WO2004093528A2 - Génération de plantes à teneur modifiée en huile - Google Patents

Génération de plantes à teneur modifiée en huile Download PDF

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WO2004093528A2
WO2004093528A2 PCT/US2004/012070 US2004012070W WO2004093528A2 WO 2004093528 A2 WO2004093528 A2 WO 2004093528A2 US 2004012070 W US2004012070 W US 2004012070W WO 2004093528 A2 WO2004093528 A2 WO 2004093528A2
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plant
sequence
oil
plants
phenotype
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WO2004093528A3 (fr
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Jonathan Lightner
Hein Tsoeng Ng
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Agrinomics Llc
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8241—Phenotypically and genetically modified plants via recombinant DNA technology
    • C12N15/8242—Phenotypically and genetically modified plants via recombinant DNA technology with non-agronomic quality (output) traits, e.g. for industrial processing; Value added, non-agronomic traits
    • C12N15/8243—Phenotypically 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
    • C12N15/8247—Phenotypically 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
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/415—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from plants

Definitions

  • composition of crop seeds 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).
  • 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.
  • TopCross High Oil system raises harvested grain oil content in maize from -3.5% to -7%, improving the energy content of the grain.
  • 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).
  • DGAT diacylglycerol acyltransferase
  • 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-function, 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
  • 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 FfJO 105.1 polypeptide.
  • the transgenic plant is selected from the group consisting of rapeseed, soy, com, 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 HJO 105.1 polypeptide, and growing the transformed progenitor cells to produce a transgenic plant, wherein the HIO105.1 polynucleotide sequence is expressed causing the high oil phenotype.
  • vector refers to a nucleic acid construct designed for transfer between different host cells.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • “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.
  • a nucleic acid sequence 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).
  • 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.
  • mutant and wild-type refers to the form in which that trait or phenotype is found in the same variety of plant in nature.
  • 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 Tl 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.
  • 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.
  • 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.
  • 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.
  • Tl refers to the generation of plants from the seed of TO plants.
  • the Tl 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.
  • T2 refers to the generation of plants by self-fertilization of the flowers of Tl plants, previously selected as being transgenic.
  • T3 plants are generated from T2 plants, etc.
  • 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 Tl 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 Tl plant.
  • 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.
  • 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.
  • 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.
  • the enhancer element can cause up-regulation genes in the vicinity, generally within about 10 kilobase (kb) of the insertion.
  • Tl 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 Tl plants, and lipids were extracted from whole seeds.
  • Gas chromatography (GC) analysis was performed to determine fatty acid content and composition of seed samples.
  • HIO105.1 genes and/or polypeptides may be employed in the development of genetically modified plants having a modified oil content phenotype ("a HIO105.1 phenotype").
  • HIO105.1 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.
  • HIO105.1 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 HJO105.1 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.
  • Arabidopsis HIO105.1 nucleic acid (genomic DNA) sequence is provided in SEQ JD NO:l and in Genbank entry GI#18405244.
  • the corresponding protein sequence is provided in SEQ ID NO:2 and in GI#15225617.
  • Nucleic acids and/or proteins that are orthologs or paralogs of Arabidopsis HJO105.1, are described in Example 3 below.
  • HIO105.1 polypeptide refers to a full-length HJO105.1 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.
  • a functionally active HIO105.1 polypeptide causes an altered oil content phenotype when mis-expressed in a plant.
  • mis- expression of the HIO 105.1 polypeptide causes a high oil phenotype in a plant.
  • a functionally active HIO105.1 polypeptide is capable of rescuing defective (including deficient) endogenous EDO105.1 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.
  • a functionally active fragment of a full length HIO105.1 polypeptide i.e., a native polypeptide having the sequence of SEQ ID NO:2 or a naturally occurring ortholog thereof
  • a HIO105.1 fragment preferably comprises a HIO105.1 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 HJO105.1 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).
  • Functionally active variants of full-length FHO105.1 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 HIO105.1 polypeptide.
  • variants are generated that change the post-translational processing of a HIO105.1 polypeptide.
  • variants may have altered protein transport or protein localization characteristics or altered protein half-life compared to the native polypeptide.
  • HJ.O105.1 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 HIO105.1 nucleic acid of this invention may be DNA, derived from genomic DNA or cDNA, or RNA.
  • a functionally active HIO105.1 nucleic acid encodes or is complementary to a nucleic acid that encodes a functionally active HIO105.1 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 HIO105.1 polypeptide.
  • a HIO105.1 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.
  • HIO105.1 polypeptides require processing events, such as proteolytic cleavage, covalent modification, etc., in order to become fully active.
  • functionally active nucleic acids may encode the mature or the pre-processed HIO105.1 polypeptide, or an intermediate form.
  • a HIO105.1 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.
  • a functionally active HIO105.1 nucleic acid is capable of being used in the generation of loss-of-function HJO105.1 phenotypes, for instance, via antisense suppression, co-suppression, etc.
  • a HK 105.1 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 HIO105.1 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.
  • a HIO105.1 polypeptide of the invention comprises a polypeptide sequence with at least 50% or 60% identity to the HIO105.1 polypeptide sequence of SEQ ID NO:2, and may have at least 70%, 80%, 85%, 90% or 95% or more sequence identity to the FQO105.1 polypeptide sequence of SEQ ID NO:2.
  • a HIO105.1 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.
  • a HIO105.1 polypeptide comprises a polypeptide sequence with at least 50%, 60 %, 70%, 80%, or 90% identity to the polypeptide sequence of SEQ ED NO:2 over its entire length.
  • a HIO105.1 polynucleotide sequence is at least 50% to 60% identical over its entire length to the HJO105.1 nucleic acid sequence presented as SEQ ID NO:l, or nucleic acid sequences that are complementary to such a HIO105.1 sequence, and may comprise at least 70%, 80%, 85%, 90% or 95% or more sequence identity to the HIO105.1 sequence presented as SEQ ID NO:l or a functionally active fragment thereof, or complementary sequences.
  • 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)).
  • a nucleic acid molecule of the invention is capable of hybridizing to a nucleic acid molecule containing the nucleotide sequence of SEQ TO 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 NaCl, 0.015 M Na citrate; pH 7.0), 5X Denhardt's solution, 0.05% sodium pyrophosphate and 100 ⁇ g/ml herring sperm DNA; hybridization for 18-20 hours at 65° C in a solution containing 6X SSC, IX Denhardt's solution, 100 ⁇ g/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).
  • SSC single strength citrate
  • 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 ⁇ g/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.
  • 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 ⁇ g/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.
  • a number of polynucleotide sequences encoding a HIO105.1 polypeptide can be produced.
  • 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 HKD 105.1. 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.
  • 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
  • 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).
  • HJO105.1 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.
  • HIO105.1 ortholog i.e., an orthologous protein
  • 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 gtl 1, as described in Sambrook, et al, 1989.
  • candidate orthologous sequence are used as bait (the "query") for the reverse BLAST against sequences from Arabidopsis or other species in which HIO105.1 nucleic acid and/or polypeptide sequences have been identified.
  • HIO105.1 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.
  • the methods of the invention involve incorporating the desired form of the HIO105.1 nucleic acid into a plant expression vector for transformation of in plant cells, and the HIO105.1 polypeptide is expressed in the host plant.
  • An isolated HIO105.1 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 HJO105.1 nucleic acid.
  • an isolated HJO105.1 nucleic acid molecule includes HJO105.1 nucleic acid molecules contained in cells that ordinarily express HIO105.1 where, for example, the nucleic acid molecule is in a chromosomal location different from that of natural cells.
  • HJO105.1 nucleic acids and polypeptides may be used in the generation of genetically modified plants having a modified oil content phenotype.
  • 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.
  • altered expression of the HIO105.1 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 HIO105.1 gene (or an ortholog, variant or fragment thereof) may be expressed in any type of plant.
  • 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.
  • campestris sunflower (Helianthus annus), cotton (Gossypium hirsutum), com (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.
  • 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-mediated 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.
  • a heterologous nucleic acid construct comprising an HIO105.1 polynucleotide may encode the entire protein or a biologically active portion thereof.
  • binary Ti-based vector systems may be used to transfer polynucleotides. Standard Agrob ⁇ cterium binary vectors are known to those of skill in the art, and many are commercially available (e.g., pBI121 Clontech Laboratories, Palo Alto, CA).
  • Agr ⁇ b ⁇ cteri wm-mediated 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.
  • Agrob ⁇ cterium 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 ⁇ l, 1989), sunflower (Everett et ⁇ l, 1987), and soybean (Christou et ⁇ l., 1989; Kline et ⁇ l, 1987).
  • HIO105.1 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 HJO105.1 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.
  • tissue-specific promoters include the tomato E4 and E8 promoters (U.S. Patent No. 5,859,330) and the tomato 2AJJ gene promoter (Van Haaren MJJ et Z., 1993).
  • HK 105.1 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 convic ⁇ lin (Bown et al, 1988, Biochem J 251:717-26), pea lectin (dePater et al, 1993, Plant Cell 5:877-86), P.
  • 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), ⁇ c prolamin (Zhou & Fan, 1993, Transgenic Res 2:141-6), wheat prolamin (Hammond-Kosack et al, 1993, EMBO J 12:545-54), maize zew (Z4, Matzke et al, 1990, Plant Mol Biol 14:323-32), and barley B-hordeins (Entwistle et al, 1991, Plant Mol Biol 17:1217-31).
  • 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 Bio
  • 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).
  • 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).
  • 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]).
  • expression profiling 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.
  • 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.
  • 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.
  • 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.
  • the invention further provides a method of identifying plants that have mutations in endogenous HI0105.1 that confer altered oil content, and generating altered oil content progeny of these plants that are not genetically modified.
  • '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.
  • HJ0105.1- specific PCR is used to identify whether a mutated plant has a HI0105.1 mutation.
  • Plants having HI0105.1 mutations may then be tested for altered oil content, or alternatively, plants may be tested for altered oil content, and then HK)105.1-specific PCR is used to determine whether a plant having altered oil content has a mutated HI0105.1 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).
  • 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 HI0105.1 gene or orthologs of HJ.0105.1 that may confer altered oil content (see Bert et al., Theor Appl Genet. 2003 Jun;107(l): 181-9; and Lionneton et al, Genome. 2002 Dec;45(6): 1203-15).
  • a HJ.0105.1 nucleic acid is used to identify whether a plant having altered oil content has a mutation in endogenous HI0105.1 or has a particular allele that causes altered oil content.
  • CaMV 35S enhancer element Transgenic plants were selected at the Tl generation based on herbicide resistance.
  • T3 seed pools were analyzed by Near Infrared Spectroscopy (NJR) intact at time of harvest. NIR 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 NJR 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 NJR 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.
  • NJR Near Infrared Spectroscopy
  • Line W000139144 (IN045421) had a NJR determined oil content of 41.0% relative to a planting day average oil content of 37.1% (110% of PDA).
  • Line W000147756
  • Line W000139144 (IN045421) had a confirmed ACTTAG insertion on Chromosome 2 at bp 16680674.
  • Line W000147756 (IN051997) had a confirmed ACTTAG insertion on Chromosome 2 at bp 16680496.
  • ACTTAG line IN045421 there was sequence identity to nucleotides 100702-100973 on Arabidopsis clone T28M21 map CIC10A06F22O13 chromosome 2 (GI#20198304), placing the left border junction upstream from 100973 (GI#20198304). The opposite flank (predicted right border junction) of this insert was not determined. Left border of IN045421 T-DNA was ⁇ 11655 bp 3' of the translation start site. For ACTTAG line IN051997, there was sequence identity to nucleotides 100613-
  • the contigged sequence is presented as SEQ JD NO: 3.
  • the contigged sequence is presented as SEQ JD NO: 4.
  • the contigged sequence is presented as SEQ ID NO: 5.
  • At2g40040 has significant homology to proteins from plant, bacteria and animal.
  • the top 8 BLAST results for At2g40040 are listed below and are included in the "Orthologue Table.
  • CHLOROPLAST PRECURSOR DEFECTIVE CHLOROPLASTS AND LEAVES PROTEIN
  • S71749 DCL protein precursor chloroplast - tomato
  • Arabidopsis thaliana >gi
  • AA5973U comes from this gene.
  • At2g40040 is a non-secretory protein that lacks a transmembrane domain
  • At2g40040 is likely to be localized to the cytoplasm or to the nucleus (44% cytoplasmic, 36% nuclear by Psort2). Pfam analysis showed that At2g40040 has no known protein motifs. BLAST analysis described above suggests that At2g40040 shares homology to a small number of plant proteins.
  • the invention further provides a method of identifying plants that have mutations in, or an allele of, endogenous HIO105.1 that confer a HIO105.1 phenotype, and generating progeny of these plants that also have the HJO105.1 phenotype and are not genetically modified.
  • TJf JNG 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.
  • HIO 105.1 -specific PCR is used to identify whether a mutated plant has a HJO105.1 mutation.
  • Plants having HJO105.1 mutations may then be tested for the HKD105.1 phenotype, or alternatively, plants may be tested for the HJO105.1 phenotype, and then HIO 105.1 -specific PCR is used to determine whether a plant having the HJO105.1 phenotype has a mutated HJO105.1 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).
  • 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 HIO105.1 gene or orthologs of HJO105.1 that may confer the HIO105.1 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).
  • QTLs Quality of Traitative Trait Locus
  • a HIO 105.1 nucleic acid is used to identify whether a plant having a HIO105.1 phenotype has a mutation in endogenous HIO 105.1 or has a particular allele that causes the HIO 105.1 phenotype compared to plants lacking the mutation or allele, and generating progeny of the identified plant that have inherited the HIO 105.1 mutation or allele and have the HIO 105.1 phenotype.
  • Harlow E and Lane D Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory Press, 1988, New York. Harlow E and Lane D, Using Antibodies: A Laboratory Manual, Cold Spring

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Abstract

La présente invention concerne des plantes qui présentent un phénotype à teneur en huile modifiée dû à l'expression altérée d'un acide nucléique HIO105.1. Cette invention se rapporte également à des procédés de génération de plantes ayant un phénotype à teneur en huile modifiée.
PCT/US2004/012070 2003-04-22 2004-04-19 Génération de plantes à teneur modifiée en huile WO2004093528A2 (fr)

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US8034993B2 (en) 2006-11-15 2011-10-11 Dow Agrosciences Llc Generation of plants with altered protein, fiber, or oil content
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WO2006076596A2 (fr) * 2005-01-12 2006-07-20 Agrinomics Llc Production de plantes a teneur en huile modifiee
US7663020B2 (en) 2006-01-11 2010-02-16 Agrinomics Llc Generation of plants with altered oil content
US7855320B2 (en) 2006-11-15 2010-12-21 Agrigenetics Inc. Generation of plants with altered protein, fiber, or oil content
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US8106253B2 (en) 2006-11-15 2012-01-31 Agrigenetics, Inc. Generation of plants with altered protein, fiber, or oil content
US8163978B2 (en) 2006-11-15 2012-04-24 Arigenetics Inc. Generation of plants with altered protein, fiber, or oil content
US8217225B2 (en) 2006-11-15 2012-07-10 Dow Agrosciences, Llc. Generation of plants with altered protein, fiber, or oil content
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US8367892B2 (en) 2006-11-15 2013-02-05 Agrigenetics, Inc. Generation of plants with altered protein, fiber, or oil content
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US7947870B2 (en) 2006-12-15 2011-05-24 Agrigenetics, Inc. Generation of plants with altered oil, protein, or fiber content
US8921651B2 (en) 2006-12-15 2014-12-30 Agrigenetics, Inc. Generation of plants with altered oil, protein, or fiber content
US7851672B2 (en) 2006-12-15 2010-12-14 Agrinomics Llc Generation of plants with altered oil, protein, or fiber content
US7851673B2 (en) 2006-12-15 2010-12-14 Agrinomics Llc Generation of plants with altered oil, protein, or fiber content
US7790954B2 (en) 2006-12-15 2010-09-07 Agrigenetics, Inc. Generation of plants with altered oil, protein, or fiber content
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US7563943B2 (en) 2006-12-15 2009-07-21 Agrinomics Llc Generation of plants with altered oil, protein, or fiber content
US9765354B2 (en) 2006-12-15 2017-09-19 Dow Agrosciences Llc. Generation of plants with altered oil, protein, or fiber content
US10400247B2 (en) 2006-12-15 2019-09-03 Dow Agrosciences Llc Generation of plants with altered oil, protein, or fiber content
US8017830B2 (en) 2007-06-18 2011-09-13 Agrinomics, Llc Generation of plants with altered oil, protein or fiber content

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