG21665.00E−44100gi|18395032|ref|NP_564151.1|expressedPEGCKHSSS
protein [Arabidopsis
thaliana]
40872085CGPG5228094gi|15241541|ref|NP_199275.1|cytochromePEGHS
P450 family protein
[Arabidopsis thaliana]
dbj|BAA98115.1| flavonoid
3′,5′-hydroxylase-like;
cytochrome P450
[Arabidopsis thaliana]
40972744CGPG55631.00E−13696gi|6321574|ref|NP_011651.1|20SHSPEGCK
proteasome beta-type
subunit; the only
nonessential 20S subunit;
Pre9p [Saccharomyces
cerevisiae]
41073039CGPG810096gi|15242124|ref|NP_197599.1|molybdopterinHSPEG
biosynthesis CNX1
protein/molybdenum
cofactor biosynthesis
enzyme CNX1 (CNX1)
[Arabidopsis thaliana]
41173054CGPG57542.00E−98100gi|6324827|ref|NP_014896.1|Nat5pPEGHSSSPEG
[Saccharomyces
cerevisiae] pir||S67150
hypothetical protein
YOR253w-yeast
(Saccharomyces
cerevisiae)
41273501CGPG6456097gi|15888752|ref|NP_354433.1|AGR_C_2631pHSPEG
[Agrobacterium
tumefaciens str. C58]
sp|Q8UFH1|ENO_AGRT5
Enolase (2-
phosphoglycerate
dehydratase) (2-phospho-
D-glycerate hydro-lyase)
41319707CGPG41791.00E−8649gi|15236282|ref|NP_195242.1|O-PEGCS
methyltransferase family 2
protein [Arabidopsis
thaliana]
41419951CGPG39415.00E−9154gi|15221582|ref|NP_177064.1|basicPEGCK
helix-loop-helix (bHLH)
family protein [Arabidopsis
thaliana]
41519967CGPG40321.00E−12767gi|4760710|dbj|BAA77395.1|SLL2-S9-PEG
protein [Brassica rapa]
41670543CGPG3815095gi|15220994|ref|NP_175222.1|E2FPEGCK
transcription factor-2
(E2F2)/transcription factor
E2Fc (E2Fc) [Arabidopsis
thaliana]
41770707CGPG12731.00E−108100gi|15219558|ref|NP_177523.1|Ssu72-PEG
like family protein
[Arabidopsis thaliana]
pir||F96765 unknown
protein F
41870719CGPG1712086gi|18394560|ref|NP_564043.1|expressedPEG
protein [Arabidopsis
thaliana]
41971134CGPG8178.00E−55100gi|15240471|ref|NP_200327.1|smallPEGHSPP
ubiquitin-like modifier 2
(SUMO) [Arabidopsis
thaliana]
42071146CGPG29281.00E−8692gi|29165403|gb|AAO65311.1|MADSPEG
affecting flowering 3 variant
II [Arabidopsis thaliana]
42171660CGPG46903.00E−80100gi|18415773|ref|NP_567637.1|methioninePEG
sulfoxide reductase
domain-containing protein/
SeIR domain-containing
protein [Arabidopsis
thaliana]
42272086CGPG52360100gi|15232215|ref|NP_191556.1|PEGPPPEG
methylenetetrahydrofolate
reductase
1 (MTHFR1) [Arabidopsis
thaliana]-
42372632CGPG48524.00E−9990gi|18425032|ref|NP_569028.1|expressedPEG
protein [Arabidopsis
thaliana]
42472716CGPG55292.00E−8589gi|6320196|ref|NP_010276.1|subunit ofPEG
the Anaphase Promoting
Complex; all known APC
subunits co-
immunoprecipitate with
epitope-tagged Apc11p;
Apc11p [Saccharomyces
cerevisiae]
42572723CGPG1848097gi|15237500|ref|NP_199487.1|humanPEG
Rev interacting-like family
protein/hRIP family protein
[Arabidopsis thaliana]
dbj|BAB08919.1| zinc finger
protein Glo3-like
[Arabidopsis thaliana]
42672987CGPG17875.00E−8177gi|15231568|ref|NP_189282.1|octicosapeptide/PEGSP
Phox/Bem1p (PB1)
domain-containing protein
[Arabidopsis thaliana]
42774109CGPG6606077gi|37524479|ref|NP_927823.1|maltodextrinPEG
phosphorylase
[Photorhabdus luminescens
subsp. laumondii TTO1]
42874140CGPG6569099gi|15613102|ref|NP_241405.1|NADP-PEGPPPEG
dependent aldehyde
dehydrogenase [Bacillus
halodurans C-125]
42974191CGPG6597096gi|22960294|ref|ZP_00007935.1|COG1850:PEG
Ribulose 1,5-
bisphosphate carboxylase,
large subunit [Rhodobacter
sphaeroides]
43074265CGPG53561.00E−117100gi|15237288|ref|NP_197727.1|GRAMPEGPPPEG
domain-containing protein/
ABA-responsive protein-
related [Arabidopsis
thaliana]
43174369CGPG60762.00E−8696gi|18409647|ref|NP_564994.1|ubiquitin-PEGCKPPPEG
conjugating enzyme family
protein [Arabidopsis
thaliana]
43270217CGPG6097gi|15231536|ref|NP_189259.1|cytochromeCKPPSP
P450 family protein
[Arabidopsis thaliana]
43372711CGPG18464.00E−7579gi|15221048|ref|NP_175816.1|transcriptionCKPPSP
initiation factor IID
(TFIID) 31 kDa subunit
(TAFII-31) family protein
[Arabidopsis thaliana]
43470932CGPG40891.00E−12956gi|15223134|ref|NP_177792.1|expressedCSHSPP
protein [Arabidopsis
thaliana]
43573518CGPG64971.00E−17763gi|22981996|ref|ZP_00027327.1|COG1012:CSCKPP
NAD-dependent
aldehyde dehydrogenases
[Burkholderia fungorum]
43619771CGPG40113.00E−9080gi|18418200|ref|NP_568342.1|rubredoxinPPHSSS
family protein
[Arabidopsis thaliana]
dbj|BAB10504.1|
gene_id: MKP11.2˜unknown
protein [Arabidopsis
thaliana] g
43773549CGPG6460090gi|37524978|ref|NP_928322.1|5-HSDSPP
carboxymethyl-2-
hydroxymuconate
semialdehyde
dehydrogenase
[Photorhabdus luminescens
subsp. laumondii TTO1]
43872994CGPG5803083gi|6322702|ref|NP_012776.1|VacuolarCKPEGCSPPPEG
transporter, exports large
neutral amino acids from
the vacuole; member of a
family of seven S. cerevisiae
genes (AVT1-7)
related to vesicular GABA-
glycine transporters; Avt3p
[Saccharomyces
cerevisiae]
43971928CGPG16170100gi|18394888|ref|NP_564120.1|catalase 3CSPEGCKPPPEG
(SEN2) [Arabidopsis
thaliana]
44072903CGPG5584091gi|6322293|ref|NP_012367.1|HistonePEGPPSS
methyltransferase with a
role in transcriptional
elongation, methylates a
lysine residue of histone
H3; associates with the C-
terminal domain of Rpo21p;
histone methylation activity
is regulated by
phosphorylation status of
Rpo21p; Set2p
[Saccharomyces
cerevisiae]
sp|P46995|SET2_YEAST
SET domain protein 2
44173017CGPG5733094gi|6325368|ref|NP_015436.1|kinasePEGPPPEG
required for late nuclear
division; Dbf20p
[Saccharomyces
cerevisiae]
44274587CGPG6774094gi|17938451|ref|NP_535240.1|succinatePEGDSHSPPSS
semialdehyde
dehydrogenase
[Agrobacterium
tumefaciens str. C58]
44372453CGPG47356.00E−6791gi|15218924|ref|NP_174236.1|auxin-CKPPSPSS
responsive family protein
[Arabidopsis thaliana]
pir||A86417 probable auxin-
induced protein, 45653-45228
44472967CGPG5742099gi|6321525|ref|NP_011602.1|CytosolicCSCKHSLLPPSS
catalase T, has a role in
protection from oxidative
damage by hydrogen
peroxide, Ctt1p
[Saccharomyces
cerevisiae]
44572961CGPG5591095gi|15228498|ref|NP_186975.1|UTP--PEGSSHSPP
glucose-1-phosphate
uridylyltransferase, putative/
UDP-glucose
pyrophosphorylase,
putative/UGPase, putative
[Arabidopsis thaliana]
44673070CGPG5627090gi|15225044|ref|NP_181451.1|proteinPEGPPSS
kinase family protein
[Arabidopsis thaliana]
44773475CGPG63850100gi|39934021|ref|NP_946297.1|glyceraldehyde-PEGPPSS
3-phosphate
dehydrogenase(GAPDH)
[Rhodopseudomonas
palustris CGA009]
44872916CGPG1814097gi|15228871|ref|NP_188303.1|proteinPPSS
phosphatase 2C, putative/
PP2C, putative
[Arabidopsis thaliana]
44972969CGPG5789094gi|6321886|ref|NP_011962.1|Low-PPSPSS
affinity glucose transporter
of the major facilitator
superfamily, expression is
induced by Hxk2p in the
presence of glucose and
repressed by Rgt1p when
glucose is limiting; Hxt1p
[Saccharomyces
cerevisiae]
45074449CGPG6659096gi|15890426|ref|NP_356098.1|AGR_L_619pPPSS
[Agrobacterium
tumefaciens str. C58]
pir||A98170 hypothetical
protein AGR_L_619
[imported]-Agrobacterium
45116615CGPG2539098gi|15890896|ref|NP_356568.1|AGR_L_1560pPP
[Agrobacterium
tumefaciens str. C58]
ref|NP_534561.1| glucose-
1-phosphate
adenylyltransferase
[Agrobacterium
tumefaciens str. C58]
45219187CGPG3310091gi|18423163|ref|NP_568731.1|squamosPP
a promoter-binding protein,
putative [Arabidopsis
thaliana]
45319648CGPG31341.00E−17996gi|18413950|ref|NP_568102.1|short-PP
chain
dehydrogenase/reductase
(SDR) family protein
[Arabidopsis thaliana]
45470354CGPG3995064gi|15241312|ref|NP_196916.1|nodulinDSPPSP
family protein [Arabidopsis
thaliana]
45570421CGPG2942088gi|30677977|ref|NP_178317.2|zinc fingerPP
(C2H2 type) family protein
[Arabidopsis thaliana]
45670459CGPG3758095gi|15233315|ref|NP_188242.1|F-boxPP
family protein [Arabidopsis
thaliana] dbj|BAB01261.1|
unnamed protein product
[Arabidopsis thaliana]
45770465CGPG37751.00E−15590gi|15236937|ref|NP_195254.1|zinc fingerPPSP
(C2H2 type) family protein
[Arabidopsis thaliana]
45870683CGPG45873.00E−6564gi|18423239|ref|NP_568751.1|polyadenylate-PP
binding protein,
putative/PABP, putative
[Arabidopsis thaliana]
45970725CGPG2097091gi|18420505|ref|NP_568066.1|expressedCSPP
protein [Arabidopsis
thaliana]
46070852CGPG1465093gi|15237075|ref|NP_195290.1|isocitratePPSP
dehydrogenase, putative/
NAD+ isocitrate
dehydrogenase, putative
[Arabidopsis thaliana]
46171112CGPG9341.00E−13094gi|15218701|ref|NP_171806.1|expressedCSPP
protein [Arabidopsis
thaliana] pir||E86161
F10O3.11 protein-
Arabidopsis thaliana
gb|AAD25802.1| Belongs to
the PF|01027
Uncharacterized protein
family UPF0005 with 7
transmembrane domains.
[Arabidopsis thaliana]
46271127CGPG945097gi|15225307|ref|NP_179604.1|26SPP
protease regulatory
complex subunit 4, putative
[Arabidopsis thaliana]
pir||E84585 26S
proteasome subunit 4
[imported]-Arabidopsis
thaliana
46371132CGPG1561098gi|15232209|ref|NP_191550.1|expressedPP
protein [Arabidopsis
thaliana]
46471217CGPG950100gi|15221476|ref|NP_172127.1|shaggy-PP
related protein kinase iota/
ASK-iota (ASK9) (GSK1)
[Arabidopsis thaliana] (EC
2.7.1.—)
46571645CGPG46883.00E−69100gi|18401105|ref|NP_566544.1|phosphotransferPP
family protein
[Arabidopsis thaliana]
46671726CGPG3894093gi|15217677|ref|NP_171725.1|no apicalHSPP
meristem (NAM) family
protein [Arabidopsis
thaliana]
46772432CGPG45621.00E−14492gi|20152540|emb|CAD29662.1|putativePPSP
auxin response factor 23
[Arabidopsis thaliana]
46872450CGPG47321.00E−170100gi|15238890|ref|NP_197366.1|zinc fingerLLPP
(C3HC4-type RING finger)
family protein [Arabidopsis
thaliana]
46972455CGPG47421.00E−14493gi|15242893|ref|NP_200597.1|anthranilatePPPEG
synthase beta subunit,
putative [Arabidopsis
thaliana]
47072727CGPG55221.00E−118100gi|6324107|ref|NP_014177.1|functionallyPP
related to TFIIB, affects
start site selection in vivo;
Ssu72p [Saccharomyces
cerevisiae]
47172817CGPG4987096gi|30679158|ref|NP_567238.2|AAA-typePP
ATPase family protein
[Arabidopsis
47272992CGPG5777090gi|6324981|ref|NP_015049.1|S-PPPEG
adenosylMethionine
Permease; Sam3p
[Saccharomyces
cerevisiae]
47373007CGPG5760093gi|6320865|ref|NP_010944.1|One ofPP
three possible beta-
subunits of the Snf1 kinase
complex, allows nuclear
localization of the Snf1
kinase complex in the
presence of a
nonfermentable carbon
source; contains glycogen-
binding domain; Gal83p
[Saccharomyces
cerevisiae]
47473073CGPG5688095gi|16331010|ref|NP_441738.1|fructosePP
1,6-bisphosphatase
[Synechocystis sp. PCC
6803]
47573506CGPG6496096gi|23062569|ref|ZP_00087347.1|COG10PP
12: NAD-dependent
aldehyde dehydrogenases
[Pseudomonas fluorescens
PfO-1]
47674107CGPG6590095gi|15965198|ref|NP_385551.1|PYRUVATEPPSS
DEHYDROGENASE
ALPHA2 SUBUNIT
PROTEIN [Sinorhizobium
meliloti 1021]
47774117CGPG6575081gi|37528116|ref|NP_931461.1|CSPP
Phenylacetaldehyde
dehydrogenase
(PAD) [Photorhabdus
luminescens subsp.
laumondii TTO1]
47874131CGPG6592096gi|16329404|ref|NP_440132.1|transaldolasePPSS
[Synechocystis sp.
PCC 6803] B-
47974344CGPG59291.00E−111100gi|15236410|ref|NP_193147.1|COP9HSPP
signalosome subunit,
putative/CSN subunit,
putative (CSN8)
[Arabidopsis thaliana]
48014320CGPG12290100gi|18418018|ref|NP_567894.1|expressedSP
protein [Arabidopsis
thaliana]
48116756CGPG21171.00E−14285gi|18391249|ref|NP_563885.1|expressedSP
protein [Arabidopsis
thaliana]
48217448CGPG26731.00E−10272gi|15239624|ref|NP_197993.1|PHDSP
finger family protein
[Arabidopsis thaliana]
gb|AAM64729.1| nucleic
acid binding protein-like
[Arabidopsis thaliana]
48317633CGPG28391.00E−14585gi|18395124|ref|NP_564171.1|basicSP
helix-loop-helix (bHLH)
family protein [Arabidopsis
thaliana]
48418876CGPG30961.00E−17289gi|18394949|ref|NP_564133.1|transporter-SP
related [Arabidopsis
thaliana] pir||G86343
hypothetical protein
T22I11.10
48519120CGPG19760100gi|15232345|ref|NP_188710.1|fertilization-SP
independent endosperm
protein (FIE) [Arabidopsis
thaliana]
48619221CGPG29581.00E−15978gi|30690446|ref|NP_182182.2|Dof zincSP
finger protein DAG2/Dof
affecting germination 2
(DAG2) [Arabidopsis
thaliana]
48770206CGPG41161.00E−13964gi|18412918|ref|NP_565249.1|phospholipid/SP
glycerol acyltransferase
family protein [Arabidopsis
48870223CGPG53093gi|15240313|ref|NP_198006.1|hexoseSP
transporter, putative
[Arabidopsis thaliana]
48970347CGPG31471.00E−12166gi|18416267|ref|NP_567693.1|Dof-typeSP
zinc finger domain-
containing protein
[Arabidopsis thaliana]
49070406CGPG1687093gi|18397470|ref|NP_564354.1|early-SP
responsive to dehydration
stress protein (ERD4)
[Arabidopsis thaliana]
49170469CGPG37911.00E−17189gi|15237581|ref|NP_198936.1|MADS-SPHS
box family protein
[Arabidopsis thaliana]
49270564CGPG1864089gi|15219067|ref|NP_173589.1|SWIRMSP
domain-containing protein/
DNA-binding family protein
gb|AAD41423.1| Contains
similarity to gb|AF033823
moira protein from
Drosophila melanogaster
and contains a PF|00249
Myb-like DNA-binding
domain.
49370601CGPG2917091gi|15235140|ref|NP_193702.1|zinc fingerSPPP
(C3HC4-type RING finger)
family protein [Arabidopsis
thaliana] pir||T04748
hypothetical protein
T16H5.30-Arabidopsis
thaliana
49470612CGPG3721096gi|18416732|ref|NP_568256.1|conservedSP
oligomeric Golgi complex
component-related/COG
complex component-related
[Arabidopsis thaliana]
49570720CGPG1358093gi|15238483|ref|NP_198387.1|lectinSP
protein kinase family
protein [Arabidopsis
thaliana]
49670735CGPG26611.00E−109100gi|15231241|ref|NP_187953.1|transcriptionSP
initiation factor IID-1
(TFIID-1)/TATA-box factor
1/TATA sequence-binding
protein 1 (TBP1)
[Arabidopsis thaliana]
49770846CGPG3771.00E−151100gi|15221223|ref|NP_177577.1|zinc fingerSP
(C3HC4-type RING finger)
family protein [Arabidopsis
thaliana] pir||D96772
probable RING zinc finger
protein
49870923CGPG4020087gi|8132347|gb|AAF73257.1|MAPSP
kinase PsMAPK2 [Pisum
sativum]
49971149CGPG3457083gi|20141566|sp|P48001|SP
HKL4_ARATHHomeobox
protein knotted-1
like 4 (KNAT4) pir||T51795
HOMEOBOX PROTEIN
KNOTTED-1 LIKE 4
(KNAT4)-
50071608CGPG46870100gi|15220438|ref|NP_72008.1|ent-SP
kaurenoic acid hydroxylase
(KAO1)/cytochrome P450
88A3, putative (CYP88A3)
[Arabidopsis thaliana]
50171739CGPG43457.00E−8980gi|18406944|ref|NP_566061.1|expressedSP
protein [Arabidopsis
thaliana]
50272014CGPG52300100gi|25410898|pir||D84423probable WD-SP
40-repeat protein [imported]-
Arabidopsis thaliana
gb|AAD14533.1| putative
stress protein [Arabidopsis
thaliana]
50372051CGPG5241093gi|18401606|ref|NP_566585.1|cyclicSP
nucleotide-binding
transporter 1/CNBT1
(CNGC20) [Arabidopsis
thaliana]
sp|Q9LD37|CG20_ARATH
Probable cyclic nucleotide-
gated ion channel 20,
chloroplast precursor
(Cyclic nucleotide-binding
transporter 1)
50474259CGPG5343096gi|15222882|ref|NP_175431.1|branched-CSHSSS
chain amino acid
aminotransferase 6/
branched-chain amino acid
transaminase 6 (BCAT6)
[Arabidopsis thaliana] s
50572463CGPG47608.00E−48100gi|15236351|ref|NP_193115.1|auxin-CSSSHSLNPP
responsive protein, putative
[Arabidopsis thaliana]
50672902CGPG5597088gi|15240576|ref|NP_199800.1|chlorideSSCSDS
channel protein (CLC-c)
[Arabidopsis thaliana]
sp|Q96282|CLCC_ARATH
Chloride channel protein
CLC-c (AtCLC-c)
50774572CGPG66401.00E−10993gi|16331001|ref|NP_441729.1|unknownCSPPSS
protein [Synechocystis sp.
PCC 6803]
50873055CGPG5768097gi|6321588|ref|NP_011665.1|HypotheticalSSCSHS
ORF; Ygr149wp
[Saccharomyces
cerevisiae]
50974103CGPG6558099gi|15833050|ref|NP_311823.1|fructose-HSPPSS
bisphosphate aldolase
class II [Escherichia coli
O157:H7] r
51072921CGPG5781093gi|6322892|ref|NP_012965.1|generalCKPEGSS
amino acid permease;
Gap1p [Saccharomyces
cerevisiae]
51172968CGPG5772099gi|6321546|ref|NP_011623.1|role inPEGLLSS
DNA replication during S
phase; Clb6p
[Saccharomyces
cerevisiae]
51219703CGPG4172083gi|7488676|pir||T07150G-box bindingHSSS
factor 2A-soybean
(fragment) gb|AAB00097.1|
G-box binding factor
51319946CGPG40971.00E−4634gi|15219099|ref|NP_175691.1|2-SS
oxoglutarate-dependent
dioxygenase, putative
[Arabidopsis thaliana]
51419980CGPG39142.00E−6349gi|28629811|gb|AAO45179.1|transcriptionCSSS
factor Myb1 [Malus
xiaojinensis]
51570435CGPG37011.00E−15091gi|15236597|ref|NP_193499.1|caseinSSPPSP
kinase II beta chain,
putative [Arabidopsis
thaliana]
51671114CGPG1657088gi|30680729|ref|NP_849990.1|K+ effluxSS
antiporter, putative (KEA4)
[Arabidopsis thaliana]
51772451CGPG4733094gi|15239622|ref|NP_197992.1|mitochondrialSS
substrate carrier family
protein [Arabidopsis
thaliana]
51872947CGPG56073.00E−6253gi|1483230|emb|CAA67968.1|MADS4SS
protein [Betula pendula]
51973012CGPG5786097gi|6324187|ref|NP_014257.1|belongsSS
to a ubiquitous family of
cytoplasmic membrane
proteins that transport only
ammonium (NH(4)(+) + NH(3)).;
Mep2p
[Saccharomyces
cerevisiae]
52073022CGPG5622086gi|15225518|ref|NP_182083.1|proteinSS
kinase family protein
[Arabidopsis thaliana]
52173488CGPG63941.00E−15494gi|16080620|ref|NP_391447.1|UTP-SSCSPP
glucose-1-phosphate
uridylyltransferase [Bacillus
subtilis]
52273901CGPG5237092gi|18400284|ref|NP_565553.1|extra-SS
large guanine nucleotide
binding protein/G-protein
(XLG)
52373964CGPG5804088gi|6319773|ref|NP_009855.1|Na+/PiSS
cotransporter, active in
early growth phase; similar
to phosphate transporters
of Neurospora crassa;
transcription regulated by
inorganic phosphate
concentrations and Pho4p;
Pho89p [
52474019CGPG57062.00E−92100gi|16079815|ref|NP_390639.1|adenineSS
phosphoribosyltransferase
[Bacillus subtilis]
52574022CGPG5724097gi|18378991|ref|NP_563659.1|glycosylSSSP
hydrolase family 3 protein
[Arabidopsis thaliana]
52674114CGPG6551099gi|15888903|ref|NP_354584.1|AGR_C_2SS
921p [Agrobacterium
tumefaciens str. C58]
pir||H97551 probable
aminotransferase aatc
52774262CGPG53530100gi|18416245|ref|NP_568226.1|histidinol-SSPP
phosphate
aminotransferase, putative
[Arabidopsis thaliana]
52874292CGPG5367096gi|15239204|ref|NP_201393.1|U-boxSS
domain-containing protein
[Arabidopsis thaliana]
52974302CGPG53841.00E−5982gi|25313155|pir||A96787protein F10A5.6PPSS
[imported]-Arabidopsis
thaliana
53074325CGPG58981.00E−17486gi|15230382|ref|NP_188576.1|cinnamyl-SS
alcohol dehydrogenase
(CAD) [Arabidopsis
thaliana]
53174429CGPG6689096gi|16077873|ref|NP_388687.1|acetoinSS
dehydrogenase E1
component (TPP-
dependent alpha subunit)
[Bacillus subtilis]
53274440CGPG66826.00E−9082gi|15613838|ref|NP_242141.1|uridineSS
kinase [Bacillus halodurans
C-125]
53374462CGPG66685.00E−6799gi|16332127|ref|NP_442855.1|unknownHSSS
protein [Synechocystis sp.
PCC 6803]
53474465CGPG66921.00E−11999gi|16078642|ref|NP_389461.1|similar toPPSS
ribulose-5-phosphate 3-
epimerase [Bacillus subtilis]
53574474CGPG66692.00E−8582gi|16331209|ref|NP_441937.1|unknownLLSS
protein [Synechocystis sp.
PCC 6803]
53674505CGPG67830100gi|16129426|ref|NP_415984.1|crypticSS
nitrate reductase 2 beta
subunit [Escherichia coli
K12]
53774507CGPG6799082gi|27479656|gb|AAO17183.1|Orf17SPSS
[Photorhabdus
luminescens]
53874562CGPG6764095gi|16077501|ref|NP_388315.1|similar toSS
pyruvate oxidase [Bacillus
subtilis]
|
Please note that this file doesn't have Table 3.
|
Screens for Identifying Trait Improving Genes
DS—Improvement of drought tolerance identified by a soil drought stress tolerance screen: Drought is a water deficit condition that imposes osmotic stress on plants. Plants are particularly vulnerable to drought during the flowering stage. The drought condition in the screening process disclosed in Example 1B started from the flowering time and was sustained to the end of harvesting. The drought tolerance-imparting DNA defined for this invention are used in recombinant DNA constructs that improve plant survival rate under drought conditions. Exemplary recombinant DNA which has been identified for conferring such drought tolerance is identified as such in Table 2. Such identified recombinant DNA is useful in generating transgenic plants that are tolerant to the drought condition imposed during flowering time and in other stages of the plant life cycle. As demonstrated from the model plant screen, in some embodiments of transgenic plants with trait-improving recombinant DNA grown under such sustained drought condition also have increased total seed weight per plant in addition to the increased survival rate within a transgenic population, providing a higher yield potential as compared to control plants.
PEG-Improvement of drought tolerance identified by PEG induced osmotic stress tolerance screen: Various drought levels can be artificially induced by using various concentrations of polyethylene glycol (PEG) to produce different osmotic potentials (Pilon-Smits et al., (1995) Plant Physiol. 107:125-130). Several physiological characteristics have been reported as being reliable indications for selection of plants possessing drought tolerance. These characteristics include the rate of seed germination and seedling growth. The traits can be assayed relatively easily by measuring the growth rate of seedling in PEG solution. Thus, a PEG-induced osmotic stress tolerance screen is a useful surrogate for drought tolerance screen. Certain embodiments of transgenic plants with trait-improving recombinant DNA identified in the PEG-induced osmotic stress tolerance screen survive drought conditions providing a higher yield potential as compared to control plants.
SS-Improvement of drought tolerance identified by high salinity stress tolerance screen: Three different factors are responsible for salt damages: (1) osmotic effects, (2) disturbances in the mineralization process, (3) toxic effects caused by the salt ions, e.g., inactivation of enzymes. While the first factor of salt stress results in the wilting of the plants that is similar to drought effect, the ionic aspect of salt stress is clearly distinct from drought. Exemplary recombinant DNA which has been identified to help plants maintain biomass, root growth and/or plant development in high salinity conditions are identified as such in Table 2. Since osmotic effect is one of the major components of salt stress, which is common to the drought stress, embodiments of trait-improving recombinant DNA identified in a high salinity stress tolerance screen also provide transgenic crops with improved drought tolerance. Embodiments of transgenic plants with trait-improving recombinant DNA identified in a high salinity stress tolerance screen survive drought conditions and/or high salinity conditions providing a higher yield potential as compared to control plants.
HS-Improvement of drought tolerance identified by heat stress tolerance screen: Heat and drought stress often occur simultaneously, limiting plant growth. Heat stress can cause the reduction in photosynthesis rate, inhibition of leaf growth and osmotic potential in plants. Thus, genes identified as heat stress tolerance conferring genes may also impart improved drought tolerance to plants. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in a heat stress tolerance screen can survive better heat stress conditions and/or drought conditions providing a higher yield potential as compared to control plants.
CK and CS-Improvement of tolerance to cold stress: Low temperature may immediately result in mechanical constraints, changes in activities of macromolecules, and reduced osmotic potential. Two screening conditions, i.e., cold shock tolerance screen (CK) and cold germination tolerance screen (CS), were set up to look for transgenic plants that display visual growth advantage at lower temperature. In cold germination tolerance screen, the transgenic Arabidopsis plants were exposed to a constant temperature of 8 degrees C. from planting until day 28 post planting. The trait-improving recombinant DNA identified by such screen are particular useful for the production of transgenic plant that can germinate more robustly in a cold temperature as compared to the wild type plants. In cold shock tolerance screen, the transgenic plants were first grown under the normal growth temperature of 22 degrees C. until day 8 post planting, and subsequently were placed under 8 degrees C. until day 28 post planting. Embodiments of transgenic plants with trait-improving recombinant DNA identified in a cold shock stress tolerance screen and/or a cold germination stress tolerance screen survive cold conditions providing a higher yield potential as compared to control plants.
Improvement of tolerance to multiple stresses: Different kinds of stresses often lead to identical or similar reaction in the plants. Genes that are activated or inactivated as a reaction to stress can either act directly in a way the genetic product reduces a specific stress, or they can act indirectly by activating other specific stress genes. By manipulating the activity of such regulatory genes, i.e., multiple stress tolerance genes, plants are enabled to react to different kinds of stresses. For examples, DNA for expressing proteins of SEQ ID NO:352 and SEQ ID NO:353 is useful to improve both heat stress tolerance and cold stress tolerance in plants. Plants transformed with DNA for expressing protein of SEQ ID NO:508 resist heat stress, salt stress and cold stress. Thus, the disclosed stress tolerance conferring genes are useful in combinations to generate transgenic plants that resist multiple stress conditions.
PP-Improvement of early plant growth and development: It is known in the art that to minimize the impact of disease on crop profitability, it is important to start the season with healthy vigorous plants. This means avoiding seed and seedling diseases, leading to increased nutrient uptake and increased yield potential. Traditionally early planting and applying fertilizer are the methods used for promoting early seedling vigor. In early development stage, plant embryos establish only the basic root-shoot axis, a cotyledon storage organ(s), and stem cell populations, called the root and shoot apical meristems, that continuously generate new organs throughout post-embryonic development. “Early growth and development” encompasses the stages of seed imbibition through the early vegetative phase. Certain DNA is identified as useful to produce transgenic plants that have advantages in one or more processes including, but not limited to, germination, seedling vigor, root growth and root morphology under non-stressed conditions. The transgenic plants starting from a more robust seedling are less susceptible to the fungal and bacterial pathogens that attach germinating seeds and seedling. Furthermore, seedlings with advantage in root growth are more resistant to drought stress due to extensive and deeper root architecture. Therefore, genes conferring the growth advantage in early stages to plants are used to generate transgenic plants that are more resistant to various stress conditions due to improved early plant development. Exemplary recombinant DNA that confers both stress tolerance and growth advantages to plants, is identified as such in Table 2, e.g., DNA encoding a protein of SEQ ID NO:444 can improve the plant early growth and development, and impart heat and cold tolerance to plants. Embodiments of transgenic plants with trait-improving recombinant DNA identified in the early plant development screen grow better under non-stress conditions and/or stress conditions providing a higher yield potential as compared to control plants.
SP-Improvement of late plant growth and development: “Late growth and development” encompasses the stages of leaf development, flower production, and seed maturity. Transgenic plants with late growth and development advantages express DNA that is identified as such in Table 2. Such plants exhibit at least one phenotypic characteristics including, but not limited to, increased rosette radius, increased rosette dry weight, seed dry weight, silique dry weight, and silique length. For example, the rosette radius and rosette dry weight are used as the indexes of photosynthesis capacity, and thereby plant source strength and yield potential of a plant. Seed dry weight, silique dry weight and silique length are used as the indexes for plant sink strength, which are considered as the direct determinants of yield. Embodiments of transgenic plants with trait-improving recombinant DNA identified in the late development screen grow better and/or have improved development during leaf development and seed maturation providing a higher yield potential as compared to control plants.
LL-Improvement of tolerance to shade stress identified in a low light screen: The effects of light on plant development are especially prominent at the seedling stage. Under normal light conditions with unobstructed direct light, a plant seeding develops according to a characteristic photomorphogenic pattern, in which plants have open and expanded cotyledons and short hypocotyls. Then the plant's energy is devoted to cotyledon and leaf development while longitudinal extension growth is minimized. Under low light condition where light quality and intensity are reduced by shading, obstruction or high population density, a seedling displays a shade-avoidance pattern, in which the seedling displays a reduced cotyledon expansion, and hypocotyls extension is greatly increased. As the result, a plant under low light condition increases significantly its stem length at the expanse of leaf, seed or fruit and storage organ development, thereby adversely affecting of yield. Recombinant DNA that enables plants to have an attenuated shade avoidance response so that the source of plant can be contributed to reproductive growth efficiently provides embodiments of those plants with higher yield as compared to the wild type plants. Embodiments of transgenic plants with trait-improving recombinant DNA identified in a shade stress tolerance screen have attenuated shade response under shade conditions providing a higher yield potential as compared to control plants. The transgenic plants generated by this invention are suitable for a higher density planting, thereby resulting increased yield per unit area.
LN-Improvement of Tolerance to Low Nitrogen Availability Stress
Nitrogen is a key factor in plant growth and crop yield. The metabolism, growth and development of plants are profoundly affected by their nitrogen supply. Restricted nitrogen supply alters shoot to root ratio, root development, activity of enzymes of primary metabolism and the rate of senescence (death) of older leaves. 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. Enhanced nitrogen use efficiency by plants should enable crops cultivated under low nitrogen availability stress condition resulted from low fertilizer input or poor soil quality.
Recombinant DNA that imparts enhanced nitrogen use efficiency in transgenic plants is identified in Table 2. Such plants exhibit one or more desirable traits including, but not limited to, increased seedling weight, increased number of green leaves, increased number of rosette leaves, altered root length and advanced flower bud formation. Such plants can also have altered amino acid or protein compositions, increased yield and/or better seed quality. Embodiments of such transgenic plants are productively cultivated under nitrogen nutrient deficient conditions, i.e., nitrogen-poor soils and low nitrogen fertilizer inputs that cause the growth of wild type plants to cease or to be so diminished as to make the wild type plants practically useless under such conditions. The transgenic plants also are advantageously used to achieve earlier maturing, faster growing, and/or higher yielding crops and/or produce more nutritious foods and animal feedstocks when cultivated using nitrogen non-limiting growth conditions.
Stacked Traits: This invention also provides transgenic plants with stacked engineered traits, e.g., a crop having an improved phenotype resulting from expression of a trait-improving recombinant DNA, in combination with herbicide and/or pest resistance traits. For example, genes of the current invention can be stacked with other traits of agronomic interest, such as a trait providing herbicide resistance, for example a glyphosate resistance trait, or insect resistance, such as using a gene from Bacillus thuringiensis to provide resistance against lepidopteran, coliopteran, homopteran, hemiopteran, and other insects. Herbicides for which resistance is useful in a plant include glyphosate herbicides, phosphinothricin herbicides, oxynil herbicides, imidazolinone herbicides, dinitroaniline herbicides, pyridine herbicides, sulfonylurea herbicides, bialaphos herbicides, sulfonamide herbicides and gluphosinate herbicides. To illustrate that the production of transgenic plants with herbicide resistance is a capability of those of ordinary skill in the art, reference is made to U.S. 2003-0106096 A1 and 2002-0112260 A1 and U.S. Pat. Nos. 5,034,322; 5,776,760, 6,107,549 and 6,376,754, all of which are incorporated herein by reference. To illustrate that the production of transgenic plants with pest resistance is a capability of those of ordinary skill in the art reference is made to U.S. Pat. Nos. 5,250,515 and 5,880,275 which disclose plants expressing an endotoxin of Bacillus thuringiensis bacteria, to U.S. Pat. No. 6,506,599 which discloses control of invertebrates which feed on transgenic plants which express dsRNA for suppressing a target gene in the invertebrate, to U.S. Pat. No. 5,986,175 which discloses the control of viral pests by transgenic plants which express viral replicase, and to U.S. Patent Application Publication 2003/0150017 A1 which discloses control of pests by a transgenic plant which express a dsRNA targeted to suppressing a gene in the pest, all of which are incorporated herein by reference.
Once one recombinant DNA has been identified as conferring an improved trait of interest in transgenic Arabidopsis plants, several methods are available for using the sequence of that recombinant trait-imparting DNA and knowledge about the protein it encodes to identify homologs of that sequence from the same plant and different plant species or other organisms, e.g., bacteria and yeast. Thus, in one aspect, this invention provides methods for identifying a homologous gene with a DNA sequence homologous to any of SEQ ID NO:1 through SEQ ID NO:269, or a homologous protein with an amino acid sequence homologous to any of SEQ ID NO:270 through SEQ ID NO:538. In another aspect, this invention provides a consensus amino acid sequence for respective homologs for each of SEQ ID NO:270 through SEQ ID NO:538. In yet another aspect, this invention also includes linking or associating one or more desired traits, or gene function with a homolog sequence disclosed herein.
The trait-improving recombinant DNA and methods of using such trait-improving recombinant DNA for generating transgenic plants with improved traits provided by this invention are not limited to any particular plant species. Indeed, the plants of this invention encompass many species of monocots and dicots and include agriculturally useful plants which are cultivated for purposes of food production or industrial applications, e.g., corn and soybean plants and cotton plants. Recombinant DNA constructs optimized for soybean transformation and recombinant DNA constructs optimized for corn transformation are disclosed in the following examples. Other plants of this invention include canola, wheat, sunflower, sorghum, alfalfa, barley, millet, rice, tobacco, fruit and vegetable crops, and turfgrass.
Thus, embodiments of this invention include the use of both DNA identified in Table 3 and homologs in recombinant DNA for transgenic crop plants with improved traits. Transgenic crop plants with improved traits are identified from populations of plants grown from transgenic events by screening to segregate the plants of this invention from plants without the improved traits. Preferred screens for transgenic crop plants identify plants with improved responses to stress conditions, e.g., assays using imposed stress conditions to detect improved responses to drought stress, nitrogen deficiency, cold growing conditions, or alternatively, under naturally present stress conditions, for example under field conditions. Biomass measures are made on greenhouse or field grown plants and include such measurements as plant height, stem diameter, root and shoot dry weights, and, for corn plants, ear length and diameter.
Trait data on morphological changes is collected by visual observation during the process of plant regeneration as well as in regenerated plants transferred to soil. Such trait data includes characteristics such as normal plants, bushy plants, taller plants, thicker stalks, narrow leaves, striped leaves, knotted phenotype, chlorosis, albino, anthocyanin production, or altered tassels, ears or roots. Other enhanced traits are identified by measurements taken under field conditions, such as days to pollen shed, days to silking, leaf extension rate, chlorophyll content, leaf temperature, stand, seedling vigor, internode length, plant height, leaf number, leaf area, tillering, brace roots, stay green, stalk lodging, root lodging, plant health, barrenness/prolificacy, green snap, and pest resistance. In addition, trait characteristics of harvested grain are confirmed, including number of kernels per row on the ear, number of rows of kernels on the ear, kernel abortion, kernel weight, kernel size, kernel density and physical grain quality.
To confirm hybrid yield in transgenic corn plants expressing trait-imparting DNA of this invention, it is useful to test hybrid plants over multiple years at multiple locations in a geographical location where corn is conventionally grown, e.g., in Iowa, Illinois and Kansas, under “normal” field conditions as well as under stress conditions, e.g., under drought or population density stress.
Transgenic crop plants are used to provide other aspects of this invention such as transgenic seeds of crop plants. Seeds of transgenic plants are used to propagate more progeny plants which contain the trait-improving recombinant DNA constructs of this invention. These progeny plants are within the scope of this invention when they contain a trait-improving recombinant DNA construct of this invention, whether or not these plants are selfed or crossed with different varieties of plants.
Screening Methods for Crop Transgenic Plants with Enhanced Agronomic Trait
Due to variability in transformation many transgenic events which survive to fertile transgenic plants that produce seeds and progeny plants do not exhibit an enhanced agronomic trait.
Thus, screening is necessary to identify the transgenic events that produce the transgenic plants and seeds of this invention. Transgenic crop plants having enhanced traits are identified from populations of plants transformed as described herein by evaluating the trait in a variety of assays to detect an enhanced agronomic trait. Useful assays include analyses to detect changes in the chemical composition, biomass, physiological properties and morphology of the plant. Changes in chemical compositions such as nutritional composition of grain are detected by analysis of the seed composition and content of protein, free amino acids, oil, free fatty acids, starch or tocopherols. Changes in biomass characteristics are detected in greenhouse or field grown plants and include plant height, stem diameter, root and shoot dry weights; and, for corn plants, ear length and diameter. Changes in physiological properties are identified by evaluating responses to stress conditions, e.g., assays using imposed stress conditions such as water deficit, nitrogen deficiency, cold growing conditions, pathogen or insect attack or light deficiency, or increased plant density. Changes in morphology are measured by visual observation of tendency of a transformed plant with an enhanced agronomic trait to also appear to be a normal plant as compared to changes toward bushy, taller, thicker, narrower leaves, striped leaves, knotted trait, chlorosis, albino, anthocyanin production, or altered tassels, ears or roots. Other screening properties include days to pollen shed, days to silking, leaf extension rate, chlorophyll content, leaf temperature, stand, seedling vigor, internode length, plant height, leaf number, leaf area, tillering, brace roots, stay green, stalk lodging, root lodging, plant health, barrenness/prolificacy, green snap, and pest resistance. In addition, phenotypic characteristics of harvested grain are evaluated, including number of kernels per row on the ear, number of rows of kernels on the ear, kernel abortion, kernel weight, kernel size, kernel density and physical grain quality.
Seeds for transgenic crop plants with enhanced agronomic traits of this invention are corn, soybean and cotton seeds, as well as seeds for canola, wheat, sunflower, sorghum, alfalfa, barley, millet, rice, tobacco, fruit and vegetable crops, and turfgrass.
A. Screening for Nitrogen Use Efficiency
Many transgenic crop plants of this invention exhibit enhanced nitrogen use efficiency as compared to control plants. Higher nitrogen soil applications increase seed protein and starch accumulation, and lead to larger seed weight and larger kernel number per ear. Recent improvements in elite high yielding corn hybrid genotypes include the ability to utilize nitrogen efficiently. DNA causing the enhanced nitrogen use efficiency in crop plants are especially useful, e.g., for improving yield. Enhanced nitrogen use efficiency is assessed by measuring changes in plant growth such as leaf area production, shoot biomass, chlorophyll content in plants grown in nitrogen limiting conditions and/or nitrogen sufficient conditions. It is useful to conduct a first screen in nitrogen limiting conditions and confirm replicate transgenic events in both nitrogen limiting and nitrogen sufficient conditions. Table 4 shows an amount of nutrients in the nutrient solution for nitrogen limiting conditions (low N) and nitrogen sufficient conditions (high N) which are useful for nitrogen use efficiency screening. For example in a greenhouse screen pots of transgenic plants and control plants are treated with 100 ml of nutrient solution three times a week on alternate days starting at 8 and 10 days after planting for high N and low N screening, respectively.
TABLE 4
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2 mM NH4NO320 mM NH4NO3
Nutrient stockLow nitrogenHigh nitrogen
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1 M NH4N032 mL/L20 mL/L
1 M KH2PO40.50.5
1 M MgSO4.7H2O22
1 M CaCl22.52.5
1 M K2SO411
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Note:
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Adjust pH to 5.6 with HCl or KOH
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After 28 days of plant growth for low N screening and 23 days for high N screening, measurements are taken for total shoot fresh mass, leaf chlorophyll, leaf area, leaf fresh mass and leaf dry mass.
B. Screening for Increased Yield
Many transgenic plants of this invention exhibit improved yield as compared to a control plant. Improved yield can result from a variety or other traits such as enhanced seed sink potential, e.g., the number and size of endosperm cells or kernels, and/or enhanced sink strength, e.g., the rate of starch biosynthesis. Sink potential is established very early during kernel development, as endosperm cell number and cell size are determined within the first few days after pollination.
Much of the increase in corn yield of the past several decades has resulted from an increase in planting density. During that period, corn yield has been increasing at a rate of 2.1 bushels/acre/year, but the planting density has increased at a rate of 250 plants/acre/year. A characteristic of modern hybrid corn is the ability of these varieties to be planted at high density. Many studies have shown that a higher than current planting density should result in more biomass production, but current germplasm does not perform well at these higher densities. One approach to increasing yield is to increase harvest index (HI), the proportion of biomass that is allocated to the kernel compared to total biomass, in high density plantings.
Effective yield screening of transgenic corn uses hybrid progeny of the transgenic event over multiple locations with plants grown under optimal production management practices, and maximum pest control. A useful target for improved yield is a 5% to 10% increase in yield as compared to yield produced by plants grown from seed for a control plant. Useful screening in multiple and diverse geographic locations, e.g., up to 16 or more locations, over one or more planting seasons, e.g., at least two planting seasons, is useful to statistically distinguish yield improvement from natural environmental effects. Useful hybrid screening includes planting multiple transgenic plants, positive and negative control plants, and pollinator plants in standard plots, e.g., 2 row plots, 20 feet long by 5 feet wide with 30 inches distance between rows and a 3 foot alley between ranges. Plants from separate transgenic events can be grouped by recombinant DNA constructs with groups randomly placed in the field. A pollinator plot of a high quality corn line is planted for every two plots to allow open pollination when using male sterile transgenic events. A useful planting density is about 30,000 plants/acre.
Surrogate indicators for screening for yield improvement include source capacity (biomass), source output (sucrose and photosynthesis), sink components (kernel size, ear size, starch in the seed), development (light response, height, density tolerance), maturity, early flowering trait and physiological responses to high density planting, e.g., at 45,000 plants per acre.
When screening for yield improvement a useful statistical measurement approach comprises three components, i.e., modeling spatial autocorrelation of the test field separately for each location, adjusting traits of recombinant DNA events for spatial dependence for each location, and conducting an across location analysis.
A first step in modeling spatial autocorrelation is estimating the covariance parameters of the semivariogram. A spherical covariance model is assumed to model the spatial autocorrelation. Because of the size and nature of the trial, it is likely that the spatial autocorrelation may change. Therefore, anisotropy is also assumed along with spherical covariance structure. The following set of equations describes the statistical form of the anisotropic spherical covariance model.
where I(•) is the indicator function,
and
{dot over (x)}=[cos(ρπ/180)(x1−x2)−sin(ρπ/180)(y1−y2)]/ωx
{dot over (y)}=[sin(ρπ/180)(x1−x2)+cos(ρπ/180)(y1−y2)]/ωy
where s1=(x1, y1) are the spatial coordinates of one location and s2=(x2, y2) are the spatial coordinates of the second location. There are 5 covariance parameters, θ=(ν,σ2, ρ, ωn,ωj) where ν is the nugget effect, σ2 is the partial sill, ρ is a rotation in degrees clockwise from north, ωn is a scaling parameter for the minor axis and ωj is a scaling parameter for the major axis of an anisotropical ellipse of equal covariance. The five covariance parameters that define the spatial trend will then be estimated by using data from heavily replicated pollinator plots via restricted maximum likelihood approach. In a multi-location field trial, spatial trend are modeled separately for each location.
After obtaining the variance parameters of the model, a variance-covariance structure is generated for the data set to be analyzed. This variance-covariance structure contains spatial information required to adjust yield data for spatial dependence. In this case, a nested model that best represents the treatment and experimental design of the study is used along with the variance-covariance structure to adjust the yield data. During this process the nursery or the seed batch effects can also be modeled and estimated to adjust the yields for any yield parity caused by seed batch differences.
After spatially adjusted data from different locations are generated, all adjusted data is combined and analyzed assuming locations as replications. In this analysis, intra and inter-location variances are combined to estimate the standard error of yield from transgenic plants and control plants. Relative mean comparisons are used to indicate statistically significant yield improvements.
C. Screening for Water Use Efficiency
Many transgenic crop plants of this invention exhibit improved yield resulting from improved water use efficiency and/or drought tolerance.
A greenhouse screen for transgenic corn plants for water use efficiency measures changes in plant growth rate, e.g., at least a 10% improvement, in height and biomass during a vegetative drought treatment, as compared to control plants. The hydration status of the shoot tissues following the drought is also measured. Shoot Initial Height (SIH) is plant height after 3 weeks of growth under optimum conditions. Shoot Wilt Height (SWH) is plant height at the end of a 6 day drought. Time course experiments have shown that at about 3 days of drought, wild type plants basically stop growing and begin to wilt. Thus a transgenic plant with improved water use efficiency will continue to grow (probably to a lesser extent than with water) and thereby end up as a significantly taller plant at the end of a drought experiment. Shoot Wilt Mass (SWM) is the amount of wet and dry matter in the shoot (plant separated from root ball at the soil line) at the end of the drought; SDM is measure after 2 to 3 weeks in a drying chamber. Shoot Turgid mass (STM) is the SWM plus the mass of the water that is transported into plant tissues in 3 days of soaking in 40 degree C. water in the dark. Experiments show that most of the water is pulled up in 24 hours but it takes 2 more days before additional increase becomes insignificant. STM-SWM is indicative of water use efficiency in plants where recovery from stress is more important than stress tolerance per se. Relative water content (RWC) is a measurement of how much (%) of the plant is water at harvest. RWC=(SWM−SDM)/(STM−SDM)*100. Fully watered corn plants are about 98% RWC. Typically, in a wilt screen the plants are about 60% RWC. Plants with higher RWC at the end of a drought are considered to be healthier plants and more fit for post-drought recovery and growth.
Relative Growth Rate (RGR) is calculated for each shoot using the formula RGR=(SWH−SIH)/((SWH+SIH)/2)*100
D. Screening for Growth Under Cold Stress
Many transgenic crop plants of this invention exhibit improved growth under cold stress, e.g., in a cold germination assay, in a cold shock assay, in an early seedling growth assay and in root-shoot biomass assay.
In a cold germination assay transgenic seeds from transgenic plants, e.g., R2 inbred seeds or F1 hybrid seeds, seeds of two types of control plants, e.g., negative segregants from the transgenic event or wild type, non-transgenic seeds of the transformed genotype, are treated with fungicide. A useful fungicide such as Captan fungicide (available from Arvesta Corp as MAESTRO® 80DF Fungicide) is applied at the rate of 0.43 mL Captan per 45 g of corn seeds which are dried to provide fungicide-coated seeds.
In a useful cold screen for transgenic corn seeds ten seeds per transgenic event are placed on filter paper (e.g., Whatman No. 1) in the lid of a Petri dish with 5 ml of water. A closed Petri dish is placed in a growth chamber set at 11 degrees C. for inbred corn seed or 9.5 degrees C. for hybrid corn seed. 2 ml of water is added on day 3 and day 10. Seeds are considered germinated if the emerged radicle size is 1 cm. Cold seeds are scored every 2 days from day 10 up to day 30. Tissue samples are collected at random on the last day of the experiment for confirmation of RNA expression. A germination index (GI) is calculated as
GI=(Σ([T+1−ni]*[Pi−Pi-1]))/T
where “T” is the number of days for the experiment, “n” is the number of days after start, “i” is number of times germination is counted including the current day, “P” is the percentage of seed germinated during any given rating. Statistical differences are calculated between positive and wild type control.
In a cold shock assay, seeds are planted in potting media and placed in a growth chamber set at 23 degrees C., relative humidity of 65% with 12 hour day and night photoperiod (300 uE/m2-min). Planted seeds are watered for 20 minute every other day by sub-irrigation and flats are rotated every third day. On day 10 after planting the transgenic positive and wild type control plants are positioned in flats in an alternating pattern. Chlorophyll fluorescence of plants is measured on the tenth day during the dark period of growth by using a Walz PAM-2000 portable fluorometer following manufacturer's instructions. After chlorophyll measurements, leaf samples from each event are collected for confirming the expression of recombinant DNA. The plants are then exposed to temperatures of 5 degrees C. for 4 days. On the fourth day chlorophyll fluorescence is measured and plants are restored to a 23 degrees C. environment for recovery over 3 days. During the recovery period the length of the V3 leaf is measured on the first and third days. After two days of recovery V2 leaf damage is determined visually by estimating percent of green V2 leaf. Statistical differences in V3 leaf growth, V2 leaf necrosis and fluorescence during pre-shock and cold shock can be used for estimation of cold shock damage on corn plants.
In an early seedling growth assay three sets of seeds are assayed. The first set is a group of transgenic seeds from transgenic plants; the second set is negative segregants of the transgenic seed; and the third seed set is seed from two cold tolerant and two cold sensitive wild-type controls. All seeds are treated with a fungicide as indicated above. Seeds are grown in germination paper (12 inch×18 inch pieces of Anchor Paper #SD7606), wetted in a solution of 0.5% KNO3 and 0.1% Thyram. For each paper fifteen seeds are placed on the line evenly spaced such that the radicles will grow toward the same edge. The wet paper is rolled up evenly and tight enough to hold the seeds in place. The roll is secured into place with two large paper clips, one at the top and one at the bottom. The rolls are incubated in a growth chamber at 23 degrees C. for three days in a randomized complete block design within an appropriate container. The chamber is set for 65% humidity with no light cycle. For the cold stress treatment the rolls are then incubated in a growth chamber at 12 degrees C. for fourteen days. The chamber is set for 65% humidity with no light cycle. For the warm treatment the rolls are incubated at 23 degrees C. for an additional two days. After the treatment the germination papers are unrolled and the seeds that did not germinate are discarded. The lengths of the radicle and coleoptile for each seed are measured. A coleoptile sample is collected from six individual kernels of each entry for confirming the expression of recombinant DNA. Statistical differences in the length of radicle and shoot during pre-shock and cold shock are used for an estimation of the effect of the cold treatment on corn plants. The analysis is conducted independently for the warm and cold treatments.
In a root-shoot biomass assay two sets of seeds are used. The first set is transgenic seeds with recombinant DNA, e.g., R2 inbred seeds or F1 hybrid seeds; the second seed set is non-transgenic, wild type negative control made from the same genotypes as the transgenic seeds. All seeds are treated with a fungicide as indicated above. The seeds are planted in potting media in pots arranged in a randomized complete block design with 6 replications. Pots are watered as and when needed by filling water up to the brim of the pot. Plants are grown in a greenhouse to a V6 stage or approximately for 28 days. Greenhouse lights are turned on after emergence of seedlings with 14 hours of light 10 hours of dark. Plants are fertilized twice each week with water-soluble fertilizer containing 200-ppm nitrogen. For measurement of root and shoot dry weight, two pots are separated carefully to remove adhering sand by washing with water. Washed roots are cut at the first node. The roots are placed in a paper bag after squeezing excess water, folded once and stapled. The shoots are then folded up to a convenient size (approximately 15 cm), placed in a paper bag. Bags are placed over a wire shelve to facilitate drying in a ventilated room maintained at 120 degrees F. to a moisture content of about 13% then weighed to determine dried root and shoot biomass.
E. Screen for Enhanced Oil, Starch, or Protein Levels in Plant Seeds
Oil concentrations are determined in kernels by Near Infrared Transmittance (NIT) from inbred and from hybrid lines. Data are also obtained for protein and starch content from this measurement.
Inbred Kernel Oil Screen
The primary transformants are selfed to produce R1 seed which is planted to segregating seed. An untransformed control line is planted every sixth row. All plants are self-pollinated. A molecular assay is conducted to determine zygosity of the transgene in each plant. Ears are harvested at maturity, and well-filled ears are chosen for proximate analysis. Proximate analysis is conducted on up to 5 homozygous ears. If 5 good homozygous ears are not available, then hemizygous ears will be used to obtain 5 good transgene-positive ears. Statistical analysis is conducted to determine whether proximate values for transgenic events are different from controls. Events with an increase in oil with a p-value of less than or equal to 0.1 are termed “putative leads.” Kernel composition is confirmed in an inbred confirmation nursery which is conducted with selected events, and is run with a design similar to that of the Gen2 nursery. A “confirmed lead event” demonstrates an increase in oil with a p-value of less than or equal to 0.1 in two nurseries.
Hybrid Kernel Oil Screen
Grain samples from the multilocation hybrid yield trials are collected at the time of harvest and are analyzed by NIT. Controls are negative segregants, untransformed controls, or pollinators. Data from 3 to 12 locations are pooled for the statistical analysis. Putative leads have increased oil with a p-value of less than or equal to 0.1.
The various aspects of the invention are illustrated by means of the following examples which are in no way intended to limit the full breath and scope of claims.
EXAMPLE 1
Identification of Recombinant DNA that Confers Improved Trait(s) to Plants
A. Expression Constructs for Arabidopsis Plant Transformation
Each gene of interest was amplified from a genomic or cDNA library using primers specific to sequences upstream and downstream of the coding region. Transformation vectors were prepared to constitutively transcribe DNA in either sense orientation (for enhanced protein expression) or anti-sense orientation (for endogenous gene suppression) under the control of an enhanced Cauliflower Mosaic Virus 35S promoter (U.S. Pat. No. 5,359,142) directly or indirectly (Moore, et al., PNAS 95:376-381, 1998; Guyer, et al., Genetics 149: 633-639, 1998; International patent application NO. PCT/EP98/07577). The transformation vectors also contain a bar gene as a selectable marker for resistance to glufosinate herbicide. The transformation of Arabidopsis plants was carried out using the vacuum infiltration method known in the art (Bethtold, et al., Methods Mol. Biol. 82:259-66, 1998). Seeds harvested from the plants, named as T1 seeds, were subsequently grown in a glufosinate-containing selective medium to select for plants which were actually transformed and which produced T2 transgenic seed.
B. Soil Drought Tolerance Screen
This example describes a soil drought tolerance screen to identify Arabidopsis plants transformed with recombinant DNA that wilt less rapidly and/or produce higher seed yield when grown in soil under drought conditions
T2 seeds were sown in flats filled with Metro/Mix® 200 (The Scotts® Company, USA). Humidity domes were added to each flat and flats were assigned locations and placed in climate-controlled growth chambers. Plants were grown under a temperature regime of 22° C. at day and 20° C. at night, with a photoperiod of 16 hours and average light intensity of 170 μmol/m2/s. After the first true leaves appeared, humidity domes were removed. The plants were sprayed with glufosinate herbicide and put back in the growth chamber for 3 additional days. Flats were watered for 1 hour the week following the herbicide treatment. Watering was continued every seven days until the flower bud primordia became apparent, at which time plants were watered for the last time.
To identify drought tolerant plants, plants were evaluated for wilting response and seed yield. Beginning ten days after the last watering, plants were examined daily until 4 plants/line had wilted. In the next six days, plants were monitored for wilting response. Five drought scores were assigned according to the visual inspection of the phenotypes: 1 for healthy, 2 for dark green, 3 for wilting, 4 severe wilting, and 5 for dead. A score of 3 or higher was considered as wilted.
At the end of this assay, seed yield measured as seed weight per plant under the drought condition was characterized for the transgenic plants and their controls and analyzed as a quantitative response according to example 1M.
Two approaches were used for statistical analysis on the wilting response. First, the risk score was analyzed for wilting phenotype and treated as a qualitative response according to the example 1L. Alternatively, the survival analysis was carried out in which the proportions of wilted and non-wilted transgenic and control plants were compared over each of the six days under scoring and an overall log rank test was performed to compare the two survival curves using S-PLUS statistical software (S-PLUS 6, Guide to statistics, Insightful, Seattle, Wash., USA). Table 5 provides a list of recombinant DNA constructs that improve drought tolerance in transgenic plants.
TABLE 5
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Survival Anaysis of
wilt response
Wilt Response Riskdiff
PepscoreSeed Weight/planttime
SEQRSp-p-top-
IDConstruct_idGeneOrientationmeanvaluecdeltavaluecwiltingvaluec
|
31910139CGPG101ANTI-SENSE0.1150.024S−0.1230.804/−0.010.469/
32011410CGPG103SENSE0.2260.003S−0.3660.926/01/
32111604CGPG48ANTI-SENSE0.250.034S0.2570.01S−0.240.38/
32212368CGPG1006SENSE0.1480.044S0.3590.02S−0.060.764/
32313502CGPG1354SENSE0.4310S0.6240S1.340.366/
32413745CGPG1576ANTI-SENSE−0.0210.711/0.6640S−0.290.453/
32513821CGPG1569SENSE0.1350.025S0.1280.402/0.240.972/
32614240CGPG1697SENSE0.3770.002S−1.3050.991/01/
32714718CGPG1082SENSE0.1680.001S0.1350.351/0.250.208/
32817022CGPG1774SENSE0.060.124T0.5630.043S00.961/
32917924CGPG2882SENSE−0.0930.914/0.2880.021S0.090.935/
33018259CGPG3368SENSE0.070.28/0.3910.058T−0.270.591/
33119171CGPG2952SENSE0.2270.005S0.8460.001S0.120.543/
33219201CGPG2332SENSE0.1240.027S−0.4350.785/0.350.256/
33319317CGPG3662SENSE0.3380S−0.0710.61/0.630.106T
33470417CGPG3427SENSE0.2530.016S−1.4240.984/01/
31570427CGPG3067SENSE−0.0330.818/1.0040.002S0.010.977/
33570467CGPG3785SENSE0.1270.023S−0.4480.946/0.710.046S
33670806CGPG712SENSE0.2460.046S0.1740.276/0.140.07T
33770818CGPG479SENSE0.070.115T0.5580.009S0.610.283/
33870820CGPG655SENSE0.1720.048S0.0360.441/0.260.554/
33970919CGPG4029SENSE0.1670.009S−0.5650.904/0.310.508/
34071623CGPG4696SENSE0.1580.047S0.4210.04S01/
39071633CGPG857SENSE0.1210.017S−0.8230.967/0.450.139T
34171662CGPG4679SENSE0.0630.013S−0.0370.631/0.160.957/
34271693CGPG4652SENSE0.0740.042S0.2460.06T0.340.616/
31671811CGPG4426SENSE0.3590.015S−0.7290.903/0.150.822/
31872081CGPG5279SENSE0.2690.005S−0.3720.987/0.170.404/
34372384CGPG4639SENSE0.1330.018S0.620.002S0.170.359/
34472439CGPG5075SENSE0.1750.013S−0.0350.604/0.230.244/
37472456CGPG4745SENSE0.530.01S−0.7370.979/−0.080.823/
34572619CGPG4835SENSE0.1780.039S0.2190.072T0.960.691/
34672624CGPG4842SENSE0.1630.021S0.3560.051T0.30.375/
34772715CGPG5521SENSE0.0820.1T0.7670.002S0.120.628/
34872754CGPG5548SENSE0.1310.031S−0.3650.974/00.923/
34972819CGPG4989SENSE0.0940.026S0.3620.069T0.030.83/
35075516CGPG7689SENSE0.0670.066T0.9650.001S0.240.464/
35175701CGPG7856SENSE0.1470.006S0.9860.015S0.150.448/
31773463CGPG6384SENSE0.1740.048S−1.3590.959/0.090.984/
45470354CGPG3995SENSE−0.0050.563/0.4440.002S10.290.9/
39771840CGPG4353SENSE0.1420.007S−0.2120.859/9.290.99/
50672902CGPG5597SENSE0.0090.162T0.0340.2T51/
43773549CGPG6460SENSE0.1190.037S−0.7740.949/6.260.25/
30273586CGPG6471SENSE0.0030.451/0.5880.002S6.340.723/
44274587CGPG6774SENSE0.2620.001S−0.1170.574/7.490.041S
38874652CGPG6168SENSE0.4750S−0.7660.92/7.480S
|
S: represents that the transgenic plants showed statistically significant trait improvement as compared to the reference (p < 0.05, p value, of the delta of a quantitative response or of the risk score of a qualitative response, is the probability that the observed difference between the transgenic plants and the reference occur by chance)
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T: represents that the transgenic plants showed a trend of trait improvement as compared to the reference with p < 0.2
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/: represents the transgenic plants didn't show any alteration or had unfavorable change in traits examined as compared to the reference in the current dataset.
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C. Stress Tolerance Screen
Under high temperatures, Arabidopsis seedlings become chlorotic and root growth is inhibited. This example sets forth the heat stress tolerance screen to identify Arabidopsis plants transformed with the gene of interest that are more resistant to heat stress based on primarily their seedling weight and root growth under high temperature.
T2 seeds were plated on ½×MS salts, 1% phytagel, with 10 μg/ml BASTA (7 per plate with 2 control seeds; 9 seeds total per plate). Plates were placed at 4° C. for 3 days to stratify seeds. Plates were then incubated at room temperature for 3 hours and then held vertically for 11 additional days at temperature of 34° C. at day and 20° C. at night. Photoperiod was 16 h. Average light intensity was ˜140 μmol/m2/s. After 14 days of growth, plants were scored for glufosinate resistance, root length, final growth stage, visual color, and seedling fresh weight. A photograph of the whole plate was taken on day 14.
The seedling weight and root length were analyzed as quantitative responses according to example 1M. The final grow stage at day 14 was scored as success if 50% of the plants had reached 3 rosette leaves and size of leaves are greater than 1 mm (Boyes, et al., (2001) The Plant Cell 13, 1499-1510). The growth stage data was analyzed as a qualitative response according to example 1L. Table 6 provides a list of recombinant DNA constructs that improve heat tolerance in transgenic plants.
TABLE 6
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PepGrowth stageRoot LengthSeedling Weight
SEQRSp-p-p-
IDConstruct_idGeneOrientationmeanvaluecdeltavaluecdeltavaluec
|
35419542CGPG3069SENSE0.8420.021S0.2960.023S1.6160S
35519618CGPG3574SENSE1.0720.005S0.3280.006S1.5690S
35619649CGPG3140SENSE0.720.042S0.2430.054T1.6650S
35719745CGPG3973SENSE0.650.016S0.190.021S1.5050S
35819768CGPG4096SENSE1.060.035S0.170.034S1.1710S
43619771CGPG4011SENSE0.8220.023S0.2010.001S1.430S
35919772CGPG3939SENSE0.2470.014S0.1510.014S1.3440S
36019779CGPG4113SENSE0.6050.051T0.1810.003S1.4360S
36119833CGPG4074SENSE0.9650.026S0.2660.007S1.010S
36219862CGPG3961SENSE0.3410.119T0.1320.007S1.220S
36319879CGPG4009SENSE0.7340.002S0.220.001S1.4990S
36470445CGPG3728SENSE0.4130.062T0.1480.114T1.2490S
36570738CGPG3195SENSE0.6870.055T0.2050.041S1.2610S
36671437CGPG4043SENSE0.0940.198T0.0920.064T1.3010S
36771572CGPG4520SENSE0.9380.052T0.4410S1.6330S
36871617CGPG1227SENSE0.8090.012S0.1430.029S1.050.003S
40872085CGPG5228SENSE1.2340.02S0.1920.043S1.1620S
36972532CGPG4780SENSE1.0280.022S0.1980.052T1.0430.001S
40972744CGPG5563SENSE0.170.146T0.040.359/0.8270.004S
37072757CGPG5572SENSE1.820.004S0.140.091T1.1210S
40772771CGPG2166SENSE1.7760.001S0.360S1.4280S
44472967CGPG5742SENSE0.2730.063T0.1470.102T1.030S
41073039CGPG810SENSE−0.0480.774/−0.1350.957/0.590.022S
41173054CGPG5754SENSE0.0550.312/0.2360.001S1.4340S
50873055CGPG5768SENSE0.1540.123T0.2690S1.5240S
37173412CGPG6448SENSE0.1870.118T0.1340.06T1.1810S
41273501CGPG6456SENSE1.60.003S0.0810.136T1.1190S
35273515CGPG6473SENSE−0.0370.758/−0.0240.604/0.6940.008S
43773549CGPG6460SENSE2.6120S0.1990.017S1.4320S
37274102CGPG6550SENSE0.340.035S0.2680.002S1.3550S
50974103CGPG6558SENSE−0.0131/−0.0210.608/0.860S
35374684CGPG6360SENSE0.440.018S0.2540.002S1.3830S
51219703CGPG4172SENSE0.2110.079T0.0590.301/1.2620S
27370423CGPG3165SENSE1.4560S0.4180S1.9120S
49170469CGPG3791SENSE0.1430.28/0.0280.349/1.0010.001S
43470932CGPG4089SENSE0.3540.1T0.030.419/1.2540S
41971134CGPG817SENSE0.5220.106T0.0770.248/1.2250S
46671726CGPG3894SENSE0.1960.225/0.0820.2T1.2430S
50572463CGPG4760SENSE1.1820.003S0.2020.026/1.7020S
44572961CGPG5591SENSE1.1950.013S0.1060.105T1.0840S
30674136CGPG6632SENSE0.8860.012S0.3060.009S1.420S
50474259CGPG5343SENSE1.0440.023S0.0810.187T1.2740S
31074318CGPG5826SENSE0.4070.075T0.1160.052T1.1180S
47974344CGPG5929SENSE1.2560.018S0.1180.125T1.2750S
53374462CGPG6668SENSE0.8460.022S0.260.011S1.4250S
31374512CGPG32SENSE0.2410.118T0.1460.044S1.0620S
44274587CGPG6774SENSE0//0.0840.054T1.0460S
|
S: represents the transgenic plants showed statistically significant trait improvement as compared to the reference (p < 0.05)
|
T: represents the transgenic plants showed a trend of trait improvement as compared to the reference with p < 0.2
|
/: represents data points not determined or the transgenic plants didn't show any alteration or had unfavorable change in traits examined as compared to the reference in the current dataset
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D. Salt Stress Tolerance Screen
This example sets forth the high salinity stress screen to identify Arabidopsis plants transformed with the gene of interest that are tolerant to high levels of salt based on their rate of development, root growth and chlorophyll accumulation under high salt conditions.
T2 seeds were plated on glufosinate selection plates containing 90 mM NaCl and grown under standard light and temperature conditions. All seedlings used in the experiment were grown at a temperature of 22° C. at day and 20° C. at night, a 16-hour photoperiod, an average light intensity of approximately 120 umol/m2. On day 11, plants were measured for primary root length. After 3 more days of growth (day 14), plants were scored for transgenic status, primary root length, growth stage, visual color, and the seedlings were pooled for fresh weight measurement. A photograph of the whole plate was also taken on day 14.
The seedling weight and root length were analyzed as quantitative responses according to example 1M. The final growth stage at day 14 was scored as success if 50% of the plants reached 3 rosette leaves and size of leaves are greater than 1 mm (Boyes, D. C., et al., (2001), The Plant Cell 13, 1499/1510). The growth stage data was analyzed as a qualitative response according to example 1L. Table 7 provides a list of recombinant DNA constructs that improve high salinity tolerance in transgenic plants
TABLE 7
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Root Length atRoot Length atSeedling Weight
PepGrowth Stageday 11day 14at day 14
SEQConstructRSp-p-p-p-
IDidGeneOrientationmeanvaluecdeltavaluecdeltavaluecdeltavaluec
|
51219703CGPG4172SENSE1.1240.139T0.1980.021S0.0720.116T0.5820.023S
51319946CGPG4097SENSE1.2010.072T0.020.89/0.0690.573/0.4430.266/
51419980CGPG3914SENSE0.9040.146T0.1010.259/0.1440.058T0.7060.016S
51570435CGPG3701SENSE1.3630.031S−0.1180.228/0.1610.038S0.0530.697/
51671114CGPG1657SENSE0.1380.399/0.2450.009S0.1870.025S0.4720.069T
51772451CGPG4733SENSE2.2260.02S0.1860.006S0.0690.23/0.4660.011S
44372453CGPG4735SENSE1.5390.031S0.2320.002S0.2160S0.7370.001S
50572463CGPG4760SENSE3.0260.002S0.1190.269/0.2020.073T1.260S
39272519CGPG4749SENSE0.5980.041S0.1260.055T0.1720.003S0.6350.008S
50672902CGPG5597SENSE1.4180.039S0.1140.286/0.2260.078T0.4260.091T
44872916CGPG1814SENSE0.6820.181T0.070.532/0.2010.046S0.3870.079T
51072921CGPG5781SENSE1.9770.029S0.1630.176T0.2110.073T0.6630.006S
51872947CGPG5607SENSE1.5050.028S0.0240.899/0.2040.022S0.4660.216/
44572961CGPG5591SENSE1.8790.007S0.2280.122T0.2290.003S0.8170.04S
44472967CGPG5742SENSE2.4270.004S0.3860.009S0.3690.001S1.2540S
51172968CGPG5772SENSE1.5310.055T0.3020.06T0.2090.073T0.7610.003S
44972969CGPG5789SENSE0.670.078T0.0290.789/0.2390.008S0.6030.013S
51973012CGPG5786SENSE2.3710.001S0.3660S0.3420S1.080S
52073022CGPG5622SENSE1.4080.036S0.220.056T0.3470S0.4920.03S
50873055CGPG5768SENSE3.2910.001S0.3690.087T0.4170.005S1.0960.005S
44673070CGPG5627SENSE2.7550.005S0.1880.392/0.2750.011S0.6850.025S
44773475CGPG6385SENSE1.110.059T0.1270.361/0.2160.001S0.4740.06T
52173488CGPG6394SENSE2.3730.013S0.3140.006S0.2620.002S1.1260.005S
52273901CGPG5237SENSE1.1410.078T0.2070.197T0.2020.097T0.6390.03S
52373964CGPG5804SENSE1.2350.043S0.4280.008S0.3170.022S0.9550.002S
52474019CGPG5706SENSE0.1050.168T0.0740.649/0.1710.106T0.7730.011S
52574022CGPG5724SENSE0.0330.327/−0.0650.616/0.1720.032S0.4840.068T
50974103CGPG6558SENSE1.2250.074T0.260.042S0.2670.004S0.5430.042S
52674114CGPG6551SENSE3.6270S0.2650.119T0.260S0.5610.063T
50474259CGPG5343SENSE2.8020.003S0.2490.098T0.2560.037S0.9950S
52774262CGPG5353SENSE0.2250.319/0.2380.062T0.2470S0.6290.006S
52874292CGPG5367SENSE0.3270.199T0.160.067T0.1050.166T0.5650.013S
52974302CGPG5384SENSE1.2460.016S0.2960.004S0.250S0.7050.004S
53074325CGPG5898SENSE1.5960.021S−0.0350.76/0.0940.106T0.6850.004S
53174429CGPG6689SENSE1.7960.008S0.2980.037S0.2070.006S0.4960.029S
53274440CGPG6682SENSE0.2230.334/0.430.007S0.2720.01S0.7440.017S
45074449CGPG6659SENSE0.6930.19T0.2040.104T0.2050.022S0.4510.095T
53374462CGPG6668SENSE2.140.028S0.2440.038S0.2390.001S0.640.013S
53474465CGPG6692SENSE1.2450.016S0.350.01S0.2150.001S0.5750.043S
53574474CGPG6669SENSE3.3120.002S0.2330.083T0.3380.003S0.5890.044S
53674505CGPG6783SENSE1.7310.043S0.2720.007S0.2080.01S0.4930.009S
53774507CGPG6799SENSE2.320.009S0.0560.567/0.2270.035S0.4760.126T
53874562CGPG6764SENSE1.4050.038S−0.0520.776/0.2150.014S0.1040.766/
50774572CGPG6640SENSE1.4250.025S0.2010.009S0.2670.001S1.1840S
27014324CGPG1560SENSE1.7080.017S0.3070.01S0.4080S0.9950.002S
35819768CGPG4096SENSE1.4960.061T0.1630.187T0.1290.013S0.660.002S
43619771CGPG4011SENSE1.6660.051T0.3190.005S0.2010.028S0.680.031S
36319879CGPG4009SENSE2.1170.029S0.160.139T0.0910.202/0.5450.028S
34772715CGPG5521SENSE1.0780.002S0.2070.141T0.1760.014S0.5190.015S
40772771CGPG2166SENSE0.5640.256/−0.0190.857/0.2060.013S0.3060.05S
44072903CGPG5584SENSE0.6450.196T−0.0310.569/0.0970.389/0.4820.015S
41173054CGPG5754SENSE1.520.035S0.1980.089T0.0980.187T0.6960.004S
47674107CGPG6590SENSE0.7720.036S0.4110S0.4310.001S1.5790S
47874131CGPG6592SENSE1.7470.044S0.3160.004S0.1150.01S0.6630.001S
44274587CGPG6774SENSE1.7540.01S0.1210.243/0.1940.001S0.6810S
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S: represents the transgenic plants showed statistically significant trait improvement as compared to the reference (p < 0.05)
|
T: represents the transgenic plants showed a trend of trait improvement as compared to the reference with p < 0.2
|
/: represents the transgenic plants didn't show any alteration or had unfavorable change in traits examined as compared to the reference in the current dataset
|
E. Polyethylene Glycol (PEG) Induced Osmotic Stress Tolerance Screen
There are numerous factors, which can influence seed germination and subsequent seedling growth, one being the availability of water. Genes, which can directly affect the success rate of germination and early seedling growth, are potentially useful agronomic traits for improving the germination and growth of crop plants under drought stress. In this assay, PEG was used to induce osmotic stress on germinating transgenic lines of Arabidopsis thaliana seeds in order to screen for osmotically resistant seed lines.
T2 seeds were plated on BASTA selection plates containing 3% PEG and grown under standard light and temperature conditions. Seeds were plated on each plate containing 3% PEG, ½×MS salts, 1% phytagel, and 10 μg/ml glufosinate. Plates were placed at 4° C. for 3 days to stratify seeds. On day 11, plants were measured for primary root length. After 3 more days of growth, i.e., at day 14, plants were scored for transgenic status, primary root length, growth stage, visual color, and the seedlings were pooled for fresh weight measurement. A photograph of the whole plate was taken on day 14.
Seedling weight and root length were analyzed as quantitative responses according to example 1M. The final growth stage at day 14 was scored as success or failure based on whether the plants reached 3 rosette leaves and size of leaves are greater than 1 mm. The growth stage data was analyzed as a qualitative response according to example 1L. Table 8 provides a list of recombinant DNA constructs that improve osmotic stress tolerance in transgenic plants.
TABLE 8
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|
Root Length atRoot Length atSeedling Weight at
PepGrowth Stageday 11day 14day 14
SEQRSp-p-p-p-
IDGeneConstruct_idOrientationmeanvaluecdeltavaluecdeltavaluecdeltavaluec
|
41319707CGPG4179SENSE2.6530.019S0.0740.58T−0.0310.81/0.4270.063T
41419951CGPG3941SENSE1.4320.134T0.0170.864T−0.080.28/0.4760.054T
41519967CGPG4032SENSE2.6910.014S0.010.934T0.190.039S0.5370.056T
41670543CGPG3815SENSE1.7350.077T0.0840.561T0.3230.007S0.6760.006S
40270681CGPG4584SENSE2.5280.006S−0.0650.682/−0.1790.05/0.3740.146T
41770707CGPG1273ANTI-1.420.095T0.2480.006S0.30.002S0.3310.007S
SENSE
41870719CGPG1712ANTI-1.430.106T−0.0070.968/0.1010.255T0.1550.349T
SENSE
41971134CGPG817SENSE1.4780.13T0.1190.15T0.0350.684T0.1980.277T
42071146CGPG2928SENSE2.6240.016S0.2270.101T0.2420.1T0.2780.296T
40571508CGPG1541SENSE3.1530.001S0.4460.054T0.3840.048S0.7820.003S
42171660CGPG4690SENSE2.8930.005S−0.0240.795/0.2250.074T0.1650.329T
40371663CGPG4638SENSE0.1160.444T−0.0610.536/0.3580.041S0.0580.702T
43971928CGPG1617SENSE2.0760.041S0.3530.013S0.2890.035S0.5310.035S
31872081CGPG5279SENSE1.2620.138T0.1740.243T0.20.197T−0.1050.714/
40872085CGPG5228SENSE40S0.220.046S0.3710.004S0.9290S
42272086CGPG5236SENSE2.5890.022S0.2810.033S0.1360.314T0.320.043S
42372632CGPG4852SENSE1.6630.053T0.2540.069T0.0940.548T0.4710.015S
42472716CGPG5529SENSE2.9140.004S0.1460.058T0.0070.925T0.5820.016S
42572723CGPG1848SENSE2.1380.066T0.0430.728T0.20.068T−0.3260.225/
40972744CGPG5563SENSE1.6360.05/0.1950.151T0.0590.751T0.5390.005S
40472769CGPG5573SENSE2.2070.055T0.0860.464T−0.1340.162/0.3890.086T
40772771CGPG2166SENSE2.5690.021S0.1690.221T0.1920.038S0.560.018S
44072903CGPG5584SENSE2.1610.061T0.0350.856T0.2450.162T0.060.871T
51072921CGPG5781SENSE2.2490.025S0.0340.788T0.2250.077T0.3060.28T
39172948CGPG5617SENSE2.2670.005S0.0540.495T0.1170.019S0.2890.077T
44572961CGPG5591SENSE1.190.14T0.0370.76T0.1360.339T0.5880.027S
51172968CGPG5772SENSE3.1420.007S0.1780.072T−0.0310.781/0.6980.016S
42672987CGPG1787SENSE2.0550.078T−0.0580.64/0.0970.144T0.3250.054T
43872994CGPG5803SENSE2.6740.013S0.2450.124T0.070.657T0.5990.035S
44173017CGPG5733SENSE40S0.3430.09T0.4620.002S0.9960S
41073039CGPG810SENSE40S0.3190.019S0.2370.05/0.4260.011S
41173054CGPG5754SENSE3.0480.002S0.5560.003S0.260.063T1.120.002S
44673070CGPG5627SENSE3.4390.001S0.1390.49T0.190.135T0.240.365T
44773475CGPG6385SENSE1.9330.033S0.040.476T0.0090.897T0.4590.073T
41273501CGPG6456SENSE1.290.121T0.1430.118T0.0430.564T0.4330.013S
42774109CGPG6606SENSE3.5170S0.1590.136T0.2490.004S0.3330.025S
42874140CGPG6569SENSE2.050.039S0.1680.138T0.1960.086T0.710.012S
42974191CGPG6597SENSE2.5650.019S0.3360.092T0.1990.112T0.540.02S
40674248CGPG5476SENSE3.1580.007S0.140.192T0.2040.051T0.3770.037S
43074265CGPG5356SENSE2.2080.023S0.3170.034S0.4190.006S0.5770.008S
43174369CGPG6076SENSE3.5220S0.3470.045S0.2720.107T0.6240.02S
44274587CGPG6774SENSE3.3250.002S0.0730.468T0.4140.002S0.5770.016S
40571508CGPG1541SENSE3.1530.001S0.4460.054T0.3840.048S0.7820.003S
43971928CGPG1617SENSE2.0760.041S0.3530.013S0.2890.035S0.5310.035S
42272086CGPG5236SENSE2.5890.022S0.2810.033S0.1360.314/0.320.043S
46972455CGPG4742SENSE1.3670.15T0.0260.764/0.0240.786/0.2550.04S
38272466CGPG4767SENSE0.7350.101T0.0680.333/0.2490.006S−0.3410.278/
37372633CGPG4853SENSE1.1790.122T0.2270.009S0.0970.065T0.4420.013S
37072757CGPG5572SENSE2.2720.017S0.1250.361/0.110.317/0.4250.047S
47272992CGPG5777SENSE2.2330.056T0.1760.261/0.1160.34/0.5110.019S
43872994CGPG5803SENSE2.6740.013S0.2450.124T0.070.657/0.5990.035S
44173017CGPG5733SENSE40S0.3430.09T0.4620.002S0.9960S
41173054CGPG5754SENSE3.0480.002S0.5560.003S0.260.063T1.120.002S
30073507CGPG6504SENSE0.3430.334/0.3470.007S0.2610.032S0.30.122T
35273515CGPG6473SENSE3.3360.002S0.2790.009S0.2410.003S0.3280.05S
42874140CGPG6569SENSE2.050.039S0.1680.138T0.1960.086T0.710.012S
43074265CGPG5356SENSE2.2080.023S0.3170.034S0.4190.006S0.5770.008S
43174369CGPG6076SENSE3.5220S0.3470.045S0.2720.107T0.6240.02S
42274587CGPG6774SENSE3.3250.002S0.0730.468/0.4140.002S0.5770.016S
|
S: represents the transgenic plants showed statistically significant trait improvement as compared to the reference (p < 0.05)
|
T: represents the transgenic plants showed a trend of trait improvement compared to the reference with p < 0.2
|
/: represents the transgenic plants didn't show any alteration or had unfavorable change in traits examined as compared to the reference in the current dataset
|
F. Cold Shock Tolerance Screen
This example set forth a screen to identify Arabidopsis plants transformed with the genes of interest that are more tolerant to cold stress subjected during day 8 to day 28 after seed planting. During these crucial early stages, seedling growth and leaf area increase were measured to assess tolerance when Arabidopsis seedlings were exposed to low temperatures. Using this screen, genetic alterations can be found that enable plants to germinate and grow better than wild type plants under sudden exposure to low temperatures.
Eleven seedlings from T2 seeds of each transgenic line plus one control line were plated together on a plate containing ½× Gamborg Salts with 0.8 Phytagel™, 1% Phytagel, and 0.3% Sucrose. Plates were then oriented horizontally and stratified for three days at 4° C. At day three, plates were removed from stratification and exposed to standard conditions (16 hr photoperiod, 22° C. at day and 20° C. at night) until day 8. At day eight, plates were removed from standard conditions and exposed to cold shock conditions (24 hr photoperiod, 8° C. at both day and night) until the final day of the assay, i.e., day 28. Rosette areas were measured at day 8 and day 28, which were analyzed as quantitative responses according to example 1M. Table 9 provides a list of recombinant nucleotides that improve cold shock stress tolerance in plants.
TABLE 9
|
|
difference in rosette
rosette arearosette areaarea between day 28
at day 8at day 28and day 8
Pepp-p-p-
SEQ IDConstruct_idGeneOrientationdeltavaluecdeltavaluecdeltavaluec
|
27014324CGPG1560SENSE0.0540.429/0.2580.017S−0.0710.631/
27117484CGPG2630SENSE−0.1890.759/0.5440.025S0.2750.121T
27219109CGPG1381ANTI-SENSE−0.0160.523/0.5410.008S0.8180.014S
27370423CGPG3165SENSE0.3160.012S0.5210.022S0.890.018S
27470424CGPG3180SENSE0.4740.003S0.6950.003S0.6930.043S
27570480CGPG3833SENSE−0.0660.591/0.1750.159T0.4740.059T
27670509CGPG2420SENSE0.0230.438/0.1170.216/0.6090.032S
27770647CGPG4334SENSE−0.5080.894/0.6040.049S0.8950.047S
27870675CGPG4519SENSE0.20.2/0.3030.153T0.5070.034S
27970829CGPG518SENSE−0.3190.823/0.8040.002S1.0820.002S
28070849CGPG596SENSE−0.0390.564/0.6980.001S0.7070.001S
28171627CGPG1270SENSE−0.1460.748/0.3490.05T0.30.12T
28271934CGPG2294SENSE−0.0680.796/0.7570S0.9220S
28372615CGPG4829SENSE0.4770.007S0.8340S0.9790.001S
28673559CGPG6535SENSE0.1430.093T−0.2650.878/−0.3440.821/
28774251CGPG5489SENSE0.3770.021S0.4390.045S0.450.07T
38970437CGPG3706SENSE−0.2730.916/0.1470.165T0.6820.034S
40270681CGPG4584SENSE0.3520.155T0.2520.261/0.2690.328/
40371663CGPG4638SENSE0.3580.013S0.0320.423/−0.0310.585/
40472769CGPG5573SENSE0.3810.049S0.8810.006S1.1020.005S
40772771CGPG2166SENSE0.9930S1.3810.003S1.5360.003S
43270217CGPG6SENSE0.2750.067T0.1260.289/0.3620.215/
43372711CGPG1846SENSE0.7740.001S0.5790.004S0.4290.038S
43872994CGPG5803SENSE0.1160.381/0.7080.068T0.7440.069T
51072921CGPG5781SENSE0.2650.057T0.310.162T0.3670.11T
41419951CGPG3941SENSE0.7290.006S0.4730.017s0.8460.006S
27370423CGPG3165SENSE0.3160.012S0.5210.022S0.890.018S
41670543CGPG3815SENSE1.5840S0.860S0.820.002S
36871617CGPG1227SENSE0.2040.136T0.4080.025S0.4580.057T
43971928CGPG1617SENSE0.1040.265/0.7860S0.8360.001S
38272466CGPG4767SENSE0.4970.017S0.5650.017S0.9630.002S
38372524CGPG4770SENSE0.4380.02S0.3770.025S0.3850.043S
40972744CGPG5563SENSE0.520.058T0.8590.026S0.4540.189T
44472967CGPG5742SENSE0.9550S0.6290.009S0.4030.189T
43573518CGPG6497SENSE0.1140.278/0.3190.01S0.1950.114T
30674136CGPG6632SENSE0.6060.007S0.5230.036S0.5980.025S
39874240CGPG5454SENSE−0.0990.644/1.2770.003S1.4980.006S
43174369CGPG6076SENSE0.6230.002S0.620.04S0.7370.096T
|
S: represents the transgenic plants showed statistically significant trait improvement as compared to the reference (p < 0.05)
|
T: represents the transgenic plants showed a trend of trait improvement compared to the reference with p < 0.2
|
/: represents the transgenic plants didn't show any alteration or had unfavorable change in traits examined as compared to the reference in the current dataset.
|
G. Cold Germination Tolerance Screen
This example sets forth a screen to identify Arabidopsis plants transformed with the genes of interests are resistant to cold stress based on their rate of development, root growth and chlorophyll accumulation under low temperature conditions.
T2 seeds were plated and all seedlings used in the experiment were grown at 8° C. Seeds were first surface disinfested using chlorine gas and then seeded on assay plates containing an aqueous solution of ½×Gamborg's B/5 Basal Salt Mixture (Sigma/Aldrich Corp., St. Louis, Mo., USA G/5788), 1% Phytagel™ (Sigma-Aldrich, P-8169), and 10 ug/ml glufosinate with the final pH adjusted to 5.8 using KOH. Test plates were held vertically for 28 days at a constant temperature of 8° C., a photoperiod of 16 hr, and average light intensity of approximately 100 umol/m2/s. At 28 days post planting, root length was measured, growth stage was observed, the visual color was assessed, and a whole plate photograph was taken.
The root length at day 28 was analyzed as a quantitative response according to example 1M. The growth stage at day 7 was analyzed as a qualitative response according to example 1L. Table 10 provides a list of recombinant DNA constructs that improve cold stress tolerance in transgenic plants.
TABLE 10
|
|
Growth stageRoot Length at
at day 28day 28
Pep SEQRSp-p-
IDConstruct_idGeneOrientationmeanvaluecdeltavaluec
|
28819631CGPG3627SENSE2.2290.052T0.0940.252/
28970121CGPG2380SENSE2.7320.042S0.1260.238/
29070654CGPG4352SENSE2.4740.026S0.2630.019S
29170696CGPG4590SENSE3.0920.01S0.0860.145T
29270713CGPG1462ANTI-SENSE40S0.2680.014S
29370740CGPG3700SENSE2.4850.024S0.2440.012S
29471321CGPG4418SENSE1.8370.126T0.0140.474/
29571835CGPG4634SENSE3.3490.002S0.3530.036S
29672934CGPG5798SENSE2.2220.023S0.2430.101T
29772945CGPG5787SENSE3.4780.001S0.2360.011S
29872980CGPG5773SENSE3.2650.003S0.2390.006S
29973504CGPG6480SENSE40S0.5210S
30073507CGPG6504SENSE40S0.4040.001S
30173573CGPG6462SENSE40S0.2680.004S
30273586CGPG6471SENSE40S0.3140.064T
30373770CGPG5435SENSE3.0910.01S0.3030.085T
30474105CGPG6574SENSE3.3290.002S0.1090.116T
30574111CGPG6622SENSE2.2260.021S0.4450.006S
30674136CGPG6632SENSE3.1920.005S0.3280.002S
30774139CGPG6561SENSE40S0.2540.092T
30874267CGPG5364SENSE3.0540.002S0.30S
30974291CGPG5363SENSE40S0.1420.142T
31074318CGPG5826SENSE40S0.2720.008S
31174319CGPG5831SENSE3.2070.005S0.2010.002S
31274324CGPG5885SENSE3.1440.007S0.2320.017S
31374512CGPG32SENSE40S0.3320.011S
31474583CGPG6649SENSE3.2490.004S0.280.001S
31570427CGPG3067SENSE1.5670.108T0.2220.044S
35273515CGPG6473SENSE40S0.3240.003S
35374684CGPG6360SENSE2.9270.004S0.4260.003S
37372633CGPG4853SENSE2.1210.027S0.2890.048S
40571508CGPG1541SENSE1.990.039S0.2630.033S
40674248CGPG5476SENSE2.3850.011S0.2170.017S
43470932CGPG4089SENSE3.2680.003S0.1460.067T
43573518CGPG6497SENSE3.3730.002S0.3520.032S
43971928CGPG1617SENSE3.0620.011S0.180.002S
50474259CGPG5343SENSE3.5110S0.3080.024S
50572463CGPG4760SENSE2.7360.01S0.0320.386/
50672902CGPG5597SENSE3.1050.009S0.2780.037S
50774572CGPG6640SENSE40S0.1250.155T
50873055CGPG5768SENSE3.1730.006S0.4070.004S
41319707CGPG4179SENSE1.8290.061T0.1690.018S
36019779CGPG4113SENSE40S0.2130.017S
36119833CGPG4074SENSE///0.2920.022S
36319879CGPG4009SENSE40S0.340.001S
51419980CGPG3914SENSE0.7980.122T0.2780.011S
27370423CGPG3165SENSE2.9060.004S0.1050.114T
45970725CGPG2097ANTI-SENSE1.9490.044S0.1220.148T
46171112CGPG934SENSE2.5790.018S0.1850.17T
44472967CGPG5742SENSE40S0.2870.007S
43872994CGPG5803SENSE1.0720.098T0.1610.04S
52173488CGPG6394SENSE40S0.2110.012S
47774117CGPG6575SENSE2.5670.02S0.1230.04S
|
S: represents the transgenic plants showed statistically significant trait improvement as compared to the reference (p < 0.05)
|
T: represents the transgenic plants showed a trend of trait improvement as compared to the reference with p < 0.2
|
/: represents data points not determined or the transgenic plants didn't show any alteration or had unfavorable change in traits examined compared to the reference in the current dataset
|
H. Shade Tolerance Screen
Plants undergo a characteristic morphological response in shade that includes the elongation of the petiole, a change in the leaf angle, and a reduction in chlorophyll content. While these changes may confer a competitive advantage to individuals, in a monoculture the shade avoidance response is thought to reduce the overall biomass of the population. Thus, genetic alterations that prevent the shade avoidance response are associated with higher yields. Genes that favor growth under low light conditions may also promote yield, as inadequate light levels frequently limit yield. This protocol describes a screen to look for Arabidopsis plants that show an attenuated shade avoidance response and/or grow better than control plants under low light intensity. Of particular interest, we were looking for plants that didn't extend their petiole length, had an increase in seedling weight relative to the reference and had leaves that were more close to parallel with the plate surface.
T2 seeds were plated on glufosinate selection plates with ½ MS medium. Seeds were sown on ½×MS salts, 1% Phytagel, 10 ug/ml BASTA. Plants were grown on vertical plates at a temperature of 22° C. at day, 20° C. at night and under low light (approximately 30 uE/m2/s, far/red ratio (655/665/725/735)-0.35 using PLAQ lights with GAM color filter #680). Twenty-three days after seedlings were sown, measurements were recorded including seedling status, number of rosette leaves, status of flower bud, petiole leaf angle, petiole length, and pooled fresh weights. A digital image of the whole plate was taken on the measurement day. Seedling weight and petiole length were analyzed as quantitative responses according to example 1M. The number of rosette leaves, flowering bud formation and leaf angel were analyzed as qualitative responses according to example 1L.
Table 11 provides a list of recombinant DNA constructs that improve shade tolerance in plants
TABLE 11
|
|
flowerbudNumberseedling
formation atLeaf Angle atPetiole length atof rosetteweight at
Pepday 23day 23day 23leaves at day 23day 23
SEQRSp-RSp-RSp-RSp-p-
IDConstruct_idOrientationmeanvaluecmeanvaluecmeanvaluecmeanvaluecdeltavaluec
|
37670426SENSE0.7190.09T0.1630.244/−0.2060.185T−0.2250.984/0.4840.003S
37770772SENSE−0.5010.858/−0.0660.724/−0.6920.004S−0.6260.983/−0.6930.023/
37871137SENSE0.260.384/0.110.168T−0.8690.029S1.0640.073T−0.4530.288/
37971529SENSE0.890.108T−0.0141/−0.440.006S1.8170.024S−0.0220.914/
38071601SENSE1.790.066T0.1950.172T−0.0570.59/−0.4830.961/0.2640.308/
38172362SENSE1.7630.072T0.2180.262/−0.1090.242/0.0030.484/0.3110.119T
37472456SENSE0.5630.313/0.7510.186T−0.8480.001S−0.6240.999/−0.850.025/
38272466SENSE−1.3821/−0.0920.645/−0.8940S1.2120.122T−0.8790.027/
38372524SENSE−0.1531/0.1520.09T−0.9520.002S−0.571/−1.2690.01/
37372633SENSE3.5130S−0.4310.977/−0.4260.001S−0.7350.994/0.2690.129T
37572963SENSE−0.9110.988/0.2360.396/−0.7530.003S−0.0830.665/−0.4850.015/
38473085SENSE−0.0730.756/1.2120.122T0.1750.097/40S0.510.027S
38574241SENSE−0.1950.935/−0.0980.64/−1.0770.01S−0.8210.999/−1.0240.002/
38674247SENSE0.430.16T0.2030.095T−0.220.197T1.1660.07T0.4830.018S
38774284SENSE0.0620.22/2.0770.038S−0.0140.943/2.3480.04S0.030.938/
38874652SENSE0.0150.442/0.0930.455/−0.0730.621/0.9670.184T0.1730.569/
36319879SENSE0.585//0//0.152//0//0.708//
29370740SENSE0.440.137T0.6090.103T0.1610.186////0.450.001S
31671811SENSE−0.0250.637/0.7250.113T−0.2050.01S///−0.5170.037/
39771840SENSE1.4980.12T0.7120.178T−0.3790.001S−0.1880.765/−0.950.124/
46872450SENSE0.0680.349/−0.0421/0.1660.016/1.620.049S0.5010.038S
37072757SENSE3.5950S0.8720.079T0.0640.138/−0.7670.997/0.5460.001S
44472967SENSE1.8290.063T1.1230.065T0.1330.196/−0.180.794/0.5090.008S
51172968SENSE0.1850.005S0.480.179T0.220.162/1.6980.085T0.3820.031S
30073507SENSE0.2480.086T0.3070.287/−0.3040.031S///0.050.86/
30774139SENSE−0.0110.556/−0.0711/−0.1240.068T−0.5111/−0.4130.124/
53574474SENSE0.7550.154T−0.1450.857/0.1420.396////0.7650.005S
40074610SENSE0.5720.222/0.1770.22/−0.180.071T///−0.3410.173/
|
S: represents the transgenic plants showed statistically significant trait improvement as compared to the reference (p < 0.05)
|
T: represents the transgenic plants showed a trend of trait improvement as compared to the reference with p < 0.2
|
/: represents data points not determined or the transgenic plants didn't show any alteration or had unfavorable change in traits examined compared to the reference in the current dataset.
|
I. Early Plant Growth and Development Screen
This example sets forth a plate based phenotypic analysis platform for the rapid detection of phenotypes that are evident during the first two weeks of growth. In this screen, we were looking for genes that confer advantages in the processes of germination, seedling vigor, root growth and root morphology under non-stressed growth conditions to plants. The transgenic plants with advantages in seedling growth and development were determined by the seedling weight and root length at day 14 after seed planting.
T2 seeds were plated on glufosinate selection plates and grown under standard conditions (˜100 □E/m2/s, 16 h photoperiod, 22° C. at day, 20° C. at night). Seeds were stratified for 3 days at 4° C. Seedlings were grown vertically (at a temperature of 22° C. at day 20° C. at night). Observations were taken on day 10 and day 14. Both seedling weight and root length at day 14 were analyzed as quantitative responses according to example 1M.
Table 12 provides a list recombinant DNA constructs that improve early plant growth and development.
TABLE 12
|
|
Root LengthSeedling Weight
Pep SEQ IDConstruct_idgeneOrientationdeltap-valuecdeltap-valuec
|
43270217CGPG6SENSE0.0380.469/0.3750.047S
43372711CGPG1846SENSE0.1320.021S0.6010.001S
43470932CGPG4089SENSE0.3280.005S0.4730.017S
43573518CGPG6497SENSE0.2870S0.6340.036S
43619771CGPG4011SENSE0.2180.076T0.5810.018S
43773549CGPG6460SENSE0.1390.003S0.3490.03S
43872994CGPG5803SENSE0.440.004S0.7910.001S
43971928CGPG1617SENSE0.0730.427/0.4940.005S
44072903CGPG5584SENSE0.2980.002S0.3990.044S
44173017CGPG5733SENSE0.2840.004S0.1990.488/
44274587CGPG6774SENSE0.1110.075T0.5380.006S
44372453CGPG4735SENSE0.2150.005S0.4160.069T
44472967CGPG5742SENSE0.1030.212/0.5680.008S
44572961CGPG5591SENSE0.1770.046S0.5480.006S
44673070CGPG5627SENSE0.2210.007S0.6520.005S
44773475CGPG6385SENSE0.0840.014S0.3360.014S
44872916CGPG1814SENSE0.1820.067T0.3530.012S
44972969CGPG5789SENSE0.1330.245/0.450.069T
45074449CGPG6659SENSE0.3140.002S0.5790.027S
45116615CGPG2539SENSE0.2230.023S0.5710.009S
45219187CGPG3310SENSE0.2640.001S0.510.08T
45319648CGPG3134SENSE0.2180.013S0.270.106T
45470354CGPG3995SENSE0.1520.046S0.4060.029S
45570421CGPG2942SENSE0.1790.225/0.5810.013S
45670459CGPG3758SENSE0.1870.036S−0.0340.884/
45770465CGPG3775SENSE−0.0090.899/0.1880.196T
45870683CGPG4587SENSE0.1330.088T0.4020.014S
45970725CGPG2097ANTI-SENSE0.3260.001S0.1160.548/
46070852CGPG1465SENSE0.2370S0.2970.127T
46171112CGPG934SENSE0.1990.013S0.3160.034S
46271127CGPG945SENSE0.0970.02S0.40.054T
46371132CGPG1561SENSE0.1950.02S0.080.524/
46471217CGPG95SENSE0.2340S0.5660.036S
46571645CGPG4688SENSE0.4750.003S0.3610.133T
46671726CGPG3894SENSE0.2230.056T0.4580.033S
46772432CGPG4562SENSE0.2090S0.5810.041S
46872450CGPG4732SENSE0.3350S0.790S
46972455CGPG4742SENSE0.2780.019S0.4820.051T
47072727CGPG5522SENSE0.1230.002S0.3150.004S
47172817CGPG4987SENSE0.2540.023S0.4850S
47272992CGPG5777SENSE0.2190.023S0.6640.015S
47373007CGPG5760SENSE0.1390.093T0.4620.008S
47473073CGPG5688SENSE0.1640.022S0.2850.247/
47573506CGPG6496SENSE0.5120S0.9860S
47674107CGPG6590SENSE0.2820.002S0.5380.057T
47774117CGPG6575SENSE0.2110.002S0.4490.005S
47874131CGPG6592SENSE0.1420.047S0.5860.003S
47974344CGPG5929SENSE0.270.01S0.4740.105T
32313502CGPG1354SENSE0.570.002S0.6250S
33018259CGPG3368SENSE0.2260.026S0.5510.021S
36119833CGPG4074SENSE0.2590S0.4720.016S
33470417CGPG3427SENSE0.1870.056T0.1130.65/
27370423CGPG3165SENSE0.030.747/0.1850.007S
51570435CGPG3701SENSE0.1310.051T0.3940.014S
49370601CGPG2917SENSE0.1770S0.3650.063T
29170696CGPG4590SENSE0.0790.205/0.3310.024S
36570738CGPG3195SENSE0.0120.864/0.4720.003S
29370740CGPG3700SENSE0.1030.082T0.3870.021S
41971134CGPG817SENSE0.0630.548/0.2790.066T
42272086CGPG5236SENSE0.0830.234/0.3980.05S
50572463CGPG4760SENSE−0.1310.416/0.4220.003S
28573014CGPG5692SENSE0.110.391/0.3730.096T
52173488CGPG6394SENSE0.0180.793/0.3980.1T
29973504CGPG6480SENSE−0.1520.479/0.5380.012S
30073507CGPG6504SENSE0.150.002S0.0530.854/
30173573CGPG6462SENSE0.1120.07T0.3750.006S
30273586CGPG6471SENSE0.3090S0.6110S
30373770CGPG5435SENSE0.210.059T0.2810.484/
50974103CGPG6558SENSE0.3740S0.5610.024S
42874140CGPG6569SENSE0.160.017S0.3760.066T
52774262CGPG5353SENSE0.2030.012S0.3750.045S
43074265CGPG5356SENSE0.1070.259T0.4320.067T
52974302CGPG5384SENSE0.1150.101T0.2690.056T
43174369CGPG6076SENSE0.1380.03S0.1950.21/
53474465CGPG6692SENSE0.20.02S0.6880.042S
50774572CGPG6640SENSE0.1620.023S0.6170S
31474583CGPG6649SENSE0.1440.023S0.4030.008S
|
S: represents the transgenic plants showed statistically significant trait improvement as compared to the reference (p < 0.05)
|
T: represents the transgenic plants showed a trend of trait improvement as compared to the reference with p < 0.2
|
/: represents the transgenic plants didn't show any alteration or had unfavorable change in traits examined as compared to the reference in the current dataset
|
J. Late Plant Growth And Development Screen
This example sets forth a soil based phenotypic platform to identify genes that confer advantages in the processes of leaf development, flowering production and seed maturity to plants.
Arabidopsis plants were grown on a commercial potting mixture (Metro Mix 360, Scotts Co., Marysville, Ohio) consisting of 30-40% medium grade horticultural vermiculite, 35-55% sphagnum peat moss, 10-20% processed bark ash, I-15% pine bark and a starter nutrient charge. Soil was supplemented with Osmocote time-release fertilizer at a rate of 30 mg/ft3. T2 seeds were imbibed in 1% agarose solution for 3 days at 4° C. and then sown at a density of 5 per 2½″ pot. Thirty-two pots were ordered in a 4 by 8 grid in standard greenhouse flat. Plants were grown in environmentally controlled rooms under a 16 h day length with an average light intensity of ˜200 μmoles/m2/s. Day and night temperature set points were 22° C. and 20° C., respectively. Humidity was maintained at 65%. Plants were watered by sub-irrigation every two days on average until mid-flowering, at which point the plants were watered daily until flowering was complete.
Application of the herbicide glufosinate was performed to select T2 individuals containing the target transgene. A single application of glufosinate was applied when the first true leaves were visible. Each pot was thinned to leave a single glufosinate-resistant seedling ˜3 days after the selection was applied.
The rosette radius was measured at day 25. The silique length was measured at day 40. The plant parts were harvested at day 49 for dry weight measurements if flowering production was stopped. Otherwise, the dry weights of rosette and silique were carried out at day 53. The seeds were harvested at day 58. All measurements were analyzed as quantitative responses according to example 1M.
Table 13 provides a list of recombinant DNA constructs that improve late plant growth and development.
TABLE 13
|
|
Rosette DrySilique Dry
PepWeightRosette RadiusSeed Dry WeightWeightSlilique Length
SEQp-p-p-p-p-
IDConstruct_idOrientationdeltavaluecdeltavaluecdeltavaluecdeltavaluecdeltavaluec
|
48014320SENSE−0.1450.94/0.1370.038S−0.7021/0.4770.002S0.0160.276/
48116756SENSE0.4850.016S0.2230.025S0.1480.042S0.4810.002S0.1470.013S
48217448SENSE−0.2880.991/−0.0540.829/0.3760.008S0.1850.034S−0.0640.981/
48317633SENSE0.0180.359/0.130.106T0.4160.055T0.3990.044S0.1160.08T
48418876SENSE0.2570.016S0.0260.448/−0.2130.786/0.3880S−0.0150.705/
48519120ANTI-−0.2520.936/0.0220.006S−1.0420.95/0.1650.076T0.0460.021S
SENSE
48619221SENSE−0.3160.986/0.1530.097T−0.350.903/0.3940.068T0.1830.028S
48770206SENSE0.1250S0.0740.18T0.7120.022S0.120.026S0.0190.403/
48870223SENSE0.1970.026S0.230.018S−0.7810.998/0.1340.039S−0.2050.915/
48970347SENSE0.1560.038S−0.0820.868/−0.1530.752/0.4050.006S0.0560.068T
49070406SENSE−0.2750.948/−0.2450.992/0.7590.025S−0.2820.949/−0.1210.939/
49170469SENSE0.0320.392/0.3480.004S−0.7330.996/0.3250.059T−0.1410.922/
49270564SENSE0.170.037S0.0510.234/0.7720S−0.3810.977/−0.0150.655/
49370601SENSE0.2310.086T0.2470.004S−0.2570.959/0.3230.024S0.0820.03S
49470612SENSE0.0530.112T0.0820.096T1.0490.011S−0.2120.992/0.070.004S
49570720ANTI-−0.160.898/0.0280.384/1.3120.009S0.2190.121T0.1280.018S
SENSE
49670735SENSE−0.0580.672/0.1560.087T0.4210.036S0.5320.003S0.0330.038S
49770846SENSE0.0860.255/0.1340.063T−0.330.918/0.1420.151T0.0110.439/
49870923SENSE0.4840.011S0.1080.081T−0.40.844/0.0910.198T0.0990.001S
49971149SENSE−1.0850.993/−0.0430.681/0.3460.017S0.1360.133T0.0660.077T
50071608SENSE−0.8490.907/−0.1320.976/0.8160.006S0.2790.004S0.0380.238/
50171739SENSE−0.2750.937/−0.1070.955/0.3340S−0.0750.815/−0.1190.874/
50272014SENSE−0.0380.94/0.070.278/0.7320.06T−0.0260.584/−0.0130.596/
50372051SENSE0.0260.28/0.3110.003S0.2220.236/0.4530.009S0.0520.168T
43270217SENSE−0.2020.893/0.2030.024S−0.0790.743/0.270.07T−0.0630.856/
45470354SENSE0.1340.147T−0.1190.684/0.480.02S−0.1190.736/0.0140.3/
33470417SENSE−0.350.988/−0.0410.637/0.690.012S−0.1360.978/0.0040.411/
51570435SENSE0.6640.014S0.1460.036S0.1380.097T0.330.038S0.0390.16T
45770465SENSE−0.1060.79////0.8830.001S−0.270.945/−0.0970.818/
46070852SENSE0.1780.031S0.1450.034S−0.5250.904/−0.3150.861/−0.0590.774/
40571508SENSE0.1950.162T0.2510.017S−0.5150.929/−0.3220.997/−0.1960.982/
29571835SENSE0.1390.055T0.1630.049S0.5380.019S0.270.068T00.496/
46772432SENSE0.1460.021S0.1390.02S0.3250.012S0.0740.149T−0.1060.879/
44372453SENSE0.2040.037S0.1160.046S−2.1980.995/0.0160.448/−0.0130.534/
43372711SENSE0.2920.058T0.1430.024S−0.1140.76/−0.040.667/−0.0930.946/
44972969SENSE0.0460.072T−0.1580.887/0.390.031S0.4770.001S0.0950.054T
42672987SENSE0.3850.006S///0.0980.104T0.1530.016S0.0570.061T
52574022SENSE0.110.226/−0.0690.844/0.710.009S−0.050.613/−0.0040.544/
28774251SENSE−0.560.961/−0.1840.916/0.6110.001S0.1740.229/−0.1370.923/
53774507SENSE0.2550.017S0.1780.03S0.3180.032S0.1880.011S0.0130.078T
31374512SENSE−0.2470.953/0.1070.015S−0.0730.86/0.1130.034S0.050.175T
|
S: represents the transgenic plants showed statistically significant trait improvement as compared to the reference (p < 0.05)
|
T: represents data points not determined or the transgenic plants showed a trend of trait improvement compared to the reference with p < 0.2
|
/: represents the transgenic plants didn't show any alteration or had unfavorable change in traits examined as compared to the reference in the current dataset
|
K. Limited Nitrogen Tolerance Screen
Under low nitrogen conditions, Arabidopsis seedlings become chlorotic and have less biomass. This example sets forth the limited nitrogen tolerance screen to identify Arabidopsis plants transformed with the gene of interest that are altered in their ability to accumulate biomass and/or retain chlorophyll under low nitrogen condition.
T2 seeds were plated on glufosinate selection plates containing 0.5×N-Free Hoagland's T 0.1 mM NH4NO3 T 0.1% sucrose T 1% phytagel media and grown under standard light and temperature conditions. At 12 days of growth, plants were scored for seedling status (i.e., viable or non-viable) and root length. After 21 days of growth, plants were scored for visual color, seedling weight, number of green leaves, number of rosette leaves, root length and formation of flowering buds. A photograph of each plant was also taken at this time point.
The seedling weight and root length were analyzed as quantitative responses according to example 1M. The number green leaves, the number of rosette leaves and the flowerbud formation were analyzed as qualitative responses according to example 1L.
Table 14 provides a list of recombinant DNA constructs that improve low nitrogen availability tolerance in plants.
TABLE 14
|
|
FlowerbudNumber of greenNumber of
formationleavesRoot Lengthrosette leavesSeedling Weight
Pep SEQRSp-RSp-p-RSp-p-
IDConstruct_idOrientationmeanvaluecmeanvaluecdeltavaluecmeanvaluecdeltavaluec
|
37572963SENSE1.10.004S0.2930.021S−0.4460.002S−0.2460.786/0.1370.001S
38970437SENSE−0.280.982/−0.080.769/0.2590.006S0.50.005S0.1330.003S
39071633SENSE0.260.26/0.2540.114T−0.10.539/0.6470.06T0.1060.023S
39172948SENSE0.5870.06T0.5390.029S−0.2370.003S0.4790.1T0.0780.121T
39272519SENSE0.7490.033S0.2090.104T−0.090.274/0.2760.264/0.1160.006S
39310475SENSE1.2560.026S0.5880.005S−0.3780.002S0.0810.319/0.0180.75/
39411120ANTI-0.7950.033S0.6080.015S−0.450.001S0.2870.106T−0.0410.387/
SENSE
39519736SENSE−0.240.907/0.3550.033S0.0140.864/0.640.006S−0.0750.005/
39671606SENSE0.6050.088T0.1760.11T−0.0330.708/1.2390.005S0.1330.002S
39771840SENSE0.4080.235/0.8790.006S−0.1370.248/0.5240.032S0.0660.198T
39874240SENSE−0.060.602/0.130.076T−0.1070.306/0.7140.034S0.1080.002S
39974331SENSE−0.441/0.0540.203/0.1320.055T1.0450.021S0.1340.003S
40074610SENSE−0.591/−0.080.922/0.2890S1.2410.017S0.1370.001S
40175527SENSE0.2420.228/0.3760.028S−0.1830.045/0.3520.083T−0.0050.8/
31671811SENSE−0.450.91////−0.1120.202/0.4380.014S−0.0540.161/
50572463SENSE−0.160.976////0.1120.109T0.3660.024S0.130.006S
35175701SENSE0.7360.048S0.070.861/−0.40.018S///−0.1090.193/
|
S: represents the transgenic plants showed statistically significant trait improvement as compared to the reference (p < 0.05)
|
T: represents the transgenic plants showed a trend of trait improvement compared than the reference with p < 0.2
|
/: represents data points not determined or the transgenic plants didn't show any alteration or had unfavorable change in traits examined as compared to the reference in the current dataset
|
L. Statistic analysis for qualitative responses
Table 15 provides a list of responses that were analyzed as qualitative responses
TABLE 15
|
|
responseScreencategories (success vs. failure)
|
wilting response RiskSoil drought tolerance screennon-wilted vs. wilted
Score
growth stage at day 14heat stress tolerance screen50% of plants reach stage1.03 vs. not
growth stage at day 14salt stress tolerance screen50% of plants reach stage1.03 vs. not
growth stage at day 14PEG induced osmotic stress tolerance50% of plants reach stage1.03 vs. not
screen
growth stage at day 7cold germination tolerance screen50% of plants reach stage 0.5 vs. not
number of rosette leavesShade tolerance screen5 leaves appeared vs. not
at day 23
flower bud formation atShade tolerance screenflower buds appear vs. not
day 23
leaf angle at day 23Shade tolerance screen>60 degree vs. <60 degree
number of green leaves atlimited nitrogen tolerance screen6 or 7 leaves appeared vs. not
day 21
number of rosette leaveslimited nitrogen tolerance screen6 or 7 leaves appeared vs. not
at day 21
Flower bud formation atlimited nitrogen tolerance screenflower buds appear vs. not
day 21
|
Plants were grouped into transgenic and reference groups and were scored as success or failure according to criteria in Table 15. First, the risk (R) was calculated, which is the proportion of plants that were scored as of failure plants within the group. Then the relative risk (RR) was calculated as the ratio of R (transgenic) to R (reference). Risk score (RS) was calculated as −log2RR. Subsequently the risk scores from multiple events for each transgene of interest were evaluated for statistical significance by t-test using S-PLUS statistical software (S-PLUS 6, Guide to statistics, Insightful, Seattle, Wash., USA). RS with a value greater than 0 indicates that the transgenic plants perform better than the reference. RS with a value less than 0 indicates that the transgenic plants perform worse than the reference. The RS with a value equal to 0 indicates that the performance of the transgenic plants and the reference don't show any difference.
M. Statistic Analysis for Quantitative Responses
Table 16 provides a list of responses that were analyzed as quantitative responses.
TABLE 16
|
|
responsescreen
|
seed yieldSoil drought stress tolerance screen
seedling weight at day 14heat stress tolerance screen
root length at day 14heat stress tolerance screen
seedling weight at day 14salt stress tolerance screen
root length at day 14salt stress tolerance screen
root length at day 11salt stress tolerance screen
seedling weight at day 14PEG induced osmotic stress tolerance screen
root length at day 11PEG induced osmotic stress tolerance screen
root length at day 14PEG induced osmotic stress tolerance screen
rosette area at day 8cold shock tolerance screen
rosette area at day28cold shock tolerance screen
difference in rosette areacold shock tolerance screen
from day 8 to day 28
root length at day 28cold germination tolerance screen
seedling weight at day 23Shade tolerance screen
petiole length at day 23Shade tolerance screen
root length at day 14Early plant growth and development screen
Seedling weight at day 14Early plant growth and development screen
Rosette dry weight atLate plant growth and development screen
day 53
rosette radius at day 25Late plant growth and development screen
seed dry weight at day 58Late plant growth and development screen
silique dry weight at day 53Late plant growth and development screen
silique length at day 40Late plant growth and development screen
Seedling weight at day 21Limited nitrogen tolerance screen
Root length at day 21Limited nitrogen tolerance screen
|
The measurements (M) of each plant were transformed by log2 calculation. The Delta was calculated as log2M(transgenic)−log2M(reference). Subsequently the mean delta from multiple events of the transgene of interest was evaluated for statistical significance by t-test using S-PLUS statistical software (S-PLUS 6, Guide to statistics, Insightful, Seattle, Wash., USA). The Delta with a value greater than 0 indicates that the transgenic plants perform better than the reference. The Delta with a value less than 0 indicates that the transgenic plants perform worse than the reference. The Delta with a value equal to 0 indicates that the performance of the transgenic plants and the reference don't show any difference.
EXAMPLE 2
Identification of Homologs
A BLAST searchable “All Protein Database” was constructed of known protein sequences using a proprietary sequence database and the National Center for Biotechnology Information (NCBI) non-redundant amino acid database (nr.aa). For each organism from which a DNA sequence provided herein was obtained, an “Organism Protein Database” was constructed of known protein sequences of the organism; the Organism Protein Database is a subset of the All Protein Database based on the NCBI taxonomy ID for the organism.
The All Protein Database was queried using amino acid sequence of cognate protein for gene DNA used in trait-improving recombinant DNA, i.e., sequences of SEQ ID NO: 240 through SEQ ID NO: 478 using “blastp” with E-value cutoff of 1e-8. Up to 1000 top hits were kept, and separated by organism names. For each organism other than that of the query sequence, a list was kept for hits from the query organism itself with a more significant E-value than the best hit of the organism. The list contains likely duplicated genes, and is referred to as the Core List. Another list was kept for all the hits from each organism, sorted by E-value, and referred to as the Hit List.
The Organism Protein Database was queried using amino acid sequences of SEQ ID NO: 270 through SEQ ID NO: 538 using “blastp” with E-value cutoff of 1e-4. Up to 1000 top hits were kept.
A BLAST searchable database was constructed based on these hits, and is referred to as “SubDB”. SubDB was queried with each sequence in the Hit List using “blastp” with E-value cutoff of 1e-8. The hit with the best E-value was compared with the Core List from the corresponding organism. The hit is deemed a likely ortholog if it belongs to the Core List, otherwise it is deemed not a likely ortholog and there is no further search of sequences in the Hit List for the same organism. Likely orthologs from a large number of distinct organisms were identified and are reported by amino acid sequences of SEQ ID NO: 539 to SEQ ID NO: 22568. The relationship of the homologs to the identified trait-improving genes on an amino acid sequence basis is found in Table 17 where the amino acid sequence of a protein encoded by a trait-improving DNA, e.g., SEQ ID NO:270, is followed by the amino acid sequences of protein encoded by homologous genes, e.g., SEQ ID NO:19844, 4248, 2761, 15944, etc. The source organism of each homolog is reported in the Sequence Listing.
TABLE 17
|
|
Sequence IDs for homolog proteins
Seq ID NO:homolog Seq ID NOs
|
270:198444248276115944117761614410470974267761010228516333
915420620164542002583881064612086001170624481476810226
12626198469302172951779463545098178964301774982110109
7542178551556217462
|
271:171554187208193387440711811317151175921887948078671
99361131510681317710519683013563121621515518601807220945
671515032519210928
|
272:0
|
273:13771855342191004310800834517501135699541719761883760
132671616981322667112161563746522270103095708183749446
128447790756947869725141871285916948186261374155257877
455015544970676161435815163131821456016722112914724261
1069320144643721413178931798417116992519953206489832837
566329431046518411249764351476313495126767513836316389
816279451495615029124332224116071130031694018847123547732
14013573511505883317658160481760957566416331373810842
189272151820097141175309137441588019484964822509122115515
6785852646617423141646588704167101937533061405016883
16322172215481136361068063473552888521794177032255714777
211891371136013968369240032004412943197491865635514902
613722370194681041021460104511717520965129161206679611329
9139110081056990587988197432008814111823145221849711952
28661546636092403167961353914806536412620206991294015426
44091245252969156629126652094736497530
|
274:1616751782412104552003611246196666400557322539854721845
24132029040361935158866071171849738
|
275:146651669412678149282148979181571395924902517146153788
10022160962124813293854113446612043603812155741893819203
228422151005414052965310183177522077642402234382709192
1721773741214120657767464452522
|
276:12496346013599704391501664
|
277:16949964081502014121885779178761461218293110531595815263
1837020984130941873473801031821641127371302820561708710686
9894752812573160431484620513280288971471610257164072727
615114846831169161014617756131937670159467750939720046
125475399186441188312531125301718821303805174931682110181
363939341419780
|
278:165319228579919821109801765634491998213335209591123813084
10281176101962317614973621375199785859494312390188061349
87592174120400137079170158991136143331063112909213612776
203237676584790651990245456768546924614134444220731
993167008677193054828365517550757921629904419475637
42093519387315884122471017714071031215957169551746920241
7267218621686422192195996365123241098564246449145643115
148851060391118609335970592851580196138391186957987
14964108115171131214747306013390221155060165361972913468
1110921989223094629096187751072111999834016607221998687
36528147220734090349120506783510890678178391447816371
57964429721542325667876175802023131649424140968115
1530414818728264224841101061075129959297212802309895
12373536622159449973711369430813974279412771165849250
6930879210185177181314850542238396749868215461588120000
190294938140241502615535163861540221036126539490417011551
37114179186191637014161112949094268921881
|
279:1357710344173715840139041268911795219121722614519885414229
7998832614001616311785101172151121043182052933204322181
21628200901801820578190811101147682834463513475630613119
1671213481692620801636142694366156159417046316616526
62504790825165411427035748127180151314717950152436671
206623487117876762548871179417157024859205271924017200
71151952312823911511770205304791203341101920645143831914
8945153589347249630981160416441193521845112451887715655
79112609125881978518328814322185148810212140021682611779
18903879201302163320930172222691188527120785364421495
146302104156768447167501043645232686823729481355919008
368618465389574161017018867145741159
|
280:1631037961020519486135811102221960155981260496622021021764
86261732311666213166121743898221351749912340207116553
1029617874914177163723
|
281:205512109613717400619762100171442517785629138551523211917
21856185641901039101362119087670105398515698911212694
14218119471810421227223481417818629829932514533131498679
17127650710375278233575947548931657287981802213688
129413817218931078152631129254929542800016102632811687
136951580740683478648613660221651788119166361370136393
159831768851244243196841700812366716120062121941587014385
9124986562116286448700886917941106972113455864469
21167855205389251103610678197717337457519974352010195
14572387021293190111292120120116471505413976211632036212988
1563623454740320517504195315208168347654159078961
|
282:19261386070761261617904886973512611204784501188747032
18024722545441144321271928373671338448215213205543826
14978217691175542501550620020659312862075018985160694571
2253637731115297451319621908120791416863119871617215399
14422124908076171801906714493131051645918285158631408518130
115661735220003299553868757191031568520563187392081519454
7820207717972
|
283:0
|
284:107505276389434861224018158121701539397651126650312792
933420684114413799108581662220849220016897177101540118589
955017571024921993200119689150584297199906431141418208
19995
|
285:179161523115741158294645219771029118062157347460182663
80369618166933960158641457817125159242182613440172498650
20159198615742197062209287666813178301085321281133945285
81392100414220175632086248815974698132334654125015737
2907146999571328865162252616496148731047118290308611953
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212962832830145536434182951795682947612043207791281
177451658679551270515449988208591768111296547225185552
985411376666953599132109641879220871313717298333313752
203011937024256946195381427315603153406427171651241910809
8003136581406442217387132842098123163116841833866508
182173578222499921344234711485519949527719885281610917
943618538186591281612308159432515203641470181931757922076
889026499329210738376151771088285959909814160535209
3144138482242819076545417056149184088112705837960422455
1984012234114980195399602130116563755122782211921098
100510264130371170220954558150631118645420632169619474
149119381411113374293230711855122362143112923650919229
1401253721236217380202721639113395513290195401922811589
13306317914568176302371469412396153691178416597369710741
1630949271339621621884116662111201408186929484152046565
143202978929474829493127749527813730612296120216645
9286224891374516653190697780152191696914762183301028010802
10479166633678167137751137033630469194721070985427060
61122245721974204767333648214526715126448351065512264
9315278616253948856341737278892802209518903370615256
1859357641111512583115681361323315136807315998563011304
19137581755801834185881254024544970174452401118696193
2151624471088951901320716465967397711171618575958412794
2139920485921818691335018263484654419667993341401318
2041811128201051673423761569970614232153571403653397107
19030716521370121034848132112253015360128639975639814067
16683211701924890815515866101317187433212352033012927
708850992302124248303174661432211383228215956341412982
1854815665109612108410824184401681937301394018821148641818
196077969654616771544184591826650001574913014142748444
4707130971593011872262171586942185025408108372192813800
518819614161174719183313499310721492125032192979211429
143982218974764391299312307197146650189945932186306683
192115651559469581359719763100974065141241468710945780
777076881511057977907211693329126271988222067192112061
7038890916914131291988116317155113235148881201202647800
75262209588710223107981531711351101051066115014290816412
2227719851120031961611003776861664620162311385070162717
2088614522525415519205413458124015787200999282114804994
628118662799296611987511156361914086209481694634566143
78667095954179262083922351132771511363687704186943644
1215437942125721638183861811121498107311377655391453020282
7762952917675151911238014865158252818164425901822018578
1329724952191345261608510965155581898229841124521040477
111402132203124655165682109313882573079767079130352800
15563509125452037117049571213793712768544831845622341
11197131071380216006428
|
534:6383104501006826617986132699010982218387373510217533
53517741619118891138491470657183563340184612028420753
1019213836524026532083335641870112506367190012013715672
13176202078314401518878795214667023181716876856016477
1363010793413652491709991522730472486845821371016562
2256295002195212129115158632635135795947954362194851
7812102161913012258195088431084251912495714118456128
906726181308120216045288739702217629921418920203687
18669170827279109461075410583448191516903187011444211182
127108108473781742199014565204452002298612888170806216
3441962940344019174011207222191481514328571766421589
1196119154124252143717489111952093321506353312843467718511
4730696956917797186877097202592096615252132211133520777
127132250214915211571359677356111140622037135631259116308
762621483421219798194585691182921613021296283283014553
4632643418295179568291204311893932187316845213606772
190392167320779128116128145681763023714694123961536914260
1339621621884116662111201408166578692948414065254015204
656514320297892947482949312774952781373061229612021
6645928622489199088931476218330108021047916663367816713
77511370336304691947210709854270606112224572197420476
733364821452671512644835106551226493152786162539488
56341737220811264315099742515838100947883348928022095
1890337061525618593576411115125835630115681361323315136
80731599811304191375817443055808588183411254024544970
1744524011088951901320716465112911647921467426327059673
2054134581240157872009992821148049942798547518142683
84354345362715897936662812071618662799296611987511156
21818361914086209481694634566143786670959541792620839
138911096515558152763513176001142611231678653261740718982
29841981711245583821039153102132203124655165682109313882
5730797670791303528001635349822203237317388134368698
50912545203711704957121379371276854483184562234115886
111971310754441600695732080537219913949918057797322459
217048464
|
535:93821006429102172438988331418461524063671900116674
1248452611896781298192857176642158911961191542143711195
20933215063533467718511473069695691779718687709720259
152521322145011335207771271322502149152115720371356312591
163087626421219798194585691182921613021296283283014553
64341829517956829476120432077912811774516586795512705
1544998820859176811129654722518555298541137666695359
9132109641879220871313717298333313752203011937024256946
195381427315340642717165156031241910809800313658140644221
738713284209812316311684183386650818217357822249992
14855134423471199495277198852816109179436185381865912816
1230815943251520364147018193175792207688902649932921073
83761517710882859599098141605352093144138482242819076
54541705614918408811270583796042245519840122341149801
953996021301165637551227822119210981005102641303711702
20954558150631118645420632169619474149119381411113374
2932307118551223621431129236509192291401253721236217380
202721639113395513290195401922814568176302371469412396
153691659736971074116309492713396216218841166621112014081
86929484152046565143202978929474829493127749527813
73061229612021664592862248913745166531906977801521916969
1476218330108021047916663367816713775113703363046919472
10709854270606112224572197420476733364821452671512644
835106551226493152786162539488563417372788928022095
1890337061525618593576411115125831156813613233151368073
159985630113041913758175580858818341125402454497017445
2401118696193215161088951901320716465967397711171618575
95841279421399204859218186913350182634846544196679933
4140131820418111282010516734237615699706142321535714036
5339710719030716521370121034848132112253015360128639975
6398140671668321170192489081551586610131718743321235
2033012927708850992302124248303174661432211383228215956
3414129821854815665109612108410824184401681937301394018821
148641818196077969654616771544184591826650001574913014
142748444470713097159301187226217158694218502540810837
21928138005188196141611747191833134993107214921250321929
79211429143982218964391299312307197146650189947475932
1863066831921156515594695813597197631009714124146871094
57807770768815110579779072116933291988212627406522067
1921120617038890916914131291988116317155113235148881201
20264780075262209588710798153171022311351101051066115014
29081641222277198511200319616110037768616646201385016231
70162717205413458124015787200999282114804994628118662
7992966119875111563619140862094816946345661437866709
5954179262083922351132771511363687704186943644121543794
212572163818386181112149810731137765539145302028277629529
17675151911238014865158252818164425901822018578132972495
2191345261608510965155581898229841124516474304477427
50672132203124655165682109313882573079767079130352800
2041650930730512545203711704957121379371276854483
184562234111197131071326816006428
|
536:82505293175191096987751653210286118115689287168020415
141041688817043102736777223966024866123339909223274344
9005164762573106161963815657895043782657336421708985
63168776223813856109910466196566879931319604120698122
213851608720487142414078242741757418938516892158093499
16714576863221362719469825219551149761274210499113229597
35699336201325283221271038131497067138867478389720869
1939813086419136692080067998453175392195657241387816687
1797
|
537:12225799119769207076346212281892015677220071721612461299
34828428486418691825950761889410621119421241428010372
9939346122101143889687193432661942668881778116971251
15687114671144472484960359818026174607270187372052218581
1656913403499920923325312847654112065138114421824610039
2117620831135321907710287963512724898434711482126918702
1205580061457119675165422122914891114591539515872930110051
684355091170710865189081203198442046940414623223461849
12095142813840167331532221786173051061114287631220456676
58948015219021489617330309015122775961961667847520224
30322111921396116520759221521815713373062122221084714596
3679210871762637431009221220223334831634026841439417353
1231720732214710166966411412211857389118621152692202983
542913258105291227068685672235511711931417713662412386
1789834801002820275129212254175942064248531038345918186
1637915333920115765177205294993473764038229719167144
1673610304331937622061411341104404734967712289207724271
1995422175302019748160838948197372211429552113732741408
67801084871241406011449179394794160582176110251496119141
166197016223598318048106701719617094904121966308403
8582618418819338092021602217350127031523717792459711159
10722044115476156121734112261210444892110814062204618198
696720318124692212376451045212647121460261091471222157
774516695110502227121574
|
538:86332106620486156591989320341186257202921015561824319452
104869599201045911178363744331322371133938083145988878
412111696160246949976018073210211691395513639140765677
273910860202151430010639135851139333927331294046313646
140375709839671693234951513640211419848132131685410018
176834171206071504125571948317558194432076013774160655097
13747713850518788183528175302816710335221711349718845
114748093223321718518392153877019176131393222281923221810
19046142146221103622118812117290991791651921842149505628
54671872972408434110002806172051863964518886678220838
77086070778822286198421689195271800877911188958492006
38231275817857154101155211047555018384903188701234618758
129811723112311318711334109431189811754449266881993513184
1365114872084168846464880316050636214301363109926297
3031262018570220212143813674224151440659917348164032064
57256211295613371368981384101754758807069727213965
929618273164567801211217834875873781983863881057919671
162798061483525304277795120765622134543935455918529
181551920915646524765391636954992130014158121261716316184
99321342166231717210687113631456211862128221603106236475
17459187452160299963042165511505522453003833411910925
11838215091540913868117531683513881720618880651042013942
968515513073107655458126733180310815770908214825413
183811427943511558222158169371241213635147115969988821962
1180116194105134703117811559317383182589184769991091971
1878031711141910405631155832171074835744222541281013894
2008969095948312015669174121924420161685022002726014202
3293446122711458218598178721569184705671896540827327
22511151671160157345450194321438714587317683591816011357
150856948533725671032122182108811016818477125371901520260
217018422244032255484126018227532192487693435310441
266057341003819976345319019167412312165811023237271523
2140224322058099471932420180138423251890110198201109744
92083182141441887514329929220542752452498697721117
9567967912352209574772129121965211510560821827137658183
143311367020503122062111622320844222621795137331105120995
26157715447822901254915082249123011418215076122710071
3792 1318647221595108801126985283213145374257876117108
4834265119705335575526681
|
EXAMPLE 3
Consensus Sequence Build
ClustalW program was selected for multiple sequence alignments of the amino acid sequence of SEQ ID NO: 379 and 10 homologs. Three major factors affecting the sequence alignments dramatically are (1) protein weight matrices; (2) gap open penalty; (3) gap extension penalty. Protein weight matrices available for ClustalW program include Blosum, Pam and Gonnet series. Those parameters with gap open penalty and gap extension penalty were extensively tested. On the basis of the test results, Blosum weight matrix, gap open penalty of 10 and gap extension penalty of 1 were chosen for multiple sequence alignment. Attached are the sequences of SEQ ID NO: 379, its homologs and the consensus sequence SEQ ID NO: 22569 at the end. The symbols for consensus sequence are (1) uppercase letters for 100% identity in all positions of multiple sequence alignment output; (2) lowercase letters for >=70% identity; symbol; (3) “X” indicated <70% identity; (4) dashes “−” meaning that gaps were in >=70% sequences.
|
|
SEQ ID NO
2406--------------------------MGSNGGSSNNNNNKVLEKPGQDQLVQQQQQQQE-
15414--------------------------MGSNGGSSNNNNNKVLEKPGQDQLVQQQQHPQE-
587------------------------------------MMGRVMEKPSQDLLQQQQQ-----
9696------------------------------------MMGRVMEKPSQDLLQQQQQ-----
5895------------------------------------MMGRVMEKPSQDLLQQQQQ-----
17251MFGNGNCDVDNEKTIITSSKWTQSEIDDHKVSMASSTGNRVMEKPGQELLQQQQQ-----
19549-----------------------------------------MEKQGQELLQQHHQQQQQQ
379-----------------------------------MQSKNMIVASSHQQQQQQQPQQPQP
21357--------MGLSSKQVSSSGLDWKQTLLEAQNLELPKPNLMRKQQQQQQQQQQQTQPNSE
17711--------MGLSSKQVSSSGLDWKQTLLEAQNLELPKPNLMRKQQQQQQQQQQQTQPNSE
13715-----------------------------------LTLTKCCMQRGSHFRSRSGSQEARS
consensus--------------------------xxxxxxxxxxxxxxxxxxxxqxxxqqqqxxxxxx
22569
|
APKCPRCDSSNTKFCYYNNYSLSQPRHFCKACKRYWTRGGTLRNVPVGGGCRRNKRVKRP
APKCPRCDSSNTKFCYYNNYSLSQPRHFCKACKRYWTRGGTLRNVPVGGGCRRNKRVERP
ALKCPRCESSNTKFCYYNNYSLSQPRHFCKACKRYWTRGGTLRNVPVGGGCRKNKRVKRP
ALKCPRCESSNTKFCYYNNYSLSQPRHFCKACKRYWTRGGTLRNVPVGGGCRKNKRVKRP
ALKCPRCESSNTKFCYYNNYSLSQPRHFCKACKRYWTRGGTLRNVPVGGGCRKNKRVKRP
ALRCPRCDSSNTKFCYYNNYSLTQPRHFCKACKRYWTRGGTLRNVPVGGGCRKNKRLKRP
ALKCPRCDSSNTKFCYYNNYSLSQPRHFCKACKRYWTRGGTLRNVPVGGGYRRNNKRSTS
QLKCPRCDSSNTKFCYYNNYSLSQPRHFCKACKRYWTRGGTLRNVPVGGSYRKNKRVKRP
SLKCPRCDSTNTKFCYYNNYNKSQPRHFCRACKRHWTKGGTLRNVPVGG-GRKNKRVKKS
SLKCPRCDSTNTKFCYYNNYNKSQPRHFCRACKRHWTKGGTLRNVPVGG-GRKNKRVRKS
GSSMSRCNSMDTKFCYYNNYNVNQPRHFCKNCQRYWTAGGSMRNVPVGAGRRKNKHTGSV
xlkcpRCxSsnTKFCYYNNYslsQPRHFCkaCkRyWTrGGtlRNVPVGggxRkNkrvxxx
|
LITTNPSSAAIDTAASNNSSN-SSSAPLQPPIDTASTS--------------NHINPLFY
ITSPCSAAIDTASNSSNSSSAPTAAASLQPQIDTASTS--------------NHINPLFY
TNHGDSSSSAANSPSSSNSNPPSQPHLDNIIASSSTTN------------HINNISPFFY
TNHGDSSSSAANSPSSSNSNPPSQPHIDNIIASSSTTN------------HINNISPFFY
TNHGDSSSSAANSPSSSNSNPPSQPHIDNIIASSSTTN------------HINNISPFFY
TYPCSNNNNIDFSASPSSSTPSSVVANPNPPSQSQQQQQQQQHHSFDIAATSNHINTMLY
SSNGPTSTTTLIKRPISTIETATTSNSSSPSSTHSSTS--------------NHMNPMFY
------STATTTTASTVSTTNSSSPNNPHQISHFSSMN----------------HHPLFY
ITPITTSSTTTTPITTATSTCTATVTTSIGNNNNNMDAMLG----------CYSHMTIQT
ITTPITTSSTTTHQSQPPLQLALPQSQPQLATTTTTWMLCW----------VVIAT----
YRHTVITPDSLASLQVDGPDLVDHKPLSPFKVNGTILKFG--------------PDAPLC
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx----------xxxxxxxxxy
|
GLPSSS-SDVNLPLFSRFGSRISSS----GFDLQLNNALGLGFSSGVLSNEASDNNGYR-
GLPSSS-SDVNLPLFSRFGSRISSS----GFDLQLNNALGLGFSSRVLSNEASDNNRYR-
GG-----DVMSSVPFPRFNLHSQLN------------ALGLGFSTGVSENGFSTSNNN--
GG-----DVMSSVPFPRFNLHSQLN------------ALGLGFSTGVSENGFSTSNNN--
GG-----DVMSSVPFPRFNLHSQLN------------ALGLGFSTGVSENGFSTSNNN--
GGNSCH-DVMNFPFSTRFNSTTRVSNPASGYDNLPQNGLGLGFSSGILMSAAGGEVNLNH
GLSSTNNPCDPNLPFSRFNITSRLSTSSGYDLQPQMNFFGLGFSSGFENNGYTNGFNTS-
GLSDHMSSCNNNLPMIPSRFSDSSK-----------TCSSSGLESEFLSSGFSSLSALG-
PLADDQKNMSSSLYQALIRPPPLLLQQQNLLNTRELEGKDFGIGIGNGNNGIFPSSTLAL
------------------------------------------------------------
ESMASILNLGEQNLSSQLDFTAGAE-----------NREETSCSSACKPVKKKDITQHN-
gxxxxxxxxxxxxxxxxxxxxxxxx----xxxxxxxxxxxxgxsxxxxxxxxxxxxxxx-
|
-------------NWFGSNNTLLSSYTSTTSTTTPAMSSLLSSSLLQQKFMTDGVD----
-------------SGFGSNNMLLSSYTSTT-TTTPAMSSLLLQQKFISGGLKNDAD----
------------SFFSAYNSMFGSSSSSTCAPSTPVMASLLSSTLLQQNLMGGGG---GG
------------SFFSAYNSMFGSSSSSTCAPSTPVMASLLSCTLLQQNFMGGGG---GG
------------SFFSAYNSMFGSSSSSTCAPSTPVMASLLSSTLLQQKLMSGGG---GG
HHHHHHDEGSYRNGFSTSNNNNYSSIFGSSSTTTPVMASLLSSTLLQQKFMGTGGGIKGG
----------------NNNYDSIFSSSTSASNNTSVMPSVLSSTLLQHKFFDDGLK----
--------LGLPHQMSHDHTINGSFINNSTTNKPFLLSGLFGSSMSSSSTLLQHP-----
P-------------IPHQSQSLLFPFSASSRSFDTNPCSVVSTSLRSSNVYNYGED----
------------------------------------------------------------
------------------------------------------------------------
------------xxxxxxxxxxxxxxxxxxxxxxxxxxsxxxxxxxxxxxxxxxxx--xx
|
--------STNTFQHGLGLTPLEQLQMASDHSSEAGMVALKDVKVELGQNNRLEWNNGAA
--------SSNTFQHGLSLTSLEQLQIASDHSSEAGMVALKDVKVELGQNNNRLEWNGGA
VKGRDHDQGDNTFHGLAPLQGLRVEGDSNNNIGSKEVKGEGQNRFEWSNNNNNNNNNGGG
VKGRDHDQGDNTFHGLAPLQGLRVEGDSNNNIGSKEVKGEGQNRFEWSNNNNNNNNNGGG
EGEEVVIMIKVATLSMAWHRYKGCKWKGIIIIVIILAQKK--------------------
GGGGGGDDDPFHHHQEMDSKEVKLGEGLQNRLDQWNMNNLNGNGGAVFQNQMENMGLSDN
----------YGSDAGSNGAFQDLQFGSKMQNQMEHIGGFYDPASSIYLNATSSSAIGVW
----------HKPMNNGGDMLGQSHLQTLASLQDLHVGGNNEDMKYKEGKLDQISGNING
---------QFKAIEEPTINSTTATIVPSTGGTNNTHHPWEIAAATSGVGLGTSSNSNYW
------------------------------------------------------------
------------------------------------------------------------
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
|
CQSQIQHVGLYDPSLYWNNSAATALGVWNDQAANIGSSVTSLI
FQSQIQHVGLYDPLLYWNN-SATALGVWNDQAANIGSSVTSLI
GQNQMEHVGLSDPNSLYWN-TATGLGAWSDQPNNIGPSVTSLI
GQNQMEHVGLSDPNSLYWN-TATGLGAWSDQPN-IGPSVTSLI
-------------------------------------------
NASLYWNNNHNNSNNNTSA-TATGLSSVWSTDQPGSNSVSSLI
NDQGANNIGSSVTSLI---------------------------
FMSSSSSLDPSNYNNMWNNASVVNGAWLDPTNNNVGSSLTSLI
NWEDFDSLVSTDLKDPWDDSDIKP-------------------
-------------------------------------------
-------------------------------------------
xxxxxxxxxxxxxxxxxxx-xxxxxxxxxxxxxxxxxxxxxxx
|
EXAMPLE 4
Corn Transformation Construct
GATEWAY™ destination vectors (available from Invitrogen Life Technologies, Carlsbad, Calif.) are constructed for insertion of trait-improving DNA for corn transformation. The elements of each destination vector are summarized in Table 18 below and include a selectable marker transcription region and a DNA insertion transcription region. The selectable marker transcription region comprises a Cauliflower Mosaic Virus 35S promoter operably linked to a gene encoding neomycin phosphotransferase II (nptII) followed by both the 3′ region of the Agrobacterium tumefaciens nopaline synthase gene (nos) and the 3′ region of the potato proteinase inhibitor II (pinII) gene. The DNA insertion transcription region comprises a rice actin 1 promoter, a rice actin 1 exon 1 intron 1 enhancer, an att-flanked insertion site and the 3′ region of the potato pinII gene. Following standard procedures provided by Invitrogen the att-flanked insertion region is replaced by recombination with trait-improving DNA, in a sense orientation for expression of a trait-improving protein and in a gene suppression orientation (i.e., either anti-sense orientation or in a sense- and anti-sense orientation) for a trait-improving suppression of a protein. Although the vector with trait-improving DNA inserted at the att-flanked insertion region is useful for plant transformation by direct DNA delivery, such as microprojectile bombardment, it is preferable to bombard target plant tissue with tandem transcription units that have been cut from the vector. For Agrobacterium-mediated transformation of plants the vector also comprises T-DNA borders from Agrobacterium flanking the transcription units.
Vectors for Agrobacterium-mediated transformation are prepared with each of the trait-improving genes having a sequence of SEQ ID NO:1 through SEQ ID NO:269 with the DNA solely in sense orientation for expression of the encoded, cognate trait-improving protein and in a gene suppression orientation for suppression of the cognate protein. Each vector is transformed into corn callus which is propagated into a plant that is grown to produce transgenic seed for each transgenic event. Progeny plants are self-pollinated to produce seed which is selected for homozygous seed. Homozygous seed is used for producing inbred plants, for introgressing the trait into elite lines, and for crossing to make hybrid seed. The progeny transgenic plants comprising the trait-improving DNA with a sequence of SEQ ID NO: 1 through SEQ ID NO: 269 have one or more improved traits identified by agronomic trait screening including, but not limited to, enhanced nitrogen use efficiency, increased yield, enhanced water use efficiency, growth under cold stress and enhanced oil, starch and protein levels. Transgenic corn including inbred and hybrids are also produced with DNA from each of the identified homologs of DNA of SEQ ID NO: 1 through SEQ ID NO: 269 to provide transgenic seeds and plants which are identified from total transgenic events by screening for the improved agronomic trait. Transgenic corn plants are also produced where the trait-improving DNA is transcribed by each of the promoters from the group selected from, a maize globulin 1 promoter, a maize oleosin promoter, a glutelin 1 promoter, an aldolase promoter, a zein Z27 promoter, a pyruvate orthophosphate dikinase (PPDK) promoter, a soybean 7S alpha promoter, a peroxiredoxin antioxidant (Per1) promoter and a CaMV 35S promoter.
Seed produced by the plants is provided to growers to enable production of corn crops with improved traits associated with the trait-improving DNA.
TABLE 18
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FUNCTIONELEMENTREFERENCE
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DNA insertionRice actin 1 promoterU.S. Pat. No. 5,641,876
transcription regionRice actin 1 exon 1, intron 1U.S. Pat. No. 5,641,876
enhancer
DNA insertionAttR1GATEWAY ™ Cloning Technology
transcription regionInstruction Manual
(att - flanked insertinCmR geneGATEWAY ™ Cloning Technology
region)Instruction Manual
ccdA, ccdB genesGATEWAY ™ Cloning Technology
Instruction Manual
attR2GATEWAY ™ Cloning Technology
Instruction Manual
DNA insertionPotato pinII 3′ regionAn et al., (1989) Plant Cell 1: 115-122
transcription region
selectable markerCaMV 35S promoterU.S. Pat. No. 5,858,742
transcription regionnptII selectable markerU.S. Pat. No. 5,858,742
nos 3regionU.S. Pat. No. 5,858,742
PinII 3′ regionAn et al., (1989) Plant Cell 1: 115-122
E. coli maintenanceColE1 origin of replication
regionF1 origin of replication
Bla ampicillin resistance
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EXAMPLE 5
Soybean Transformation Construct
Constructs for use in transformation of soybean are prepared by restriction enzyme based cloning into a common expression vector. Elements of an exemplary common expression vector are shown in Table 19 below and include a selectable marker expression cassette and a gene of interest expression cassette. The selectable marker expression cassette comprises Arabidopsis act 7 gene (AtAct7) promoter with intron and 5′UTR, the transit peptide of Arabidopsis EPSPS, the synthetic CP4 coding region with dicot preferred codon usage and a 3′ UTR of the nopaline synthase gene. The gene of interest expression cassette comprises a Cauliflower Mosaic Virus 35S promoter operably linked to a trait-improving gene in a sense orientation for expression of a trait-improving protein and in a gene suppression orientation (i.e., either anti-sense orientation or in a sense- and anti-sense orientation for a trait-improving suppression of a protein.
Vectors similar to that described above are constructed for use in Agrobacterium mediated soybean transformation systems, with each of the trait-improving DNA having a sequence of SEQ ID NO:1 though SEQ ID NO:269 and the respective identified homologs with the DNA in sense orientation for expression of the encoded, cognate protein and in a gene suppression arrangement for suppression of the cognate protein. Each vector is transformed into soybean embryo tissue to produce transgenic events which are grown into plants that produce progeny transgenic plants and seed for screening to identify the transgenic soybean plants of this invention that exhibit the enhanced agronomic trait imparted by DNA with a sequence of SEQ ID NO:1 through SEQ ID NO:269 or a respective homolog. The transgenic soybean plants of this invention are identified by agronomic trait screening including, but not limited to, enhanced nitrogen use efficiency, increased yield, enhanced water use efficiency, growth under cold stress and enhanced oil, starch and protein levels. Transgenic soybean plants are also produced where the trait-improving DNA is transcribed by a napin promoter and Arabidopsis SSU promoter.
Seed produced by the plants is provided to growers to enable production of soybean crops with improved traits associated with the trait-improving DNA.
TABLE 19
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FunctionElementReference
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Agro transformationB-ARGtu.right borderDepicker, A. et al (1982) Mol
Appl Genet 1: 561-573
Antibiotic resistanceCR-Ec.aadA-SPC/STR
Repressor of primers from the ColE1 plasmidCR-Ec.rop
Origin of replicationOR-Ec.oriV-RK2
Agro transformationB-ARGtu.left borderBarker, R. F. et al (1983) Plant
Mol Biol 2: 335-350
Plant selectable marker expression cassetteArabidopsis act 7 geneMcDowell et al., (1996) Plant
(AtAct7) promoter withPhysiol. 111: 699-711.
intron and 5′UTR
5′ UTR of Arabidopsis act 7 gene
Intron in 5′UTR of AtAct7
Transit peptide region ofKlee, H. J. et at (1987) MGG
Arabidopsis EPSPS210: 437-442
Synthetic CP4 coding region with
dicot preferred codon usage
A 3′ UTR of the nopaline synthaseU.S. Pat. No. 5,858,742
gene of Agrobacterium
tumefaciens Ti plasmid
Plant gene of interest expression cassettePromoter for 35S RNA fromU.S. Pat. No. 5,322,938
CaMV containing a duplication of
the −90 to −350 region
Gene of interest insertion site
Cotton E6 3′ endGenBank accession U30508
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EXAMPLE 6
Cotton Transformation
Vectors similar to that described above for soybean transformation are constructed for use in 5 Agrobacterium mediated cotton transformation systems, with each of the trait-improving DNA having a sequence of SEQ ID NO:1 though SEQ ID NO:269 and the respective identified homologs with the DNA in sense orientation for expression of the encoded, cognate protein and in a gene suppression arrangement for suppression of the cognate protein. Each vector is transformed into cotton embryo tissue to produce transgenic events which are grown into plants that produce progeny transgenic plants and seed for screening to identify the transgenic soybean plants of this invention that exhibit the enhanced agronomic trait imparted by DNA with a sequence of SEQ ID NO:1 through SEQ ID NO:269 or a respective homolog. The transgenic cotton plants of this invention are identified by agronomic trait screening including, but not limited to, enhanced nitrogen use efficiency, increased yield, enhanced water use efficiency, growth under cold stress and enhanced oil, starch and protein levels. Transgenic cotton plants are also produced where the trait-improving DNA is transcribed by a napin promoter and Arabidopsis SSU promoter.
Seed produced by the plants is provided to growers to enable production of cotton crops with improved traits associated with the trait-improving DNA.