WO2006047358A1 - Production de plantes a teneur en huile modifiee - Google Patents

Production de plantes a teneur en huile modifiee Download PDF

Info

Publication number
WO2006047358A1
WO2006047358A1 PCT/US2005/038077 US2005038077W WO2006047358A1 WO 2006047358 A1 WO2006047358 A1 WO 2006047358A1 US 2005038077 W US2005038077 W US 2005038077W WO 2006047358 A1 WO2006047358 A1 WO 2006047358A1
Authority
WO
WIPO (PCT)
Prior art keywords
plant
oil
sequence
plants
seed
Prior art date
Application number
PCT/US2005/038077
Other languages
English (en)
Other versions
WO2006047358A9 (fr
Inventor
John P. Davies
Hein Tsoeng Ng (Medard)
Jonathan Lightner
Sandra Peters
D. Ry Wagner
Original Assignee
Agrinomics Llc
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Agrinomics Llc filed Critical Agrinomics Llc
Publication of WO2006047358A1 publication Critical patent/WO2006047358A1/fr
Publication of WO2006047358A9 publication Critical patent/WO2006047358A9/fr

Links

Classifications

    • 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
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/0004—Oxidoreductases (1.)
    • C12N9/0071—Oxidoreductases (1.) acting on paired donors with incorporation of molecular oxygen (1.14)
    • 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

Definitions

  • Decreasing oil may improve the quality of isolated starch by reducing undesired flavors associated with oil oxidation.
  • increasing oil content may increase overall value.
  • feed grains such as corn and wheat
  • 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.
  • compositional alteration can provide compositional alteration and improvement of oil yield.
  • Compositional alterations include high oleic soybean and corn oil (U.S. Pat Nos 6,229,033 and 6,248,939), and laurate-containing seeds (U.S. 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, U.S. Pat. No: 5,704,160).
  • HOC High-Oil Corn
  • 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 about 3.5% to about 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.
  • T-DNA mutagenesis screens (Feldmann et ah, 1989) that detected altered fatty acid composition identified the omega 3 desaturase (FAD3) and delta- 12 desaturase (FAD2) genes (U.S. 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 HIO 123.3 polypeptide.
  • 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 invention also provides a transgenic plant cell having a high oil phenotype.
  • the transgenic plant cell comprises a transformation vector comprising a nucleotide sequence that encodes or is complementary to a sequence that encodes a High Oil (hereinafter "HIO123.3") polypeptide.
  • HIO123.3 High Oil
  • the transgenic plant cell is selected from the group consisting of rapeseed, soy, corn, sunflower, cotton, cocoa, safflower, oil palm, coconut palm, flax, castor and peanut.
  • the plant cell is a seed, pollen, propagule, or embryo cell.
  • the invention further provides feed, meal, grain, food, or seed comprising a nucleic acid sequence that encodes a HIO123.3 polypeptide.
  • the invention also provides feed, meal, grain, food, or seed comprising the HIO123.3 polypeptide, or an ortholog thereof.
  • 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 HIO123.3 polypeptide, and growing the transformed progenitor cells to produce a transgenic plant, wherein the HIO 123.3 polynucleotide sequence is expressed causing the high oil phenotype.
  • the invention provides a plant that is the direct progeny or the indirect progeny of a plant grown from said progenitor cells.
  • the invention further provides plant cells obtained from said transgenic plant.
  • the invention also provides plant cells from a plant that is the direct progeny or the indirect progeny of a plant grown from said progenitor cells.
  • the present invention also provides a container of over about 10,000, more preferably about 20,000, and even more preferably about 40,000 seeds where over about 10%, more preferably about 25%, more preferably about 50%, and even more preferably about 75% or more preferably about 90% of the seeds are seeds derived from a plant of the present invention.
  • the present invention also provides a container of over about 10 kg, more preferably about 25 kg, and even more preferably about 50 kg seeds where over about 10%, more preferably about 25%, more preferably about 50%, and even more preferably about 75% or more preferably about 90% of the seeds are seeds derived from a plant of the present invention.
  • Any of the plants or parts thereof of the present invention may be processed to produce a feed, food, meal, or oil preparation.
  • a particularly preferred plant part for this purpose is a seed, hi a preferred embodiment the feed, food, meal, or oil preparation is designed for ruminant animals.
  • Methods to produce feed, food, meal, and oil preparations are known in the art. See, for example, U.S. Patents 4,957,748; 5,100,679; 5,219,596; 5,936,069; 6,005,076; 6,146,669; and 6,156,227.
  • the meal of the present invention may be blended with other meals, hi a preferred embodiment, the meal produced from plants of the present invention or generated by a method of the present invention constitutes greater than about 0.5%, about 1%, about 5%, about 10%, about 25%, about 50%, about 75%, or about 90% by volume or weight of the meal component of any product, hi another embodiment, the meal preparation may be blended and can constitute greater than about 10%, about 25%, about 35%, about 50%, or about 75% of the blend by volume.
  • 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.
  • 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.
  • control sequence i.e. promoter or enhancer
  • 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.
  • 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.
  • mi-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).
  • 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.
  • 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.
  • 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.
  • Various methods for the introduction of a desired polynucleotide sequence encoding the desired protein into plant cells include, but are not limited to: (1) physical methods such as microinjection, electroporation, and microprojectile mediated delivery (biolistics or gene gun technology); (2) virus mediated delivery methods; and (3) Agrobacterium- mediated transformation methods.
  • Agrobacterium-mediated DNA transfer process and the biolistics or microproj ectile bombardment mediated process (i.e., the gene gun).
  • the biolistics or microproj ectile bombardment mediated process i.e., the gene gun.
  • plant plastids may be transformed utilizing a microproj ectile-mediated delivery of the desired polynucleotide.
  • Agrobacterium-mediated transformation is achieved through the use of a genetically engineered soil bacterium belonging to the genus Agrob ⁇ cterium.
  • a number of wild-type and disarmed strains of Agrob ⁇ cterium tumef ⁇ ciens and Agrob ⁇ cterium rhizogenes harboring Ti or Ri plasmids can be used for gene transfer into plants. Gene transfer is done via the transfer of a specific DNA known as "T- DNA” that can be genetically engineered to carry any desired piece of DNA into many plant species.
  • Agrobacterium-mediated genetic transformation of plants involves several steps.
  • the first step in which the virulent Agrob ⁇ cterium and plant cells are first brought into contact with each other, is generally called “inoculation”.
  • the Agrob ⁇ cterium and plant cells/tissues are permitted to be grown together for a period of several hours to several days or more under conditions suitable for growth and T-DNA transfer.
  • This step is termed "co-culture”.
  • the plant cells are treated with bactericidal or bacteriostatic agents to kill the Agrob ⁇ cterium remaining in contact with the explant and/or in the vessel containing the explant.
  • particles are coated with nucleic acids and delivered into cells by a propelling force.
  • Exemplary particles include those comprised of tungsten, platinum, and preferably, gold.
  • An illustrative embodiment of a method for delivering DNA into plant cells by acceleration is the Biolistics Particle Delivery System (BioRad, Hercules, CA), which can be used to propel particles coated with DNA or cells through a screen, such as a stainless steel or Nytex screen, onto a filter surface covered with monocot plant cells cultured in suspension.
  • Microprojectile bombardment techniques are widely applicable, and may be used to transform virtually any plant species.
  • species that have been transformed by microprojectile bombardment include monocot species such as maize (International Publication No. WO 95/06128 (Adams et al.)), barley, wheat (U.S. Patent No. 5,563,055 (Townsend et al.) incorporated herein by reference in its entirety), rice, oat, rye, sugarcane, and sorghum; as well as a number of dicots including tobacco, soybean (U.S. Patent No. 5,322,783 (Tomes et al), incorporated herein by reference in its entirety), sunflower, peanut, cotton, tomato, and legumes in general (U.S. Patent No.
  • the DNA introduced into the cell contains a gene that functions in- a regenerable plant tissue to produce a compound that confers upon the plant tissue resistance to an otherwise toxic compound.
  • Genes of interest for use as a selectable, screenable, or scorable marker would include but are not limited to GUS, green fluorescent protein (GFP), luciferase (LUX), antibiotic or herbicide tolerance genes.
  • antibiotic resistance genes include the penicillins, kanamycin (and neomycin, G418, bleomycin); methotrexate (and trimethoprim); chloramphenicol; kanamycin and tetracycline.
  • Polynucleotide molecules encoding proteins involved in herbicide tolerance are known in the art, and include, but are not limited to a polynucleotide molecule encoding 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) described in U.S. Patent No. 5,627,061 (Barry, et al), U.S. Patent No 5,633,435 (Barry, et al), and U.S.
  • EPSPS 5-enolpyruvylshikimate-3-phosphate synthase
  • Patent No 6,040,497 (Spencer, et al.) and aroA described in U.S. Patent No. 5,094,945 (Comai) for glyphosate tolerance
  • a polynucleotide molecule encoding bromoxynil nitrilase (Bxn) described in U.S. Patent No. 4,810,648 (Duerrschnabel, et al.) for Bromoxynil tolerance
  • This regeneration and growth process typically includes the steps of selecting transformed cells and culturing those individualized cells through the usual stages of embryonic development through the rooted plantlet stage. Transgenic embryos and seeds are similarly regenerated. The resulting transgenic rooted shoots are thereafter planted in an appropriate plant growth medium such as soil. Cells that survive the exposure to the selective agent, or cells that have been scored positive in a screening assay, may be cultured in media that supports regeneration of plants. Developing plantlets are transferred to soil less plant growth mix, and hardened off, prior to transfer to a greenhouse or growth chamber for maturation.
  • transformable as used herein is meant a cell or tissue that is capable of further propagation to give rise to a plant.
  • Those of skill in the art recognize that a number of plant cells or tissues are transformable in which after insertion of exogenous DNA and appropriate culture conditions the plant cells or tissues can form into a differentiated plant.
  • Tissue suitable for these purposes can include but is not limited to immature embryos, scutellar tissue, suspension cell cultures, immature inflorescence, shoot meristem, nodal explants, callus tissue, hypocotyl tissue, cotyledons, roots, and leaves.
  • Any suitable plant culture medium can be used.
  • suitable media would include but are not limited to MS-based media (Murashige and Skoog, Physiol. Plant, 15:473-497, 1962) or N6-based media (Chu et al, Scientia Sinica 18:659, 1975) supplemented with additional plant growth regulators including but not limited to auxins, cytokinins, ABA, and gibberellins.
  • auxins cytokinins
  • ABA cytokinins
  • gibberellins gibberellins.
  • tissue culture media can either be purchased as a commercial preparation, or custom prepared and modified.
  • media and media supplements such as nutrients and growth regulators for use in transformation and regeneration and other culture conditions such as light intensity during incubation, pH, and incubation temperatures that can be optimized for the particular variety of interest.
  • an expression cassette is stably incorporated in transgenic plants and confirmed to be operable, it can be introduced into other plants by sexual crossing. Any of a number of standard breeding techniques can be used, depending upon the species to be crossed.
  • ACTTAG Arabidopsis activation tagging
  • 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).
  • the enhancer element can cause up-regulation of genes in the vicinity, generally within about 10 kilobase (kb) of the enhancers. Tl plants were exposed to the selective agent in order to specifically recover transformed plants.
  • NMR Near Infrared Spectroscopy
  • HIO123.3 genes and/or polypeptides may be employed in the development of genetically modified plants having a modified oil content phenotype ("a HIO123.3 phenotype").
  • HIO123.3 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. HIO123.3 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 HIO 123.3 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 HIO123.3 nucleic acid (genomic DNA) sequence is provided in SEQ ID NO: 1 and in Genbank entry GI#30689833.
  • the corresponding protein sequence is provided in SEQ ID NO:2 and in GI#30689834.
  • Nucleic acids and/or proteins that are orthologs or paralogs of Arabidopsis HIO123.3 are described in Example 3 below.
  • HIO123.3 polypeptide refers to a full-length HIO123.3 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 HIO123.3 polypeptide causes an altered oil content phenotype when mis-expressed in a plant.
  • mis-expression of the HIO123.3 polypeptide causes a high oil phenotype in a plant.
  • a functionally active HIO 123.3 polypeptide is capable of rescuing defective (including deficient) endogenous HIO123.3 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 HIO123.3 polypeptide i.e., a native polypeptide having the sequence of SEQ ID NO:2 or a naturally occurring ortholog thereof
  • a HIO 123.3 fragment preferably comprises a HIO 123.3 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 HIO123.3 protein.
  • Functional . domains can be identified using the PFAM program (Bateman A et ah, 1999 Nucleic Acids Res 27:260-262).
  • a preferred HIO123.3 fragment comprises of one or more flavonol synthase family proteins.
  • variants of full-length HIO 123.3 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 HIO123.3 polypeptide, hi some cases, variants are generated that change the post-translational processing of a HIO123.3 polypeptide. For instance, variants may have altered protein transport or protein localization characteristics or altered protein half-life compared to the native polypeptide.
  • HIO 123.3 nucleic acid encompasses nucleic acids with the sequence provided in or complementary to the sequence provided in SEQ ID NO:1, as well as functionally active fragments, derivatives, or orthologs thereof.
  • a HIO123.3 nucleic acid of this invention may be DNA, derived from genomic DNA or cDNA, or RNA.
  • a functionally active HIO 123.3 nucleic acid encodes or is complementary to a nucleic acid that encodes a functionally active HIO 123.3 polypeptide.
  • 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 HIO123.3 polypeptide.
  • a HIO123.3 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.
  • functionally active nucleic acids may encode the mature or the pre-processed HIO123.3 polypeptide, or an intermediate form.
  • a HIO123.3 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 HIO 123.3 nucleic acid is capable of being used in the generation of loss-of-function HIO 123.3 phenotypes, for instance, via antisense suppression, co-suppression, etc.
  • a HIO 123.3 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 HIO123.3 polypeptide having at least 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95% or more sequence identity to the polypeptide sequence presented in SEQ E) NO:2.
  • a HIO 123.3 polypeptide of the invention comprises a polypeptide sequence with at least 50% or 60% identity to the HIO123.3 polypeptide sequence of SEQ E) NO:2, and may have at least 70%, 80%, 85%, 90% or 95% or more sequence identity to the HIO123.3 polypeptide sequence of SEQ E) NO:2, such as one or more flavonol synthase family proteins.
  • Pfam analysis shows that HIO123.3 is a member of the 2OG-Fe(II) oxygenase superfamily (PF03171). This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily (Aravind and Koonin (2001) Genome Biol 2:RESEARCH0007).
  • HIO123.3 is a member of the flavonol synthase family, which in turn is a member of the 2-oxoglutarate-dependent dioxygenases subfamily (Pelletier (1997) Plant Physiol. 113,1437-1445).
  • a HIO123.3 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 HIO123.3 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 flavonol synthase family proteins.
  • a HIO 123.3 polynucleotide sequence is at least 50% to
  • HIO123.3 nucleic acid sequence presented as SEQ ID NO:1 60% identical over its entire length to the HIO123.3 nucleic acid sequence presented as SEQ ID NO:1, or nucleic acid sequences that are complementary to such a HIO123.3 sequence, and may comprise at least 70%, 80%, 85%, 90% or 95% or more sequence identity to the HIO123.3 sequence presented as SEQ ID NO:1 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. MoI. Biol. (1990) 215:403-410) 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 DD NO:1.
  • 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 ID NO:1 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), hi other embodiments, moderately string
  • SSC
  • 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 HIO123.3 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 HIO 123.3. 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, hi 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.
  • Programs for multiple sequence alignment may be used to highlight conserved regions and/or residues of orthologous proteins and to generate phylogenetic trees.
  • CLUSTAL Thimpson JD et al, 1994, Nucleic Acids Res 22:4673-4680
  • 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 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 HIO123.3 coding sequence may be used as a probe. HIO123.3 ortholog nucleic acids may hybridize to the nucleic acid of SEQ ID NO: 1 under high, moderate, or low stringency conditions.
  • HIO123.3 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. 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 123.3 nucleic acid and/or polypeptide sequences have been identified.
  • HIO123.3 nucleic acids and polypeptides maybe 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 HIO 123.3 nucleic acid into a plant expression vector for transformation of plant cells, and the HIO123.3 polypeptide is expressed in the host plant.
  • An isolated HIO123.3 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 HIO 123.3 nucleic acid.
  • an isolated HIO 123.3 nucleic acid molecule includes HIO123.3 nucleic acid molecules contained in cells that ordinarily express HIO 123.3 where, for example, the nucleic acid molecule is in a chromosomal location different from that of natural cells.
  • HIO123.3 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 HIO123.3 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 HIO123.3 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), corn (Zea mays), cocoa ⁇ ieobroma cacao), safflower (Cai'thamus 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 Agrobacte ⁇ um-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 a HIO123.3 polynucleotide may encode the entire protein or a biologically active portion thereof.
  • binary Ti-based vector systems may be used to transfer polynucleotides.
  • a construct or vector may include a plant promoter to express the nucleic acid molecule of choice, hi a preferred embodiment, the promoter is a plant promoter.
  • the optimal procedure for transformation of plants with Agrobacterium vectors will vary with the type of plant being transformed.
  • Exemplary methods for Agrobacterium-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.
  • Agrobacterium 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).
  • HIO 123.3 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 are available for controlling the expression of a HIO 123.3 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 nopaline synthase (NOS) promoter (Ebert et al, Proc. Natl. Acad. Sd.
  • the octopine synthase (OCS) promoter (which is carried on tumor- inducing plasmids of Agrobacterium tumefaciens), the caulimovirus promoters such as the cauliflower mosaic virus (CaMV) 19S promoter (Lawton et al., Plant MoI. Biol. 9:315-324, 1987) and the CaMV 35S promoter (Odell et al., Nature 313:810- 812, 1985 and Jones JD et al, 1992), the melon actin promoter (published PCT application WO0056863), the figwort mosaic virus 35S-promoter (U.S.
  • Patent No. 5,378,619 the light-inducible promoter from the small subunit of ribulose-l,5-bis- phosphate carboxylase (ssRUBISCO), the Adh promoter (Walker et al., Proc. Natl. Acad. ScL (U.S.A.) 84:6624-6628, 1987), the sucrose synthase promoter (Yang et al., Proc. Natl. Acad. Sci.
  • ssRUBISCO the light-inducible promoter from the small subunit of ribulose-l,5-bis- phosphate carboxylase
  • Adh promoter Walker et al., Proc. Natl. Acad. ScL (U.S.A.) 84:6624-6628, 1987
  • sucrose synthase promoter Yamamoto et al., Proc. Natl. Acad. Sci.
  • tissue-specific promoters include the tomato E4 and E8 promoters (U.S. Patent No. 5,859,330) and the tomato 2AII gene promoter (Van Haaren MJJ et al, 1993).
  • HIO123.3 expression is under control of regulatory sequences from genes whose expression is associated with early seed and/or embryo development.
  • the promoter used is a seed-enhanced promoter. Examples of such promoters include the 5' regulatory regions from such genes as napin (Kridl et al, Seed Sci. Res. 1:209:219, 1991), globulin (Belanger and Kriz, Genet., 129: 863-872, 1991, GenBank Accession No.
  • soybean a 1 subunit of ⁇ -conglycinin (Chen et al, Proc. Natl. Acad. Sd. 83:8560- 8564, 1986), Viciafaba USP (P-Vf.Usp, SEQ ID NO: 1, 2, and 3 in (US 2003/229918) and Zea mays L3 oleosin promoter (Hong et al, Plant MoI. Biol, 34(3):549-555, 1997).
  • zeins which are a group of storage proteins found in corn endosperm. Genomic clones for zein genes have been isolated (Pedersen et al, Cell 22:1015-1026, 1982; and Russell et al, Transgenic
  • promoters from these clones including the 15 kD, 16 kD, 19 kD, 22 kD, 27 kD and genes, could also be used.
  • Other promoters known to function, for example, in corn include the promoters for the following genes: waxy, Brittle, Shrunken 2, Branching enzymes I and II, starch synthases, debranching enzymes, oleosins, glutelins and sucrose synthases.
  • Legume genes whose promoters are associated with early seed and embryo development include V.
  • 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; "GIuB-I,” Takaiwa et al, 1996, Plant MoI Biol 30:1207-21; Washida et al, 1999, Plant MoI Biol 40:1-12; "Gt3,” Leisy et al, 1990, Plant MoI Biol 14:41-50), ⁇ ceprolamin (Zhou & Fan, 1993, Transgenic Res 2:141-6), wheat prolamin (Hammond-Kosack et al, 1993, EMBO J 12:545-54), maize zein (ZA, Matzke et al, 1990, Plant MoI Biol 14:323-32), and barley B-hor deins (Entwistle et al, 1991, Plant MoI 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 MoI Biol 1993 23:671-83; Ellerstrom et al, 1996, Plant MoI Biol 32:1019-27), Brassica napus oleosin (Keddie et al, 1994, Plant MoI Biol 24:327-40), Arabidopsis oleosin (Plant et al, 1994, Plant MoI Biol 25:193-205), Arabidopsis FAEl (Rossak et al, 2001, Plant MoI Biol 46:717-25), Canavalia gladiata conA (Yamamoto et al, 1995
  • 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). Additional promoters that may be utilized are described, for example, in U.S. Patents 5,378,619; 5,391,725; 5,428,147; 5,447,858; 5,608,144; 5,608,144; 5,614,399; 5,633,441; 5,633,435; and 4,633,436.
  • 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.
  • 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 maybe 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, or an allele of, endogenous HIO123.3 that confer a HIO123.3 phenotype, and generating progeny of these plants that also have the HIO123.3 phenotype and are not genetically modified, hi 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. HIO123.3- specific PCR is used to identify whether a mutated plant has a HIO 123.3 mutation.
  • Plants having HIO123.3 mutations may then be tested for the HIO123.3 phenotype, or alternatively, plants may be tested for the HIO123.3 phenotype, and then HIO123.3-specific PCR is used to determine whether a plant having the HIO123.3 phenotype has a mutated HIO 123.3 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 HIO123.3 gene or orthologs of HIO123.3 that may confer the HIO123.3 phenotype (see Foolad et al, Theor Appl Genet. (2002) 104(6-7):945- 958; Rothan et al, Theor Appl Genet (2002) 105(l):145-159); Dekkers and Hospital, Nat Rev Genet. (2002) Jan;3(l):22-32).
  • QTLs Quality of Traitative Trait Locus
  • a HIO 123.3 nucleic acid is used to identify whether a plant having a HIO 123.3 phenotype has a mutation in endogenous HIO123.3 or has a particular allele that causes the HIO123.3 phenotype compared to plants lacking the mutation or allele, and generating progeny of the identified plant that have inherited the HIO123.3 mutation or allele and have the HIO123.3 phenotype.
  • Transgenic plants were selected at the Tl generation based on herbicide resistance.
  • T3 seed pools were analyzed by Near Infrared Spectroscopy (NIR) intact at time of harvest.
  • NIR infrared spectra were captured using a Bruker 22 N/F near infrared spectrometer.
  • Bruker Software was used to estimate total seed oil and total seed protein content using data from NIR analysis and reference methods according to the manufacturers instructions. Oil content predicting calibrations were developed following the general method of AOCS Procedure Ami -92, Official Methods and Recommended Practices of the American Oil Chemists Society, 5th Ed., AOCS, Champaign 111).
  • Line W000087875 (IN024655) had a NIR determined oil content of 39.6% relative to a flat average oil content of 35.6% (111% of Flat Average).
  • Line W000207424 (IN086963) had a NER. determined oil content of 31.8% relative to a flat average oil content of 26.0 (111 % of Flat Average).
  • Line W000087875 (IN024655) had a confirmed ACTTAG insertion on Chromosome 2 at bp 18472754.
  • Line W000207424 (IN086963) had a confirmed ACTTAG insertion on Chromosome 2 at bp 18476435.
  • ACTTAG line IN024655 there was sequence identity to nucleotides 85859 - 86191 on Arabidopsis BAC clone F16B22 chromosome 2 (GI#20197021), placing the left border junction upstream from nucleotide 86191 (GI#20197021). Left border of IN024655 T-DNA was about 1326 bp 5' of the translation start site.
  • ACTTAG line IN086963 there was sequence identity to nucleotides
  • the candidate gene At2g44800 is supported by NCBI entry gi
  • Triticum aestivum Gossypium hirsutum, Zea mays, Glycine max, Mentha x piperita, Populus tremula, Oryza sativa, Lycopersicon esculentum, Solanum tuberosum, and Beta vulgaris.
  • the contigged sequence is presented as SEQ ID NO: 4.
  • the contigged sequence is presented as SEQ ID NO: 6.
  • the contigged sequence is presented as SEQ ID NO: 7.
  • the contigged sequence is presented as SEQ ID NO: 8.
  • the contigged sequence is presented as SEQ ID NO: 9.
  • the contigged sequence is presented as SEQ ID NO: 11.
  • At4g10490 Arabidopsis > ⁇ i
  • 15235124l Length 348 BLASTP thaliana > ⁇ i
  • At2g44800 is a non-secretory protein that lacks a transmembrane domain (predicted by TMHMM (Krogh et al J MoI Biol. 2001 305:567-80)) and signal peptide (predicted by SignalP). At2g44800 is a member of the flavonol synthase family which suggests it is localized to the cytoplasm. However, Psort2 predicts an alternate cellularization of At2g44800 (40% nuclear, 28% cytoplasmic, 16% mitochondrial, 8% vacuolar by Psort2).
  • At2g44800 is a member of the 2OG-Fe(II) oxygenase superfamily (PF03171). This family contains members of the 2- oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily. At2g44800 is a member of the flavonol synthase family, which in turns, belongs to the subfamily of 2-oxoglutarate-dependent dioxygenases.
  • Flavonoids are pigmented secondary products in plants that are likely to have important function in plant reproduction by attracting pollinators and seed dispersers, protection against ultra-violet light, protection against aluminum toxicity in maize, and regulation of the polar transport of the plant hormone auxin. Alteration in expression of At2g44800 is likely to lead to changes in the quantity and quality of flavonoids in plants.
  • *seq-f refers to "sequence-from” and seq-t refers to "sequence-to.”
  • the two periods following the seq-t number indicate that the matching region was within the sequence and did not extend to either end.
  • the two brackets indicate that the match spanned the entire length of the profile HMM.
  • hmm-f and hmm-t refer to the beginning and ending coordinates of the matching portion of the profile HMM.
  • At2g44800 causes high seed oil phenotype
  • oil content in seeds from transgenic plants over-expressing this gene was compared with oil content in seeds from non-transgenic control plants.
  • Arabidopsis plants of the CoI-O ecotype were transformed by Agrobacterium mediated transformation using the floral dip method with a construct containing the coding sequences of the HIO123.3 gene (At2g44800) behind the CsVMV promoter and in front of the nos terminator or a control gene unrelated to pathogen resistance. Both of these constructs contain the nptl ⁇ gene directed by the RE4 promoter to confer kanamycin resistance in plants and serve as a selectable marker.
  • Tl seed was harvested from the transformed plants and transformants selected by germinating seed on agar medium containing kanamycin. Kanamycin resistant transformants, identified as healthy green plants, were transplanted to soil after 7 days. Control plants were germinated on agar medium without kanamycin, transplanted to soil after 7 days. Twenty-two plants containing the CsVMV::HIO123.3 transgene along with 10 CoI-O control plants were grown in the same flat in the growth room. All plants were allowed to self-fertilize and set seed.
  • phenotype T2 seed pools were analyzed by Near Infrared Spectroscopy (NTJR.) at time of harvest.
  • NTJR. Near Infrared Spectroscopy
  • infrared spectra were captured using a Bruker 22 N/F spectrometer.
  • Bruker Software was used to estimate total seed oil and total seed protein content using data from NIR analysis and reference methods according to the manufacturers instructions.
  • Oil contents predicted by our calibration (ren oil 1473 Id + sline.q2, Predicts Hexane Extracted Oil), followed the general method of AOCS Procedure AM1-92, Official Methods and Recommended Practices of the American Oil Chemists Society, 5th Ed., AOCS, Champaign, 111. Seed from transgenic plants and control plants grown in the same flat were compared and the results are presented in Table 3.
  • Transformed explants of rapeseed, soy, corn, sunflower, cotton, cocoa, safflower, oil palm, coconut palm, flax, castor and peanut are obtained through Agrobacterium tumefaciens-mediated transformation or microparticle bombardment. Plants are regenerated from transformed tissue. The greenhouse grown plants are then analyzed for the gene of interest expression levels as well as oil levels.
  • Oil levels (on a mass basis and as a percent of tissue weight) of first generation single corn kernels and dissected germ and endosperm are determined by low-resolution 1 H nuclear magnetic resonance (NMR) (Tiwari et al, JAOCS, 51:104-109 (1974); or Rubel, JAOCS, 71:1057-1062 (1994)), whereby NMR relaxation times of single kernel samples are measured, and oil levels are calculated based on regression analysis using a standard curve generated from analysis of corn kernels with varying oil levels as determined gravimetrically following accelerated solvent extraction.
  • NMR nuclear magnetic resonance
  • Oil levels and protein levels in second generation seed are determined by NIT spectroscopy, whereby NIT spectra of pooled seed samples harvested from individual plants are measured, and oil and protein levels are calculated based on regression analysis using a standard curve generated from analysis of corn kernels with varying oil or protein levels, as determined gravimetrically following accelerated solvent extraction or elemental (%N) analysis, respectively.
  • One-way analysis of variance and the Student's T-test are performed to identify significant differences in oil (% kernel weight) and protein (% kernel weight) between seed from marker positive and marker negative plants.
  • the levels of free amino acids are analyzed from each of the transgenic events using the following procedure.
  • Quantitative determination of total amino acids from corn is performed by the following method. Kernels are ground and approximately 60 mg of the resulting meal is acid-hydrolyzed using 6 N HCl under reflux at 100 0 C for 24 hrs. Samples are dried and reconstituted in 0.1 N HCl followed by precolumn derivatization with ⁇ -phthalaldehyde (OPAO for HPLC analysis. The amino acids are separated by a reverse-phase Zorbax Eclipse XDB-C 18 HPLC column on an Agilent 1100 HPLC (Agilent, Palo Alto, CA). The amino acids are detected by fluorescence.
  • Total tryptophan is measured in corn kernels using an alkaline hydrolysis method as described (Approved Methods of the American Association of Cereal Chemists -10 th edition, AACC ed, (2000) 07-20 Measurement of Tryptophan - Alakline Hydrolysis).
  • Tocopherol and tocotrienol levels in seeds are assayed by methods well- known in the art. Briefly, 10 mg of seed tissue are added to 1 g of microbeads (Biospec Product Inc, Barlesville, OK) in a sterile microfuge tube to which 500 ⁇ l 1% pyrogallol (Sigma Chemical Co., St. Louis, MO)/ethanol have been added. The mixture is shaken for 3 minutes in a mini Beadbeater (Biospec) on "fast" speed, then filtered through a 0.2 ⁇ m filter into an autosampler tube.
  • the filtered extracts are analyzed by HPLC using a Zorbax silica HPLC column (4.6 mm> ⁇ 250 mm) with a fluorescent detection, an excitation at 290 nm, an emission at 336 nm, and bandpass and slits.
  • Solvent composition and running conditions are as listed below with solvent A as hexane and solvent B as methyl-t-butyl ether.
  • the injection volume is 20 ⁇ l
  • the flow rate is 1.5 ml/minute
  • the run time is 12 minutes at 40 0 C.
  • the solvent gradient is 90% solvent A, 10% solvent B for 10 minutes; 25% solvent A, 75% solvent B for 11 minutes; and 90% solvent A, 10% solvent B for 12 minutes.
  • Tocopherol standards in 1% pyrogallol/ethanol are run for comparison ( ⁇ - tocopherol, ⁇ -tocopherol, ⁇ -tocopherol, ⁇ -tocopherol, and tocopherol (tocol)).
  • Standard curves for alpha, beta, delta, and gamma tocopherol are calculated using Chemstation software (Hewlett Packard).
  • Tocotrienol standards in 1% pyrogallol/ethanol are run for comparison ( ⁇ -tocotrienol, ⁇ - tocotrienol, ⁇ - tocotrienol, ⁇ - tocotrienol).
  • Standard curves for ⁇ -, ⁇ -, ⁇ -, and ⁇ -tocotrienol are calculated using Chemstation software (Hewlett Packard).
  • Carotenoid levels within transgenic corn kernels are determined by a standard protocol (Craft, Meth. Enzymol., 213:185-205 (1992)). Plastiquinols and phylloquinones are determined by standard protocols (Threlfall et al., Methods in Enzymology, XVIII, part C, 369-396 (1971); and Ramadan et al, Eur. Food Res. Technol, 214(6):521-527 (2002)).

Landscapes

  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Engineering & Computer Science (AREA)
  • Chemical & Material Sciences (AREA)
  • Zoology (AREA)
  • Biotechnology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Wood Science & Technology (AREA)
  • Organic Chemistry (AREA)
  • General Engineering & Computer Science (AREA)
  • Biomedical Technology (AREA)
  • Molecular Biology (AREA)
  • Microbiology (AREA)
  • Biochemistry (AREA)
  • General Health & Medical Sciences (AREA)
  • Medicinal Chemistry (AREA)
  • Oil, Petroleum & Natural Gas (AREA)
  • Nutrition Science (AREA)
  • Cell Biology (AREA)
  • Physics & Mathematics (AREA)
  • Biophysics (AREA)
  • Plant Pathology (AREA)
  • Breeding Of Plants And Reproduction By Means Of Culturing (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)

Abstract

La présente invention concerne des plantes qui présentent un phénotype de teneur en huile modifiée par suite d'une expression altérée de l'acide nucléique HIO123.3. L'invention concerne également des méthodes de production de plantes avec phénotype de teneur en huile modifié.
PCT/US2005/038077 2004-10-22 2005-10-20 Production de plantes a teneur en huile modifiee WO2006047358A1 (fr)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US62111004P 2004-10-22 2004-10-22
US60/621,110 2004-10-22

Publications (2)

Publication Number Publication Date
WO2006047358A1 true WO2006047358A1 (fr) 2006-05-04
WO2006047358A9 WO2006047358A9 (fr) 2006-06-08

Family

ID=35874421

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2005/038077 WO2006047358A1 (fr) 2004-10-22 2005-10-20 Production de plantes a teneur en huile modifiee

Country Status (1)

Country Link
WO (1) WO2006047358A1 (fr)

Cited By (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2008092505A1 (fr) * 2007-02-01 2008-08-07 Enza Zaden Beheer B.V. Plantes résistantes à la maladie
CN110540999A (zh) * 2019-08-21 2019-12-06 中国农业科学院油料作物研究所 一种转基因油菜及其产品筛查阳性质粒分子pYCSC-1905及其应用
US10501754B2 (en) 2007-02-01 2019-12-10 Enza Zaden Beheer B.V. Disease resistant potato plants
US10597675B2 (en) 2013-07-22 2020-03-24 Scienza Biotechnologies 5 B.V. Downy mildew resistance providing genes in sunflower
US10787673B2 (en) 2007-02-01 2020-09-29 Enza Zaden Beheer B.V. Disease resistant Brassica plants
US11299746B2 (en) 2014-06-18 2022-04-12 Enza Zaden Beheer B.V. Disease resistant pepper plants
US11685926B2 (en) 2007-02-01 2023-06-27 Enza Zaden Beheer B.V. Disease resistant onion plants

Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2001083697A2 (fr) * 2000-05-01 2001-11-08 Exelixis Plant Sciences, Inc. Systeme permettant de decouvrir la fonction de genes chez des plantes
WO2002010210A2 (fr) * 2001-08-28 2002-02-07 Bayer Cropscience Ag Polypeptides permettant d'identifier de nouveaux composes herbicides actifs
WO2003079766A2 (fr) * 2002-03-20 2003-10-02 Agrinomics, Llc Generation de plantes a teneur en huile alteree

Patent Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2001083697A2 (fr) * 2000-05-01 2001-11-08 Exelixis Plant Sciences, Inc. Systeme permettant de decouvrir la fonction de genes chez des plantes
WO2002010210A2 (fr) * 2001-08-28 2002-02-07 Bayer Cropscience Ag Polypeptides permettant d'identifier de nouveaux composes herbicides actifs
WO2003079766A2 (fr) * 2002-03-20 2003-10-02 Agrinomics, Llc Generation de plantes a teneur en huile alteree

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
DATABASE EMBL [online] 11 December 1997 (1997-12-11), "Arabidopsis thaliana chromosome 2 clone F16B22 map m336, complete sequence.", XP002370556, retrieved from EBI accession no. EM_PRO:AC003672 Database accession no. AC003672 *
DATABASE GENEBANK 20 August 2002 (2002-08-20), TOWN, C.D. ET AL.: "Arabidopsis thaliana chromosome 2 CHR2v07142002 genomic sequence", XP002370558, retrieved from ENTREZ Database accession no. NM_130044 *
DATABASE Geneseq [online] 31 May 2002 (2002-05-31), "Herbicidally active polypeptide SEQ ID NO 1332.", XP002370557, retrieved from EBI accession no. GSN:ABB92121 Database accession no. ABB92121 *

Cited By (13)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9994861B2 (en) 2007-02-01 2018-06-12 Enza Zaden Beheer B.V. Disease resistant grape plants
WO2008092659A1 (fr) * 2007-02-01 2008-08-07 Enza Zaden Beheer B.V. Plantes résistantes aux maladies
US8742207B2 (en) 2007-02-01 2014-06-03 Enza Zaden Beheer B.V. Disease resistant plants
US9121029B2 (en) 2007-02-01 2015-09-01 Enza Zaden Beheer B.V. Disease resistant plants
US9546373B2 (en) 2007-02-01 2017-01-17 Enza Zaden Beheer B.V. Disease resistant plants
US9932600B2 (en) 2007-02-01 2018-04-03 Enza Zaden Beheer B.V. Disease resistant tomato plants
WO2008092505A1 (fr) * 2007-02-01 2008-08-07 Enza Zaden Beheer B.V. Plantes résistantes à la maladie
US10501754B2 (en) 2007-02-01 2019-12-10 Enza Zaden Beheer B.V. Disease resistant potato plants
US10787673B2 (en) 2007-02-01 2020-09-29 Enza Zaden Beheer B.V. Disease resistant Brassica plants
US11685926B2 (en) 2007-02-01 2023-06-27 Enza Zaden Beheer B.V. Disease resistant onion plants
US10597675B2 (en) 2013-07-22 2020-03-24 Scienza Biotechnologies 5 B.V. Downy mildew resistance providing genes in sunflower
US11299746B2 (en) 2014-06-18 2022-04-12 Enza Zaden Beheer B.V. Disease resistant pepper plants
CN110540999A (zh) * 2019-08-21 2019-12-06 中国农业科学院油料作物研究所 一种转基因油菜及其产品筛查阳性质粒分子pYCSC-1905及其应用

Also Published As

Publication number Publication date
WO2006047358A9 (fr) 2006-06-08

Similar Documents

Publication Publication Date Title
US7563942B2 (en) Generation of plants with altered oil content
US20170183678A1 (en) Generation of plants with altered protein, fiber, or oil content
WO2006047358A1 (fr) Production de plantes a teneur en huile modifiee
WO2004093532A2 (fr) Generation de plantes avec un contenu en huile modifie
WO2004093528A2 (fr) Génération de plantes à teneur modifiée en huile
WO2008079545A2 (fr) Génération de plantes avec une teneur en protéines, fibres, ou huile modifiée
WO2008061156A2 (fr) Génération de végétaux à teneur modifiée en protéines, en fibres ou en huile
US7851677B2 (en) Generation of plants with altered oil content
US7745695B2 (en) Generation of plants with altered oil content
US7858846B2 (en) Generation of plants with altered oil content
WO2005103269A2 (fr) Production de plantes avec teneur en huile modifiee
US7528296B2 (en) Generation of plants with altered oil content
US7554009B2 (en) Generation of plants with altered oil content
WO2008061157A2 (fr) Génération de végétaux à teneur modifiée en protéines, en fibres ou en huile
WO2006047159A1 (fr) Creation de plantes a teneur modifiee en huile
US20090035442A1 (en) Generation of plants with altered oil, protein or fiber content
US7663020B2 (en) Generation of plants with altered oil content
WO2006076596A2 (fr) Production de plantes a teneur en huile modifiee
WO2008061159A2 (fr) Génération de plantes avec une teneur en protéines, en fibres ou en huile modifiée

Legal Events

Date Code Title Description
AK Designated states

Kind code of ref document: A1

Designated state(s): AE AG AL AM AT AU AZ BA BB BG BW BY BZ CA CH CN CO CR CU CZ DK DM DZ EC EE EG ES FI GB GD GH GM HR HU ID IL IN IS JP KE KG KP KR KZ LC LK LR LS LT LU LV LY MD MG MK MN MW MX MZ NA NG NO NZ OM PG PH PL PT RO RU SC SD SG SK SL SM SY TJ TM TN TR TT TZ UG US UZ VC VN YU ZA ZM

AL Designated countries for regional patents

Kind code of ref document: A1

Designated state(s): BW GH GM KE LS MW MZ NA SD SZ TZ UG ZM ZW AM AZ BY KG MD RU TJ TM AT BE BG CH CY DE DK EE ES FI FR GB GR HU IE IS IT LU LV MC NL PL PT RO SE SI SK TR BF BJ CF CG CI CM GA GN GQ GW MR NE SN TD TG

COP Corrected version of pamphlet

Free format text: PAGE 1, DESCRIPTION, REPLACED BY CORRECT PAGE 1

121 Ep: the epo has been informed by wipo that ep was designated in this application
NENP Non-entry into the national phase

Ref country code: DE

122 Ep: pct application non-entry in european phase

Ref document number: 05815614

Country of ref document: EP

Kind code of ref document: A1