# Patent

## Title
Generation of plants with altered protein, fiber, or oil content

## Abstract

The present invention is directed to plants that display an improved oil quantity phenotype or an improved meal quality phenotype due to altered expression of an IMQ nucleic acid. The invention is further directed to methods of generating plants with an improved oil quantity phenotype or improved meal quality phenotype.

## Background
CROSS REFERENCE TO RELATED APPLICATIONS
This application is a divisional of U.S. patent application Ser. No. 13/217,169, filed Aug. 24, 2011, now U.S. Pat. No. 8,217,224 which is a divisional of U.S. patent application Ser. No. 11/940,269, filed Nov. 14, 2007, now U.S. Pat. No. 8,030,541, issued Oct. 4, 2011, which claims the benefit of U.S. Provisional Application No. 60/866,055, filed Nov. 15, 2006, each of which is incorporated herein by reference in its entirety.


FIELD OF THE DISCLOSURE
The present disclosure is related to transgenic plants with altered oil, protein, and/or fiber content, as well as methods of making plants having altered oil, protein, and/or fiber content and producing oil from such plants.
INCORPORATION-BY-REFERENCE OF MATERIAL SUBMITTED AS AN ASCII TEXT FILE
A Sequence Listing is submitted herewith as an ASCII compliant text file named “Sequence_Listing.txt”, created on May 9, 2012, and having a size of  ̃260 kilobytes, as permitted under 37 CFR 1.821(c). The material in the aforementioned file is hereby incorporated by reference in its entirety.
BACKGROUND
The ability to manipulate the composition of crop seeds, particularly the content and composition of seed oil and protein, as well as the available metabolizable energy (“AME”) in the seed meal in livestock, has important applications in the agricultural industries, relating both to processed food oils and to animal feeds. 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 U.S. soybean crop is crushed by the soy processing industry. Soy processing yields purified oil, which is sold at high value, while the remaining seed meal is sold for livestock feed (U.S. Soybean Board, 2001 Soy Stats). Canola seed is also crushed to produce oil and the co-product canola meal (Canola Council of Canada). Canola meal contains a high percentage of protein and a good balance of amino acids but because it has a high fiber and phytate content, it is not readily digested by livestock (Slominski, B. A., et al., 1999 Proceedings of the 10th International Rapeseed Congress, Canberra, Australia) and has a lower value than soybean meal.
Over 55% of the corn produced in the U.S. is used as animal feed (Iowa Corn Growers Association). The value of the corn is directly related to its ability to be digested by livestock. Thus, it is desirable to maximize both oil content of seeds and the AME of meal. For processed oilseeds such as soy and canola, increasing the absolute oil content of the seed will increase the value of such grains, while increasing the AME of meal will increase its value. For processed corn, either an increase or a decrease in oil content may be desired, depending on how the other major constituents are to be used. Decreasing oil may improve the quality of isolated starch by reducing undesired flavors associated with oil oxidation. Alternatively, when the starch is used for ethanol production, where flavor is unimportant, increasing oil content may increase overall value.
In many feed grains, such as corn and wheat, it is desirable to increase seed oil content, because oil has higher energy content than other seed constituents such as carbohydrate. Oilseed processing, like most grain processing businesses, is a capital-intensive business; thus small shifts in the distribution of products from the low valued components to the high value oil component can have substantial economic impacts for grain processors. In addition, increasing the AME of meal by adjusting seed protein and fiber content and composition, without decreasing seed oil content, can increase the value of animal feed.
Biotechnological manipulation of oils has been shown to provide compositional alteration and improvement of oil yield. Compositional alterations include high oleic acid 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 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 content in current HOC fields has 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.
Manipulation of seed composition has identified several components that improve the nutritive quality, digestibility, and AME in seed meal. Increasing the lysine content in canola and soybean (Falco et al., 1995 Bio/Technology 13:577-582) increases the availability of this essential amino acid and decreases the need for nutritional supplements. Soybean varieties with increased seed protein were shown to contain considerably more metabolizable energy than conventional varieties (Edwards et al., 1999, Poultry Sci. 79:525-527). Decreasing the phytate content of corn seed has been shown to increase the bioavailability of amino acids in animal feeds (Douglas et al., 2000, Poultry Sci. 79:1586-1591) and decreasing oligosaccharide content in soybean meal increases the metabolizable energy in the meal (Parsons et al., 2000, Poultry Sci. 79:1127-1131).
Soybean and canola are the most obvious target crops for the processed oil and seed meal markets since both crops are crushed for oil and the remaining meal sold for animal feed. A large body of commercial work (e.g., U.S. Pat. No. 5,952,544; PCT Application No. WO9411516) demonstrates that Arabidopsis is an excellent model for oil metabolism in these crops. Biochemical screens of seed oil composition have identified Arabidopsis genes for many critical biosynthetic enzymes and have led to identification of agronomically important gene orthologs. For instance, screens using chemically mutagenized populations have identified lipid mutants whose seeds display altered fatty acid composition (Lemieux et al., 1990, Theor. Appl. Genet. 80, 234-240; James and Dooner, 1990, Theor. Appl. Genet. 80, 241-245). T-DNA mutagenesis screens (Feldmann et al., 1989, Science 243: 1351-1354) that detected altered fatty acid composition identified the omega 3 desaturase (FADS) and delta-12 desaturase (FAD2) genes (U.S. Pat. No. 5,952,544; Yadav et al., 1993, Plant Physiol. 103, 467-476; Okuley et al., 1994, Plant Cell 6(1):147-158). 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, Plant Physiol. 118:91-101).
Another screen, designed to identify enzymes involved in production of very long chain fatty acids, identified a mutation in the gene encoding a diacylglycerol acyltransferase (DGAT) as being responsible for reduced triacyl glycerol accumulation in seeds (Katavic V et al., 1995, Plant Physiol. 108(1):399-409). It was further shown that seed-specific over-expression of the DGAT cDNA was associated with increased seed oil content (Jako et al., 2001, Plant Physiol. 126(2):861-74). Arabidopsis is also a model for understanding the accumulation of seed components that affect meal quality. For example, Arabidopsis contains albumin and globulin seed storage proteins found in many dicotyledonous plants including canola and soybean (Shewry 1995, Plant Cell 7:945-956). The biochemical pathways for synthesizing components of fiber, such as cellulose and lignin, are conserved within the vascular plants, and mutants of Arabidopsis affecting these components have been isolated (reviewed in Chapel and Carpita 1998, Current Opinion in Plant Biology 1:179-185).
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, Science 258: 1350-1353; Weigel D et al., 2000, Plant Physiology, 122:1003-1013). The inserted construct provides a molecular tag for rapid identification of the native plant whose mis-expression causes the mutant phenotype. Activation tagging may also cause loss-of-function phenotypes. The insertion may result in disruption of a native plant gene, in which case the phenotype is generally recessive.
Activation tagging has been used in various species, including tobacco and Arabidopsis, to identify many different kinds of mutant phenotypes and the genes associated with these phenotypes (Wilson et al., 1996, Plant Cell 8: 659-671; Schaffer et al., 1998, Cell 93: 1219-1229; Fridborg et al., 1999, Plant Cell 11: 1019-1032; Kardailsky et al., 1999, Science 286: 1962-1965; and Christensen S et al., 1998, 9th International Conference on Arabidopsis Research, Univ. of Wisconsin-Madison, June 24-28, Abstract 165).
SUMMARY
Provided herein are transgenic plants having an Improved Seed Quality phenotype. Transgenic plants with an Improved Seed Quality phenotype may include an improved oil quantity and/or an improved meal quality. Transgenic plants with improved meal quality have an Improved Meal Quality (IMQ) phenotype and transgenic plants with improved oil quantity have an Improved Oil Quantity (IOQ) phenotype. The IMQ phenotype in a transgenic plant may include altered protein and/or fiber content in any part of the transgenic plant, for example in the seeds. The IOQ phenotype in a transgenic plant may include altered oil content in any part of the transgenic plant, for example in the seeds. In particular embodiments, a transgenic plant may include an IOQ phenotype and/or an IMQ phenotype. In some embodiments of a transgenic plant, the IMQ phenotype may be an increase in protein content in the seed and/or a decrease in the fiber content of the seed. In other embodiments of a transgenic plant, the IOQ phenotype is an increase in the oil content of the seed (a high oil phenotype). Also provided is seed meal derived from the seeds of transgenic plants, wherein the seeds have altered protein content and/or altered fiber content. Further provided is oil derived from the seeds of transgenic plants, wherein the seeds have altered oil content. Any of these changes can lead to an increase in the AME from the seed or seed meal from transgenic plants, relative to control, non-transgenic, or wild-type plants. Also provided herein is meal, feed, or food produced from any part of the transgenic plant with an IMQ phenotype and/or IOQ phenotype.
In certain embodiments, the disclosed transgenic plants comprise a transformation vector comprising an IMQ nucleotide sequence that encodes or is complementary to a sequence that encodes an “IMQ” polypeptide. In particular embodiments, expression of an IMQ polypeptide in a transgenic plant causes an altered oil content, an altered protein content, and/or an altered fiber content in the transgenic plant. In preferred embodiments, the transgenic plant is selected from the group consisting of plants of the Brassica species, including canola and rapeseed, soy, corn, sunflower, cotton, cocoa, safflower, oil palm, coconut palm, flax, castor, peanut, wheat, oat and rice. Also provided is a method of producing oil or seed meal, comprising growing the transgenic plant and recovering oil and/or seed meal from said plant. The disclosure further provides feed, meal, grain, or seed comprising a nucleic acid sequence that encodes an IMQ polypeptide. The disclosure also provides feed, meal, grain, or seed comprising the IMQ polypeptide, or an ortholog thereof.
Examples of the disclosed transgenic plant are produced by a method that comprises introducing into progenitor cells of the plant a plant transformation vector comprising an IMQ nucleotide sequence that encodes, or is complementary to a sequence that encodes, an IMQ polypeptide, and growing the transformed progenitor cells to produce a transgenic plant, wherein the IMQ polynucleotide sequence is expressed, causing an IOQ phenotype and/or and IMQ phenotype in the transgenic plant. In some specific, non-limiting examples, the method produces transgenic plants wherein expression of the IMQ polypeptide causes a high (increased) oil, high (increased) protein, and/or low (decreased) fiber phenotype in the transgenic plant, relative to control, non-transgenic, or wild-type plants.
Additional methods are disclosed herein of generating a plant having an IMQ and/or an IOQ phenotype, wherein a plant is identified that has an allele in its IMQ nucleic acid sequence that results in an IMQ phenotype and/or an IOQ phenotype, compared to plants lacking the allele. The plant can generate progeny, wherein the progeny inherit the allele and have an IMQ phenotype and/or an IOQ phenotype. In some embodiments of the method, the method employs candidate gene/QTL methodology or TILLING methodology.
Also provided herein is a transgenic plant cell having an IMQ phenotype and/or an IOQ phenotype. The transgenic plant cell comprises a transformation vector comprising an IMQ nucleotide sequence that encodes or is complementary to a sequence that encodes an IMQ polypeptide. In preferred embodiments, the transgenic plant cell is selected from the group consisting of plants of the Brassica species, including canola and rapeseed, soy, corn, sunflower, cotton, cocoa, safflower, oil palm, coconut palm, flax, castor, peanut, wheat, oat and rice. In other embodiments, the plant cell is a seed, pollen, propagule, or embryo cell. The disclosure also provides plant cells from a plant that is the direct progeny or the indirect progeny of a plant grown from said progenitor cells.


DETAILED DESCRIPTION
Terms
Unless otherwise indicated, all technical and scientific terms used herein have the same meaning as they would to one skilled in the art of the present disclosure. Practitioners are particularly directed to Sambrook et al. (Molecular Cloning: A Laboratory Manual (Second Edition), Cold Spring Harbor Press, Plainview, N.Y., 1989) and Ausubel F M et al. (Current Protocols in Molecular Biology, John Wiley & Sons, New York, N.Y., 1993) for definitions and terms of the art. It is to be understood that this disclosure is not limited to the particular methodology, protocols, and reagents described, as these may vary.
As used herein, the term “IMQ phenotype” refers to plants, or any part of a plant (for example, seeds, or meal produced from seeds), with an altered protein and/or fiber content (phenotype). As provided herein, altered protein and/or fiber content includes either an increased or decreased level of protein and/or fiber content in plants, seeds or seed meal. Any combination of these changes can lead to an IMQ phenotype. For example, in one specific non-limiting example, an IMQ phenotype can refer to increased protein and decreased fiber content. In another specific non-limiting example, an IMQ phenotype can refer to unchanged protein and decreased fiber content. In yet another specific non-limiting example, an IMQ phenotype can refer to increased protein and unchanged fiber content. It is also provided that any combination of these changes can lead to an increase in the AME (available metabolizable energy) from the seed or meal generated from the seed. An IMQ phenotype also includes an improved seed quality (ISQ) phenotype or an improved seed meal quality phenotype.
As used herein, the term “IOQ phenotype” refers to plants, or any part of a plant (for example, seeds), with an altered oil content (phenotype). As provided herein, altered oil content includes an increased, for example a high, oil content in plants or seeds. In some embodiments, a transgenic plant can express both an IOQ phenotype and an IMQ phenotype. In specific, non-limiting examples, a transgenic plant having a combination of an IOQ phenotype and an IMQ phenotype can lead to an increase in the AME (available metabolizable energy) from the seed or meal generated from the seed. An IOQ phenotype also includes an improved seed quality (ISQ) phenotype.
As used herein, the term “available metabolizable energy” (AME) refers to the amount of energy in the feed that is able to be extracted by digestion in an animal and is correlated with the amount of digestible protein and oil available in animal meal. AME is determined by estimating the amount of energy in the feed prior to feeding and measuring the amount of energy in the excreta of the animal following consumption of the feed. In one specific, non-limiting example, a transgenic plant with an increase in AME includes transgenic plants with altered seed protein and/or fiber content and without a decrease in seed oil content (seed oil content remains unchanged or is increased), resulting in an increase in the value of animal feed derived from the seed.
As used herein, the term “content” refers to the type and relative amount of, for instance, a seed or seed meal component.
As used herein, the term “fiber” refers to non-digestible components of the plant seed including cellular components such as cellulose, hemicellulose, pectin, lignin, and phenolics.
As used herein, the term “meal” refers to seed components remaining following the extraction of oil from the seed. Examples of components of meal include protein and fiber.
As used herein, the term “vector” refers to a nucleic acid construct designed for transfer between different host cells. An “expression vector” refers to a vector that has the ability to incorporate and express heterologous DNA fragments in a foreign cell. Many prokaryotic and eukaryotic expression vectors are commercially available. Selection of appropriate expression vectors is within the knowledge of those having skill in the art.
A “heterologous” nucleic acid construct or sequence has a portion of the sequence that is not native to the plant cell in which it is expressed. Heterologous, with respect to a control sequence refers to a control sequence (i.e. promoter or enhancer) that does not function in nature to regulate the same gene the expression of which it is currently regulating. Generally, heterologous nucleic acid sequences are not endogenous to the cell or part of the genome in which they are present, and have been added to the cell by infection, transfection, microinjection, electroporation, or the like. A “heterologous” nucleic acid construct may contain a control sequence/DNA coding sequence combination that is the same as, or different from, a control sequence/DNA coding sequence combination found in the native plant. Specific, non-limiting examples of a heterologous nucleic acid sequence include an IMQ nucleic acid sequence, or a fragment, derivative (variant), or ortholog thereof.
As used herein, the term “gene” means the segment of DNA involved in producing a polypeptide chain, which may or may not include regions preceding and following the coding region, e.g. 5′ untranslated (5′ UTR) or “leader” sequences and 3′ UTR or “trailer” sequences, as well as intervening sequences (introns) between individual coding segments (exons) and non-transcribed regulatory sequences.
As used herein, “recombinant” includes reference to a cell or vector, that has been modified by the introduction of a heterologous nucleic acid sequence or that the cell is derived from a cell so modified. Thus, for example, recombinant cells express genes that are not found in identical form within the native (non-recombinant) form of the cell or express native genes that are otherwise abnormally expressed, under expressed, or not expressed at all as a result of deliberate human intervention.
As used herein, the term “gene expression” refers to the process by which a polypeptide is produced based on the nucleic acid sequence of a gene. The process includes both transcription and translation; accordingly, “expression” may refer to either a polynucleotide or polypeptide sequence, or both. Sometimes, expression of a polynucleotide sequence will not lead to protein translation. “Over-expression” refers to increased expression of a polynucleotide and/or polypeptide sequence relative to its expression in a wild-type (or other reference [e.g., non-transgenic]) plant and may relate to a naturally-occurring or non-naturally occurring sequence. “Ectopic expression” refers to expression at a time, place, and/or increased level that does not naturally occur in the non-altered or wild-type plant. “Under-expression” refers to decreased expression of a polynucleotide and/or polypeptide sequence, generally of an endogenous gene, relative to its expression in a wild-type plant. The terms “mis-expression” and “altered expression” encompass over-expression, under-expression, and ectopic expression.
The term “introduced” in the context of inserting a nucleic acid sequence into a cell, includes “transfection,” “transformation,” and “transduction” and includes reference to the incorporation of a nucleic acid sequence into a eukaryotic or prokaryotic cell where the nucleic acid sequence may be incorporated into the genome of the cell (for example, chromosome, plasmid, plastid, or mitochondrial DNA), converted into an autonomous replicon, or transiently expressed (for example, transfected mRNA).
As used herein, a “plant cell” refers to any cell derived from a plant, including cells from undifferentiated tissue (e.g., callus), as well as from plant seeds, pollen, propagules, and embryos.
As used herein, the terms “native” and “wild-type” relative to a given plant trait or phenotype refers to the form in which that trait or phenotype is found in the same variety of plant in nature. In one embodiment, a wild-type plant is also a control plant. In another embodiment, a wild-type plant is a non-transgenic plant.
As used herein, the term “modified” regarding a plant trait, refers to a change in the phenotype of a transgenic plant (for example, a transgenic plant with any combination of an altered oil content, an altered protein content, and/or an altered fiber content) in any part of the transgenic plant, for example the seeds, relative to a similar non-transgenic plant. As used herein, the term “altered” refers to either an increase or a decrease of a plant trait or phenotype (for example, oil content, protein content, and/or fiber content) in a transgenic plant, relative to a similar non-transgenic plant. In one specific, non-limiting example, a transgenic plant with a modified trait includes a plant with an increased oil content, increased protein content, and/or decreased fiber content relative to a similar non-transgenic plant. In another specific, non-limiting example, a transgenic plant with a modified trait includes unchanged oil content, increased protein content, and/or decreased fiber content relative to a similar non-transgenic plant. In yet another specific, non-limiting example, a transgenic plant with a modified trait includes an increased oil content, increased protein content, and/or unchanged fiber content relative to a similar non-transgenic plant. Specific, non-limiting examples of a change in phenotype include an IMQ phenotype or an IOQ phenotype.
An “interesting phenotype (trait)” with reference to a transgenic plant refers to an observable or measurable phenotype demonstrated by a T1 and/or subsequent generation plant, which is not displayed by the corresponding non-transgenic plant (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 (for example, increased oil content, increased protein content, and/or decreased fiber content in seeds of 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 phenotype or quality. Such transgenic plants may have an improved phenotype, such as an IMQ phenotype or an IOQ phenotype.
The phrase “altered oil content phenotype” refers to a measurable phenotype of a genetically modified (transgenic) 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 (non-transgenic) plant. A high oil phenotype refers to an increase in overall oil content. The phrase “altered protein content phenotype” refers to measurable phenotype of a genetically modified plant, where the plant displays a statistically significant increase or decrease in overall protein content (i.e., the percentage of seed mass that is protein), as compared to the similar, but non-modified plant. A high protein phenotype refers to an increase in overall protein content. The phrase “altered fiber content phenotype” refers to measurable phenotype of a genetically modified plant, where the plant displays a statistically significant increase or decrease in overall fiber content (i.e., the percentage of seed mass that is fiber), as compared to the similar, but non-modified plant. A low fiber phenotype refers to decrease in overall fiber content.
As used herein, a “mutant” polynucleotide sequence or gene differs from the corresponding wild-type polynucleotide sequence or gene either in terms of sequence or expression, where the difference contributes to a modified or altered plant phenotype or trait. Relative to a plant or plant line, the term “mutant” refers to a plant or plant line which has a modified or altered plant phenotype or trait, where the modified or altered phenotype or trait is associated with the modified or altered expression of a wild-type polynucleotide sequence or gene.
As used herein, the term “T1” refers to the generation of plants from the seed of TO plants. The T1 generation is the first set of transformed plants that can be selected by application of a selection agent, e.g., an antibiotic or herbicide, for which the transgenic plant contains the corresponding resistance gene. The term “T2” refers to the generation of plants by self-fertilization of the flowers of T1 plants, previously selected as being transgenic. T3 plants are generated from T2 plants, etc. As used herein, the “direct progeny” of a given plant derives from the seed (or, sometimes, other tissue) of that plant and is in the immediately subsequent generation; for instance, for a given lineage, a T2 plant is the direct progeny of a T1 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 T1 plant.
As used herein, the term “plant part” includes any plant organ or tissue, including, without limitation, seeds, embryos, meristematic regions, callus tissue, leaves, roots, shoots, gametophytes, sporophytes, pollen, and microspores. Plant cells can be obtained from any plant organ or tissue and cultures prepared therefrom. Provided herein is a transgenic plant cell having an IMQ phenotype and/or an IOQ phenotype. The transgenic plant cell comprises a transformation vector comprising an IMQ nucleotide sequence that encodes or is complementary to a sequence that encodes an IMQ polypeptide. In preferred embodiments, the transgenic plant cell is selected from the group consisting of plants of the Brassica species, including canola and rapeseed, soy, corn, sunflower, cotton, cocoa, safflower, oil palm, coconut palm, flax, castor, peanut, wheat, oat and rice. In other embodiments, the plant cell is a seed, pollen, propagule, or embryo cell. The disclosure 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 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 monocotyledonous and dicotyledonous plants.
As used herein, “transgenic plant” includes a plant that comprises within its genome a heterologous polynucleotide. The heterologous polynucleotide can be either stably integrated into the genome, or can be extra-chromosomal. Preferably, the polynucleotide of the present invention is stably integrated into the genome such that the polynucleotide is passed on to successive generations. A plant cell, tissue, organ, or plant into which the heterologous polynucleotides have been introduced is considered “transformed,” “transfected,” or “transgenic.” Direct and indirect progeny of transformed plants or plant cells that also contain the heterologous polynucleotide are also considered transgenic.
Disclosed herein are transgenic plants having an Improved Seed Quality phenotype. Transgenic plants with an Improved Seed Quality phenotype may include an improved oil quantity and/or an improved meal quality. Transgenic plants with improved meal quality have an IMQ phenotype and transgenic plants with improved oil quantity have an IOQ phenotype. The IMQ phenotype in a transgenic plant may include altered protein and/or fiber content in any part of the transgenic plant, for example in the seeds. The IOQ phenotype in a transgenic plant may include altered oil content in any part of the transgenic plant, for example in the seeds. In particular embodiments, a transgenic plant may include an IOQ phenotype and/or an IMQ phenotype. In some embodiments of a transgenic plant, the IMQ phenotype may be an increase in protein content in the seed and/or a decrease in the fiber content of the seed. In other embodiments of a transgenic plant, the IOQ phenotype is an increase in the oil content of the seed (a high oil phenotype). Also provided is seed meal derived from the seeds of transgenic plants, wherein the seeds have altered protein content and/or altered fiber content. Further provided is oil derived from the seeds of transgenic plants, wherein the seeds have altered oil content. Any of these changes can lead to an increase in the AME from the seed or seed meal from transgenic plants, relative to control, non-transgenic, or wild-type plants. Also provided herein is meal, feed, or food produced from any part of the transgenic plant with an IMQ phenotype and/or IOQ phenotype.
In certain embodiments, the disclosed transgenic plants comprise a transformation vector comprising an IMQ nucleotide sequence that encodes or is complementary to a sequence that encodes an “IMQ” polypeptide. In particular embodiments, expression of an IMQ polypeptide in a transgenic plant causes an altered oil content, an altered protein content, and/or an altered fiber content in the transgenic plant. In preferred embodiments, the transgenic plant is selected from the group consisting of plants of the Brassica species, including canola and rapeseed, soy, corn, sunflower, cotton, cocoa, safflower, oil palm, coconut palm, flax, castor, peanut, wheat, oat and rice. Also provided is a method of producing oil or seed meal, comprising growing the transgenic plant and recovering oil and/or seed meal from said plant. The disclosure further provides feed, meal, grain, or seed comprising a nucleic acid sequence that encodes an IMQ polypeptide. The disclosure also provides feed, meal, grain, or seed comprising the IMQ polypeptide, or an ortholog thereof.
Various methods for the introduction of a desired polynucleotide sequence encoding the desired protein into plant cells are available and known to those of skill in the art and 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 (see, for example, WO 2007/053482 and WO 2005/107437, which are incorporated herein by reference in their entirety).
The most commonly used methods for transformation of plant cells are the Agrobacterium-mediated DNA transfer process and the biolistics or microprojectile bombardment mediated process (i.e., the gene gun). Typically, nuclear transformation is desired but where it is desirable to specifically transform plastids, such as chloroplasts or amyloplasts, plant plastids may be transformed utilizing a microprojectile-mediated delivery of the desired polynucleotide.
Agrobacterium-mediated transformation is achieved through the use of a genetically engineered soil bacterium belonging to the genus Agrobacterium. A number of wild-type and disarmed strains of Agrobacterium tumefaciens and Agrobacterium 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 Agrobacterium and plant cells are first brought into contact with each other, is generally called “inoculation.” Following the inoculation, the Agrobacterium 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.” Following co-culture and T-DNA delivery, the plant cells are treated with bactericidal or bacteriostatic agents to kill the Agrobacterium remaining in contact with the explant and/or in the vessel containing the explant. If this is done in the absence of any selective agents to promote preferential growth of transgenic versus non-transgenic plant cells, then this is typically referred to as the “delay” step. If done in the presence of selective pressure favoring transgenic plant cells, then it is referred to as a “selection” step. When a “delay” is used, it is typically followed by one or more “selection” steps.
With respect to microprojectile bombardment (U.S. Pat. No. 5,550,318; U.S. Pat. No. 5,538,880, U.S. Pat. No. 5,610,042; and PCT Publication WO 95/06128; each of which is specifically incorporated herein by reference in its entirety), 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, Calif.), 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. Examples of species that have been transformed by microprojectile bombardment include monocot species such as maize (PCT Publication No. WO 95/06128), barley, wheat (U.S. Pat. No. 5,563,055, 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. Pat. No. 5,322,783, incorporated herein by reference in its entirety), sunflower, peanut, cotton, tomato, and legumes in general (U.S. Pat. No. 5,563,055, incorporated herein by reference in its entirety).
To select or score for transformed plant cells regardless of transformation methodology, 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. Examples of antibiotic resistance genes include the penicillins, kanamycin (and neomycin, G418, bleomycin), methotrexate (and trimethoprim), chloramphenicol, 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. Pat. No. 5,627,061, U.S. Pat. No. 5,633,435, and U.S. Pat. No. 6,040,497 and aroA described in U.S. Pat. No. 5,094,945 for glyphosate tolerance; a polynucleotide molecule encoding bromoxynil nitrilase (Bxn) described in U.S. Pat. No. 4,810,648 for Bromoxynil tolerance; a polynucleotide molecule encoding phytoene desaturase (crtI) described in Misawa et al. (Plant J. 4:833-840, 1993) and Misawa et al. (Plant J. 6:481-489, 1994) for norflurazon tolerance; a polynucleotide molecule encoding acetohydroxyacid synthase (AHAS, also known as ALS) described in Sathasiivan et al. (Nucl. Acids Res. 18:2188-2193, 1990) for tolerance to sulfonylurea herbicides; and the bar gene described in DeBlock et al. (EMBO J. 6:2513-2519, 1987) for glufosinate and bialaphos tolerance.
The regeneration, development, and cultivation of plants from various transformed explants are well documented in the art. 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.
The present invention can be used with any transformable cell or tissue. By 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. Examples of 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. Those of skill in the art are familiar with the variety of tissue culture media, which when supplemented appropriately, support plant tissue growth and development and are suitable for plant transformation and regeneration. These tissue culture media can either be purchased as a commercial preparation, or custom prepared and modified. Those of skill in the art are aware that 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.
One of ordinary skill will appreciate that, after 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.
Identification of Plants with an Improved Oil Quantity Phenotype and/or Improved Meal Quality Phenotype
An Arabidopsis activation tagging screen (ACTTAG) was used to identify the association between 1) ACTTAG plant lines with an altered protein, fiber and/or oil content (phenotype, for example, see columns 4, 5 and 6, respectively, of Table 1, below) and 2) the nucleic acid sequences identified in column 3 of Tables 2 and 3, wherein each nucleic acid sequence is provided with a gene alias or an IMQ designation (IMQ#; see column 1 in Tables 1, 2, and 3). Briefly, and as further described in the Examples, a large number of Arabidopsis plants were mutated with the pSKI015 vector, which comprises a T-DNA from the Ti plasmid of Agrobacterium tumefaciens, a viral enhancer element, and a selectable marker gene (Weigel et al., 2000, Plant Physiology, 122:1003-1013). When the T-DNA inserts into the genome of transformed plants, the enhancer element can cause up-regulation of genes in the vicinity, generally within about nine kilobases (kb) of the enhancers. T1 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. T1 plants were allowed to grow to maturity, self-fertilize and produce seed. T2 seed was harvested, labeled and stored. To amplify the seed stocks, about eighteen T2 were sown in soil and, after germination, exposed to the selective agent to recover transformed T2 plants. T3 seed from these plants was harvested and pooled. Oil, protein and fiber content of the seed were estimated using Near Infrared Spectroscopy (NIR) as described in the Examples.
Quantitative determination of fatty acid (FA) content (column 7, Table 1) in T2 seeds was performed using the following methods. A sample of 15 to 20 T2 seeds from each line tested. This sample generally contained plants with homozygous insertions, no insertions, and hemizygous insertions in a standard 1:1:2 ratios. The seed sample was massed on UMT-2 ultra-microbalance (Mettler-Toledo Co., Ohio, USA) and then transferred to a glass extraction vial. Lipids were extracted from the seeds and trans-esterified in 500 μl 2.5% H2SO4 in MeOH for 3 hours at 80° C., following the method of Browse et al. (Biochem J 235:25-31, 1986) with modifications. A known amount of heptadecanoic acid was included in the reaction as an internal standard. 750 μl of water and 400 μl of hexane were added to each vial, which was then shaken vigorously and allowed to phase separate. Reaction vials were loaded directly onto gas chromatography (GC) for analysis and the upper hexane phase was sampled by the autosampler. Gas chromatography with Flame Ionization detection was used to separate and quantify the fatty acid methyl esters. Agilent 6890 Plus GC's were used for separation with Agilent Innowax columns (30 m×0.25 mm ID, 250 um film thickness). The carrier gas was Hydrogen at a constant flow of 2.5 ml/minute. 1 μl of sample was injected in splitless mode (inlet temperature 220° C., Purge flow 15 ml/min at 1 minute). The oven was programmed for an initial temperature of 105° C., initial time 0.5 minutes, followed by a ramp of 60° C. per minute to 175° C., a 40° C./minute ramp to 260° C. with a final hold time of 2 minutes. Detection was by Flame Ionization (Temperature 275° C., Fuel flow 30.0 ml/min, Oxidizer 400.0 ml/min). Instrument control and data collection and analysis were monitored using the Millennium Chromatography Management System (Version 3.2, Waters Corporation, Milford, Mass.). Peaks were initially identified by comparison with standards. Integration and quantification were performed automatically, but all analyses were subsequently examined manually to verify correct peak identification and acceptable signal to noise ratio before inclusion of the derived results in the study.
The association of an IMQ nucleic acid sequence with an IMQ phenotype or an IOQ phenotype was discovered by analysis of the genomic DNA sequence flanking the T-DNA insertion in the ACTTAG line identified in column 3 of Table 1. An ACTTAG line is a family of plants derived from a single plant that was transformed with a T-DNA element containing four tandem copies of the CaMV 35S enhancers. Accordingly, the disclosed IMQ nucleic acid sequences and/or polypeptides may be employed in the development of transgenic plants having an improved seed quality phenotype, including an IMQ phenotype and/or an IOQ phenotype. IMQ nucleic acid sequences may be used in the generation of transgenic plants, such as oilseed crops, that provide improved oil yield from oilseed processing and result in an increase in the quantity of oil recovered from seeds of the transgenic plant. IMQ nucleic acid sequences may also be used in the generation of transgenic plants, such as feed grain crops, that provide an IMQ phenotype resulting in increased energy for animal feeding, for example, seeds or seed meal with an altered protein and/or fiber content, resulting in an increase in AME. IMQ nucleic acid sequences may further be used to increase the oil content of specialty oil crops, in order to augment yield and/or recovery of desired unusual fatty acids. Transgenic plants that have been genetically modified to express IMQ polypeptides can be used in the production of seeds, wherein the transgenic plants are grown, and oil and seed meal are obtained from plant parts (e.g. seed) using standard methods.
IMO Nucleic Acids and Polypeptides
The IMQ designation for each of the IMQ nucleic acid sequences discovered in the activation tagging screen described herein are listed in column 1 of Tables 1-3, below. The disclosed IMQ polypeptides are listed in column 5 of Table 2 and column 4 of Table 3. As used herein, the term “IMQ polypeptide” refers to any polypeptide that when expressed in a plant causes an IMQ phenotype and/or an IOQ phenotype in any part of the plant, for example the seeds. In one embodiment, an IMQ polypeptide refers to a full-length IMQ protein, or a fragment, derivative (variant), or ortholog thereof that is “functionally active,” such that the protein fragment, derivative, or ortholog exhibits one or more or the functional activities associated with one or more of the disclosed full-length IMQ polypeptides, for example, the amino acid sequences provided in the GenBank entry referenced in column 5 of Table 2, which correspond to the amino acid sequences set forth as SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO: 20, SEQ ID NO: 22, SEQ ID NO: 24, SEQ ID NO: 26, SEQ ID NO: 28, SEQ ID NO: 30, SEQ ID NO: 32, SEQ ID NO: 34, SEQ ID NO: 36, SEQ ID NO: 38, SEQ ID NO: 40, SEQ ID NO: 42, SEQ ID NO: 44, SEQ ID NO: 46, SEQ ID NO: 48, SEQ ID NO: 50, SEQ ID NO: 52, SEQ ID NO: 54, SEQ ID NO: 56, SEQ ID NO: 58, SEQ ID NO: 60, SEQ ID NO: 62, SEQ ID NO: 64, SEQ ID NO: 66, SEQ ID NO: 68, SEQ ID NO: 70, SEQ ID NO: 72, SEQ ID NO: 74, SEQ ID NO: 76, SEQ ID NO: 78, SEQ ID NO: 80, SEQ ID NO: 82, SEQ ID NO: 84, SEQ ID NO: 86, SEQ ID NO: 88, SEQ ID NO: 90, SEQ ID NO: 92, SEQ ID NO: 94, SEQ ID NO: 96, SEQ ID NO: 98, or SEQ ID NO: 100, or an ortholog thereof. In one preferred embodiment, a functionally active IMQ polypeptide causes an IMQ phenotype and/or an IOQ phenotype in a transgenic plant. In another embodiment, a functionally active IMQ polypeptide causes an altered oil, protein, and/or fiber content phenotype (for example, an altered seed meal content phenotype) when mis-expressed in a plant. In other preferred embodiments, mis-expression of the IMQ polypeptide causes a high oil (such as, increased oil), high protein (such as, increased protein), and/or low fiber (such as, decreased fiber) phenotype in a plant. In another embodiment, mis-expression of the IMQ polypeptide causes an improved AME of meal. In yet another embodiment, a functionally active IMQ polypeptide can rescue defective (including deficient) endogenous IMQ activity when expressed in a plant or in plant cells; the rescuing polypeptide may be from the same or from a different species as the species with the defective polypeptide activity. The disclosure also provides feed, meal, grain, food, or seed comprising the IMQ polypeptide, or a fragment, derivative (variant), or ortholog thereof.
In another embodiment, a functionally active fragment of a full length IMQ polypeptide (for example, a functionally active fragment of a native polypeptide having the amino acid sequence set forth as SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO: 20, SEQ ID NO: 22, SEQ ID NO: 24, SEQ ID NO: 26, SEQ ID NO: 28, SEQ ID NO: 30, SEQ ID NO: 32, SEQ ID NO: 34, SEQ ID NO: 36, SEQ ID NO: 38, SEQ ID NO: 40, SEQ ID NO: 42, SEQ ID NO: 44, SEQ ID NO: 46, SEQ ID NO: 48, SEQ ID NO: 50, SEQ ID NO: 52, SEQ ID NO: 54, SEQ ID NO: 56, SEQ ID NO: 58, SEQ ID NO: 60, SEQ ID NO: 62, SEQ ID NO: 64, SEQ ID NO: 66, SEQ ID NO: 68, SEQ ID NO: 70, SEQ ID NO: 72, SEQ ID NO: 74, SEQ ID NO: 76, SEQ ID NO: 78, SEQ ID NO: 80, SEQ ID NO: 82, SEQ ID NO: 84, SEQ ID NO: 86, SEQ ID NO: 88, SEQ ID NO: 90, SEQ ID NO: 92, SEQ ID NO: 94, SEQ ID NO: 96, SEQ ID NO: 98, or SEQ ID NO: 100, or a naturally occurring ortholog thereof) retains one or more of the biological properties associated with the full-length IMQ polypeptide, such as signaling activity, binding activity, catalytic activity, or cellular or extra-cellular localizing activity. An IMQ fragment preferably comprises an IMQ 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 an IMQ protein. Functional domains of IMQ genes are listed in column 8 of Table 2 and can be identified using the PFAM program (Bateman A et al., 1999, Nucleic Acids Res. 27:260-262) or INTERPRO (Mulder et al., 2003, Nucleic Acids Res. 31, 315-318) program. Functionally active variants of full-length IMQ 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 IMQ polypeptide. In some cases, variants are generated that change the post-translational processing of an IMQ polypeptide. For instance, variants may have altered protein transport or protein localization characteristics, or altered protein half-life, compared to the native polypeptide.
As used herein, the term “IMQ nucleic acid” refers to any polynucleotide that when expressed in a plant causes an IMQ phenotype and/or an IOQ phenotype in any part of the plant, for example the seeds. In one embodiment, an IMQ polynucleotide encompasses nucleic acids with the sequence provided in or complementary to the GenBank entry referenced in column 3 of Table 2, which correspond to nucleic acid sequences set forth as SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 9, SEQ ID NO: 11, SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 19, SEQ ID NO: 21, SEQ ID NO: 23, SEQ ID NO: 25, SEQ ID NO: 27, SEQ ID NO: 29, SEQ ID NO: 31, SEQ ID NO: 33, SEQ ID NO: 35, SEQ ID NO: 37, SEQ ID NO: 39, SEQ ID NO: 41, SEQ ID NO: 43, SEQ ID NO: 45, SEQ ID NO: 47, SEQ ID NO: 49, SEQ ID NO: 51, SEQ ID NO: 53, SEQ ID NO: 55, SEQ ID NO: 57, SEQ ID NO: 59, SEQ ID NO: 61, SEQ ID NO: 63, SEQ ID NO: 65, SEQ ID NO: 67, SEQ ID NO: 69, SEQ ID NO: 71, SEQ ID NO: 73 SEQ ID NO: 75, SEQ ID NO: 77, SEQ ID NO: 79, SEQ ID NO: 81, SEQ ID NO: 83, SEQ ID NO: 85, SEQ ID NO: 87, SEQ ID NO: 89, SEQ ID NO: 91, SEQ ID NO: 93, SEQ ID NO: 95, SEQ ID NO: 97, or SEQ ID NO: 99, as well as functionally active fragments, derivatives, or orthologs thereof. An IMQ nucleic acid of this disclosure may be DNA, derived from genomic DNA or cDNA, or RNA. Genomic sequences of the genes listed in Table 2 are known and available in public databases such as GenBank.
In one embodiment, a functionally active IMQ nucleic acid encodes or is complementary to a nucleic acid that encodes a functionally active IMQ polypeptide. A functionally active IMQ nucleic acid also includes 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 IMQ polypeptide. An IMQ nucleic acid can include other non-coding sequences, which may or may not be transcribed; such sequences include 5′ and 3′ UTRs, polyadenylation signals and regulatory sequences that control gene expression, among others, as are known in the art. Some polypeptides require processing events, such as proteolytic cleavage, covalent modification, etc., in order to become fully active. Accordingly, functionally active nucleic acids may encode the mature or the pre-processed IMQ polypeptide, or an intermediate form. An IMQ polynucleotide can also include heterologous coding sequences, for example, sequences that encode a marker included to facilitate the purification of the fused polypeptide, or a transformation marker. In another embodiment, a functionally active IMQ nucleic acid is capable of being used in the generation of loss-of-function IMQ phenotypes, for instance, via antisense suppression, co-suppression, etc. The disclosure also provides feed, meal, grain, food, or seed comprising a nucleic acid sequence that encodes an IMQ polypeptide.
In one preferred embodiment, an IMQ nucleic acid used in the disclosed methods comprises a nucleic acid sequence that encodes, or is complementary to a sequence that encodes, an IMQ polypeptide having at least 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity to a disclosed IMQ polypeptide sequence, for example the amino acid sequence set forth as SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO: 20, SEQ ID NO: 22, SEQ ID NO: 24, SEQ ID NO: 26, SEQ ID NO: 28, SEQ ID NO: 30, SEQ ID NO: 32, SEQ ID NO: 34, SEQ ID NO: 36, SEQ ID NO: 38, SEQ ID NO: 40, SEQ ID NO: 42, SEQ ID NO: 44, SEQ ID NO: 46, SEQ ID NO: 48, SEQ ID NO: 50, SEQ ID NO: 52, SEQ ID NO: 54, SEQ ID NO: 56, SEQ ID NO: 58, SEQ ID NO: 60, SEQ ID NO: 62, SEQ ID NO: 64, SEQ ID NO: 66, SEQ ID NO: 68, SEQ ID NO: 70, SEQ ID NO: 72, SEQ ID NO: 74, SEQ ID NO: 76, SEQ ID NO: 78, SEQ ID NO: 80, SEQ ID NO: 82, SEQ ID NO: 84, SEQ ID NO: 86, SEQ ID NO: 88, SEQ ID NO: 90, SEQ ID NO: 92, SEQ ID NO: 94, SEQ ID NO: 96, SEQ ID NO: 98, or SEQ ID NO: 100.
In another embodiment, an IMQ polypeptide comprises a polypeptide sequence with at least 50% or 60% identity to a disclosed IMQ polypeptide sequence (for example, the amino acid sequence set forth as SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO: 20, SEQ ID NO: 22, SEQ ID NO: 24, SEQ ID NO: 26, SEQ ID NO: 28, SEQ ID NO: 30, SEQ ID NO: 32, SEQ ID NO: 34, SEQ ID NO: 36, SEQ ID NO: 38, SEQ ID NO: 40, SEQ ID NO: 42, SEQ ID NO: 44, SEQ ID NO: 46, SEQ ID NO: 48, SEQ ID NO: 50, SEQ ID NO: 52, SEQ ID NO: 54, SEQ ID NO: 56, SEQ ID NO: 58, SEQ ID NO: 60, SEQ ID NO: 62, SEQ ID NO: 64, SEQ ID NO: 66, SEQ ID NO: 68, SEQ ID NO: 70, SEQ ID NO: 72, SEQ ID NO: 74, SEQ ID NO: 76, SEQ ID NO: 78, SEQ ID NO: 80, SEQ ID NO: 82, SEQ ID NO: 84, SEQ ID NO: 86, SEQ ID NO: 88, SEQ ID NO: 90, SEQ ID NO: 92, SEQ ID NO: 94, SEQ ID NO: 96, SEQ ID NO: 98, or SEQ ID NO: 100) and may have at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity to a disclosed IMQ polypeptide sequence. In a further embodiment, an IMQ polypeptide comprises 50%, 60%, 70%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity to a disclosed IMQ polypeptide sequence, and may include a conserved protein domain of the IMQ polypeptide (such as the protein domain(s) listed in column 8 of Table 2). In another embodiment, an IMQ polypeptide comprises a polypeptide sequence with at least 50%, 60%, 70%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity to a functionally active fragment of the polypeptide referenced in column 5 of Table 2. In yet another embodiment, an IMQ polypeptide comprises a polypeptide sequence with at least 50%, 60%, 70%, 80%, 90%, 95%, 97%, 98%, or 99% identity to the polypeptide sequence of the GenBank entry referenced in column 5 of Table 2 over its entire length and comprises a conserved protein domain(s) listed in column 8 of Table 2.
In another aspect, an IMQ polynucleotide sequence is at least 50% to 60% identical over its entire length to a disclosed IMQ nucleic acid sequence, such as the nucleic acid sequence set forth as SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 9, SEQ ID NO: 11, SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 19, SEQ ID NO: 21, SEQ ID NO: 23, SEQ ID NO: 25, SEQ ID NO: 27, SEQ ID NO: 29, SEQ ID NO: 31, SEQ ID NO: 33, SEQ ID NO: 35, SEQ ID NO: 37, SEQ ID NO: 39, SEQ ID NO: 41, SEQ ID NO: 43, SEQ ID NO: 45, SEQ ID NO: 47, SEQ ID NO: 49, SEQ ID NO: 51, SEQ ID NO: 53, SEQ ID NO: 55, SEQ ID NO: 57, SEQ ID NO: 59, SEQ ID NO: 61, SEQ ID NO: 63, SEQ ID NO: 65, SEQ ID NO: 67, SEQ ID NO: 69, SEQ ID NO: 71, SEQ ID NO: 73 SEQ ID NO: 75, SEQ ID NO: 77, SEQ ID NO: 79, SEQ ID NO: 81, SEQ ID NO: 83, SEQ ID NO: 85, SEQ ID NO: 87, SEQ ID NO: 89, SEQ ID NO: 91, SEQ ID NO: 93, SEQ ID NO: 95, SEQ ID NO: 97, or SEQ ID NO: 99, or nucleic acid sequences that are complementary to such an IMQ sequence, and may comprise at least 70%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity to the disclosed IMQ sequence, or a functionally active fragment thereof, or complementary sequences. In another embodiment, a disclosed IMQ nucleic acid comprises a nucleic acid sequence as shown in SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 9, SEQ ID NO: 11, SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 19, SEQ ID NO: 21, SEQ ID NO: 23, SEQ ID NO: 25, SEQ ID NO: 27, SEQ ID NO: 29, SEQ ID NO: 31, SEQ ID NO: 33, SEQ ID NO: 35, SEQ ID NO: 37, SEQ ID NO: 39, SEQ ID NO: 41, SEQ ID NO: 43, SEQ ID NO: 45, SEQ ID NO: 47, SEQ ID NO: 49, SEQ ID NO: 51, SEQ ID NO: 53, SEQ ID NO: 55, SEQ ID NO: 57, SEQ ID NO: 59, SEQ ID NO: 61, SEQ ID NO: 63, SEQ ID NO: 65, SEQ ID NO: 67, SEQ ID NO: 69, SEQ ID NO: 71, SEQ ID NO: 73 SEQ ID NO: 75, SEQ ID NO: 77, SEQ ID NO: 79, SEQ ID NO: 81, SEQ ID NO: 83, SEQ ID NO: 85, SEQ ID NO: 87, SEQ ID NO: 89, SEQ ID NO: 91, SEQ ID NO: 93, SEQ ID NO: 95, SEQ ID NO: 97, or SEQ ID NO: 99, or nucleic acid sequences that are complementary to such an IMQ sequence, and nucleic acid sequences that have substantial sequence homology to a such IMQ sequences. As used herein, the phrase “substantial sequence homology” refers to those nucleic acid sequences that have slight or inconsequential sequence variations from such IMQ sequences, i.e., the sequences function in substantially the same manner and encode an IMQ polypeptide.
As used herein, “percent (%) sequence identity” with respect to a specified subject sequence, or a specified portion thereof, is defined as the percentage of nucleotides or amino acids in an identified 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-2.0a19 (Altschul et al., J. Mol. 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 “percent (%) 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 performing 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 disclosed IMQ nucleic acid sequences (for example, the nucleic acid sequence set forth as SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 9, SEQ ID NO: 11, SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 19, SEQ ID NO: 21, SEQ ID NO: 23, SEQ ID NO: 25, SEQ ID NO: 27, SEQ ID NO: 29, SEQ ID NO: 31, SEQ ID NO: 33, SEQ ID NO: 35, SEQ ID NO: 37, SEQ ID NO: 39, SEQ ID NO: 41, SEQ ID NO: 43, SEQ ID NO: 45, SEQ ID NO: 47, SEQ ID NO: 49, SEQ ID NO: 51, SEQ ID NO: 53, SEQ ID NO: 55, SEQ ID NO: 57, SEQ ID NO: 59, SEQ ID NO: 61, SEQ ID NO: 63, SEQ ID NO: 65, SEQ ID NO: 67, SEQ ID NO: 69, SEQ ID NO: 71, SEQ ID NO: 73 SEQ ID NO: 75, SEQ ID NO: 77, SEQ ID NO: 79, SEQ ID NO: 81, SEQ ID NO: 83, SEQ ID NO: 85, SEQ ID NO: 87, SEQ ID NO: 89, SEQ ID NO: 91, SEQ ID NO: 93, SEQ ID NO: 95, SEQ ID NO: 97, or SEQ ID NO: 99). 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., 1989, Molecular Cloning: A Laboratory Manual (Second Edition), Cold Spring Harbor Press, Plainview, N.Y.).
In some embodiments, a nucleic acid molecule of the disclosure is capable of hybridizing to a nucleic acid molecule containing the disclosed nucleotide sequence under stringent hybridization conditions that are: prehybridization of filters containing nucleic acid for 8 hours to overnight at 65° C. in a solution comprising 6× single strength citrate (SSC) (1×SSC is 0.15 M NaCl, 0.015 M Na citrate; pH 7.0), 5×Denhardt's solution, 0.05% sodium pyrophosphate and 100 μg/ml herring sperm DNA; hybridization for 18-20 hours at 65° C. in a solution containing 6×SSC, 1×Denhardt's solution, 100 μg/ml yeast tRNA and 0.05% sodium pyrophosphate; and washing of filters at 65° C. for 1 h in a solution containing 0.1×SSC and 0.1% SDS (sodium dodecyl sulfate). In other embodiments, moderately stringent hybridization conditions are used that are: pretreatment of filters containing nucleic acid for 6 h at 40° C. in a solution containing 35% formamide, 5×SSC, 50 mM Tris-HCl (pH 7.5), 5 mM EDTA, 0.1% PVP, 0.1% Ficoll, 1% BSA, and 500 μg/ml denatured salmon sperm DNA; hybridization for 18-20 h at 40° C. in a solution containing 35% formamide, 5×SSC, 50 mM Tris-HCl (pH 7.5), 5 mM EDTA, 0.02% PVP, 0.02% Ficoll, 0.2% BSA, 100 μg/ml salmon sperm DNA, and 10% (wt/vol) dextran sulfate; followed by washing twice for 1 hour at 55° C. in a solution containing 2×SSC and 0.1% SDS. Alternatively, low stringency conditions can be used that comprise: incubation for 8 hours to overnight at 37° C. in a solution comprising 20% formamide, 5×SSC, 50 mM sodium phosphate (pH 7.6), 5×Denhardt's solution, 10% dextran sulfate, and 20 μg/ml denatured sheared salmon sperm DNA; hybridization in the same buffer for 18 to 20 hours; and washing of filters in 1×SSC at about 37° C. for 1 hour.
As a result of the degeneracy of the genetic code, a number of polynucleotide sequences encoding an IMQ polypeptide can be produced. For example, codons may be selected to increase the rate at which expression of the polypeptide occurs in a particular host species, in accordance with the optimum codon usage dictated by the particular host organism (see, e.g., Nakamura et al., 1999, Nucleic Acids Res. 27:292). Such sequence variants may be used in the methods disclosed herein.
The disclosed methods may use orthologs of a disclosed Arabidopsis IMQ nucleic acid sequence. Representative putative orthologs of each of the disclosed Arabidopsis IMQ genes are identified in column 3 of Table 3, below. Methods of identifying the orthologs in other plant species are known in the art. In general, 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 M A and Bork P, 1998, Proc. Natl. Acad. Sci., 95:5849-5856; Huynen M A et al., 2000, Genome Research, 10:1204-1210).
Programs for multiple sequence alignment, such as CLUSTAL (Thompson J D et al., 1994, Nucleic Acids Res. 22:4673-4680) may be used to highlight conserved regions and/or residues of orthologous proteins and to generate phylogenetic trees. In a phylogenetic tree representing multiple homologous sequences from diverse species (e.g., retrieved through BLAST analysis), orthologous sequences from two species generally appear closest on the tree with respect to all other sequences from these two species. Structural threading or other analysis of protein folding (e.g., using software by ProCeryon, Biosciences, Salzburg, Austria) may also identify potential orthologs. Nucleic acid hybridization methods may also be used to find orthologous genes and are preferred when sequence data are not available. Degenerate PCR and screening of cDNA or genomic DNA libraries are common methods for finding related gene sequences and are well known in the art (see, e.g., Sambrook, 1989, Molecular Cloning: A Laboratory Manual (Second Edition), Cold Spring Harbor Press, Plainview, N.Y.; Dieffenbach and Dveksler, 1995, PCR Primer: A Laboratory Manual, Cold Spring Harbor Laboratory Press, NY). 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 IMQ coding sequence may be used as a probe. IMQ ortholog nucleic acids may hybridize to the nucleic acid of SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 9, SEQ ID NO: 11, SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 19, SEQ ID NO: 21, SEQ ID NO: 23, SEQ ID NO: 25, SEQ ID NO: 27, SEQ ID NO: 29, SEQ ID NO: 31, SEQ ID NO: 33, SEQ ID NO: 35, SEQ ID NO: 37, SEQ ID NO: 39, SEQ ID NO: 41, SEQ ID NO: 43, SEQ ID NO: 45, SEQ ID NO: 47, SEQ ID NO: 49, SEQ ID NO: 51, SEQ ID NO: 53, SEQ ID NO: 55, SEQ ID NO: 57, SEQ ID NO: 59, SEQ ID NO: 61, SEQ ID NO: 63, SEQ ID NO: 65, SEQ ID NO: 67, SEQ ID NO: 69, SEQ ID NO: 71, SEQ ID NO: 73 SEQ ID NO: 75, SEQ ID NO: 77, SEQ ID NO: 79, SEQ ID NO: 81, SEQ ID NO: 83, SEQ ID NO: 85, SEQ ID NO: 87, SEQ ID NO: 89, SEQ ID NO: 91, SEQ ID NO: 93, SEQ ID NO: 95, SEQ ID NO: 97, or SEQ ID NO: 99 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 DNA clone.
Alternatively, it is possible to initiate an EST project to generate a database of sequence information for the plant species of interest. In another approach, antibodies that specifically bind known IMQ polypeptides are used for ortholog isolation (see, e.g., Harlow and Lane, 1988, 1999, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory Press, New York). Western blot analysis can determine that an IMQ ortholog (i.e., a protein orthologous to a disclosed IMQ polypeptide) is present in a crude extract of a particular plant species. When reactivity is observed, the sequence encoding the candidate ortholog may be isolated by screening expression libraries representing the particular plant species. Expression libraries can be constructed in a variety of commercially available vectors, including lambda gt11, 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 IMQ nucleic acid and/or polypeptide sequences have been identified.
IMQ 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 T A et al., 1991, Methods Enzymol. 204:125-39), may be used to introduce desired changes into a cloned nucleic acid.
In general, the methods disclosed herein involve incorporating the desired form of the IMQ nucleic acid into a plant expression vector for transformation of plant cells, and the IMQ polypeptide is expressed in the host plant. Transformed plants and plant cells expressing an IMQ polypeptide express an IMQ phenotype and/or an IOQ phenotype and, in one specific, non-limiting example, may have high (increased) oil, high (increased) protein, and/or low (decreased) fiber content.
An “isolated” IMQ 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 IMQ nucleic acid. However, an isolated IMQ nucleic acid molecule includes IMQ nucleic acid molecules contained in cells that ordinarily express IMQ where, for example, the nucleic acid molecule is in a chromosomal location different from that of natural cells.
Generation of Genetically Modified Plants with an Improved Oil Quantity Phenotype and/or an Improved Meal Quality Phenotype
The disclosed IMQ nucleic acids and polypeptides may be used in the generation of transgenic plants having a modified or altered oil, protein, and/or fiber content phenotype. As used herein, an “altered oil content (phenotype)” may refer to altered oil content in any part of the plant. In a preferred embodiment, altered expression of the IMQ gene in a plant is used to generate plants with a high oil content (phenotype). As used herein, an “altered protein content (phenotype)” may refer to altered protein content in any part of the plant. In a preferred embodiment, altered expression of the IMQ gene in a plant is used to generate plants with a high (or increased) protein content (phenotype). As used herein, an “altered fiber content (phenotype)” may refer to altered fiber content in any part of the plant. In a preferred embodiment, altered expression of the IMQ gene in a plant is used to generate plants with a low (or decreased) fiber content (phenotype). The altered oil, protein, and/or fiber content is often observed in seeds. Examples of a transgenic plant include plants comprising a plant transformation vector with a nucleotide sequence that encodes or is complementary to a sequence that encodes an IMQ polypeptide having the amino acid sequence as set forth in SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO: 20, SEQ ID NO: 22, SEQ ID NO: 24, SEQ ID NO: 26, SEQ ID NO: 28, SEQ ID NO: 30, SEQ ID NO: 32, SEQ ID NO: 34, SEQ ID NO: 36, SEQ ID NO: 38, SEQ ID NO: 40, SEQ ID NO: 42, SEQ ID NO: 44, SEQ ID NO: 46, SEQ ID NO: 48, SEQ ID NO: 50, SEQ ID NO: 52, SEQ ID NO: 54, SEQ ID NO: 56, SEQ ID NO: 58, SEQ ID NO: 60, SEQ ID NO: 62, SEQ ID NO: 64, SEQ ID NO: 66, SEQ ID NO: 68, SEQ ID NO: 70, SEQ ID NO: 72, SEQ ID NO: 74, SEQ ID NO: 76, SEQ ID NO: 78, SEQ ID NO: 80, SEQ ID NO: 82, SEQ ID NO: 84, SEQ ID NO: 86, SEQ ID NO: 88, SEQ ID NO: 90, SEQ ID NO: 92, SEQ ID NO: 94, SEQ ID NO: 96, SEQ ID NO: 98, or SEQ ID NO: 100, or an ortholog thereof.
Transgenic plants, such as corn, soybean and canola containing the disclosed nucleic acid sequences, can be used in the production of vegetable oil and meal. Vegetable oil is used in a variety of food products, while meal from seed is used as an animal feed. After harvesting seed from transgenic plants, the seed is cleaned to remove plant stalks and other material and then flaked in roller mills to break the hulls. The crushed seed is heated to 75-100° C. to denature hydrolytic enzymes, lyse the unbroken oil containing cells, and allow small oil droplets to coalesce. Most of the oil is then removed (and can be recovered) by pressing the seed material in a screw press. The remaining oil is removed from the presscake by extraction with and organic solvents, such as hexane. The solvent is removed from the meal by heating it to approximately 100° C. After drying, the meal is then granulated to a consistent form. The meal, containing the protein, digestible carbohydrate, and fiber of the seed, may be mixed with other materials prior to being used as an animal feed.
The methods described herein for generating transgenic plants are generally applicable to all plants. Although activation tagging and gene identification is carried out in Arabidopsis, the IMQ nucleic acid sequence (or an ortholog, variant or fragment thereof) may be expressed in any type of plant. In a preferred embodiment, oil-producing plants 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 (Theobroma cacao), safflower (Carthamus tinctorius), oil palm (Elaeis guineensis), coconut palm (Cocos nucifera), flax (Linum usitatissimum), castor (Ricinus communis), and peanut (Arachis hypogaea), as well as wheat, rice and oat. 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 may also be a source of unique fatty acids. In other embodiments, any plant expressing the IMQ nucleic acid sequence can also express increased protein and/or decreased fiber content in a specific plant part or organ, such as in seeds.
The skilled artisan will recognize that a wide variety of transformation techniques exist in the art, and new techniques are continually becoming available. Any technique that is suitable for the target host plant can be employed within the scope of the present invention. For example, the constructs can be introduced in a variety of forms including, but not limited to, as a strand of DNA, in a plasmid, or in an artificial chromosome. The introduction of the constructs into the target plant cells can be accomplished by a variety of techniques, including, but not limited to, Agrobacterium-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. Depending upon the intended use, a heterologous nucleic acid construct comprising an IMQ polynucleotide may encode the entire protein or a biologically active portion thereof.
In one embodiment, binary Ti-based vector systems may be used to transfer polynucleotides. Standard Agrobacterium binary vectors are known to those of skill in the art, and many are commercially available (e.g., pBI121 Clontech Laboratories, Palo Alto, Calif.). A construct or vector may include a plant promoter to express the nucleic acid molecule of choice. In 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 plants of the Brassica species, including canola and rapeseed, (De Block et al., 1989, Plant Physiol., 91:694-701), sunflower (Everett et al., 1987, Bio/Technology, 5:1201), soybean (Christou et al., 1989, Proc. Natl. Acad. Sci USA, 86:7500-7504; Kline et al., 1987, Nature, 327:70), wheat, rice and oat.
Expression (including transcription and translation) of an IMQ nucleic acid sequence 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 an IMQ 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. Pat. Nos. 5,783,393 and 5,783,394), the nopaline synthase (NOS) promoter (Ebert et al., Proc. Natl. Acad. Sci. (U.S.A.) 84:5745-5749, 1987), 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 Mol. Biol. 9:315-324, 1987) and the CaMV 35S promoter (Odell et al., Nature 313:810-812, 1985 and Jones J D et al, 1992, Transgenic Res., 1:285-297), the figwort mosaic virus 35S-promoter (U.S. Pat. No. 5,378,619), the light-inducible promoter from the small subunit of ribulose-1,5-bis-phosphate carboxylase (ssRUBISCO), the Adh promoter (Walker et al., Proc. Natl. Acad. Sci. (U.S.A.) 84:6624-6628, 1987), the sucrose synthase promoter (Yang et al., Proc. Natl. Acad. Sci. (U.S.A.) 87:4144-4148, 1990), the R gene complex promoter (Chandler et al., The Plant Cell 1:1175-1183, 1989), the chlorophyll a/b binding protein gene promoter, the CsVMV promoter (Verdaguer B et al., 1998, Plant Mol Biol., 37:1055-1067), and the melon actin promoter (published PCT application WO0056863). Exemplary tissue-specific promoters include the tomato E4 and E8 promoters (U.S. Pat. No. 5,859,330) and the tomato 2AII gene promoter (Van Haaren M J J et al., 1993, Plant Mol Bio., 21:625-640).
In one preferred embodiment, expression of the IMQ nucleic acid sequence is under control of regulatory sequences from genes whose expression is associated with early seed and/or embryo development. Indeed, in a preferred embodiment, 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. L22295), gamma zein Z 27 (Lopes et al., Mol Gen Genet., 247:603-613, 1995), L3 oleosin promoter (U.S. Pat. No. 6,433,252), phaseolin (Bustos et al., Plant Cell, 1(9):839-853, 1989), arcelin5 (U.S. Application No. 2003/0046727), a soybean 7S promoter, a 7Sα promoter (U.S. Application No. 2003/0093828), the soybean 7Sα′ beta conglycinin promoter, a 7S α′ promoter (Beachy et al., EMBO J., 4:3047, 1985; Schuler et al., Nucleic Acid Res., 10(24):8225-8244, 1982), soybean trypsin inhibitor (Riggs et al., Plant Cell 1(6):609-621, 1989), ACP (Baerson et al., Plant Mol. Biol., 22(2):255-267, 1993), stearoyl-ACP desaturase (Slocombe et al., Plant Physiol. 104(4):167-176, 1994), soybean a′ subunit of β-conglycinin (Chen et al., Proc. Natl. Acad. Sci. 83:8560-8564, 1986), Vicia faba USP (P-Vf.Usp, SEQ ID NO: 1, 2, and 3 in (U.S. Application No. 2003/229918) and Zea mays L3 oleosin promoter (Hong et al., Plant Mol. Biol., 34(3):549-555, 1997). Also included are the zeins, which are a group of storage proteins found in corn endosperm. Genomic clones for zein genes have been isolated (Pedersen et al., Cell, 29:1015-1026, 1982; and Russell et al., Transgenic Res. 6(2):157-168) and the 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. faba legumin (Baumlein et al., 1991, Mol. Gen. Genet. 225:121-8; Baumlein et al., 1992, Plant J. 2:233-9), V. faba usp (Fiedler et al., 1993, Plant Mol. Biol. 22:669-79), pea convicilin (Bown et al., 1988, Biochem. J. 251:717-26), pea lectin (dePater et al., 1993, Plant Cell 5:877-86), P. vulgaris beta phaseolin (Bustos et al., 1991, EMBO J. 10:1469-79), P. vulgaris DLEC2 and PHS [beta] (Bobb et al., 1997, Nucleic Acids Res. 25:641-7), and soybean beta-Conglycinin, 7S storage protein (Chamberland et al., 1992, Plant Mol. Biol. 19:937-49).
Cereal genes whose promoters are associated with early seed and embryo development include rice glutelin (“GluA-3,” Yoshihara and Takaiwa, 1996, Plant Cell Physiol. 37:107-11; “GluB-1,” Takaiwa et al., 1996, Plant Mol. Biol. 30:1207-21; Washida et al., 1999, Plant Mol. Biol. 40:1-12; “Gt3,” Leisy et al., 1990, Plant Mol. Biol. 14:41-50), rice prolamin (Zhou & Fan, 1993, Transgenic Res. 2:141-6), wheat prolamin (Hammond-Kosack et al., 1993, EMBO J. 12:545-54), maize zein (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).
Other genes whose promoters are associated with early seed and embryo development include oil palm GLO7A (7S globulin, Morcillo et al., 2001, Physiol. Plant 112:233-243), Brassica napus napin, 2S storage protein, and napA gene (Josefsson et al., 1987, J. Biol. Chem. 262:12196-201; Stalberg et al., 1993, Plant Mol. Biol. 1993 23:671-83; Ellerstrom et al., 1996, Plant Mol. Biol. 32:1019-27), Brassica napus oleosin (Keddie et al., 1994, Plant Mol. Biol. 24:327-40), Arabidopsis oleosin (Plant et al., 1994, Plant Mol. Biol. 25:193-205), Arabidopsis FAE1 (Rossak et al., 2001, Plant Mol. Biol. 46:717-25), Canavalia gladiata conA (Yamamoto et al., 1995, Plant Mol. Biol. 27:729-41), and Catharanthus roseus strictosidine synthase (Str, Ouwerkerk and Memelink, 1999, Mol. Gen. Genet. 261:635-43). In another preferred embodiment, regulatory sequences from genes expressed during oil biosynthesis are used (see, e.g., U.S. 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. Pat. Nos. 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.
In yet another aspect, in some cases it may be desirable to inhibit the expression of the endogenous IMQ nucleic acid sequence in a host cell. Exemplary methods for practicing this aspect of the invention include, but are not limited to antisense suppression (Smith, et al., 1988, Nature, 334:724-726; van der Krol et al., 1988, BioTechniques, 6:958-976); co-suppression (Napoli, et al., 1990, Plant Cell, 2:279-289); ribozymes (PCT Publication WO 97/10328); and combinations of sense and antisense (Waterhouse, et al., 1998, Proc. Natl. Acad. Sci. USA, 95:13959-13964). 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, Proc. Natl. Acad. Sci. USA, 85:8805-8809), a partial cDNA sequence including fragments of 5′ coding sequence, (Cannon et al., 1990, Plant Mol. Biol., 15:39-47), or 3′ non-coding sequences (Ch'ng et al., 1989, Proc. Natl. Acad. Sci. USA, 86:10006-10010). Cosuppression techniques may use the entire cDNA sequence (Napoli et al., 1990, Plant Cell, 2:279-289; van der Krol et al., 1990, Plant Cell, 2:291-299), or a partial cDNA sequence (Smith et al., 1990, Mol. Gen. Genetics, 224:477-481).
Standard molecular and genetic tests may be performed to further analyze the association between a nucleic acid sequence and an observed phenotype. Exemplary techniques are described below.
1. DNA/RNA Analysis
The stage- and tissue-specific gene expression patterns in mutant versus wild-type lines may be determined, for instance, by in situ hybridization. Analysis of the methylation status of the gene, especially flanking regulatory regions, may be performed. Other suitable techniques include over-expression, 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, Arch. Virol. Suppl. 15:189-201).
In a preferred application expression profiling, generally by microarray analysis, is used to simultaneously measure differences or induced changes in the expression of many different genes. Techniques for microarray analysis are well known in the art (Schena M et al., Science 1995 270:467-470; Baldwin D et al., 1999, Cur. Opin. Plant Biol. 2(2):96-103; Dangond F, Physiol Genomics (2000) 2:53-58; van Hal N L 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 over-expression of the gene of interest, which may help to place an unknown gene in a particular pathway.
2. Gene Product Analysis
Analysis of gene products may include recombinant protein expression, antisera production, immunolocalization, biochemical assays for catalytic or other activity, analysis of phosphorylation status, and analysis of interaction with other proteins via yeast two-hybrid assays.
3. Pathway Analysis
Pathway analysis may include placing a gene or gene product within a particular biochemical, metabolic or signaling pathway based on its mis-expression phenotype or by sequence homology with related genes. Alternatively, analysis may comprise genetic crosses with wild-type lines and other mutant lines (creating double mutants) to order the gene in a pathway, or determining the effect of a mutation on expression of downstream “reporter” genes in a pathway.
Generation of Mutated Plants with an Improved Oil Quantity Phenotype and/or Improved Meal Quality Phenotype
Additional methods are disclosed herein of generating a plant having an IMQ and/or an IOQ phenotype, wherein a plant is identified that has an allele in its IMQ nucleic acid sequence that results in an IMQ phenotype and/or an IOQ phenotype, compared to plants lacking the allele. The plant can generate progeny, wherein the progeny inherit the allele and have an IMQ phenotype and/or an IOQ phenotype. For example, provided herein is a method of identifying plants that have mutations in the endogenous IMQ nucleic acid sequence that confer an IMQ phenotype and/or an IOQ phenotype and generating progeny of these plants with an IMQ and/or IOQ phenotype that are not genetically modified. In some embodiments, the plants have an IMQ phenotype with an altered protein and/or fiber content or seed meal content, or an IOQ phenotype, with an altered oil content.
In one method, called “TILLING” (for targeting induced local lesions in genomes), mutations are induced in the seed of a plant of interest, for example, using EMS (ethylmethane sulfonate) treatment. The resulting plants are grown and self-fertilized, and the progeny are used to prepare DNA samples. PCR amplification and sequencing of the IMQ nucleic acid sequence is used to identify whether a mutated plant has a mutation in the IMQ nucleic acid sequence. Plants having IMQ mutations may then be tested for altered oil, protein, and/or fiber content, or alternatively, plants may be tested for altered oil, protein, and/or fiber content, and then PCR amplification and sequencing of the IMQ nucleic acid sequence is used to determine whether a plant having altered oil, protein, and/or fiber content has a mutated IMQ nucleic acid sequence. TILLING can identify mutations that may alter the expression of specific genes or the activity of proteins encoded by these genes (see Colbert et al., 2001, Plant Physiol. 126:480-484; McCallum et al., 2000, Nature Biotechnology 18:455-457).
In another method, a candidate gene/Quantitative Trait Locus (QTLs) approach can be used in a marker-assisted breeding program to identify alleles of or mutations in the IMQ nucleic acid sequence or orthologs of the IMQ nucleic acid sequence that may confer altered oil, protein, and/or fiber content (see Bert et al., Theor Appl Genet., 2003 June; 107(1):181-9; and Lionneton et al., Genome, 2002 December; 45(6):1203-15). Thus, in a further aspect of the disclosure, an IMQ nucleic acid is used to identify whether a plant having altered oil, protein, and/or fiber content has a mutation an endogenous IMQ nucleic acid sequence or has a particular allele that causes altered oil, protein, and/or fiber content.
While the disclosure has been described with reference to specific methods and embodiments, it will be appreciated that various modifications and changes may be made without departing from the disclosure. All publications cited herein are expressly incorporated herein by reference for the purpose of describing and disclosing compositions and methodologies that might be used in connection with the disclosure. All cited patents, patent applications, and sequence information in referenced public databases are also incorporated by reference.
EXAMPLES
Example 1
Generation of Plants with an IMQ Phenotype and/or an IOQ Phenotype by Transformation with an Activation Tagging Construct
This Example describes the generation of transgenic plants with altered oil, protein, and/or fiber content.
Mutants were generated using the activation tagging “ACTTAG” vector, pSKI015 (GI#6537289; Weigel D et al., 2000, Plant Physiology, 122:1003-1013). Standard methods were used for the generation of Arabidopsis transgenic plants, and were essentially as described in published application PCT WO0183697. Briefly, TO Arabidopsis (Col-0) plants were transformed with Agrobacterium carrying the pSKI015 vector, which comprises T-DNA derived from the Agrobacterium Ti plasmid, an herbicide resistance selectable marker gene, and the 4×CaMV 35S enhancer element. Transgenic plants were selected at the T1 generation based on herbicide resistance. T2 seed (from T1 plants) was harvested and sown in soil. T2 plants were exposed to the herbicide to kill plants lacking the ACTTAG vector. T2 plants were grown to maturity, allowed to self-fertilize and set seed. T3 seed (from the T2 plants) was harvested in bulk for each line.
T3 seed was analyzed by Near Infrared Spectroscopy (NIR) at the time of harvest. NIR spectra were captured using a Bruker 22 near infrared spectrometer. Bruker Software was used to estimate total seed oil, total seed protein and total seed fiber content using data from NIR analysis and reference methods according to the manufacturer's instructions. Oil content predicting calibrations were developed following the general method of AOCS Procedure Am1-92, Official Methods and Recommended Practices of the American Oil Chemists Society, 5th Ed., AOCS, Champaign, Ill. A NIR protein content predicting calibration was developed using total nitrogen content data of seed samples following the general method of Dumas Procedure AOAC 968.06 (Official Methods of Analysis of AOAC International 17th Edition AOAC, Gaithersburg, Md.). A fiber content predicting calibration was developed by measuring crude fiber content in a set of seed samples. Fiber content of in a known mass of seed was determined using the method of Honig and Rackis, (1979, J. Agri. Food Chem., 27: 1262-1266). Digestible protein content of in a known mass of seed was determined by quantifying the individual amino acids liberated by an acid hydrolysis Steine and Moore (1958, Anal. Chem., 30:1185-1190). The quantification was performed by the Amino Quant (Agilent). The undigested protein remaining associated with the non digestible fraction is measured by the same method described for the whole seed homogenate. Digestible protein content is determined by subtracting the amount of undigested protein associated with the non digestible fraction from the total amount of protein in the seed sample.
Seed oil, protein, digestible protein and fiber values in 82,274 lines were determined by NIR spectroscopy and normalized to allow comparison of seed component values in plants grown at different times. Oil, protein and fiber values were normalized by calculating the average oil, protein and fiber values in seed from all plants planted on the same day (including a large number of other ACTTAG plants, including control, wild-type, or non-transgenic plants). The seed components for each line was expressed as a “percent relative value” which was calculated by dividing the component value for each line with the average component value for all lines planted on the same day (which should approximate the value in control, wild-type, or non-transgenic plants). The “percent relative protein” and “percent relative fiber” were calculated similarly.
Inverse PCR was used to recover genomic DNA flanking the T-DNA insertion. The PCR product was subjected to sequence analysis and placed on the genome using a basic BLASTN search and/or a search of the Arabidopsis Information Resource (TAIR) database (available at the publicly available website). Promoters within 9 kb of the enhancers in the ACTTAG element are considered to be within “activation space.” Genes with T-DNA inserts within coding sequences were not considered to be within “activation space.” The ACTTAG lines with the above average oil and protein values, and below average fiber values were identified and are listed in column 3 of Table 1.













TABLE 1








4.
5.







Relative
Relative
6.





Seed
Seed
Relative


1. Gene

3. ACTTAG
Protein
Fiber
Seed Oil
7.


alias
2. Tair
Line
Content
Content
Content
GC FA





















IMQ34.3
At2g31480
W000137133
135.45%
89.55%
82.65%



IMQ34.4
At2g31490
W000137133
135.45%
89.55%
82.65%


IMQ35.1
At2g34030
W000041983
122.86%
92.93%
80.44%


IMQ35.2
At2g34040
W000041983
122.86%
92.93%
80.44%


IMQ35.2
At2g34040
W000041983
122.86%
92.93%
80.44%


IMQ35.3
At2g34050
W000041983
122.86%
92.93%
80.44%


IMQ35.4
At2g34060
W000041983
122.86%
92.93%
80.44%


IMQ36.1
At2g34400
W000146178
109.53%
93.15%
94.98%


IMQ36.2
At2g34410
W000146178
109.53%
93.15%
94.98%


IMQ36.2
At2g34410
W000146178
109.53%
93.15%
94.98%


IMQ36.2
At2g34410
W000146178
109.53%
93.15%
94.98%


IMQ36.3
At2g34420
W000146178
109.53%
93.15%
94.98%


IMQ36.3
At2g34420
W000146178
109.53%
93.15%
94.98%


IMQ36.4
At2g34430
W000146178
109.53%
93.15%
94.98%


IMQ36.5
At2g34440
W000146178
109.53%
93.15%
94.98%


IMQ36.6
At2g34450
W000146178
109.53%
93.15%
94.98%


IMQ36.6
At2g34450
W000146178
109.53%
93.15%
94.98%


IMQ37.1
At3g03800
W000168536
105.07%
88.55%
98.42%


IMQ37.2
At3g03810
W000168536
105.07%
88.55%
98.42%


IMQ37.3
At3g03820
W000168536
105.07%
88.55%
98.42%


IMQ37.4
At3g03830
W000168536
105.07%
88.55%
98.42%


IMQ37.5
At3g03840
W000168536
105.07%
88.55%
98.42%


IMQ37.6
At3g03847
W000168536
105.07%
88.55%
98.42%
97.87%


IMQ37.7
At3g03850
W000168536
105.07%
88.55%
98.42%


IMQ38.1
At3g07100
W000182714
101.56%
90.13%
99.68%


IMQ38.2
At3g07110
W000182714
101.56%
90.13%
99.68%


IMQ38.2
At3g07110
W000182714
101.56%
90.13%
99.68%


IMQ38.3
At3g07120
W000182714
101.56%
90.13%
99.68%


IMQ38.4
At3g07130
W000182714
101.56%
90.13%
99.68%


IMQ38.5
At3g07140
W000182714
101.56%
90.13%
99.68%


IMQ38.5
At3g07140
W000182714
101.56%
90.13%
99.68%


IMQ38.6
At3g07150
W000182714
101.56%
90.13%
99.68%


IMQ39.1
At3g15480
W000190425
151.85%
106.23%
57.69%


IMQ39.2
At3g15490
W000190425
151.85%
106.23%
57.69%
69.66%


IMQ39.3
At3g15500
W000190425
151.85%
106.23%
57.69%


IMQ40.1
At3g16580
W000085366
119.68%
89.13%
84.56%
99.63%


IMQ40.2
At3g16590
W000085366
119.68%
89.13%
84.56%


IMQ40.3
At3g16600
W000085366
119.68%
89.13%
84.56%


IMQ40.4
At3g16610
W000085366
119.68%
89.13%
84.56%


IMQ40.5
At3g16620
W000085366
119.68%
89.13%
84.56%


IMQ41.1
At3g17640
W000192636
101.54%
86.92%
102.79%
107.27%


IMQ41.2
At3g17650
W000192636
101.54%
86.92%
102.79%


IMQ41.3
At3g17660
W000192636
101.54%
86.92%
102.79%


IMQ41.4
At3g17670
W000192636
101.54%
86.92%
102.79%


IMQ41.5
At3g17680
W000192636
101.54%
86.92%
102.79%
107.27%


IMQ41.5
At3g17680
W000192636
101.54%
86.92%
102.79%


IMQ41.6
At3g17690
W000192636
101.54%
86.92%
102.79%
107.27%


IMQ42.1
At3g19850
W000093675
112.46%
94.21%
95.25%


IMQ42.2
At3g19860
W000093675
112.46%
94.21%
95.25%


IMQ42.2
At3g19860
W000093675
112.46%
94.21%
95.25%























TABLE 2











7. Putative





3. Nucleic

5.

biochemical


1. Gene

Acid seq.
4. SEQ ID
Polypeptide
6. SEQ ID
function/protein
8. Conserved protein


alias
2. Tair
GI#
NO
seq. GI#
NO
name
domain







IMQ34.3
At2g31480
gi|42569515
SEQ ID
gi|42569516
SEQ ID
unknown protein






NO: 1

NO: 2


IMQ34.4
At2g31490
gi|18402681
SEQ ID
gi|18402682
SEQ ID
unknown protein





NO: 3

NO: 4


IMQ35.1
At2g34030
gi|42569600
SEQ ID
gi|42569601
SEQ ID
calcium ion binding
IPR002048 Calcium-





NO: 5

NO: 6

binding EF-hand


IMQ35.2
At2g34040
gi|30685905
SEQ ID
gi|30685906
SEQ ID
unknown protein
IPR008383 Apoptosis





NO: 7

NO: 8

inhibitory 5


IMQ35.2
At2g34040
gi|30685899
SEQ ID
gi|18403429
SEQ ID
unknown protein
IPR008383 Apoptosis





NO: 9

NO: 10

inhibitory 5


IMQ35.3
At2g34050
gi|30685908
SEQ ID
gi|18403431
SEQ ID
unknown protein
IPR010591 ATP11





NO: 11

NO: 12


IMQ35.4
At2g34060
gi|30685912
SEQ ID
gi|15226205
SEQ ID
peroxidase
IPR002016 Haem





NO: 13

NO: 14

peroxidase,









plant/fungal/bacterial;









IPR000823 Plant









peroxidase


IMQ36.1
At2g34400
gi|18403542
SEQ ID
gi|15226301
SEQ ID
unknown protein
IPR002885





NO: 15

NO: 16

Pentatricopeptide repeat;









IPR008940 Protein









prenyltransferase


IMQ36.2
At2g34410
gi|79324292
SEQ ID
gi|79324293
SEQ ID
O-acetyltransferase
IPR012419 Cas1p-like





NO: 17

NO: 18


IMQ36.2
At2g34410
gi|79324284
SEQ ID
gi|79324285
SEQ ID
O-acetyltransferase
IPR012419 Cas1p-like





NO: 19

NO: 20


IMQ36.2
At2g34410
gi|42569608
SEQ ID
gi|42569609
SEQ ID
O-acetyltransferase
IPR012419 Cas1p-like





NO: 21

NO: 22


IMQ36.3
At2g34420
gi|30686050
SEQ ID
gi|30686051
SEQ ID
LHB1B2
IPR001344 Chlorophyll





NO: 23

NO: 24

A-B binding protein


IMQ36.3
At2g34420
gi|30686047
SEQ ID
gi|18403546
SEQ ID
LHB1B2
IPR001344 Chlorophyll





NO: 25

NO: 26

A-B binding protein


IMQ36.4
At2g34430
gi|30686053
SEQ ID
gi|18403549
SEQ ID
LHB1B1; chlorophyll
IPR001344 Chlorophyll





NO: 27

NO: 28
binding
A-B binding protein


IMQ36.5
At2g34440
gi|18403551
SEQ ID
gi|15226309
SEQ ID
transcription factor
IPR002100 Transcription





NO: 29

NO: 30

factor, MADS-box


IMQ36.6
At2g34450
gi|79324302
SEQ ID
gi|79324303
SEQ ID
unknown protein
IPR000910 HMG1/2





NO: 31

NO: 32

(high mobility group) box


IMQ36.6
At2g34450
gi|30686062
SEQ ID
gi|18403553
SEQ ID
transcription factor
IPR000910 HMG1/2





NO: 33

NO: 34

(high mobility group) box


IMQ37.1
At3g03800
gi|18396673
SEQ ID
gi|15228637
SEQ ID
SYP131; t-SNARE
IPR000727 Target





NO: 35

NO: 36

SNARE coiled-coil









region;









IPR006011 Syntaxin, N-









terminal;









IPR006012









Syntaxin/epimorphin









family


IMQ37.2
At3g03810
gi|30678945
SEQ ID
gi|30678946
SEQ ID
unknown protein
IPR004348 Hypothetical





NO: 37

NO: 38

plant protein


IMQ37.3
At3g03820
gi|18396679
SEQ ID
gi|15228639
SEQ ID
unknown protein
IPR003676 Auxin





NO: 39

NO: 40

responsive SAUR









protein


IMQ37.4
At3g03830
gi|30678954
SEQ ID
gi|15228640
SEQ ID
unknown protein
IPR003676 Auxin





NO: 41

NO: 42

responsive SAUR









protein


IMQ37.5
At3g03840
gi|42563470
SEQ ID
gi|15228641
SEQ ID
unknown protein
IPR003676 Auxin





NO: 43

NO: 44

responsive SAUR









protein


IMQ37.6
At3g03847
gi|22330828
SEQ ID
gi|22330829
SEQ ID
unknown protein
IPR003676 Auxin





NO: 45

NO: 46

responsive SAUR









protein


IMQ37.7
At3g03850
gi|30678958
SEQ ID
gi|30678959
SEQ ID
unknown protein





NO: 47

NO: 48


IMQ38.1
At3g07100
gi|30680128
SEQ ID
gi|30680129
SEQ ID
protein binding/
IPR006896





NO: 49

NO: 50
transporter
Sec23/Sec24 trunk









region;









IPR006900









Sec23/Sec24 helical









region;









IPR006895 Zinc finger,









Sec23/Sec24-type;









IPR006706 Extensin-like









region;









IPR007123 Gelsolin









region


IMQ38.2
At3g07110
gi|79313148
SEQ ID
gi|79313149
SEQ ID
structural constituent
IPR005822 Ribosomal





NO: 51

NO: 52
of ribosome
protein L13;









IPR005755 Ribosomal









protein L13, archea and









eukaryotic form;









IPR005823 Ribosomal









protein L13, bacterial









and organelle form


IMQ38.2
At3g07110
gi|30680131
SEQ ID
gi|15231394
SEQ ID
structural constituent
IPR005822 Ribosomal





NO: 53

NO: 54
of ribosome
protein L13;









IPR005755 Ribosomal









protein L13, archea and









eukaryotic form;









IPR005823 Ribosomal









protein L13, bacterial









and organelle form


IMQ38.3
At3g07120
gi|30680134
SEQ ID
gi|15231396
SEQ ID
protein binding/
IPR001841 Zinc finger,





NO: 55

NO: 56
ubiquitin-protein
RING-type








ligase/zinc ion








binding


IMQ38.4
At3g07130
gi|42563571
SEQ ID
gi|15231398
SEQ ID
hydrolase/protein
IPR004843





NO: 57

NO: 58
serine/threonine
Metallophosphoesterase








phosphatase


IMQ38.5
At3g07140
gi|42570456
SEQ ID
gi|30680143
SEQ ID
GPI-anchor
IPR007245 Gpi16





NO: 59

NO: 60
transamidase
subunit, GPI









transamidase









component


IMQ38.5
At3g07140
gi|30680141
SEQ ID
gi|18397852
SEQ ID
GPI-anchor
IPR007245 Gpi16





NO: 61

NO: 62
transamidase
subunit, GPI









transamidase









component


IMQ38.6
At3g07150
gi|18397855
SEQ ID
gi|15231401
SEQ ID
unknown protein





NO: 63

NO: 64


IMQ39.1
At3g15480
gi|30683621
SEQ ID
gi|18400781
SEQ ID
unknown protein
IPR009606 Protein of





NO: 65

NO: 66

unknown function









DUF1218


IMQ39.2
At3g15490
gi|42564187
SEQ ID
gi|42564188
SEQ ID
unknown protein
IPR005061 Protein of





NO: 67

NO: 68

unknown function









DUF292, eukaryotic


IMQ39.3
At3g15500
gi|30683631
SEQ ID
gi|15232604
SEQ ID
ATNAC3;
IPR003441 No apical





NO: 69

NO: 70
transcription factor
meristem (NAM) protein


IMQ40.1
At3g16580
gi|30684147
SEQ ID
gi|18401179
SEQ ID
unknown protein
IPR001810 Cyclin-like F-





NO: 71

NO: 72

box;









IPR006527 F-box protein









interaction domain


IMQ40.2
At3g16590
gi|18401181
SEQ ID
gi|15228255
SEQ ID
unknown protein
IPR006527 F-box protein





NO: 73

NO: 74

interaction domain;









IPR001810 Cyclin-like F-









box


IMQ40.3
At3g16600
gi|18401188
SEQ ID
gi|15228256
SEQ ID
ATP binding/ATP-
IPR000330 SNF2-





NO: 75

NO: 76
dependent helicase/
related;








DNA binding/
IPR001410 DEAD/DEAH








helicase/nucleic
box helicase;








acid binding/protein
IPR001650 Helicase, C-








binding/ubiquitin-
terminal








protein ligase/zinc








ion binding


IMQ40.4
At3g16610
gi|18401191
SEQ ID
gi|15228257
SEQ ID
unknown protein
IPR001841 Zinc finger,





NO: 77

NO: 78

RING-type;









IPR002885









Pentatricopeptide repeat


IMQ40.5
At3g16620
gi|30684161
SEQ ID
gi|15228272
SEQ ID
ATTOC120; protein
IPR006703 AIG1;





NO: 79

NO: 80
translocase
IPR002917 GTP-binding









protein, HSR1-related;









IPR005688 Chloroplast









protein import









component Toc34;









IPR005690 Chloroplast









protein import









component Toc86/159


IMQ41.1
At3g17640
gi|18401587
SEQ ID
gi|15229088
SEQ ID
protein binding
IPR001611 Leucine-rich





NO: 81

NO: 82

repeat;









IPR007090 Leucine-rich









repeat, plant specific


IMQ41.2
At3g17650
gi|18401589
SEQ ID
gi|18401590
SEQ ID
PDE321;
IPR004813 Oligopeptide





NO: 83

NO: 84
oligopeptide
transporter OPT








transporter
superfamily;









IPR004814 Oligopeptide









transporter OPT;









IPR004648 Tetrapeptide









transporter, OPT1/isp4


IMQ41.3
At3g17660
gi|18401594
SEQ ID
gi|15229090
SEQ ID
DNA binding
IPR001164 Arf GTPase





NO: 85

NO: 86

activating protein


IMQ41.4
At3g17670
gi|18401598
SEQ ID
gi|15229091
SEQ ID
unknown protein
IPR001440 TPR repeat





NO: 87

NO: 88


IMQ41.5
At3g17680
gi|79313276
SEQ ID
gi|79313277
SEQ ID
unknown protein
IPR011684 KIP1-like





NO: 89

NO: 90


IMQ41.5
At3g17680
gi|30684630
SEQ ID
gi|30684631
SEQ ID
unknown protein
IPR011684 KIP1-like





NO: 91

NO: 92


IMQ41.6
At3g17690
gi|30684635
SEQ ID
gi|15229093
SEQ ID
ATCNGC19;
IPR005821 Ion transport





NO: 93

NO: 94
calmodulin binding/
protein;








cyclic nucleotide
IPR000595 Cyclic








binding/ion channel
nucleotide-binding


IMQ42.1
At3g19850
gi|42565033
SEQ ID
gi|42565034
SEQ ID
protein binding/
IPR004249 NPH3;





NO: 95

NO: 96
signal transducer
IPR000210 BTB/POZ


IMQ42.2
At3g19860
gi|79313298
SEQ ID
gi|79313299
SEQ ID
DNA binding
IPR001092 Basic helix-





NO: 97

NO: 98

loop-helix dimerisation









region bHLH;









IPR003106 Leucine









zipper, homeobox-









associated


IMQ42.2
At3g19860
gi|30685522
SEQ ID
gi|15230975
SEQ ID
DNA binding/
IPR001092 Basic helix-





NO: 99

NO: 100
transcription factor
loop-helix dimerisation









region bHLH;









IPR003106 Leucine









zipper, homeobox-









associated



















TABLE 3









4.
5. Orthologous Genes: Nucleic Acid/Polypeptide seq. GI#













1. Gene

3. Nucleic
Polypeptide
Nucleic Acid




alias
2. Tair
Acid seq. GI#
seq. GI#
GI#
Polypeptide GI#
Species





IMQ34.3
At2g31480
gi|42569515
gi|42569516





IMQ34.4
At2g31490
gi|18402681
gi|18402682
gi|15146360
gi|57899156
Oryza sativa (japonica cultivar-group)






gi|34910867
gi|34910868
Oryza sativa (japonica cultivar-group)






gi|34909561
gi|34909562
Oryza sativa (japonica cultivar-group)


IMQ35.1
At2g34030
gi|42569600
gi|42569601
gi|30690570
gi|15218787
Arabidopsis thaliana






gi|18403422
gi|15226191
Arabidopsis thaliana






gi|30695447
gi|30695448
Arabidopsis thaliana


IMQ35.2
At2g34040
gi|30685905
gi|30685906
gi|30685899
gi|18403429
Arabidopsis thaliana






gi|42562386
gi|42562387
Arabidopsis thaliana






gi|50907460
gi|50907461
Oryza sativa (japonica cultivar-group)






gi|66526466
gi|66526467
Apis mellifera


IMQ35.2
At2g34040
gi|30685899
gi|18403429
gi|30685905
gi|30685906
Arabidopsis thaliana






gi|42562386
gi|42562387
Arabidopsis thaliana






gi|50907460
gi|50907461
Oryza sativa (japonica cultivar-group)






gi|66526466
gi|66526467
Apis mellifera


IMQ35.3
At2g34050
gi|30685908
gi|18403431
gi|50907446
gi|50907447
Oryza sativa (japonica cultivar-group)






gi|66814293
gi|66814294
Dictyostelium discoideum






gi|50751555
gi|50751556
Gallus gallus


IMQ35.4
At2g34060
gi|30685912
gi|15226205
gi|50918940
gi|50918941
Oryza sativa (japonica cultivar-group)






gi|55701112
gi|55701113
Oryza sativa (japonica cultivar-group)






gi|537318
gi|537319
Medicago sativa


IMQ36.1
At2g34400
gi|18403542
gi|15226301
gi|18398256
gi|15231970
Arabidopsis thaliana






gi|18399739
gi|15230593
Arabidopsis thaliana






gi|18420159
gi|15233645
Arabidopsis thaliana


IMQ36.2
At2g34410
gi|79324292
gi|79324293
gi|79324284
gi|79324285
Arabidopsis thaliana






gi|42569608
gi|42569609
Arabidopsis thaliana






gi|30694937
gi|18422663
Arabidopsis thaliana






gi|42562401
gi|42562402
Arabidopsis thaliana






gi|20161482
gi|55297065
Oryza sativa (japonica cultivar-group)


IMQ36.2
At2g34410
gi|79324284
gi|79324285
gi|79324292
gi|79324293
Arabidopsis thaliana






gi|42569608
gi|42569609
Arabidopsis thaliana






gi|30694937
gi|18422663
Arabidopsis thaliana






gi|42562401
gi|42562402
Arabidopsis thaliana






gi|20161482
gi|55297065
Oryza sativa (japonica cultivar-group)


IMQ36.2
At2g34410
gi|42569608
gi|42569609
gi|79324292
gi|79324293
Arabidopsis thaliana






gi|79324284
gi|79324285
Arabidopsis thaliana






gi|30694937
gi|18422663
Arabidopsis thaliana






gi|42562401
gi|42562402
Arabidopsis thaliana






gi|20161482
gi|55297065
Oryza sativa (japonica cultivar-group)


IMQ36.3
At2g34420
gi|30686050
gi|30686051
gi|30686047
gi|18403546
Arabidopsis thaliana






gi|30690951
gi|15220615
Arabidopsis thaliana






gi|30690948
gi|18397288
Arabidopsis thaliana






gi|30690947
gi|18397286
Arabidopsis thaliana


IMQ36.3
At2g34420
gi|30686047
gi|18403546
gi|30690951
gi|15220615
Arabidopsis thaliana






gi|30690948
gi|18397288
Arabidopsis thaliana






gi|30690947
gi|18397286
Arabidopsis thaliana






gi|31323255
gi|31323256
Brassica oleracea


IMQ36.4
At2g34430
gi|30686053
gi|18403549
gi|21137
gi|21138
Sinapis alba






gi|18266038
gi|18266039
Brassica oleracea






gi|30690951
gi|15220615
Arabidopsis thaliana


IMQ36.5
At2g34440
gi|18403551
gi|15226309
gi|18397662
gi|15230767
Arabidopsis thaliana






gi|30682570
gi|30682571
Arabidopsis thaliana






gi|18424355
gi|15239333
Arabidopsis thaliana


IMQ36.6
At2g34450
gi|79324302
gi|79324303
gi|30686062
gi|18403553
Arabidopsis thaliana






gi|20161570
gi|56202161
Oryza sativa (japonica cultivar-group)






gi|63020535
gi|63020536
Cucumis sativus






gi|34910913
gi|34910914
Oryza sativa (japonica cultivar-group)


IMQ36.6
At2g34450
gi|30686062
gi|18403553
gi|20161570
gi|56202161
Oryza sativa (japonica cultivar-group)






gi|63020535
gi|63020536
Cucumis sativus






gi|42562198
gi|18394900
Arabidopsis thaliana


IMQ37.1
At3g03800
gi|18396673
gi|15228637
gi|18415700
gi|18415701
Arabidopsis thaliana






gi|51963279
gi|51963280
Oryza sativa (japonica cultivar-group)






gi|50934370
gi|50934371
Oryza sativa (japonica cultivar-group)






gi|55741415
gi|55741416
Oryza sativa (japonica cultivar-group)


IMQ37.2
At3g03810
gi|30678945
gi|30678946
gi|46063406
gi|50878393
Oryza sativa (japonica cultivar-group)






gi|30689847
gi|30689848
Arabidopsis thaliana






gi|30679041
gi|22329335
Arabidopsis thaliana


IMQ37.3
At3g03820
gi|18396679
gi|15228639
gi|42563470
gi|15228641
Arabidopsis thaliana






gi|30678958
gi|30678959
Arabidopsis thaliana






gi|30678954
gi|15228640
Arabidopsis thaliana


IMQ37.4
At3g03830
gi|30678954
gi|15228640
gi|30678958
gi|30678959
Arabidopsis thaliana






gi|18396679
gi|15228639
Arabidopsis thaliana






gi|42563470
gi|15228641
Arabidopsis thaliana


IMQ37.5
At3g03840
gi|42563470
gi|15228641
gi|18396679
gi|15228639
Arabidopsis thaliana






gi|30678958
gi|30678959
Arabidopsis thaliana






gi|30678954
gi|15228640
Arabidopsis thaliana


IMQ37.6
At3g03847
gi|22330828
gi|22330829
gi|42567926
gi|15238721
Arabidopsis thaliana






gi|42567924
gi|15238716
Arabidopsis thaliana






gi|30686621
gi|15238715
Arabidopsis thaliana


IMQ37.7
At3g03850
gi|30678958
gi|30678959
gi|30678954
gi|15228640
Arabidopsis thaliana






gi|42563470
gi|15228641
Arabidopsis thaliana






gi|18396679
gi|15228639
Arabidopsis thaliana


IMQ38.1
At3g07100
gi|30680128
gi|30680129
gi|50921574
gi|50921575
Oryza sativa (japonica cultivar-group)






gi|74199102
gi|74199103
Mus musculus






gi|31340743
gi|30424898
Mus musculus


IMQ38.2
At3g07110
gi|79313148
gi|79313149
gi|30680131
gi|15231394
Arabidopsis thaliana






gi|30695535
gi|15239698
Arabidopsis thaliana






gi|30687674
gi|15230197
Arabidopsis thaliana






gi|42566745
gi|15235617
Arabidopsis thaliana


IMQ38.2
At3g07110
gi|30680131
gi|15231394
gi|30695535
gi|15239698
Arabidopsis thaliana






gi|30687674
gi|15230197
Arabidopsis thaliana






gi|42566745
gi|15235617
Arabidopsis thaliana


IMQ38.3
At3g07120
gi|30680134
gi|15231396
gi|42565172
gi|15230243
Arabidopsis thaliana






gi|42570141
gi|42570142
Arabidopsis thaliana






gi|18413925
gi|15235589
Arabidopsis thaliana


IMQ38.4
At3g07130
gi|42563571
gi|15231398
gi|13925770
gi|13925771
Glycine max






gi|62177682
gi|62177683
Medicago truncatula






gi|50920094
gi|50920095
Oryza sativa (japonica cultivar-group)


IMQ38.5
At3g07140
gi|42570456
gi|30680143
gi|30680141
gi|18397852
Arabidopsis thaliana






gi|77548247
gi|77550830
Oryza sativa (japonica cultivar-group)






gi|73992512
gi|73992513
Canis familiaris


IMQ38.5
At3g07140
gi|30680141
gi|18397852
gi|42570456
gi|30680143
Arabidopsis thaliana






gi|77548247
gi|77550830
Oryza sativa (japonica cultivar-group)






gi|73992512
gi|73992513
Canis familiaris


IMQ38.6
At3g07150
gi|18397855
gi|15231401
gi|19386744
gi|57900451
Oryza sativa (japonica cultivar-group)






gi|34907011
gi|34907012
Oryza sativa (japonica cultivar-group)


IMQ39.1
At3g15480
gi|30683621
gi|18400781
gi|42562716
gi|18404242
Arabidopsis thaliana






gi|38016520
gi|38016521
Gossypium barbadense






gi|50936920
gi|50936921
Oryza sativa (japonica cultivar-group)


IMQ39.2
At3g15490
gi|42564187
gi|42564188
gi|18397647
gi|15226014
Arabidopsis thaliana






gi|50918206
gi|50918207
Oryza sativa (japonica cultivar-group)






gi|30683233
gi|15222251
Arabidopsis thaliana


IMQ39.3
At3g15500
gi|30683631
gi|15232604
gi|42562715
gi|15219112
Arabidopsis thaliana






gi|66394515
gi|66394516
Glycine max






gi|6175245
gi|6175246
Lycopersicon esculentum


IMQ40.1
At3g16580
gi|30684147
gi|18401179
gi|42569040
gi|15225992
Arabidopsis thaliana






gi|18398432
gi|15223198
Arabidopsis thaliana






gi|18401705
gi|18401706
Arabidopsis thaliana


IMQ40.2
At3g16590
gi|18401181
gi|15228255
gi|18391359
gi|15221240
Arabidopsis thaliana






gi|30684644
gi|18401609
Arabidopsis thaliana






gi|18391361
gi|15221246
Arabidopsis thaliana


IMQ40.3
At3g16600
gi|18401188
gi|15228256
gi|18403060
gi|18403061
Arabidopsis thaliana






gi|18402451
gi|15231009
Arabidopsis thaliana






gi|51964729
gi|51964730
Oryza sativa (japonica cultivar-group)


IMQ40.4
At3g16610
gi|18401191
gi|15228257
gi|50941690
gi|50941691
Oryza sativa (japonica cultivar-group)






gi|18483227
gi|18483237
Sorghum bicolor






gi|34906109
gi|34906110
Oryza sativa (japonica cultivar-group)






gi|28564706
gi|57899529
Oryza sativa (japonica cultivar-group)


IMQ40.5
At3g16620
gi|30684161
gi|15228272
gi|30679717
gi|15227268
Arabidopsis thaliana






gi|37536637
gi|37536638
Oryza sativa (japonica cultivar-group)






gi|44662984
gi|44662985
Physcomitrella patens


IMQ41.1
At3g17640
gi|18401587
gi|15229088
gi|50931366
gi|50931367
Oryza sativa (japonica cultivar-group)






gi|51339056
gi|55733924
Oryza sativa (japonica cultivar-group)






gi|30678565
gi|30678566
Arabidopsis thaliana


IMQ41.2
At3g17650
gi|18401589
gi|18401590
gi|30694308
gi|18402162
Arabidopsis thaliana






gi|42562981
gi|15218799
Arabidopsis thaliana






gi|74267415
gi|74267416
Oryza sativa (japonica cultivar-group)


IMQ41.3
At3g17660
gi|18401594
gi|15229090
gi|30696440
gi|18423615
Arabidopsis thaliana






gi|50510177
gi|50510178
Oryza sativa (japonica cultivar-group)






gi|60596222
gi|76152990
Schistosoma japonicum


IMQ41.4
At3g17670
gi|18401598
gi|15229091
gi|53749471
gi|53749491
Solanum demissum






gi|50929586
gi|50929587
Oryza sativa (japonica cultivar-group)






gi|50928358
gi|50928359
Oryza sativa (japonica cultivar-group)


IMQ41.5
At3g17680
gi|79313276
gi|79313277
gi|30684630
gi|30684631
Arabidopsis thaliana






gi|22330106
gi|22330107
Arabidopsis thaliana






gi|53749471
gi|53749473
Solanum demissum






gi|50916296
gi|50916297
Oryza sativa (japonica cultivar-group)


IMQ41.5
At3g17680
gi|30684630
gi|30684631
gi|22330106
gi|22330107
Arabidopsis thaliana






gi|53749471
gi|53749473
Solanum demissum






gi|50916296
gi|50916297
Oryza sativa (japonica cultivar-group)


IMQ41.6
At3g17690
gi|30684635
gi|15229093
gi|42564623
gi|18401606
Arabidopsis thaliana






gi|50913256
gi|50913257
Oryza sativa (japonica cultivar-group)






gi|51091189
gi|51091194
Oryza sativa (japonica cultivar-group)


IMQ42.1
At3g19850
gi|42565033
gi|42565034
gi|22330149
gi|22330150
Arabidopsis thaliana






gi|50929590
gi|50929591
Oryza sativa (japonica cultivar-group)






gi|50938220
gi|50938221
Oryza sativa (japonica cultivar-group)


IMQ42.2
At3g19860
gi|79313298
gi|79313299
gi|30685522
gi|15230975
Arabidopsis thaliana






gi|51536177
gi|51536178
Oryza sativa (japonica cultivar-group)






gi|30690567
gi|30690568
Arabidopsis thaliana






gi|22329203
gi|22329204
Arabidopsis thaliana


IMQ42.2
At3g19860
gi|30685522
gi|15230975
gi|51536177
gi|51536178
Oryza sativa (japonica cultivar-group)






gi|22329203
gi|22329204
Arabidopsis thaliana






gi|30690567
gi|30690568
Arabidopsis thaliana









Example 2
Analysis of the Arabidopsis IMO Sequence
Sequence analyses were performed with BLAST (Altschul et al., 1990, J. Mol. Biol. 215:403-410), PFAM (Bateman et al., 1999, Nucleic Acids Res. 27:260-262), INTERPRO (Mulder et al. 2003 Nucleic Acids Res. 31, 315-318), PSORT (Nakai K, and Horton P, 1999, Trends Biochem. Sci. 24:34-6), and/or CLUSTAL (Thompson J D et al., 1994, Nucleic Acids Res. 22:4673-4680). Conserved domains for each protein are listed in column 8 of Table 2.
Example 3
To test whether over-expression of the genes in Tables 1 and 2 alter the seed composition phenotype, protein, digestible protein, oil and fiber content in seeds from transgenic plants expressing these genes was compared with protein, digestible protein, oil and fiber content in seeds from non-transgenic control plants. To do this, the genes were cloned into plant transformation vectors behind the strong constitutive CsVMV promoter and the seed specific PRU promoter. These constructs were transformed into Arabidopsis plants using the floral dip method. The plant transformation vector contains a gene, which provides resistance to a toxic compound, and serves as a selectable marker. Seed from the transformed plants were plated on agar medium containing the toxic compound. After 7 days, transgenic plants were identified as healthy green plants and transplanted to soil. Non-transgenic control plants were germinated on agar medium, allowed to grow for 7 days and then transplanted to soil. Transgenic seedlings and non-transgenic control plants were transplanted to two inch pots that were placed in random positions in a 10 inch by 20 inch tray. The plants were grown to maturity, allowed to self-fertilize and set seed. Seed was harvested from each plant and its oil content estimated by Near Infrared (NIR) Spectroscopy using methods previously described. The effect of each construct on seed composition was examined in at least two experiments.
Table 4 lists constructs tested for causing a significant increase in oil, protein, digestible protein or a significant decrease in fiber were identified by a two-way Analysis of Variance (ANOVA) test at a p-value≦0.05. The ANOVA p-values for Protein, Oil, Digestible Protein and Fiber are listed in columns 4-7, respectively. Those with a significant p-value are listed in bold. The Average values for Protein, Oil, Digestible Protein and Fiber are listed in columns 8-11, respectively and were calculated by averaging the average values determined for the transgenic plants in each experiment.

















TABLE 4










6. ANOVA
7.


10.






4. ANOVA
5. ANOVA
Digestible
ANOVA


Digestible


1. Gene
2. TAIR
3. Construct
Protein
Oil
Protein
Fiber
8. Protein
9. Oil
Protein
11. Fiber

























IMQ37.5
At3g03840
CsVMV::At3g03840
0.433
0.415
0.033
0.197
101.7%
98.7%
102.4%
98.7%


IMQ37.6
At3g03847
CsVMV::At3g03847
0.998
0.503
0.634
0.864
100.2%
99.4%
100.5%
99.8%


IMQ37.6
At3g03847
Pru::At3g03847
0.007
0.002
0.115
0.547
104.6%
94.4%
101.2%
100.6%


IMQ39.1
At3g15480
Pru::At3g15480
0.521
0.450
0.026
0.011
100.9%
100.4%
101.4%
97.6%


IMQ39.2
At3g15490
CsVMV::At3g15490
0.192
0.463
0.176
0.035
103.1%
99.1%
101.7%
97.8%


IMQ39.2
At3g15490
Pru::At3g15490
0.125
0.551
<0.0001
<0.0001
100.9%
99.4%
101.4%
97.8%


IMQ40.1
At3g16580
CsVMV::At3g16580
0.436
0.321
0.050
0.173
101.3%
99.0%
101.6%
98.9%


IMQ40.1
At3g16580
Pru::At3g16580
0.269
0.972
0.005
0.003
101.3%
99.7%
101.7%
97.4%


IMQ40.3
At3g16600
Pru::At3g16600
0.019
0.019
0.220
0.136
102.8%
97.0%
99.5%
101.5%


IMQ41.1
At3g17640
CsVMV::At3g17640
0.991
0.671
0.864
0.725
99.9%
99.5%
99.8%
99.8%


IMQ41.1
At3g17640
Pru::At3g17640
0.024
0.006
0.041
0.003
97.1%
105.0%
101.3%
96.8%


IMQ41.5
At3g17680
CsVMV::At3g17680
0.567
0.873
0.803
0.290
101.3%
100.2%
100.3%
98.9%


IMQ41.5
At3g17680
Pru::At3g17680
0.569
0.252
0.009
0.004
99.3%
101.8%
102.1%
96.7%


IMQ41.6
At3g17690
CsVMV::At3g17690
0.388
0.856
0.060
0.039
102.7%
99.8%
102.4%
97.3%


IMQ41.6
At3g17690
Pru::At3g17690
0.263
0.726
0.003
0.009
102.0%
99.2%
103.0%
96.5%









Example 4
To test whether over-expression of the genes identified in Tables 1-4 alter the seed composition phenotype, protein, digestible protein, oil, and fiber content in seeds from transgenic plants expressing these genes is compared with protein, digestible protein, oil and fiber content in seeds from non-transgenic control plants. Any one of the genes identified in Tables 1-4 is used to transform Brassica napus (canola). To do this, the genes are cloned into plant transformation vectors behind the strong constitutive CsVMV promoter and the seed specific phaseolin promoter. These constructs (which include a gene encoding a selection agent) are transformed into canola plants.
Transformation of canola is accomplished via Agrobacterium-mediated transformation. Seeds are surface-sterilized with 10% commercial bleach for 10 minutes and rinsed 3 times with sterile distilled water. The seeds are then placed on one half concentration of MS basal medium (Murashige and Skoog, Physiol. Plant. 15:473-497, 1962) and maintained under growth regime set at 25° C., and a photoperiod of 16 hrs light/8 hrs dark.
Hypocotyl segments (3-5 mm) are excised from 5-7 day old seedlings and placed on callus induction medium K1D1 (MS medium with 1 mg/l kinetin and 1 mg/l 2,4-D) for 3 days as pre-treatment. The segments are then transferred into a petri plate, treated with Agrobacterium Z7075 or LBA4404 strain containing pDAB721. The Agrobacterium is grown overnight at 28° C. in the dark on a shaker at 150 rpm and subsequently re-suspended in the culture medium.
After 30 minute treatment of the hypocotyl segments with Agrobacterium, these are placed back on the callus induction medium for 3 days. Following co-cultivation, the segments are placed on K1D1TC (callus induction medium containing 250 mg/l Carbenicillin and 300 mg/l Timentin) for one week of recovery. Alternately, the segments are placed directly on selection medium K1D1H1 (above medium with 1 mg/l selection agent, for example an herbicide). Carbenicillin and Timentin are antibiotics used to kill the Agrobacterium. The selection agent is used to allow the growth of the transformed cells.
Callus samples from independent events are tested by PCR. All the samples tested are positive for the presence of the transformed gene, whereas the non-transformed controls are negative. Callus samples are confirmed to express the appropriate protein as determined by ELISA.
Callused hypocotyl segments are then placed on B3Z1H1 (MS medium, 3 mg/l benzylamino purine, 1 mg/l Zeatin, 0.5 gm/l MES [2-(N-morpholino) ethane sulfonic acid], 5 mg/l silver nitrate, 1 mg/l selection agent, Carbenicillin and Timentin) shoot regeneration medium. After shoots start to regenerate (approximately 3 weeks), hypocotyl segments along with the shoots are transferred to B3Z1H3 medium (MS medium, 3 mg/l benzylamino purine, 1 mg/l Zeatin, 0.5 gm/l MES [2-(N-morpholino) ethane sulfonic acid], 5 mg/l silver nitrate, 3 mg/l selection agent, Carbenicillin and Timentin) for 3 weeks.
Shoots are excised from the hypocotyl segments and transferred to shoot elongation medium MESH10 (MS, 0.5 gm/l MES, 10 mg/l selection agent, Carbenicillin, Timentin) for 2-4 weeks. The elongated shoots are cultured for root induction on MSI.1 (MS with 0.1 mg/l Indolebutyric acid). Once the plants have a well established root system, these are transplanted into soil. The plants are acclimated under controlled environmental conditions in the Conviron for 1-2 weeks before transfer to the greenhouse. The transformed TO plants self-pollinate in the greenhouse to obtain T1 seed. Transgenic plants are selected at the T1 generation based on resistance to a selection agent. T2 seed (from T1 plants) is harvested and sown in soil. T2 plants are grown to maturity, allowed to self-fertilize and set seed. T3 seed (from the T2 plants) is harvested in bulk for each line. Seed oil, protein, digestible protein, and fiber values are measured as discussed in Example 1.

## Claims

1. A method of producing meal, comprising:
growing a transgenic plant comprising a plant transformation vector comprising a nucleotide sequence that encodes or is the complement of a sequence that encodes an IMQ polypeptide comprising the amino acid sequence as set forth in SEQ ID NO: 76, whereby the transgenic plant has an improved meal quality phenotype, relative to control plants; and
recovering meal from the transgenic plant, thereby producing meal.

2. The method of claim 1, wherein the meal is produced from seeds of the transgenic plant.

3. A method of producing an improved meal quality phenotype in a plant, said method comprising:
a) introducing into progenitor cells of the plant a plant transformation vector comprising a nucleotide sequence that encodes or is the compliment of a sequence that encodes an IMQ polypeptide comprising the amino acid sequence set forth in SEQ ID NO: 76,
b) growing the transformed progenitor cells to produce a transgenic plant, wherein the nucleotide sequence is expressed, and the transgenic plant exhibits an improved meal quality phenotype relative to control plants, and
c) recovering meal from the transgenic plant,

thereby producing the improved meal quality phenotype in the plant.

4. A method of generating a plant having an improved meal quality phenotype, comprising:
a) identifying a plant that has an allele in its ortholog of the A. thaliana IMQ gene where the wildtype A. thaliana gene has the nucleic acid sequence set forth as SEQ ID NO: 75, which allele results in improved meal quality phenotype, compared to a control plant lacking the allele, wherein identifying a plant comprises analyzing the sequence of the allele in the plant;
b) generating progeny of said identified plant; and
c) identifying from among the progeny at least one plant that inherits the allele and has an improved meal quality phenotype relative to the control plant lacking the allele,

thereby generating a plant having an improved meal quality phenotype.

5. The method of claim 4 that employs candidate gene/QTL methodology.

6. The method of claim 4 that employs TILLING methodology.