WO2004093532A2 - Generation of plants with altered oil content - Google Patents

Generation of plants with altered oil content Download PDF

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WO2004093532A2
WO2004093532A2 PCT/US2004/012279 US2004012279W WO2004093532A2 WO 2004093532 A2 WO2004093532 A2 WO 2004093532A2 US 2004012279 W US2004012279 W US 2004012279W WO 2004093532 A2 WO2004093532 A2 WO 2004093532A2
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plant
sequence
oil
plants
phenotype
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WO2004093532A3 (en )
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Jonathan Lightner
Hein Tsoeng Ng
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Agrinomics Llc
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    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07KPEPTIDES
    • C07K14/00Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/415Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from plants
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09Recombinant DNA-technology
    • C12N15/63Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/82Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8241Phenotypically and genetically modified plants via recombinant DNA technology
    • C12N15/8242Phenotypically and genetically modified plants via recombinant DNA technology with non-agronomic quality (output) traits, e.g. for industrial processing; Value added, non-agronomic traits
    • C12N15/8243Phenotypically and genetically modified plants via recombinant DNA technology with non-agronomic quality (output) traits, e.g. for industrial processing; Value added, non-agronomic traits involving biosynthetic or metabolic pathways, i.e. metabolic engineering, e.g. nicotine, caffeine
    • C12N15/8247Phenotypically and genetically modified plants via recombinant DNA technology with non-agronomic quality (output) traits, e.g. for industrial processing; Value added, non-agronomic traits involving biosynthetic or metabolic pathways, i.e. metabolic engineering, e.g. nicotine, caffeine involving modified lipid metabolism, e.g. seed oil composition
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes

Abstract

The present invention is directed to plants that display an altered oil content phenotype due to altered expression of a HIO106.2 nucleic acid. The invention is further directed to methods of generating plants with an altered oil content phenotype.

Description

GENERATION OF PLANTS WITH ALTERED OIL CONTENT

REFERENCE TO RELATED APPLICATIONS

This application claims priority to U.S. provisional patent application 60/464,487 iled 4/22/2003, the contents of which are hereby incorporated by reference

BACKGROUND OF THE INVENTION

The ability to manipulate the composition of crop seeds, particularly the content and composition of seed oils, has important applications in the agricultural industries, relating both to processed food oils and to oils for animal feeding. Seeds of agricultural crops contain a variety of valuable constituents, including oil, protein and starch. Industrial processing can separate some or all of these constituents for individual sale in specific applications. For instance, nearly 60% of the US soybean crop is crushed by the soy processing industry. Soy processing yields purified oil, which is sold at high value, while the remainder is sold principally for lower value livestock feed (US Soybean Board, 2001 Soy Stats). Canola seed is crushed to produce oil and the co-product canola meal (Canola Council of Canada). Nearly 20% of the 1999/2000 US corn crop was industrially refined, primarily for production of starch, ethanol and oil (Corn Refiners Association). Thus, it is often desirable to maximize oil content of seeds. For instance, for processed oilseeds such as soy and canola, increasing the absolute oil content of the seed will increase the value of such grains. For processed corn it may be desired to either increase or decrease oil content, depending on utilization of other major constituents. Decreasing oil may improve the quality of isolated starch by reducing undesired flavors associated with oil oxidation. Alternatively, in ethanol production, where flavor is unimportant, increasing oil content may increase overall value. In many fed grains, such as corn and wheat, it is desirable to increase seed oil content, because oil has higher energy content than other seed constituents such as carbohydrate. Oilseed processing, like most grain processing businesses, is a capital-intensive business; thus small shifts in the distribution of products from the low valued components to the high value oil component can have substantial economic impacts for grain processors.

Biotechnological manipulation of oils can provide compositional alteration and improvement of oil yield. Compositional alterations include high oleic soybean and corn oil (US Pat Nos 6,229,033 and 6,248,939), and laurate-containing seeds (US Pat No 5,639,790), among others. Work in compositional alteration has predominantly focused on processed oilseeds but has been readily extendable to non-oilseed crops, including corn. While there is considerable interest in increasing oil content, the only currently practiced biotechnology in this area is High-Oil Corn (HOC) technology (DuPont, US PAT NO: 5,704,160). HOC employs high oil pollinators developed by classical selection breeding along with elite (male-sterile) hybrid females in a production system referred to as TopCross. The TopCross High Oil system raises harvested grain oil content in maize from ~3.5% to -7%, improving the energy content of the grain.

While it has been fruitful, the HOC production system has inherent limitations. First, the system of having a low percentage of pollinators responsible for an entire field's seed set contains inherent risks, particularly in drought years. Second, oil contents in current HOC fields have plateaued at about 9% oil. Finally, high-oil corn is not primarily a biochemical change, but rather an anatomical mutant (increased embryo size) that has the indirect result of increasing oil content. For these reasons, an alternative high oil strategy, particularly one that derives from an altered biochemical output, would be especially valuable.

The most obvious target crops for the processed oil market are soy and rapeseed, and a large body of commercial work (e.g., US Pat No: 5,952,544; PCT application WO9411516) demonstrates that Arabidopsis is an excellent model for oil metabolism in these crops. Biochemical screens of seed oil composition have identified Arabidopsis genes for many critical biosynthetic enzymes and have led to identification of agronomically important gene orthologs. For instance, screens using chemically mutagenized populations have identified lipid mutants whose seeds display altered fatty acid composition (Lemieux et al, 1990; James and Dooner, 1990). T-DNA mutagenesis screens (Feldmann et al, 1989) that detected altered fatty acid composition identified the omega 3 desaturase (FAD3) and delta-12 desaturase (FAD2) genes (US Pat No 5952544; Yadav et al, 1993; Okuley et al, 1994). A screen which focused on oil content rather than oil quality, analyzed chemically-induced mutants for wrinkled seeds or altered seed density, from which altered seed oil content was inferred (Focks and Benning, 1998). Another screen, designed to identify enzymes involved in production of very long chain fatty acids, identified a mutation in the gene encoding a diacylglycerol acyltransferase (DGAT) as being responsible for reduced triacyl glycerol accumulation in seeds (Katavic V et al, 1995). It was further shown that seed-specific over-expression of the DGAT cDNA was associated with increased seed oil content (Jako et al, 2001). Activation tagging in plants refers to a method of generating random mutations by insertion of a heterologous nucleic acid construct comprising regulatory sequences (e.g., an enhancer) into a plant genome. The regulatory sequences can act to enhance transcription of one or more native plant genes; accordingly, activation tagging is a fruitful method for generating gain-of-f unction, generally dominant mutants (see, e.g., Hayashi et al, 1992; Weigel D et al 2000). The inserted construct provides a molecular tag for rapid identification of the native plant whose mis-expression causes the mutant phenotype. Activation tagging may also cause loss-of-function phenotypes. The insertion may result in disruption of a native plant gene, in which case the phenotype is generally recessive. Activation tagging has been used in various species, including tobacco and

Arabidopsis, to identify many different kinds of mutant phenotypes and the genes associated with these phenotypes (Wilson et al, 1996, Schaffer et al, 1998, Fridborg et al, 1999; Kardailsky et al, 1999; Christensen S et al, 1998).

SUMMARY OF THE INVENTION

The invention provides a transgenic plant having a high oil phenotype. The transgenic plant comprises a transformation vector comprising a nucleotide sequence that encodes or is complementary to a sequence that encodes a HIO 106.2 polypeptide. In preferred embodiments, the transgenic plant is selected from the group consisting of rapeseed, soy, corn, sunflower, cotton, cocoa, safflower, oil palm, coconut palm, flax, castor and peanut. The invention further provides a method of producing oil comprising growing the transgenic plant and recovering oil from said plant.

The transgenic plant of the invention is produced by a method that comprises introducing into progenitor cells of the plant a plant transformation vector comprising a nucleotide sequence that encodes or is complementary to a sequence that encodes a HJO106.2 polypeptide, and growing the transformed progenitor cells to produce a transgenic plant, wherein the HIO106.2 polynucleotide sequence is expressed causing the high oil phenotype.

DETAILED DESCRD?TION OF THE INVENTION

Definitions

Unless otherwise indicated, all technical and scientific terms used herein have the same meaning as they would to one skilled in the art of the present invention. Practitioners are particularly directed to Sambrook et al, 1989, and Ausubel FM et al, 1993, for definitions and terms of the art. It is to be understood that this invention is not limited to the particular methodology, protocols, and reagents described, as these may vary.

As used herein, the term "vector" refers to a nucleic acid construct designed for transfer between different host cells. An "expression vector" refers to a vector that has the ability to incorporate and express heterologous DNA fragments in a foreign cell. Many prokaryotic and eukaryotic expression vectors are commercially available. Selection of appropriate expression vectors is within the knowledge of those having skill in the art.

A "heterologous" nucleic acid construct or sequence has a portion of the sequence that is not native to the plant cell in which it is expressed. Heterologous, with respect to a control sequence refers to a control sequence (i.e. promoter or enhancer) that does not function in nature to regulate the same gene the expression of which it is currently regulating. Generally, heterologous nucleic acid sequences are not endogenous to the cell or part of the genome in which they are present, and have been added to the cell, by infection, transfection, microinjection, electroporation, or the like. A "heterologous" nucleic acid construct may contain a control sequence/DNA coding sequence combination that is the same as, or different from a control sequence/DNA coding sequence combination found in the native plant.

As used herein, the term "gene" means the segment of DNA involved in producing a polypeptide chain, which may or may not include regions preceding and following the coding region, e.g. 5' untranslated (5' UTR) or "leader" sequences and 3' UTR or "trailer" sequences, as well as intervening sequences (introns) between individual coding segments (exons) and non-transcribed regulatory sequence.

As used herein, "recombinant" includes reference to a cell or vector, that has been modified by the introduction of a heterologous nucleic acid sequence or that the cell is derived from a cell so modified. Thus, for example, recombinant cells express genes that are not found in identical form within the native (non-recombinant) form of the cell or express native genes that are otherwise abnormally expressed, under expressed or not expressed at all as a result of deliberate human intervention. As used herein, the term "gene expression" refers to the process by which a polypeptide is produced based on the nucleic acid sequence of a gene. The process includes both transcription and translation; accordingly, "expression" may refer to either a polynucleotide or polypeptide sequence, or both. Sometimes, expression of a polynucleotide sequence will not lead to protein translation. "Over-expression" refers to increased expression of a polynucleotide and/or polypeptide sequence relative to its expression in a wild-type (or other reference [e.g., non-transgenic]) plant and may relate to a naturally-occurring or non-naturally occurring sequence. "Ectopic expression" refers to expression at a time, place, and/or increased level that does not naturally occur in the non- altered or wild-type plant. "Under-expression" refers to decreased expression of a polynucleotide and/or polypeptide sequence, generally of an endogenous gene, relative to its expression in a wild-type plant. The terms "mis-expression" and "altered expression" encompass over-expression, under-expression, and ectopic expression.

The term "introduced" in the context of inserting a nucleic acid sequence into a cell, means "transfection", or "transformation" or "transduction" and includes reference to the incorporation of a nucleic acid sequence into a eukaryotic or prokaryotic cell where the nucleic acid sequence may be incorporated into the genome of the cell (for example, chromosome, plasmid, plastid, or mitochondrial DNA), converted into an autonomous replicon, or transiently expressed (for example, transfected mRNA). As used herein, a "plant cell" refers to any cell derived from a plant, including cells from undifferentiated tissue (e.g., callus) as well as plant seeds, pollen, progagules and embryos.

As used herein, the terms "native" and "wild-type" relative to a given plant trait or phenotype refers to the form in which that trait or phenotype is found in the same variety of plant in nature.

As used herein, the term "modified" regarding a plant trait, refers to a change in the phenotype of a transgenic plant relative to the similar non-transgenic plant. An "interesting phenotype (trait)" with reference to a transgenic plant refers to an observable or measurable phenotype demonstrated by a TI and/or subsequent generation plant, which is not displayed by the corresponding non-transgenic (i.e., a genotypically similar plant that has been raised or assayed under similar conditions). An interesting phenotype may represent an improvement in the plant or may provide a means to produce improvements in other plants. An "improvement" is a feature that may enhance the utility of a plant species or variety by providing the plant with a unique and/or novel quality. An "altered oil content phenotype" refers to measurable phenotype of a genetically modified plant, where the plant displays a statistically significant increase or decrease in overall oil content (i.e., the percentage of seed mass that is oil), as compared to the similar, but non- modified plant. A high oil phenotype refers to an increase in overall oil content. As used herein, a "mutant" polynucleotide sequence or gene differs from the corresponding wild type polynucleotide sequence or gene either in terms of sequence or expression, where the difference contributes to a modified plant phenotype or trait. Relative to a plant or plant line, the term "mutant" refers to a plant or plant line which has a modified plant phenotype or trait, where the modified phenotype or trait is associated with the modified expression of a wild type polynucleotide sequence or gene.

As used herein, the term "TI" refers to the generation of plants from the seed of TO plants. The TI generation is the first set of transformed plants that can be selected by application of a selection agent, e.g., an antibiotic or herbicide, for which the transgenic plant contains the corresponding resistance gene. The term "T2" refers to the generation of plants by self-fertilization of the flowers of TI plants, previously selected as being transgenic. T3 plants are generated from T2 plants, etc. As used herein, the "direct progeny" of a given plant derives from the seed (or, sometimes, other tissue) of that plant and is in the immediately subsequent generation; for instance, for a given lineage, a T2 plant is the direct progeny of a TI plant. The "indirect progeny" of a given plant derives from the seed (or other tissue) of the direct progeny of that plant, or from the seed (or other tissue) of subsequent generations in that lineage; for instance, a T3 plant is the indirect progeny of a TI plant.

As used herein, the term "plant part" includes any plant organ or tissue, including, without limitation, seeds, embryos, meristematic regions, callus tissue, leaves, roots, shoots, gametophytes, sporophytes, pollen, and microspores. Plant cells can be obtained from any plant organ or tissue and cultures prepared therefrom. The class of plants which can be used in the methods of the present invention is generally as broad as the class of higher plants amenable to transformation techniques, including both monocotyledenous and dicotyledenous plants.

As used herein, "transgenic plant" includes a plant that comprises within its genome a heterologous polynucleotide. The heterologous polynucleotide can be either stably integrated into the genome, or can be extra-chromosomal. Preferably, the polynucleotide of the present invention is stably integrated into the genome such that the polynucleotide is passed on to successive generations. A plant cell, tissue, organ, or plant into which the heterologous polynucleotides have been introduced is considered "transformed", "transfected", or "transgenic". Direct and indirect progeny of transformed plants or plant cells that also contain the heterologous polynucleotide are also considered transgenic. Identification of Plants with an Altered Oil Content Phenotype

We used an Arabidopsis activation tagging screen to identify the association between the gene we have designated "HIO106.2," (At2g34220; GI#18403485) encoding a non-secretory protein that lacks a transmembrane domain (GI#15226250), and an altered oil content phenotype (specifically, a high oil phenotype). Briefly, and as further described in the Examples, a large number of Arabidopsis plants were mutated with the pSKI015 vector, which comprises a T-DNA from the Ti plasmid of Agrobacterium tumifaciens, a viral enhancer element, and a selectable marker gene (Weigel et al, 2000). When the T-DNA inserts into the genome of transformed plants, the enhancer element can cause up-regulation genes in the vicinity, generally within about 10 kilobase (kb) of the insertion. TI plants were exposed to the selective agent in order to specifically recover transformed plants that expressed the selectable marker and therefore harbored T-DNA insertions. Samples of approximately 15-20 T2 seeds were collected from transformed TI plants, and lipids were extracted from whole seeds. Gas chromatography (GC) analysis was performed to determine fatty acid content and composition of seed samples.

An Arabidopsis line that showed a high-oil phenotype was identified wherein oil content (i.e., fatty acids) constituted approximately 38.4% relative to a planting day average oil content of 35.5% (108% of PDA). The association of the HIO106.2 gene with the high oil phenotype was discovered by analysis of the genomic DNA sequence flanking the T-DNA insertion in the identified line. Accordingly, HIO106.2 genes and/or polypeptides may be employed in the development of genetically modified plants having a modified oil content phenotype ("a HIO106.2 phenotype"). HIO106.2 genes may be used in the generation of oilseed crops that provide improved oil yield from oilseed processing and in the generation of feed grain crops that provide increased energy for animal feeding. HIO106.2 genes may further be used to increase the oil content of specialty oil crops, in order to augment yield of desired unusual fatty acids. Transgenic plants that have been genetically modified to express HIO106.2 can be used in the production of oil, wherein the transgenic plants are grown, and oil is obtained from plant parts (e.g. seed) using standard methods.

HIO106.2 Nucleic Acids and Polypeptides

Arabidopsis HTO106.2 nucleic acid (genomic DNA) sequence is provided in SEQ ID NO:l and in Genbank entry GI#18403485. The corresponding protein sequence is provided in SEQ ID NO:2 and in GI#15226250. Nucleic acids and/or proteins that are orthologs or paralogs of Arabidopsis HIO106.2, are described in Example 3 below.

As used herein, the term "HIO106.2 polypeptide" refers to a full-length HIO106.2 protein or a fragment, derivative (variant), or ortholog thereof that is "functionally active," meaning that the protein fragment, derivative, or ortholog exhibits one or more or the functional activities associated with the polypeptide of SEQ ID NO:2. In one preferred embodiment, a functionally active HJO106.2 polypeptide causes an altered oil content phenotype when mis-expressed in a plant. In a further preferred embodiment, mis- expression of the HIO 106.2 polypeptide causes a high oil phenotype in a plant. In another embodiment, a functionally active HJO106.2 polypeptide is capable of rescuing defective (including deficient) endogenous HIO106.2 activity when expressed in a plant or in plant cells; the rescuing polypeptide may be from the same or from a different species as that with defective activity. In another embodiment, a functionally active fragment of a full length HJO106.2 polypeptide (i.e., a native polypeptide having the sequence of SEQ ID NO: 2 or a naturally occurring ortholog thereof) retains one of more of the biological properties associated with the full-length HIO 106.2 polypeptide, such as signaling activity, binding activity, catalytic activity, or cellular or extra-cellular localizing activity. A HIO106.2 fragment preferably comprises a HIO106.2 domain, such as a C- or N-terminal or catalytic domain, among others, and preferably comprises at least 10, preferably at least 20, more preferably at least 25, and most preferably at least 50 contiguous amino acids of a HIO106.2 protein. Functional domains can be identified using the PFAM program (Bateman A et al, 1999 Nucleic Acids Res 27:260-262; website at pfam.wustl.edu). A preferred H106.2 fragment comprises of one or more plant specific domains, including PF04780 and PF04781. Functionally active variants of full-length HIO 106.2 polypeptides or fragments thereof include polypeptides with amino acid insertions, deletions, or substitutions that retain one of more of the biological properties associated with the full- length HIO106.2 polypeptide. In some cases, variants are generated that change the post- translational processing of a HKH06.2 polypeptide. For instance, variants may have altered protein transport or protein localization characteristics or altered protein half-life compared to the native polypeptide.

As used herein, the term "HIO106.2 nucleic acid" encompasses nucleic acids with the sequence provided in or complementary to the sequence provided in SEQ ID NO:l, as well as functionally active fragments, derivatives, or orthologs thereof. A HIO106.2 nucleic acid of this invention may be DNA, derived from genomic DNA or cDNA, or RNA.

In one embodiment, a functionally active HIO106.2 nucleic acid encodes or is complementary to a nucleic acid that encodes a functionally active HIO106.2 polypeptide. Included within this definition is genomic DNA that serves as a template for a primary RNA transcript (i.e., an mRNA precursor) that requires processing, such as splicing, before encoding the functionally active HJO106.2 polypeptide. A HIO106.2 nucleic acid can include other non-coding sequences, which may or may not be transcribed; such sequences include 5' and 3' UTRs, polyadenylation signals and regulatory sequences that control gene expression, among others, as are known in the art. Some polypeptides require processing events, such as proteolytic cleavage, covalent modification, etc., in order to become fully active. Accordingly, functionally active nucleic acids may encode the mature or the pre-processed HIO 106.2 polypeptide, or an intermediate form. A HIO 106.2 polynucleotide can also include heterologous coding sequences, for example, sequences that encode a marker included to facilitate the purification of the fused polypeptide, or a transformation marker.

In another embodiment, a functionally active HJO106.2 nucleic acid is capable of being used in the generation of loss-of-function HIO106.2 phenotypes, for instance, via antisense suppression, co-suppression, etc. In one preferred embodiment, a HIO 106.2 nucleic acid used in the methods of this invention comprises a nucleic acid sequence that encodes or is complementary to a sequence that encodes a HIO106.2 polypeptide having at least 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95% or more sequence identity to the polypeptide sequence presented in SEQ ID NO:2. In another embodiment a HIO106.2 polypeptide of the invention comprises a polypeptide sequence with at least 50% or 60% identity to the HIO106.2 polypeptide sequence of SEQ ID NO:2, and may have at least 70%, 80%, 85%, 90% or 95% or more sequence identity to the HIO106.2 polypeptide sequence of SEQ D NO:2. In another embodiment, a HIO106.2 polypeptide comprises a polypeptide sequence with at least 50%, 60%, 70%, 80%, 85%, 90% or 95% or more sequence identity to a functionally active fragment of the polypeptide presented in SEQ ID NO:2, such as one or more plant specific domains, including PF04780 and PF04781. In yet another embodiment, a HIO106.2 polypeptide comprises a polypeptide sequence with at least 50%, 60 %, 70%, 80%, or 90% identity to the polypeptide sequence of SEQ ID NO: 2 over its entire length and comprises of one or more plant specific domains, including PF04780 and PF04781.

In another aspect, a HIO106.2 polynucleotide sequence is at least 50% to 60% identical over its entire length to the HIO106.2 nucleic acid sequence presented as SEQ ID NO:l, or nucleic acid sequences that are complementary to such a HIO106.2 sequence, and may comprise at least 70%, 80%, 85%, 90% or 95% or more sequence identity to the HJO106.2 sequence presented as SEQ ID NO:l or a functionally active fragment thereof, or complementary sequences.

As used herein, "percent (%) sequence identity" with respect to a specified subject sequence, or a specified portion thereof, is defined as the percentage of nucleotides or amino acids in the candidate derivative sequence identical with the nucleotides or amino acids in the subject sequence (or specified portion thereof), after aligning the sequences and introducing gaps, if necessary to achieve the maximum percent sequence identity, as generated by the program WU-BLAST-2.0al9 (Altschul et al, J. Mol. Biol. (1997) 215:403-410; website at blast.wustl.edu/blast/README.html) with search parameters set to default values. The HSP S and HSP S2 parameters are dynamic values and are established by the program itself depending upon the composition of the particular sequence and composition of the particular database against which the sequence of interest is being searched. A "% identity value" is determined by the number of matching identical nucleotides or amino acids divided by the sequence length for which the percent identity is being reported. "Percent (%) amino acid sequence similarity" is determined by doing the same calculation as for determining % amino acid sequence identity, but including conservative amino acid substitutions in addition to identical amino acids in the computation. A conservative amino acid substitution is one in which an amino acid is substituted for another amino acid having similar properties such that the folding or activity of the protein is not significantly affected. Aromatic amino acids that can be substituted for each other are phenylalanine, tryptophan, and tyrosine; interchangeable hydrophobic amino acids are leucine, isoleucine, methionine, and valine; interchangeable polar amino acids are glutamine and asparagine; interchangeable basic amino acids are arginine, lysine and histidine; interchangeable acidic amino acids are aspartic acid and glutamic acid; and interchangeable small amino acids are alanine, serine, threonine, cysteine and glycine.

Derivative nucleic acid molecules of the subject nucleic acid molecules include sequences that selectively hybridize to the nucleic acid sequence of SEQ ID NO:l. The stringency of hybridization can be controlled by temperature, ionic strength, pH, and the presence of denaturing agents such as formamide during hybridization and washing. Conditions routinely used are well known (see, e.g., Current Protocol in Molecular Biology, Vol. 1, Chap. 2.10, John Wiley & Sons, Publishers (1994); Sambrook et al, Molecular Cloning, Cold Spring Harbor (1989)). In some embodiments, a nucleic acid molecule of the invention is capable of hybridizing to a nucleic acid molecule containing the nucleotide sequence of SEQ ID NO:l under stringent hybridization conditions that are: prehybridization of filters containing nucleic acid for 8 hours to overnight at 65° C in a solution comprising 6X single strength citrate (SSC) (IX SSC is 0.15 M NaCI, 0.015 M Na citrate; pH 7.0), 5X Denhardt's solution, 0.05% sodium pyrophosphate and 100 μg/ml herring sperm DNA; hybridization for 18-20 hours at 65° C in a solution containing 6X SSC, IX Denhardt's solution, 100 μg/ml yeast tRNA and 0.05% sodium pyrophosphate; and washing of filters at 65° C for 1 h in a solution containing 0.1X SSC and 0.1% SDS (sodium dodecyl sulfate). In other embodiments, moderately stringent hybridization conditions are used that are: pretreatment of filters containing nucleic acid for 6 h at 40° C in a solution containing 35% formamide, 5X SSC, 50 mM Tris-HCl (pH 7.5), 5 mM EDTA, 0.1%) PVP, 0.1% Ficoll, 1% BSA, and 500 g/ml denatured salmon sperm DNA; hybridization for 18-20 h at 40° C in a solution containing 35% formamide, 5X SSC, 50 mM Tris-HCl (pH 7.5), 5 mM EDTA, 0.02% PVP, 0.02% Ficoll, 0.2% BSA, 100 μg ml salmon sperm DNA, and 10% (wt/vol) dextran sulfate; followed by washing twice for 1 hour at 55° C in a solution containing 2X SSC and 0.1% SDS. Alternatively, low stringency conditions can be used that comprise: incubation for 8 hours to overnight at 37° C in a solution comprising 20% formamide, 5 x SSC, 50 mM sodium phosphate (pH 7.6), 5X Denhardt's solution, 10% dextran sulfate, and 20 μg/ml denatured sheared salmon sperm DNA; hybridization in the same buffer for 18 to 20 hours; and washing of filters in 1 x SSC at about 37° C for 1 hour.

As a result of the degeneracy of the genetic code, a number of polynucleotide sequences encoding a HIO106.2 polypeptide can be produced. For example, codons may be selected to increase the rate at which expression of the polypeptide occurs in a particular host species, in accordance with the optimum codon usage dictated by the particular host organism (see, e.g., Nakamura et al, 1999). Such sequence variants may be used in the methods of this invention.

The methods of the invention may use orthologs of the Arabidopsis HIO 106.2. Methods of identifying the orthologs in other plant species are known in the art. Normally, orthologs in different species retain the same function, due to presence of one or more protein motifs and/or 3-dimensional structures. In evolution, when a gene duplication event follows speciation, a single gene in one species, such as Arabidopsis, may correspond to multiple genes (paralogs) in another. As used herein, the term "orthologs" encompasses paralogs. When sequence data is available for a particular plant species, orthologs are generally identified by sequence homology analysis, such as BLAST analysis, usually using protein bait sequences. Sequences are assigned as a potential ortholog if the best hit sequence from the forward BLAST result retrieves the original query sequence in the reverse BLAST (Huynen MA and Bork P, Proc Natl Acad Sci (1998) 95:5849-5856; Huynen MA et al, Genome Research (2000) 10: 1204-1210). Programs for multiple sequence alignment, such as CLUSTAL (Thompson JD et al, 1994, Nucleic Acids Res 22:4673-4680) may be used to highlight conserved regions and/or residues of orthologous proteins and to generate phylogenetic trees. In a phylogenetic tree representing multiple homologous sequences from diverse species (e.g., retrieved through BLAST analysis), orthologous sequences from two species generally appear closest on the tree with respect to all other sequences from these two species. Structural threading or other analysis of protein folding (e.g., using software by ProCeryon, Biosciences, Salzburg, Austria) may also identify potential orthologs. Nucleic acid hybridization methods may also be used to find orthologous genes and are preferred when sequence data are not available. Degenerate PCR and screening of cDNA or genomic DNA libraries are common methods for finding related gene sequences and are well known in the art (see, e.g., Sambrook, 1989; Dieffenbach and Dveksler, 1995). For instance, methods for generating a cDNA library from the plant species of interest and probing the library with partially homologous gene probes are described in Sambrook et al. A highly conserved portion of the Arabidopsis FLTO106.2 coding sequence may be used as a probe. HJO106.2 ortholog nucleic acids may hybridize to the nucleic acid of SEQ ID NO:l under high, moderate, or low stringency conditions. After amplification or isolation of a segment of a putative ortholog, that segment may be cloned and sequenced by standard techniques and utilized as a probe to isolate a complete cDNA or genomic clone. Alternatively, it is possible to initiate an EST project to generate a database of sequence information for the plant species of interest. In another approach, antibodies that specifically bind known HIO106.2 polypeptides are used for ortholog isolation (see, e.g., Harlow and Lane, 1988, 1999). Western blot analysis can determine that a HIO106.2 ortholog (i.e., an orthologous protein) is present in a crude extract of a particular plant species. When reactivity is observed, the sequence encoding the candidate ortholog may be isolated by screening expression libraries representing the particular plant species. Expression libraries can be constructed in a variety of commercially available vectors, including lambda gtll, as described in Sambrook, et al, 1989. Once the candidate ortholog(s) are identified by any of these means, candidate orthologous sequence are used as bait (the "query") for the reverse BLAST against sequences from Arabidopsis or other species in which HIO 106.2 nucleic acid and/or polypeptide sequences have been identified.

HIO106.2 nucleic acids and polypeptides may be obtained using any available method. For instance, techniques for isolating cDNA or genomic DNA sequences of interest by screening DNA libraries or by using polymerase chain reaction (PCR), as previously described, are well known in the art. Alternatively, nucleic acid sequence may be synthesized. Any known method, such as site directed mutagenesis (Kunkel TA et al, 1991), may be used to introduce desired changes into a cloned nucleic acid.

In general, the methods of the invention involve incorporating the desired form of the HIO106.2 nucleic acid into a plant expression vector for transformation of in plant cells, and the HIO106.2 polypeptide is expressed in the host plant.

An isolated HJO106.2 nucleic acid molecule is other than in the form or setting in which it is found in nature and is identified and separated from least one contaminant nucleic acid molecule with which it is ordinarily associated in the natural source of the HIO106.2 nucleic acid. However, an isolated HIO106.2 nucleic acid molecule includes HIO106.2 nucleic acid molecules contained in cells that ordinarily express HIO106.2 where, for example, the nucleic acid molecule is in a chromosomal location different from that of natural cells.

Generation of Genetically Modified Plants with an Altered Oil Content Phenotype

HKM06.2 nucleic acids and polypeptides may be used in the generation of genetically modified plants having a modified oil content phenotype. As used herein, a "modified oil content phenotype" may refer to modified oil content in any part of the plant; the modified oil content is often observed in seeds. In a preferred embodiment, altered expression of the HIO106.2 gene in a plant is used to generate plants with a high oil phenotype.

The methods described herein are generally applicable to all plants. Although activation tagging and gene identification is carried out in Arabidopsis, the HIO 106.2 gene (or an ortholog, variant or fragment thereof) may be expressed in any type of plant. In a preferred embodiment, the invention is directed to oil-producing plants, which produce and store triacylglycerol in specific organs, primarily in seeds. Such species include soybean (Glycine max), rapeseed and canola (including Brassica napus, B. campestήs), sunflower (Helianthus annus), cotton (Gossypium hirsutum), corn (Zea mays), cocoa (Theobroma cacao), safflower (Carthamus tinctorius), oil palm (Elaeis guineensis), coconut palm (Cocos nucifera), flax (Linum usitatissimum), castor (Ricinus communis) and peanut (Arachis hypogaea). The invention may also be directed to fruit- and vegetable-bearing plants, grain-producing plants, nut-producing plants, rapid cycling Brassica species, alfalfa (Medicago sativa), tobacco (Nicotiana), turfgrass (Poaceae family), other forage crops, and wild species that may be a source of unique fatty acids. The skilled artisan will recognize that a wide variety of transformation techniques exist in the art, and new techniques are continually becoming available. Any technique that is suitable for the target host plant can be employed within the scope of the present invention. For example, the constructs can be introduced in a variety of forms including, but not limited to as a strand of DNA, in a plasmid, or in an artificial chromosome. The introduction of the constructs into the target plant cells can be accomplished by a variety of techniques, including, but not limited to Agrobacterium-m.edia.ted transformation, electroporation, microinjection, microprojectile bombardment calcium-phosphate-DNA co-precipitation or liposome-mediated transformation of a heterologous nucleic acid. The transformation of the plant is preferably permanent, i.e. by integration of the introduced expression constructs into the host plant genome, so that the introduced constructs are passed onto successive plant generations. Depending upon the intended use, a heterologous nucleic acid construct comprising an HIO 106.2 polynucleotide may encode the entire protein or a biologically active portion thereof. In one embodiment, binary Ti-based vector systems may be used to transfer polynucleotides. Standard Agrobαcterium binary vectors are known to those of skill in the art, and many are commercially available (e.g., pBI121 Clontech Laboratories, Palo Alto, CA).

The optimal procedure for transformation of plants with Agrobαcterium vectors will vary with the type of plant being transformed. Exemplary methods for

Agrobαcterium- ediated transformation include transformation of explants of hypocotyl, shoot tip, stem or leaf tissue, derived from sterile seedlings and/or plantlets. Such transformed plants may be reproduced sexually, or by cell or tissue culture. Agrobαcterium transformation has been previously described for a large number of different types of plants and methods for such transformation may be found in the scientific literature. Of particular relevance are methods to transform commercially important crops, such as rapeseed (De Block et al, 1989), sunflower (Everett et al, 1987), and soybean (Christou et al, 1989; Kline et al, 1987). Expression (including transcription and translation) of HIO 106.2 may be regulated with respect to the level of expression, the tissue type(s) where expression takes place and/or developmental stage of expression. A number of heterologous regulatory sequences (e.g., promoters and enhancers) are available for controlling the expression of a HIO 106.2 nucleic acid. These include constitutive, inducible and regulatable promoters, as well as promoters and enhancers that control expression in a tissue- or temporal-specific manner. Exemplary constitutive promoters include the raspberry E4 promoter (U.S. Patent Nos. 5,783,393 and 5,783,394), the 35S CaMV (Jones JD et al, 1992), the CsVMV promoter (Verdaguer B et al, 1998) and the melon actin promoter (published PCT application WO0056863). Exemplary tissue-specific promoters include the tomato E4 and E8 promoters (U.S. Patent No. 5,859,330) and the tomato 2AIJ gene promoter (Van Haaren MJJ et Z., 1993).

In one preferred embodiment, HIO106.2 expression is under control of regulatory sequences from genes whose expression is associated with early seed and/or embryo development. Legume genes whose promoters are associated with early seed and embryo development include V. faba legumin (Baumlein et al, 1991, Mol Gen Genet 225:121-8; Baumlein et al, 1992, Plant J 2:233-9), V. faba usp (Fiedler et al, 1993, Plant Mol Biol 22:669-79), pea convicilin (Bown et al, 1988, Biochem J 251:717-26), pea lectin (dePater et al, 1993, Plant Cell 5:877-86), P. vulgaήs beta phaseolin (Bustos et al, 1991, EMBO J 10:1469-79), P. vulgaris DLEC2 and PHS [beta] (Bobb et al, 1997, Nucleic Acids Res 25:641-7), and soybean beta-Conglycinin, 7S storage protein (Chamberland et al, 1992, Plant Mol Biol 19:937-49). Cereal genes whose promoters are associated with early seed and embryo development include rice glutelin ("GluA-3," Yoshihara and Takaiwa, 1996, Plant Cell Physiol 37:107-11; "GluB-1," Takaiwa et al, 1996, Plant Mol Biol 30:1207-21; Washida et al, 1999, Plant Mol Biol 40:1-12; "Gt3," Leisy et al, 1990, Plant Mol Biol 14:41-50), rice prolamin (Zhou & Fan, 1993, Transgenic Res 2: 141-6), wheat prolamin (Hammond-Kosack et al, 1993, EMBO J 12:545-54), maize ze (TA, Matzke et al, 1990, Plant Mol Biol 14:323-32), and barley B-hordeins (Entwistle et al, 1991, Plant Mol Biol 17:1217-31). Other genes whose promoters are associated with early seed and embryo development include oil palm GLO7A (7S globulin, Morcillo et al, 2001, Physiol Plant 112:233-243), Brassica napus napin, 2S storage protein, and napA gene (Josefsson et al, 1987, J Biol Chem 262:12196-201; Stalberg et al, 1993, Plant Mol Biol 1993 23:671-83; Ellerstrom et al, 1996, Plant Mol Biol 32:1019-27), Brassica napus oleosin (Keddie et al, 1994, Plant Mol Biol 24:327-40), Arabidopsis oleosin (Plant et al, 1994, Plant Mol Biol 25:193-205), Arabidopsis FAE1 (Rossak et al, 2001, Plant Mol Biol 46:717-25), Canavalia gladiata conA (Yamamoto et al, 1995, Plant Mol Biol 27:729-41), and Catharanthus roseus strictosidine synthase (Str, Ouwerkerk and Memelink, 1999, Mol Gen Genet 261:635-43). In another preferred embodiment, regulatory sequences from genes expressed during oil biosynthesis are used (see, e.g., US Pat No: 5,952, 544). Alternative promoters are from plant storage protein genes (Bevan et al, 1993, Philos Trans R Soc Lond B Biol Sci 342:209-15).

In yet another aspect, in some cases it may be desirable to inhibit the expression of endogenous HIO106.2 in a host cell. Exemplary methods for practicing this aspect of the invention include, but are not limited to antisense suppression (Smith, et /.,1988; van der Krol et al, 1988); co-suppression (Napoli, et al, 1990); ribozymes (PCT Publication WO 97/10328); and combinations of sense and antisense (Waterhouse, et al, 1998). Methods for the suppression of endogenous sequences in a host cell typically employ the transcription or transcription and translation of at least a portion of the sequence to be suppressed. Such sequences may be homologous to coding as well as non-coding regions of the endogenous sequence. Antisense inhibition may use the entire cDNA sequence

(Sheehy et al, 1988), a partial cDNA sequence including fragments of 5' coding sequence, (Cannon et al, 1990), or 3' non-coding sequences (Ch'ng et al, 1989). Cosuppression techniques may use the entire cDNA sequence (Napoli et al, 1990; van der Krol et al, 1990), or a partial cDNA sequence (Smith et al, 1990).

Standard molecular and genetic tests may be performed to further analyze the association between a gene and an observed phenotype. Exemplary techniques are described below.

1. DNA/RNA analysis The stage- and tissue-specific gene expression patterns in mutant versus wild-type lines may be determined, for instance, by in situ hybridization. Analysis of the methylation status of the gene, especially flanking regulatory regions, may be performed. Other suitable techniques include overexpression, ectopic expression, expression in other plant species and gene knock-out (reverse genetics, targeted knock-out, viral induced gene silencing [VIGS, see Baulcombe D, 1999]).

In a preferred application expression profiling, generally by microarray analysis, is used to simultaneously measure differences or induced changes in the expression of many different genes. Techniques for microarray analysis are well known in the art (Schena M et al, Science (1995) 270:467-470; Baldwin D et al, 1999; Dangond F, Physiol Genomics (2000) 2:53-58; van Hal NL et al, J Biotechnol (2000) 78:271-280; Richmond T and Somerville S, Curr Opin Plant Biol (2000) 3:108-116). Expression profiling of individual tagged lines may be performed. Such analysis can identify other genes that are coordinately regulated as a consequence of the overexpression of the gene of interest, which may help to place an unknown gene in a particular pathway.

2. Gene Product Analysis

Analysis of gene products may include recombinant protein expression, antisera production, immunolocalization, biochemical assays for catalytic or other activity, analysis of phosphorylation status, and analysis of interaction with other proteins via yeast two-hybrid assays.

3. Pathway Analysis

Pathway analysis may include placing a gene or gene product within a particular biochemical, metabolic or signaling pathway based on its mis-expression phenotype or by sequence homology with related genes. Alternatively, analysis may comprise genetic crosses with wild-type lines and other mutant lines (creating double mutants) to order the gene in a pathway, or determining the effect of a mutation on expression of downstream "reporter" genes in a pathway.

Generation of Mutated Plants with an Altered Oil Content Phenotype

The invention further provides a method of identifying plants that have mutations in endogenous HI0106.2 that confer altered oil content, and generating altered oil content progeny of these plants that are not genetically modified. In one method, called "TTTJJ G" (for targeting induced local lesions in genomes), mutations are induced in the seed of a plant of interest, for example, using EMS treatment. The resulting plants are grown and self-fertilized, and the progeny are used to prepare DNA samples. HI0106.2- specific PCR is used to identify whether a mutated plant has a HI0106.2 mutation. Plants having HI0106.2 mutations may then be tested for altered oil content, or alternatively, plants may be tested for altered oil content, and then M0106.2-specific PCR is used to determine whether a plant having altered oil content has a mutated HI0106.2 gene. TILLING can identify mutations that may alter the expression of specific genes or the activity of proteins encoded by these genes (see Colbert et al (2001) Plant Physiol 126:480-484; McCallum et al (2000) Nature Biotechnology 18:455-457). In another method, a candidate gene/Quantitative Trait Locus (QTLs) approach can be used in a marker-assisted breeding program to identify alleles of or mutations in the HJ0106.2 gene or orthologs of HI0106.2 that may confer altered oil content (see Bert et al., Theor Appl Genet. 2003 Jun; 107(1): 181-9; and Lionneton et al, Genome. 2002 Dec;45(6): 1203-15). Thus, in a further aspect of the invention, a HJ.0106.2 nucleic acid is used to identify whether a plant having altered oil content has a mutation in endogenous HJ.0106.2 or has a particular allele that causes altered oil content.

While the invention has been described with reference to specific methods and embodiments, it will be appreciated that various modifications and changes may be made without departing from the invention. All publications cited herein are expressly incorporated herein by reference for the purpose of describing and disclosing compositions and methodologies that might be used in connection with the invention. All cited patents, patent applications, and sequence information in referenced websites and public databases are also incorporated by reference.

EXAMPLES

EXAMPLE 1

Generation of Plants with a HJO106.2 Phenotype by Transformation with an Activation Tagging Construct

Mutants were generated using the activation tagging "ACTTAG" vector, pSKI015 (GI#6537289; Weigel D et al, 2000). Standard methods were used for the generation of Arabidopsis transgenic plants, and were essentially as described in published application PCT WO0183697. Briefly, TO Arabidopsis (Col-0) plants were transformed with Agrobacterium carrying the pSKI015 vector, which comprises T-DNA derived from the Agrobacterium Ti plasmid, an herbicide resistance selectable marker gene, and the 4X CaMV 35S enhancer element. Transgenic plants were selected at the TI generation based on herbicide resistance.

T3 seed pools were analyzed by Near Infrared Spectroscopy (NTR) intact at time of harvest. NJR. infrared spectra were captured using a Bruker 22 N/F. Bruker Software was used to estimate total seed oil and total seed protein content using data from NTR analysis and reference methods according to the manufacturers instructions. Oil contents predicted by our calibration (PDX Oil 3, Predicts Hexane Extracted Oil) were compared for 40,000 individual ACTTAG lines. To identify high oil lines the NTR oil result was compared to the mean oil result for all ACTTAG lines planted on the same day (Relative oil content). Subsequent to seed compositional analysis ACTTAG flanking sequence was determined. 22,000 lines with recovered flanking sequences were considered in this analysis. From 22,000 placed ACTTAG lines 819 (-4%) had high oil (defined as oil content of >=107% of the planting day average oil content). The genome coordinates in this subset of high oil ACTTAG lines was evaluated and lines having 2 or more independent ACTTAG insertions, also displaying high oil, were identified and the flanking sequence confirmed by PCR and sequencing.

Line W000151578 (L 047787) had a NTR determined oil content of 37.7% relative to a planting day average oil content of 34.4% (110% of PDA). Line W000112024 (TN034777) had a NIR determined oil content of 38.4% relative to a planting day average oil content of 35.5%( 108% of PDA).

Line W000151578 (IN047787) had a confirmed ACTTAG insertion on Chromosome 2 at bp 14400020.

Line W000112024 (L 034777) had a confirmed ACTTAG insertion on Chromosome 2 at bp 14407000.

EXAMPLE 2 Characterization of the T-DNA Insertion in Plants Exhibiting the Altered Oil Content Phenotype.

We performed standard molecular analyses, essentially as described in patent application PCT WO0183697, to determine the site of the T-DNA insertion associated with the altered oil content phenotype. Briefly, genomic DNA was extracted from plants exhibiting the altered oil content phenotype. PCR, using primers specific to the pSKI015 vector, confirmed the presence of the 35S enhancer in plants from lines I 047787 and JN034777, and Southern blot analysis verified the genomic integration of the ACTTAG T- DNA and showed the presence of the T-DNA insertions in each of the transgenic lines. Inverse PCR was used to recover genomic DNA flanking the T-DNA insertion, which was then subjected to sequence analysis using a basic BLASTN search and/or a search of the Arabidopsis Information Resource (TAJR) database (available at the arabidopsis.org website). For ACTTAG line IN047787, there was sequence identity to nucleotides 21803-22156 on Arabidopsis clone F13P17 map ve016 chromosome 2

(GI#20197153), placing the left border junction downstream from 21803 (GI#20197153). The opposite flank (predicted right border junction) of this insert is not determined. Left border of IN047787 T-DNA is ~ 19 bp 5' of the translation start site.

For ACTTAG line L 034777, there was sequence identity to nucleotides 28624- 28769 on Arabidopsis clone F13P17 map ve016 chromosome 2 (GI#20197153), placing the left border junction downstream from 28624 (GI#20197153). The opposite flank (predicted right border junction) of this insert was not determined. Left border LN034777 T-DNA is ~ 6999 bp 3' of the translation start site.

EXAMPLE 3

Analysis of Arabidopsis ΕΩ.O106.2 Sequence

Sequence analyses were performed with BLAST (Altschul et al, 1997, J. Mol. Biol. 215:403-410), PFAM (Bateman et al, 1999, Nucleic Acids Res 27:260-262), PSORT (Nakai K, and Horton P, 1999,Trends Biochem Sci 24:34-6), and/or CLUSTAL (Thompson JD et al, 1994, Nucleic Acids Res 22:4673-4680).

TBLASTN against est_others results:

At2g34220 has limited homology to sequences in the EST databases (including Arabidopsis ESTs). It is likely that At2g34220 and its homologues are expressed at low levels.

BLASTP against all.aa results:

The protein At2g34220 has homology to putative or hypothetical proteins from Arabidopsis. The top 10 BLAST results for At2g34220 are listed below and are included in the "Orthologue Table. 1. At2g34220 itself (several redundant entries)

>gi|15226250|ref|NP_180969.1| hypothetical protein; protein id: At2g34220.1 [Arabidopsis thaliana] >gi|7485475|ρir||T02310 hypothetical protein At2g34220 [imported] - Arabidopsis thaliana >gi|3337353|gb|AAC27398.1| hypothetical protein [Arabidopsis thaliana]

Score = 3506 (1239.2 bits), Expect = 0., P = 0.

2. At2g34240 from Arabidopsis (several redundant entries)

>gi|15226253|ref|NP_180971.1| hypothetical protein; protein id: At2g34240.1 [Arabidopsis thaliana] >gi|7485477|ρir||T02312 hypothetical protein At2g34240

[imported] - Arabidopsis thaliana >gi|3337355|gb|AAC27400.1| hypothetical protein [Arabidopsis thaliana]

Score = 2286 (809.8 bits), Expect = 1.6e-236, P = 1.6e-236

3. At2g34230 from Arabidopsis (several redundant entries)

>gi|15226252|ref|NP_l 80970.11 hypothetical protein; protein id: At2g34230.1 [Arabidopsis thaliana] >gi|7485476|pir||T02311 hypothetical protein At2g34230 [imported] - Arabidopsis thaliana >gi|3337354|gb|AAC27399.1| hypothetical protein [Arabidopsis thaliana] Score = 2219 (786.2 bits), Expect = 2.0e-229, P = 2.0e-229

4. Atlg65130 from Arabidopsis (several redundant entries)

>gi|15217861|ref|NP_176692.1| hypothetical protein; protein id: Atlg65130.1 [Arabidopsis thaliana] Score = 714 (256.4 bits), Expect = 2. le-69, P = 2. le-69

The following sequences are other redundant entries of Atlg65130. However, they differ from the sequences listed above by a few nucleotides. This is likely to be the result of sequencing errors or of single nucleotide polymorphisms with little or no effect on activity.

>gi|254O4528 |pir| [B 96675 hypothetical protein T23K8.4 [imported] - Arabidopsis thaliana >gi|4646196|gb|AAD26869.1|AC007230_3 Contains similarity to F13P17.8 gi|3337355 hypothetical protein from Arabidopsis thaliana BAC gb|AC004481 5. Atlg65110 from Arabidopsis (several redundant entries)

>gi|15217858|ref|NP_176690.11 hypothetical protein; protein id: Atlg65110.1 [Arabidopsis thaliana]

Score = 682 (245.1 bits), Expect = 7.4e-66, P = 7.4e-66

The following sequences are other redundant entries of Atlg65110. However, they differ from the sequences listed above by a few nucleotides. This is likely to be the result of sequencing errors or of single nucleotide polymorphisms with little or no effect on activity. >gi|25404524|pir||H96674 hypothetical protein T23K8.2 [imported] - Arabidopsis thaliana >gi|4646195|gb|AAD26868.1|AC007230_2 Contains similarity to F13P17.8 gi|3337355 hypothetical protein from Arabidopsis thaliana BAG gb|AC004481. EST gb|AA394560 comes from this gene

6. Atlg65120 from Arabidopsis (several redundant entries)

>gi|15217860|ref|NP_176691.1| hypothetical protein; protein id: Atlg65120.1 [Arabidopsis thaliana]

Score = 651 (234.2 bits), Expect = 2.6e-62, P = 2.6e-62

The following sequences are other redundant entries of Atlg65120. However, they differ from the sequences listed above by a few nucleotides. This is likely to be the result of sequencing errors or of single nucleotide polymorphisms with little or no effect on activity.

>gi|25404526|ρir||A96675 hypothetical protein T23K8.3 [imported] - Arabidopsis thaliana >gi|4646208|gb|AAD26881.1|AC007230_15 Contains similarity to F13P17.8 gi|3337355 hypothetical protein from Arabidopsis thaliana BAG gb|AC004481

7. Atlg52450 from Arabidopsis (several redundant entries)

>gi|15218999|ref|NP_175654.1| hypothetical protein; protein id: Atlg52450.1 [Arabidopsis thaliana] >gi|25405552|pir||H96564 F6D8.33 [imported] - Arabidopsis thaliana >gi|5903057|gb|AAD55616.1|AC008016_26 F6D8.33 [Arabidopsis thaliana] Score = 643 (231.4 bits), Expect = l.βe-61, P = 1.6e-61 8. Atlg65200 from Arabidopsis

>gi|15217870|ref|NP_176699.1| hypothetical protein; protein id: Atlg65200.1 [Arabidopsis thaliana]

Score = 623 (224.4 bits), Expect = 2.0e-59, P = 2.0e-59

9. Atlg52430 from Arabidopsis (several redundant entries)

>gi|15218996|ref|NP_175652.1| hypothetical protein; protein id: Atlg52430.1 [Arabidopsis thaliana] >gi|25405550|ρir||F96564 hypothetical protein F6D8.35 [imported] - Arabidopsis thaliana >gi|5903058|gb|AAD55617.1|AC008016_27 Strong similarity to F6D8.33. [Arabidopsis thaliana]

Score = 623 (224.4 bits), Expect = 2.3e-59, P = 2.3e-59

10. Atlg52430 from Arabidopsis (2 redundant entries)

>gi|15240389|ref|NP_201000.1| putative protein; protein id: At5g61940.1 [Arabidopsis thaliana]

Score = 621 (223.7 bits), Expect = 3.2e-59, P = 3.2e-59

The following sequence is another redundant entry of At5g61940. However, it differs from the sequences listed above by a few nucleotides. This is likely to be the result of sequencing errors or of single nucleotide polymorphisms with little or no effect on activity.

>gi|9758394|dbj|BAB08881.1| gb|AAD55616.1~gene_id:K22G18.7~strong similarity to unknown protein [Arabidopsis thaliana]

Closest Arabidopsis homologs:

Figure imgf000024_0001
Figure imgf000025_0001

At2g34220 is a non-secretory protein that lacks a transmembrane domain (predicted by TMHMM) and signal peptide (predicted by SignalP). At2g34220 is likely to be localized to the nucleus or to the cytoplasm (44% cytoplasmic, 40% nuclear, 8% mitochondrial by Psort2).

Pfam analysis showed that At2g34220 contains two plant specific domains (PF04780, PF04781).

Model Domain seq-f seq-t hmm-f hrnm-t score E-value

PF04781 1/1 18 144 1 126 [ ] 246.1 5.6e-71 PF04780 1/1 192 647 1 468 [ ] 866.0 1.4e-257 EXAMPLE 4

Generation of Mutated Plants with a HKH06.2 Phenotype

The invention further provides a method of identifying plants that have mutations in, or an allele of, endogenous HJO106.2 that confer a HJO106.2 phenotype, and generating progeny of these plants that also have the HIO106.2 phenotype and are not genetically modified. In one method, called 'TILLING" (for targeting induced local lesions in genomes), mutations are induced in the seed of a plant of interest, for example, using EMS treatment. The resulting plants are grown and self -fertilized, and the progeny are used to prepare DNA samples. HJO106.2-specific PCR is used to identify whether a mutated plant has a HEO106.2 mutation. Plants having HJO106.2 mutations may then be tested for the HIO106.2 phenotype, or alternatively, plants may be tested for the HJO106.2 phenotype, and then HJO106.2-specific PCR is used to determine whether a plant having the HIO 106.2 phenotype has a mutated HIO 106.2 gene. TILLING can identify mutations that may alter the expression of specific genes or the activity of proteins encoded by these genes (see Colbert et al. (2001) Plant Physiol 126:480-484; McCallum et al. (2000) Nature Biotechnology 18:455-457).

In another method, a candidate gene/Quantitative Trait Locus (QTLs) approach can be used in a marker-assisted breeding program to identify alleles of or mutations in the HJO106.2 gene or orthologs of HIO106.2 that may confer the HIO106.2 phenotype (see Foolad et al, Theor Appl Genet. (2002) 104(6-7):945-958; Rothan et al, Theor Appl

Genet (2002) 105(1): 145-159); Dekkers and Hospital, Nat Rev Genet. (2002) Jan;3(l):22- 32).

Thus, in a further aspect of the invention, a HIO106.2 nucleic acid is used to identify whether a plant having a HEO106.2 phenotype has a mutation in endogenous HIO106.2 or has a particular allele that causes the HJ.0106.2 phenotype compared to plants lacking the mutation or allele, and generating progeny of the identified plant that have inherited the EQO106.2 mutation or allele and have the HJO106.2 phenotype.

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Claims

IT IS CLAIMED:
1. A transgenic plant comprising a plant transformation vector comprising a nucleotide sequence that encodes or is complementary to a sequence that encodes a HJ0106.2 polypeptide comprising the amino acid sequence of SEQ ID NO:2, or an ortholog thereof, whereby the transgenic plant has a high oil phenotype relative to control plants.
2. The transgenic plant of claim 1, which is selected from the group consisting of rapeseed, soy, corn, sunflower, cotton, cocoa, safflower, oil palm, coconut palm, flax, castor and peanut.
3. A plant part obtained from the plant according to claim 1.
4. The plant part of claim 3, which is a seed.
5. A method of producing oil comprising growing the transgenic plant of claim 1 and recovering oil from said plant.
6. A method of producing a high oil phenotype in a plant, said method comprising: a) introducing into progenitor cells of the plant a plant transformation vector comprising a nucleotide sequence that encodes or is complementary to a sequence that encodes a HI0106.2 polypeptide comprising the amino acid sequence of SEQ ID NO:2, or an ortholog thereof, and b) growing the transformed progenitor cells to produce a transgenic plant, wherein said polynucleotide sequence is expressed, and said transgenic plant exhibits an altered oil content phenotype relative to control plants.
7. A plant obtained by a method of claim 6.
8. The plant of claim 7, which is selected from the group consisting of rapeseed, soy, corn, sunflower, cotton, cocoa, safflower, oil palm, coconut palm, flax, castor and peanut.
9. A method of generating a plant having a high oil phenotype comprising identifying a plant that has an allele in its HI0106.2 gene that results in increased oil content compared to plants lacking the allele and generating progeny of said identified plant, wherein the generated progeny inherit the allele and have the high oil phenotype.
10. The method of claim 9 that employs candidate gene/QTL methodology.
11. The method of claim 9 that employs TILLING methodology.
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