# Patent

## Title
FAD-2 mutants and high oleic plants

## Abstract

The present invention relates to plants, seeds and products derived thereof, in particular to Brassica plants, seeds products derived thereof, that have mutant sequences conferring high oleic acid profile on the seed oil. More particularly, the invention relates to mutant delta-12 fatty acid desaturase sequences, also referred to herein as FAD2 sequences, —in-such-plants which confer high oleic acid profile on the seed oil.

## Background
FIELD OF THE INVENTION
The present invention relates to plants, seeds and products derived thereof, in particular to Brassica plants, seeds products derived thereof, that have mutant sequences conferring high oleic acid profile to the seed oil.
More particularly, the invention relates to mutant delta-12 fatty acid desaturase sequences, also referred to herein as mutant FAD2 sequences, in such plants which confer high oleic acid profile on the seed oil.
BACKGROUND
Delta-12 fatty acid desaturase (also known as oleic desaturase or oleate desaturase) is involved in the enzymatic conversion of oleic acid to linoleic acid.
Varieties with high level of oleic acid (possibly combined with low level of linolenic acid) are sought for many different applications (food applications, health applications, biodiesel applications and many others).
Mutant seeds providing an oil exhibiting a high oleic acid content (oleic acid content higher that 70 wt. % based upon the total weight of fatty acids present in the oil) previously reported in the literature had very poor agronomic value and/or bad root characteristics, and/or very low yield capacity.
There is still a need for material having stable, high oleic acid content (possibly combined with stable low linolenic acid content) across locations and across years, with also good agronomic performances and with normal oilseed rape morphology. In particular, the plants should have no fasciation and should have normal root development.
SUMMARY OF THE INVENTION
The present invention relates to a plant or a plant part or a seed containing a first FAD2 gene and possibly a second FAD2 gene, said first or said second FAD2 gene having a deletion at or corresponding to position 1421 (also referred to as DEL.1421) relative to a wild-type FAD2 gene, such as wild-type FAD2 gene of SEQ ID NO 9.
Another object of the present invention is a plant or a plant part or a seed containing a first FAD2 gene having a deletion at or corresponding to position 1421 relative to a wild-type FAD2 gene, such as wild-type FAD2 gene of SEQ ID NO 9, and a second FAD2 gene encoding a FAD-2 protein having an amino acid substitution at or corresponding to position 118 relative to a wild-type FAD-2 protein, such as the wild-type PAD-2 protein of SEQ ID NO 2 or 6.
A plant or a plant part or a seed of the invention preferably contains a nucleic acid sequence corresponding to SEQ ID NO 1 or 5, wherein the nucleotide (C) at position 215 is deleted, or contains a (variant) nucleic acid sequence, of at least 80%, preferably at least 85%, more preferably at least 90% and even more preferably at least 95%, 96%, 97%, 98% or 99% identity with SEQ ID NO 1 or 5, wherein the nucleotide corresponding to position 215 is deleted.
A plant or a plant part or a seed according to the invention can contain a (variant) nucleic acid sequence of at least 80%, preferably at least 85%, more preferably at least 90% and even more preferably at least 95%, 96%, 97%, 98% or 99% identity with SEQ ID NO 9, wherein the nucleotide corresponding to position 1421 is deleted (i.e. further deleted of the nucleotide corresponding to position 1421). Preferably, a plant or a plant part or a seed according to the invention contains a nucleic acid sequence corresponding to SEQ ID NO 9, wherein the nucleotide at position 1421 is deleted (i.e. further deleted of the nucleotide corresponding to position 1421).
A plant or a plant part or a seed according to the invention can contain a (variant) nucleic acid sequence of at least 80%, preferably at least 85%, more preferably at least 90% and even more preferably at least 95%, 96%, 97%, 98% or 99% identity with SEQ ID NO 10, wherein the nucleotide corresponding to position 1453 is deleted (i.e. further deleted of the nucleotide corresponding to position 1453). Preferably, a plant or a plant part or a seed according to the invention contains a nucleic acid sequence corresponding to SEQ ID NO 10, wherein the nucleotide at position 1453 is deleted (i.e. further deleted of the nucleotide corresponding to position 1453).
A preferred plant or a plant part or a seed according to the invention, further contains a nucleic acid sequence encoding a FAD-2 protein having an amino acid substitution at or corresponding to position 118 relative to a wild-type FAD-2 protein, such as the wild-type FAD-2 protein of SEQ ID NO 2 or 6. Preferably, said substituted amino acid at or corresponding to position 118 is phenylalanine.
A plant or a plant part or a seed according to the invention can be obtained by a mutagenesis treatment, more particularly by an Ethyl Methane Sulfonate (EMS) treatment.
Another object of the present invention is an isolated nucleic acid molecule comprising (or consisting of) the nucleic acid sequence of SEQ ID NO 1 or 5 wherein the nucleotide at position 215 is deleted (i.e. SEQ ID NO 1 or 5 further deleted of the nucleotide corresponding to position 215).
Also object of the invention is a (variant) nucleic acid molecule encoding a FAD2 protein (or a fragment of said protein), of at least 80%, preferably at least 85%, more preferably at least 90% and even more preferably at least 95%, 96%, 97%, 98% or 99% identity with SEQ ID NO 1 or 5, wherein the nucleotide corresponding to position 215 is deleted (i.e. further deleted of the nucleotide corresponding to position 215).
An isolated nucleic acid molecule according to the invention can comprise (or consist of) a (variant) nucleic acid sequence encoding a FAD2 protein (or a fragment), of at least 80%, preferably at least 85%, more preferably at least 90% and even more preferably at least 95%, 96%, 97%, 98% or 99% identity with SEQ ID NO 9, wherein the nucleotide corresponding to position 1421 is deleted (i.e. further deleted of the nucleotide corresponding to position 1421). Preferably, a nucleic acid molecule according to the invention comprises (or consists of) a nucleic acid sequence of SEQ ID NO 9, wherein the nucleotide at position 1421 is deleted (i.e. of SEQ ID NO 9 further deleted of the nucleotide corresponding to position 1421).
An isolated nucleic acid molecule according to the invention can comprise (or consist of) a (variant) nucleic acid sequence encoding a FAD2 protein (or a fragment), of at least 80%, preferably at least 85%, more preferably at least 90% and even more preferably at least 95%, 96%, 97%, 98% or 99% identity with SEQ ID NO 10, wherein the nucleotide corresponding to position 1453 is deleted (i.e. further deleted of the nucleotide corresponding to position 1453). Preferably, a nucleic acid molecule according to the invention comprises (or consists of) a nucleic acid sequence of SEQ ID NO 10, wherein the nucleotide at position 1453 is deleted (i.e. of SEQ ID NO 10 further deleted of the nucleotide corresponding to position 1453).
A preferred nucleic acid molecule of the invention comprises (or consists of) a nucleic acid sequence of SEQ ID NO 3, its complementary form or the RNA forms thereof.
Also object of the invention is a fragment of at least 10 nucleotides, preferably of at least 15, 20, 25, or 40 nucleotides, more preferably of at least 50 or 100 nucleotides of an isolated nucleic acid molecule of the invention, said fragment comprising the mutated codon resulting from said deletion.
Another object of the invention is a method of producing high oleic plant lines comprising:

    a) inducing mutagenesis, preferably by means of EMS treatment, in at least some cells from a plant, more particularly of a Brassica plant, and preferably of a Brassica napus variety that has a oleic acid content of less than 70%;
    b) regenerating plants from at least one of said mutagenized cells;
    c) selecting regenerated plants which have a nucleic acid sequence according to the invention, and
    d) deriving further generations of plants from said regenerated plants.


Said regenerated plants comprise a nucleic acid sequence of at least 80%, preferably at least 85%, more preferably at least 906 and even more preferably at least 95%, 96%, 97%, 98% or 99% identity with SEQ ID NO 9, wherein the nucleotide corresponding to position 1421 is deleted (i.e. further deleted of the nucleotide corresponding to position 1421), or a nucleic acid sequence of at least 80%, preferably at least 85%, more preferably at least 90% and even more preferably at least 95%, 96%, 97%, 98% or 99% identity with SEQ ID NO 10, wherein the nucleotide corresponding to position 1453 is deleted (i.e. further deleted of the nucleotide corresponding to position 1453).
Preferably, said regenerated plants comprise a nucleic acid sequence of SEQ ID NO 9 wherein the nucleotide 1421 is deleted (i.e. of SEQ ID NO 9 further deleted of the nucleotide corresponding to position 1421), or a nucleic acid sequence of SEQ ID NO 10 wherein the nucleotide 1453 is deleted (i.e. of SEQ ID NO 10 further deleted of the nucleotide corresponding to position 1453), or a nucleic acid sequence of SEQ ID NO 3.
More preferably, said regenerated plants further comprise a nucleic acid sequence encoding a FAD-2 protein having an amino acid substitution at or corresponding to position 118 relative to a wild-type FAD-2 protein, such as the wild-type FAD-2 protein of SEQ ID NO 2 or 6. Preferably, said substituted amino acid at or corresponding to position 118 is phenylalanine.
Step c) can comprise any method known in the art for identifying said mutation(s) (DEL.1421, DEL.1453, DEL.215 and possibly SNP1590), in particular step c) can comprise the use of restriction fragment length polymorphism (RFLP), random amplification polymorphism detection (RAPD), or polymerase chain reaction (PCR) method.
Another object is a method of producing high oleic plant lines comprising:

    i. crossing a first plant of the invention with a second plant,
    ii. obtaining seeds from the cross of step (a),
    iii. growing fertile plants from such seeds,
    iv. obtaining progeny seeds from the plants of step (c), and
    v. identifying those seeds among the progeny that have high oleic acid content.


Step (v) of identifying said seeds can comprise the use of a nucleic acid molecule according to the invention.
More particularly, step (v) can comprise any method known in the art for identifying said mutation(s) according to the invention, and more particularly, step (v) can comprise the use of restriction fragment length polymorphism (RFLP), random amplification polymorphism detection (RAPD), or polymerase chain reaction (PCR) method.
Another object relates to a vegetable oil obtained from the seeds of the invention, said oil comprising more than (about) 72%, 75%, 80%, or 85% of oleic acid based upon the total weight of the fatty acids present in said oil.
Preferably, a vegetable oil according to the invention further comprises less than (about) 4%, 3.5%, 3%, 2%, 1% or 0.5% of linolenic acid.



BRIEF DESCRIPTION OF THE FIGURE
FIGS. 1A-1E correspond to the list of sequences of the present invention.
FIG. 2a shows the notification of acceptance for the deposit of the MSP05 variety.
FIG. 2b shows the first page of the viability statement for the MSP05 variety.
FIG. 2c shows the second page of the viability statement for the MSP05 variety.
FIG. 2d shows the notification of acceptance for the deposit of the 28DHS.086 variety.
FIG. 2e shows the first page of the viability statement for the 28DHS.086 variety.
FIG. 2f shows the second page of the viability statement for the 28DHS.086 variety.
FIG. 2g shows the notification of acceptance for the deposit of the MSP12 variety.
FIG. 2h shows the first page of the viability statement for the MSP12 variety.
FIG. 2i shows the second page of the viability statement for the MSP12 variety.



DETAILED DESCRIPTION OF THE INVENTION
The present invention relates to plants, more particularly to Brassica plants, preferably to Brassica napus varieties, which provide an oil having a oleic acid content higher than 70 wt. %, based upon the total weight of fatty acids present in the oil.
More particularly, a plant of the invention has at least one mutated FAD2 gene according to the invention.
Preferably, said mutated FAD2 gene confers high oleic acid content (i.e. a oleic acid content higher than 70 wt. %, based upon the total weight of fatty acids present in the oil) to seeds of said plants and to oil extracted from said seeds.
The present invention relates also to any part or any product of said plant bearing said at least one mutated FAD2 gene.
In the context of the present invention, a part or product of a plant is meant to encompass a leaf, cotyledon, stem, petiole, stalk, seed or any other tissue or fragment of tissue of said plant.
The present invention relates also to any progeny of said plant bearing said at least one mutated FAD2 gene of the invention.
In the context of the present invention, the term “progeny” refers to direct and indirect descendants, offspring and derivatives of a plant or plants of the invention and includes the first, second, third and/or subsequent generations, which may be produced by self crossing, crossing with plants with the same or different genotypes, and may be modified by range of suitable genetic engineering techniques.
The present invention also relates to said mutated FAD2 genes that confer high oleic acid content in seeds when present in a plant.
In particular, the invention relates to novel isolated nucleic acid molecules corresponding to novel variant forms of FAD2 genes having a deleted nucleotide at or corresponding to position 1421 relative to a wild type FAD2 gene, such as the wild type FAD2 gene represented by SEQ ID NO 9.
Said deletion alters the functionality of the resulting FAD2 gene product, whereby the level of oleic acid is increased, in plant expressing the mutant sequence(s), compared to the corresponding level in plant expressing the wild-type sequence(s).
In particular, a nucleic acid molecule of the invention can comprise (or consist of) a nucleotide sequence having at least 80%, preferably at least 85%, more preferably at least 90% and even more preferably at least 95%, 96%, 97%, 98% or 99% identity with any of SEQ ID NO 9, or with the complementary form or RNA form thereof, wherein the nucleotide at or corresponding to position 1421 is deleted (i.e. further deleted of the nucleotide corresponding to position 1421).
A nucleic acid molecule of the invention containing said deletion at or corresponding to position 1421 (also referred to as DEL.1421) can be derived from Brassica napus varieties, such as CONTACT, CABRIOLET, 28DHS.086 and/or MSP12 varieties.
The term “at position 1421” is to be understood as designating the nucleotide position 1421 in a wild-type FAD2 gene represented by SEQ ID NO 9, but also as referring to the nucleotide corresponding to said position in a wild-type or variant FAD2 gene that would have a different nucleic acid sequence due to deletions or additional nucleotides in the sequence.
The term “corresponding to position” as used herein means that a position is not only determined by the number of the preceding nucleotides. The position of a given nucleotide in accordance with the present invention may vary due to deletions or additional nucleotides in the nucleic acid sequence. Thus, under a “corresponding position” in accordance with the present invention it is to be understood that the nucleotide referred to may differ in the indicated number but still has similar neighbouring nucleotides in the linear sequence. For example, position 1453 in SEQ ID NO 10 or position 215 in SEQ ID NO 1 or 5 is such a position.
Similarly, the term “at position 118”, is to be understood as designating the amino acid position 118 in a wild-type FAD2 protein represented by SEQ ID NO 2 or 6, but also as referring to the amino acid corresponding to said position in a wild-type or variant FAD2 protein that would have a different amino acid sequence due to deletions or additional amino acids in the polypeptide.
The term “corresponding to position” as used herein means that a position is not only determined by the number of the preceding amino acids. The position of a given amino acid in accordance with the present invention may vary due to deletions or additional amino acids in the polypeptide. Thus, under a “corresponding position” in accordance with the present invention it is to be understood that the amino acid(s) referred to may differ in the indicated number but still has (have) similar neighbouring amino acids in the linear sequence.
In another aspect, a nucleic acid molecule of the invention encodes a FAD2 protein having a substituted amino acid at or corresponding to position 118 relative to a wild type FAD2 protein, such as the wild type FAD2 protein represented by SEQ ID NO 2 or 6.
An isolated nucleic acid molecule of the invention contains at least one mutation, said mutation resulting in said substitution at or corresponding to position 118, preferably a substitution of tryptophan, more preferably a substitution of phenylalanine, for leucine, relative to a wild-type FAD2 protein, such as the wild-type FAD2 protein represented by SEQ ID NO 2 or 6.
Said mutation(s) alter(s) the functionality of the resulting FAD2 gene product, whereby the level of oleic acid is modified, preferably increased, in plant expressing the mutant sequence(s), compared to the corresponding level in plant expressing the wild-type sequence(s).
More particularly, a nucleic acid molecule of the invention encodes a FAD2 protein having a substitution of a phenylalanine for a leucine at position 118 relative to a wild type FAD2 protein represented by the amino acid sequence of SEQ ID NO 6.
A nucleic acid molecule of the invention can comprise (or consist of) a nucleic acid sequence of SEQ ID NO 1, 5, 9 or 10, wherein the codon encoding the amino acid at position 118 has at least one mutation to encode an amino acid different from leucine, and preferably to encode a phenylalanine at position 118 according to a FAD2 protein of the invention.
In other words, a nucleic acid molecule of the invention can comprise (or consist of) a nucleic acid sequence of SEQ ID NO 1, 5, 9 or 10, further comprising at least one mutation in the codon encoding the amino acid at position 118, to encode an amino acid different from leucine, and preferably to encode a phenylalanine at position 118.
A preferred nucleic acid molecule of the invention comprises (or consists of) a nucleic acid sequence of SEQ ID NO 7.
In another aspect, a nucleic acid molecule of the invention can encode a FAD2 protein having a deletion at position 118 relative to a wild type FAD2 protein, such as a wild type FAD2 protein represented by the amino acid sequence of SEQ ID NO 2 or 6.
More particularly, a nucleic acid molecule of the invention can encode a FAD2 protein having a leucine deleted at position 118 relative to a wild type FAD2 protein represented by the amino acid sequence of SEQ ID NO 2 or 6.
A nucleic acid molecule of the invention can comprise (or consist of) a nucleic acid sequence of SEQ ID NO 1, 5, 7, 9 or 10, wherein the codon encoding the amino acid at position 118 has been deleted (i.e. of SEQ ID NO 1, 5, 7, 9 or 10 further deleted of the codon encoding the amino acid at position 118).
It will be appreciated by the skilled person that the nucleic acid sequences of SEQ ID NO 1, 5, 7, 9 and 10 are not the only sequences that can be used to provide a FAD2 protein of the invention. Also contemplated are any nucleic acid molecules having different sequences but which, because of the degeneracy of the genetic code, encode a FAD2 protein comprising a substitution of an amino acid at position 118 (or corresponding to position 118) relative to the wild-type amino acid sequence, such as the wild-type FAD2 protein represented by SEQ ID NO 2 or 6.
In particular, a nucleic acid molecule of the invention can comprise (or consist of) a nucleotide sequence having at least 80%, preferably at least 85%, more preferably at least 90% and even more preferably at least 95%, 96%, 97%, 98% or 99% identity with any of SEQ ID NO 1, 5, 7, 9 and 10, or with the complementary form or RNA form thereof, encoding a FAD2 protein having an amino acid substitution at position 118 relative to a wild-type FAD2 protein.
A nucleic acid molecule of the invention having said mutation(s) resulting in said amino acid substitution at position 118 can be derived from Brassica napus varieties, such as 28DHS.086 variety and/or MSP12 variety.
More particularly, a nucleic acid molecule of the invention has a mutation at position 1590 (also referred to as SNP1590) of the acid nucleic sequence of SEQ ID NO 10, which causes a change in genetic codon from CTT to TTT, resulting in a substitution of an amino acid at position 118 relative to the wild-type amino acid sequence, such as the wild-type FAD2 protein represented by SEQ ID NO 6.
An isolated nucleic acid molecule of the invention containing said SNP1590 mutation, resulting in a substitution of phenylalanine for leucine at position 118, alters the functionality of the resulting FAD2 gene product, whereby the level of oleic acid is increased in plant expressing the mutant sequence, compared to the corresponding level in plant expressing the wild-type sequence.
In the framework of the invention, the term “SNP1590” refers to the single nucleotide polymorphism corresponding to said mutation at position 1590 of the nucleic acid of SEQ ID NO 10, and can refer also to the corresponding mutation in any nucleic acid molecule encoding a FAD2 protein of the invention having a substituted amino acid at position 118 (or corresponding to position 118) relative to the wild-type FAD2 protein, such as the wild-type FAD2 protein represented by SEQ ID NO 2 or 6.
Any fragment of a nucleic acid molecule of the invention of at least 10, 15, 20, 25, 50, 100 or more nucleotides and comprising at least one mutation resulting in a FAD2 protein according to the invention is contemplated.
In particular, a fragment of a nucleic acid molecule of the invention of at least 10, 15, 20, 25, 50, 100 or more nucleotides comprising said deletion DEL1421, DEL1453 or DEL215 or said SNP1590 is contemplated.
Also contemplated is a fragment of a nucleic acid molecule of the invention of at least 20, 25, 50, 100 or more nucleotides comprising said DEL1421 and said SNP1590.
Such fragments can be used as primers, as probes and/or as markers.
The nucleic acid fragments of the invention can be used as markers in plant genetic mapping.
In particular, the nucleic acid fragments of the invention can be used as markers in plant breeding programs.
Such markers may include restriction fragment length polymorphism (RFLP), random amplification polymorphism detection (RAPD), polymerase chain reaction (PCR) or self-sustained sequence replication (3SR) markers, for example.
Marker-assisted breeding techniques may be used to identify and follow a plant according to the invention or its progeny, also object of the invention, during the breeding process.
Marker-assisted breeding techniques may be used in addition to, or as an alternative to, other sorts of identification techniques.
An example of marker-assisted breeding is the use of PCR primers that specifically amplify a nucleic acid molecule of the invention.
The invention thereby provides methods for segregation and selection analysis of genetic crosses involving plants having nucleic acid sequences of the invention.
Also object of the present invention is a nucleic acid molecule of at least 10 or 15 nucleotides, preferably 20, 25, 50, 100 or more nucleotides, that hybridizes under stringent conditions to any nucleic acid sequence of SEQ ID NO 1, 3, 5, 7, and 9 to 12, which contains (or further contains) a mutation according to the invention.
An example of stringent hybridization conditions is hybridization at about 50° C., or at about 60° C. or higher, and 0.1×SSC (buffer of 0.15M NaCl, 0.015M trisodium citrate).
A method of the invention may for example involve determining the presence in a genome of particular FAD2 alleles containing at least said deletion at (or corresponding to) position 1421 relative to a wild type FAD2 gene, such as the wild type FAD2 gene represented by SEQ ID 9 and/or said substitution, SNP1590, (resulting in a substitution of phenylalanine for leucine) at (or corresponding to) position 118 relative to a wild type FAD2 protein, such as the wild type FAD2 protein represented by SEQ ID NO 2 or 6.
Such a determination may for example be achieved with a range of techniques, such as PCR amplification, DNA fingerprinting, RNA fingerprinting, gel blotting and RFLP analysis, nuclease protection assays, sequencing of the relevant nucleic acid fragment, the generation of antibodies (monoclonal or polyclonal), or alternative methods adapted to distinguish the protein produced by the relevant alleles from other variant forms of that protein or from the wild-type.
More particularly, such fragments can be used in method of marker assisted selection for high oleic traits in plants, preferably in Brassica species, more particularly in Brassica napus varieties.
Another aspect of the present invention is related to a recombinant nucleotide sequence comprising, operably linked to a nucleotide sequence according to the invention, one or more adjacent regulatory sequence(s). Said adjacent regulatory sequence(s) is/are preferably originating from homologous organisms.
However said adjacent regulatory sequences may also be originating from heterologous organisms.
Said adjacent regulatory sequences are specific sequences such as promoters, enhancers, secretion signal sequences and/or terminators.
Another aspect of the invention is related to a vector comprising a nucleic acid molecule of the invention, possibly operably linked to one or more adjacent regulatory sequence(s) originating from homologous or from heterologous organisms.
In the present context “vector” is defined as any biochemical construct which may be used for the introduction of a nucleotide sequence (by transduction, transfection, transformation, infection, conjugation, etc.) into a cell.
Advantageously, a vector according to the invention is selected from the group consisting of plasmids (including replicative and integrative plasmids), viruses, phagemids, chromosomes, transposons, liposomes, cationic vesicles, or a mixture thereof. Said vector may already comprise one or more adjacent regulatory sequence(s), allowing the expression of said nucleic acid molecule and its transcription into a polypeptide of the invention.
The present invention also encompasses any peptide, which may still have a delta-12 oleate desaturase activity, resulting from the expression of a nucleic acid of the invention containing said deletion (DEL1421, DEL1453 or DEL215), such as the peptide of SEQ ID NO 4.
Nucleic acid molecules, recombinant nucleic acid molecules, and/or vectors of the present invention are useful to transform target plants, and thereby confer altered FAD2 gene product, whereby the level of oleic acid is modified, preferably increased, in plant expressing a mutant FAD2 of the invention, compared to the corresponding level in plant expressing the wild-type sequence.
The present invention is also related to a transformed host cell, or recombinant host cell, containing (or having incorporated) one or more of the nucleotide sequences and/or vectors according to the invention having the deletion 1421.
In the present context, a “transformed host cell” or “recombinant cell”, also referred to as “transformant”, is a cell having incorporated one or more of the nucleotide sequences and/or vectors according to the invention. The transformed host cell may be a cell in which said vector(s) and/or said nucleotide sequence(s) is/are introduced by means of genetic transformation, preferably by means of homologous recombination, or by any other well known methods used for obtaining a recombinant organism.
Any method by which the novel sequence can be incorporated into the host genome is contemplated by the present invention.
More particularly, any method by which the novel sequence can be incorporated into the host genome, and stably inherited by its progeny, is contemplated by the present invention.
A broad range of known techniques currently exist for achieving direct or indirect transformation of higher plants with exogenous DNA.
Transformation of plant cells can be mediated by the use of vectors. A common method of achieving transformation is the use of Agrobacterium tumefaciens to introduce a foreign gene into the target plant cell.
Plant viruses also provide a possible means for transfer of exogenous DNA.
Direct uptake of plant cells can also be employed. Typically, protoplasts of the target plant are placed in culture in the presence of the nucleic acid molecules to be transferred, and an agent which promotes the uptake of said nucleic acid molecules by protoplast. Useful agents in this regard are polyethylene glycol or calcium phosphate.
Alternatively, nucleic acid molecules uptake can be stimulated by electroporation. In this method, an electrical pulse is used to open temporary pores in a protoplast cell membrane, and said nucleic acid molecules in the surrounding solution are then drawn into the cell through the pores. Similarly, microinjection can be employed to deliver said nucleic acid molecules directly into a cell, and preferably directly into the nucleus of the cell.
In these techniques, transformation occurs in a plant cell in culture. Subsequent to the transformation event, plant cells can be regenerated to whole plants.
Techniques for the regeneration of mature plants from callus or protoplast culture are well known.
Alternate methods are also available which do not necessarily require the use of isolated cells, and therefore, plant regeneration techniques, to achieve transformation. These are generally referred to as “ballistic” or “particle acceleration” methods, in which nucleic acid molecules coated metal particles are propelled into plant cells by either a gunpowder charge or electrical discharge. In this manner, plant cells in culture or plant reproductive organs or cells, e.g. pollen, can be stably transformed with the nucleic acid molecules of interest.
The present invention can be applied to transformation of virtually any type of plant, monocotyledons or dicotyledons.
Suitable plants to be transformed are preferably oil producing crops, such as sunflower, soybean, cotton, corn, etc., preferably Brassica species, more preferably Brassica napus varieties.
The present invention relates to a plant or a plant part or a seed containing a first FAD2 gene and possibly a second FAD2 gene, said first or said second FAD2 gene having said deletion (DEL.1421, DEL.1453 or DEL.215).
More particularly, a plant or a plant part or a seed of the invention contains a first FAD2 gene and possibly a second FAD2 gene, said first or said second FAD2 gene having a deletion at or corresponding to position 1421 (also referred to as DEL.1421) relative to a wild-type FAD2 gene, such as wild-type FAD2 gene of SEQ ID NO 9.
Preferably, a plant or a plant part or a seed of the invention contains a first FAD2 gene having a deletion at or corresponding to position 1421 relative to a wild-type FAD2 gene, such as wild-type FAD2 gene of SEQ ID NO 9, and a second FAD2 gene encoding a FAD-2 protein having an amino acid substitution at or corresponding to position 118 relative to a wild-type FAD-2 protein, such as the wild-type FAD-2 protein of SEQ ID NO 2 or 6.
In particular, a plant or a plant part or a seed of the invention preferably contains a nucleic acid sequence corresponding to SEQ ID NO 1 or 5, wherein the nucleotide (C) at position 215 is deleted (i.e. corresponding to SEQ ID NO 1 or 5 further deleted of the nucleotide at position 215), or contains a (variant) nucleic acid sequence, of at least 80%, preferably at least 85%, more preferably at least 90% and even more preferably at least 95%, 96%, 97%, 98% or 99% identity with SEQ ID NO 1 or 5, wherein the nucleotide corresponding to position 215 is deleted (i.e. with SEQ ID NO 1 or 5 further deleted of the nucleotide corresponding to position 215).
Examples of such plants are CONTACT and CABRIOLET varieties, which are registered varieties.
A preferred plant or a plant part or a seed according to the invention, further contains a nucleic acid sequence encoding a FAD-2 protein having an amino acid substitution at or corresponding to position 118 relative to a wild-type FAD-2 protein, such as the wild-type FAD-2 protein of SEQ ID NO 2 or 6. Preferably, said substituted amino acid at or corresponding to position 118 is phenylalanine.
Examples of such plants are 28DHS.086 and MSP12 varieties.
MSP05 variety is maintained as a Budapest Treaty patent deposit with NCIMB, 23 St. Machar Drive, Aberdeen, AB24 3RY, Scotland, under accession number NCIMB 41233 made Jul. 9, 2004.
28DHS.086 variety is maintained as a Budapest Treaty patent deposit with NCIMB, Bucksburn, Aberdeen, AB21 9YA, Scotland, under accession number NCIMB 41365 made Dec. 22, 2005.
MSP12 variety is maintained as a Budapest Treaty patent deposit with NCIMB, Bucksburn, Aberdeen, AB21 9YA, Scotland, under accession number NCIMB 41374 made Feb. 10, 2006.
A mutated plant or a plant part or a seed according to the invention exhibits the surprising advantage of developing a good rooting system. More particularly, having regard to a mutated Brassica napus variety according to the invention, the principal root and the secondary rooting system have a length comparable (similar) to respectively the principal root and the secondary rooting system of wild-type varieties. In comparison, mutated Brassica napus obtained by carrying out the method described in WO98/56239 shows a principal root much smaller than the wild-types and a secondary rooting system severely impaired.
A plant or a plant part or a seed according to the invention can be obtained by a mutagenesis treatment, more particularly by an Ethyl Methane Sulfonate (EMS) treatment.
Another object of the invention is a method of producing high oleic plant lines comprising: (a) crossing a first plant with a second plant having at least one FAD2 gene having said deletion according to the invention, (b) obtaining seeds from the cross of step (a), (c) growing fertile plants from such seeds; (d) obtaining progeny seeds from the plants of step (c), and (e) identifying those seeds among the progeny that have high oleic acid content.
In said method of producing high oleic plant lines, said second plant preferably have a second mutant FAD2 gene having said SNP1590 mutation.
In another aspect, the invention provides a method for increasing the oleic acid content of plants, more particularly of Brassica plants, and preferably of Brassica napus plants comprising the steps of:

    (a) inducing mutagenesis in at least some cells from a plant, more particularly of a Brassica plant, and preferably of a Brassica napus plant that has a oleic acid content of less than 70%;
    (b) regenerating plants from at least one of said mutagenized cells;
    (c) selecting regenerated plants which have a nucleic acid sequence of the invention and/or which expresses a FAD2 protein of the invention; and
    (d) deriving further generations of plants from said regenerated plants.


Preferably, the seeds obtained from said plants provide an oil having an oleic acid content of more than 70 wt. %, more preferably of more than 75 wt. %, based upon the total weight of fatty acid present the oil.
Another object of the invention is a vegetable oil obtained from at least one plant according to the invention, which vegetable oil comprises more than (about) 70%, 72%, 75%, 80%, or 85% of oleic acid.
More particularly, a vegetable oil of the invention, obtained preferably from at least one Brassica species of the invention, more preferably from at least one Brassica napus variety according to the invention, comprises more than (about) 70%, 72%, 75%, 80%, or 85% of oleic acid. Said oil can further comprise less than (about) 4%, 3.5%, 3%, 29%, 19% or 0.5% of linolenic acid, based upon the total weight of the fatty acids present in the oil.
Preferably, said oil comprises more than (about) 70%, 72%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89% or 90%, preferably between (about) 70% and (about) 90%, more preferably between (about) 72% and (about) 89% of oleic acid. Said oil can further comprise less than (about) 4%, 3.5%, 3%, 2%, 1%, or 0.5%, preferably between (about) 4% and (about) 0.4% of linolenic acid, based upon the total weight of the fatty acids present in the oil.
According to a preferred embodiment, two double low winter rapeseed varieties (ENVOL and LIBERATOR) were submitted to an Ethyl Methane Sulfonate (EMS) treatment in 1992. The EMS treatment was performed at 2.5% and 5% for 4 h or 8 h.
The M1 generation was grown in a greenhouse after 8 weeks of vernalization in a growth chamber and then harvested in July 93.
M1 seeds were planted in the field in September 93, bagged at the beginning of flowering and M2 seeds harvested in July 94.
M2 seeds were planted in September 94, bagged at the beginning of flowering and M3 seeds harvested in July 95.
The progenies were then analysed for fatty acid composition using gas chromatography based analytical method, as commonly known in this area of technology.
All progenies showing an oleic content higher than 68% were kept.
Selected progeny was replanted in the field in September 1995, bagged in April then harvested in July 1996.
At this stage progenies were screened for good agronomic and morphological characteristics, such as good germination capacity, good autumn vigor, good winter hardiness, good rooting system, good blackleg and light leaf spot resistance as well as excellent lodging resistance.
Material which was too tall and too late was eliminated as well as material showing strong fasciation.
Analysis of the remaining progeny was again done by gas chromatography to select individuals with oleic acid levels higher than 68%. All of these individuals were planted in the field in September 1996-1997.
A progeny called MUT 152-96 looked particularly interesting in terms of agronomic and morphological characteristics, as well as for its oleic acid content. It was cultivated in isolation during the crop season of September 1.996-1997. The most interesting progenies in terms of agronomic and morphological characteristics were selected for bagging and crossing.
Crossing was performed with double low winter oilseed rape varieties having a conventional fatty acid profile (i.e. oleic acid below 70%) or with low linolenic acid content (i.e. less than about 3.5%) in order to develop lines with a high oleic acid content associated with low linolenic acid content (HOLL).
The material was progressed into pedigree breeding, self pollination until at least the F7 generation.
At all generations strong selection pressure was applied against fasciation and for normal plant development and normal rooting system.
Fatty acid composition was monitored in each generation and only material with oleic acid content higher than 75% and linolenic acid content below 3.5% was kept.
Different HOLL varieties were obtained by this process such as for example MSP05.
And by crossing MSP05 variety and CABRIOLET variety, 28DHS.086 variety was obtained.
MSP12 was developed by the same breeding process than MSP05 but as among starting parent CONTACT was used instead of parents having a conventional fatty acid profile.
The double low varieties with conventional fatty acid profiles used in this work were BRISTOL, CAPITOL, CAPVERT, VIVOL and CAIMAN and these varieties have been multiplied or maintained using the same maintenance scheme as described here above for the HOLL lines (in accordance with the technical rules published by the “GNIS” and edited by SEDIS, e.g. see 2003 edition, vol. 1, pp. 135-147 related to crop plants).
Basic seed was used for the determination of fatty acid content in trials—small research trials (6 to 12 m2) or development trials (500 m2) and for the sequencing work.
EXAMPLES
Example 1
The seeds were grinded in a first solution consisting of methanol (800 ml), trimethyl-pentane (200 ml) and 5 g of Na OH. About 3 ml of solution was used for about 10 g of seeds (in other words about 10 to 50 seeds for 1 ml of solution).
Extraction was performed during 20 minutes and thereafter a second solution, consisting of trimethylamine (900 ml), and propanol, 2-(100 ml), was added at the same volume as the first solution.
The resulting solution was vortexed and allowed to rest until formation of an upper phase.
The upper phase was sampled and transferred into viols.
One microliter of same was injected in a gas chromatograph (Fisons from thermo-electron with a column DB3-30 meter with a diameter of 0.25 mm and a thickness of 25 micrometer). Running time was about 4 min.
The oleic acid content results are summarized in table 1.









TABLE 1





Varieties
Oleic acid content (wt. %)
Appreciation







CONTACT
71.8-75.2
High


CABRIOLET
73.2-76.8
High


28DHS086
80.3-83.1
Very high


MSP12
80.3-83.5
Very high


MSP05
78.1-81.9
Very high


BRISTOL
61.4-65.7
Normal


VIVOL
60.8-63.2
Normal


CAPVERT
58.9-65.9
Normal


CAIMAN
61.9-64.0
Normal


CAPITOL
59.7-64.6
Normal









The oleic acid content is based on the total weight of the fatty acid in the extracted oil.
Example 2
Plant materials used for sequencing are:

    
    
        mutant lines with higher oleic fatty acid content: CONTACT, CABRIOLET and 28DHS.086; and
        wild type varieties with normal oleic acid content: Bristol, Capitol, Vivol, Capvert and Caiman.
    
    


All these lines were grown in a growth chamber and the cotyledons and stems were collected from 7-day-old plants.
The plant tissues were freeze-dried and used for DNA extraction.
DNA was isolated with Qiagen Plant DNA kits (Qiagen INC.-USA, Valencia Calif.).
PCR was performed with TaqGold protocol (AB Biosystem, Inc,).
Reaction mix includes 2.5 μl 10× buffer, 0.2 μl TaqGold, 0.2 μl dNTP (25 mM), 2 μl primers (5 uM) and 10 ul DNA template (2 ng/ul) and 10.1 ul H2O.
PCR cycles were as follows: 94° C. 5 min; 8 cycles of 94° C. 40 sec, 62° C. 40 sec, 72° C. 1 min, 94° C. 40 sec, 60° C. 40 sec, 72° C. 1 min, 94° C. 40 sec, 58° C. 40 sec, 72° C. 1 min, 94° C. 40 sec, 56° C. 40 sec, 72° C. 1 min; 3 cycles of 94° C. 40 sec, 55° C. 40 sec, 72° C. 1 min; hold at 72° C. for 7 min.
PCR products were analyzed on 1% agarose gel.
For sequencing, 5 μl PCR products were removed to a new tube and 1 μl ExonucleaseI (1:50 dilution) and 1 μl Shrimp Alkaline Phosphatase (1:5 dilution).
The mix was incubated at 37° C. for 20 min and then 80° C. for 15 min to inactivate the enzymes.
40 μl H2O was added and 6 μl were used as template with 1 μl sequencing primer.
Sequencing was done on 3730 DNA Analyzer (Applied Biosystems).
Sequences were assembled and aligned using SeqMan II program of the LaserGene (DNASTAR, INC, Madison. WI).
Example 3
Four Brassica napus delta-12 oleate desaturase (FAD2) gene sequences, 4684997, 46399190, 8705228 and 4092878, were downloaded from Genebank (NCBI). These sequences were used as queries to blast against Monsanto sequence database.
Using the “blastn” programs (NCBI), a number of high score hits were obtained. All the hit sequences were downloaded and reassembled with the SeqmanII program (DNASTAR Inc, Madison, Wis., USA).
Two distinct transcripts were identified and designated as Fad2-1 (SEQ ID NO 11) and Fad2-2 (SEQ ID NO 12). Fad2-1 and Fad2-2 share a high sequence homology, with 97% sequence identity.
To identify causative mutations associated with high oleic acid content in the mutant lines and their progenies, nested locus-specific primers were designed to cover the entire sequences.
The 3′ end of a primer was always located at a nucleotide that differentiated Fad2-1 from Fad2-2 except those located at 5′ and 3′ ends of the consensus sequences where there was not differential nucleotide between the two genes.
The primers were also designed in such way that one amplicon would overlap with another to ensure full coverage of the entire sequence. These primers were arrayed and used to generate locus-specific amplicons on mutants and wild types. Sequencing results indicated that all the locus-specific PCR primers behaved as expected.
Sequences belonging to the same gene were assembled together using SeqManII program.
The consensus genomic sequences of the wild-type Fad2-l and Fad2-2 genes are represented respectively by SEQ ID NO 9 and 10.
Table 2 summarizes the sequence features of both Fad2-1 and Fad2-2 genes.









TABLE 2





Features
FAD2-1 position
FAD2-2 position







Gene
  1-2601
  1-2666


5′ UTR
  1-1206
  1-1238


Exon
 1-108
 1-111


Intron
 109-1202
 112-1234


Exon
1207-2601
1235-2619


CDS
1207-2361
1239-2393


3 ′UTR
2362-2601
2394-2666









The features are based on the consensus genomic sequences from multiple reads on different genotypes.
Both Fad2-1 and Fad2-2 genes have one intron each.
The intron sizes are slightly different between two genes. For Fad2-1, intron spans 1105 bp starting from position 109 to 1213, while for Fad2-2, intron consists of 1123 bp starting from position 112 to 1234 on the consensus sequences.
The intron is located at 5′ UTR region.
Putative translation initiation codons are located at 1207 and 1239 for Fad2-1 and Fad2-2 genes, respectively.
The translation termination codons are located at 2370-2372 and 2391-2393, respectively for Fad2-1 and Fad2-2.
3′ UTR sequences are 247 base pairs for Fad2-1 and 273 base pairs for Fad2-2 genes.
A deletion at position 1421 (called DEL.1421) of FAD2-1 gene caused a frame-shift in genetic codons, resulting in premature termination of the polypeptides.
A point mutation at position 1590 (SNP1590) of FAD2-2 gene (as represented by SEQ ID NO 7) caused an amino acid residue change from leucine (CTT) to phenylalanine (TTT).
Both leucine and phenylalanine are hydrophobic in nature and share some common amino acid properties, but phenylalanine contains a large rigid aromatic group on the side chain that causes some change in the function of the enzyme.
Moreover, in combination with DEL.215, this mutation causes more visible effect on the phenotype.
Combination of different alleles at these mutations created a gradient on oleic content as observed on different mutant lines (see table 1).
Two mutant lines, 28DHS.086 and MSP12, carried double mutations at DEL1421 and SNP1590. Since both mutations were missense mutations, the FAD2 gene functions are severely affected, resulting in the highest oleic content in the mutant line.
It is to be noted that Brassica napus varieties carrying only the SNP1590 mutation exhibits a normal oleic acid content (i.e. an oleic acid content equivalent to the oleic acid content of the wild-types).
Two mutant lines, CONTACT and CABRIOLET, carried a single point mutation at DEL.1421, resulting in an oleic content slightly below in comparison with the double mutants.
In summary, the sequence data strongly indicated that these mutations, at Fad2-1 and Fad2-2 are associated with oleic contents on different mutant lines.
The identification of causative sequence variations is crucial to design diagnostic assays specifically for each mutant allele.
Knowledge of association between sequence variations and phenotypes can allow to design marker assays to accurately predict the oleic acid content in plants without the need of wet chemical analysis of the fatty acid content.

## Claims

1. An isolated nucleic acid molecule encoding a FAD2 protein having reduced desaturase activity, wherein the molecule comprises a nucleotide sequence selected from the group consisting of:
(a) the nucleotide sequence of SEQ ID NO: 1 wherein the nucleotide at position 215 is deleted;
(b) the nucleotide sequence of SEQ ID NO: 5 wherein the nucleotide at position 215 is deleted;
(c) the nucleotide sequence of SEQ ID NO: 3, its complementary form, or the RNA form thereof;
(d) a nucleotide sequence having at least 95% identity with the nucleotide sequence of SEQ ID NO: 1 wherein the nucleotide corresponding to position 215 is deleted;
(e) a nucleotide sequence having at least 95% identity with the nucleotide sequence of SEQ ID NO: 5 wherein the nucleotide corresponding to position 215 is deleted;
(f) a nucleotide sequence fragment comprising at least 10 contiguous nucleotides of an isolated nucleic acid molecule of (a), wherein the fragment comprises a mutated codon resulting from the deletion at position 215; and
(g) a nucleotide sequence fragment comprising at least 10 contiguous nucleotides of an isolated nucleic acid molecule of (b), wherein the fragment comprises a mutated codon resulting from the deletion at position 215.

2. The isolated nucleic acid molecule of claim 1, further comprising a nucleotide sequence selected from the group consisting of:
(a) the nucleotide sequence of SEQ ID NO: 9 wherein the nucleotide at position 1421 is deleted;
(b) a nucleotide sequence having at least 95% identity with the nucleotide sequence of SEQ ID NO: 9 wherein the nucleotide corresponding to position 1421 is deleted; and
(c) a nucleotide sequence fragment comprising at least 10 contiguous nucleotides of an isolated nucleic acid molecule of (a), wherein the fragment comprises a mutated codon resulting from the deletion at position 1421.

3. An isolated nucleic acid molecule encoding a FAD2 protein having reduced desaturase activity, wherein the molecule comprises a nucleotide sequence selected from the group consisting of:
(a) the nucleotide sequence of SEQ ID NO: 9 wherein the nucleotide at position 1421 is deleted;
(b) the nucleotide sequence of SEQ ID NO: 10 wherein the nucleotide at position 1453 is deleted;
(c) a nucleotide sequence having at least 95% identity with the nucleotide sequence of SEQ ID NO: 9 wherein the nucleotide corresponding to position 1421 is deleted;
(d) a nucleotide sequence having at least 95% identity with the nucleotide sequence of SEQ ID NO: 10 wherein the nucleotide corresponding to position 1453 is deleted;
(e) a nucleotide sequence fragment comprising at least 10 contiguous nucleotides of an isolated nucleic acid molecule of (a), wherein the fragment comprises a mutated codon resulting from said deletion; and
(f) a nucleotide sequence fragment comprising at least 10 contiguous nucleotides of an isolated nucleic acid molecule of (b), wherein the fragment comprises a mutated codon resulting from said deletion.

4. A vector comprising a nucleic acid molecule according to claim 1.

5. A host cell comprising a nucleic acid molecule according to claim 1.

6. A plant stably transformed with a vector of claim 4.

7. A method of enhancing the oleic acid content in a plant comprising transforming a plant with the vector of claim 4.

8. A method of producing high oleic plant lines, the method comprising:
(a) inducing mutagenesis in a cell from a plant that has an oleic acid content of less than 70%;
(b) regenerating a plant from said mutagenized cell;
(c) selecting regenerated plants which have a nucleic acid sequence according to claim 1; and
(d) deriving further generations of plants from said regenerated plants.

9. The method according to claim 8, wherein the cell from a plant is from a Brassica plant.

10. The method according to claim 9, wherein the Brassica plant is a Brassica napus plant.

11. The method according to claim 8, wherein said regenerated plant further comprises a nucleic acid sequence encoding a FAD2 protein having an amino acid substitution at or corresponding to position 118 relative to a wild-type FAD2 protein of SEQ ID NO: 2 or SEQ ID NO: 6.

12. The method according to claim 8, wherein the mutagenesis is induced by ethyl methane sulfonate treatment.

13. A plant obtained by the method according to claim 8.

14. A method of producing high oleic plant lines, the method comprising:
(a) crossing a first plant of claim 6 with a second plant,
(b) obtaining seeds from the cross of step (a),
(c) growing fertile plants from the seeds,
(d) obtaining progeny seeds from the plants of step (c), and
(e) identifying those seeds among the progeny that have high oleic acid content.

15. A method of producing high oleic plant lines, the method comprising:
(a) crossing a first plant of claim 13 with a second plant,
(b) obtaining seeds from the cross of step (a),
(c) growing fertile plants from the seeds,
(d) obtaining progeny seeds from the plants of step (c), and
(e) identifying those seeds among the progeny that have high oleic acid content.

16. An assay kit comprising a first container containing a nucleic acid molecule of claim 1.