# Patent

## Title
Modification of flavonoid biosynthesis in plants

## Abstract

The present invention relates to nucleic acids encoding flavonoid biosynthetic enzymes, flavonoid-regulating transcription factors and a flavonoid-specific membrane transporter in plants, and the use thereof for the modification of flavonoid biosynthesis in plants. The present invention also relates to constructs and vectors including such nucleic acids, and related polypeptides. More particularly, the protein involved in flavonoid biosynthesis is selected from the group consisting of TRANSPARENT TESTA 12 (TT12), TRANSPARENT TESTA GLABRA 1 (TTG1), TRANSPARENT TESTA 2 (TT2), TRANSPARENT TESTA 8 (TT8), leucoanthocyanidin dioxygenase (LDOX), cinnamate-4-hydroxylase (C4H), 4-coumaroyl:CoA-ligase (4CL); and functionally active fragments and variants thereof.

## Background
The present invention relates generally to nucleic acid fragments and their encoded amino acid sequences for flavonoid biosynthetic enzymes in plants, and the use thereof for the modification of flavonoid biosynthesis in plants.
Flavonoids constitute a relatively diverse family of aromatic molecules that are derived from phenylalanine and malonyl-coenzyme A (CoA, via the fatty acid pathway). These compounds include six major subgroups that are found in most higher plants: the chalcones, flavones, flavonols, flavandiols, anthocyanins and condensed tannins (or proanthocyanidins). A seventh group, the aurones, is widespread, but not ubiquitous.
Some plant species also synthesize specialised forms of flavonoids, such as the isoflavonoids that are found in legumes and a small number of non-legume plants. Similarly, sorghum and maize are among the few species known to synthesize 3-deoxyanthocyanins (or phlobaphenes in the polymerised form). The stilbenes, which are closely related to flavonoids, are synthesised by another group of unrelated species that includes grape, peanut and pine.
Besides providing pigmentation to flowers, fruits, seeds, and leaves, flavonoids also have key roles in signalling between plants and microbes, in male fertility of some species, in defense as antimicrobial agents and feeding deterrents, and in UV protection.
Flavonoids also have significant activities when ingested by animals, and there is great interest in their potential health benefits, particularly for compounds such as isoflavonoids, which have been linked to anticancer benefits, and stilbenes that are believed to contribute to reduced heart disease.
The major branch pathways of flavonoid biosynthesis start with general phenylpropanoid metabolism and lead to the nine major subgroups: the colorless chalcones, aurones, isoflavonoids, flavones, flavonols, flavandiols, anthocyanins, condensed tannins, and phlobaphene pigments. The enzyme phenylalanine ammonia-lyase (PAL) of the general phenylpropanoid pathway will lead to the production of cinnamic acid. Cinnamate-4-hydroxylase (C4H) will produce p-coumaric acid which will be converted through the action of 4-coumaroyl:CoA-ligase (4CL) to the production of 4-coumaroyl-CoA and malonyl-CoA.
In the phenylpropanoid pathway, chalcone synthase (CHS) uses malonyl CoA and 4-coumaryl CoA as substrates. Chalcone reductase (CHR) balances the production of 5-hydroxy- or 5-deoxyflavonoids. The next enzyme, chalcone isomerase (CHI) catalyses ring closure to form a flavanone, but the reaction can also occur spontaneously. Further enzymes in the pathway are: flavanone 3-hydroxylase (F3H), dihydroflavonol 4-reductase (DFR), flavonoid 3′-hydroxylase (F3′H) and flavonoid 3′,5′ hydroxylase (F3′5′H).
In the branch of the phenylpropanoid pathway that is specific to condensed tannin and anthocyanin production, leucoanthocyanidins can be reduced to catechins by leucoanthocyanidin reductase (LAR) or to anthocyanidins by leucoanthocyanidin dioxygenase (LDOX). Anthocyanidins can be converted to anthocyanins by the addition of sugar groups, or to epicatechins by anthocyanidin reductase (ANR), encoded by the BANYULS gene. Catechins and epicatechins are the subunits of condensed tannins (CTs), which in Arabidopsis are thought to be transported into the vacuole by a multidrug secondary transporter-like protein, TRANSPARENT TESTA 12 (TT12), and polymerised by an unknown mechanism.
Enzymes in the flavonoid pathway have been found to be controlled by a range of transcription factors in Arabidopsis, maize and petunia. In Arabidopsis, condensed tannin biosynthesis requires the function of TRANSPARENT TESTA 2 (TT2), a myb family factor, TRANSPARENT TESTA 8 (TT8), a myc family factor and TRANSPARENT TESTA GLABRA 1 (TTG1), a WD40 family factor, among other transcription factors. These three proteins are thought to form a transcription complex that coordinately activates multiple flavonoid pathway enzymes in order to promote condensed tannin production in Arabidopsis seeds. Other myc and myb family transcription factors regulate distinct parts of the flavonoid pathway in maize, petunia and other plant species.
While nucleic acid sequences encoding some flavonoid biosynthetic enzymes have been isolated for certain species of plants, for example certain C4H, 4CL, LDOX, TT12-like transporters and TT8-like, TT4-like and TTG1-like transcription factors, there remains a need for materials useful in modifying flavonoid biosynthesis; in modifying protein binding, metal chelation, anti-oxidation, and UV-light absorption; in modifying plant pigment production; in modifying plant defense to biotic stresses such as viruses, microorganisms, insects, fungal pathogens; in modifying forage quality, for example by disrupting protein foam and conferring protection from rumen pasture bloat, particularly in forage legumes and grasses, including alfalfa, medics, clovers, ryegrasses and fescues. There is also a need for methods of using such materials.
It is an object of the present invention to overcome, or at least alleviate, one or more of the difficulties or deficiencies associated with the prior art or to assist in meeting the needs stated above.
In one aspect, the present invention provides a substantially purified or isolated nucleic acid or nucleic acid fragment encoding a flavonoid biosynthesis-regulating transcription factor selected from the group consisting of TRANSPARENT TESTA GLABRA 1 (TTG1), TRANSPARENT TESTA 2 (TT2), and TRANSPARENT TESTA 8 (TT8); a flavonoid biosynthetic enzyme selected from the group consisting of leucoanthocyanidin dioxygenase (LDOX), cinnamate-4-hydroxylase (C4H) and 4-coumaroyl:CoA-ligase (4CL); and a flavonoid transporter TRANSPARENT TESTA 12 (TT12); from a clover (Trifolium), medic (Medicago), ryegrass (Lolium) or fescue (Festuca) species; or a functionally active fragment or variant thereof. The present invention further provides substantially purified or isolated nucleic acids or nucleic acid fragments complementary and antisense to the nucleic acids or nucleic acid fragments of the present invention.
The present invention also provides substantially purified or isolated nucleic acids or nucleic acid fragments encoding amino acid sequences for a class of proteins which are related to C4H, 4CL, LDOX, TT12, TT2, TT8 and TTG1, or functionally active fragments or variants thereof. Such proteins are referred to herein as C4H-like, 4CL-like, LDOX-like, TT12-like, TT2-like, TT8-like and TTG1-like, respectively. Proteins are related in that either one of both of the following criteria apply: (i) the genes which encode these proteins are expressed in a similar manner to C4H, 4CL, LDOX, TT12, TT2, TT8 or TTG1, and (ii) the polypeptides have similar functional activity to C4H, 4CL, LDOX, TT12, TT2, TT8 and TTG1. In a preferred embodiment, the related proteins are at least 70%, preferably at least 80%, more preferably at least 90% homologous to C4H, 4CL, LDOX, TT12, TT2, TT8 or TTG1. Also provided are substantially isolated nucleic acids or nucleic acid fragments complementary and antisense to C4H-like, 4CL-like, LDOX-like, TT12-like, TT2-like, TT8-like and TTG1-like-encoding nucleic acid fragments.
The individual or simultaneous enhancement or otherwise manipulation of the expression of C4H, 4CL, LDOX, TT12, TT2, TT8, TTG1 or -like polypeptides in plants may enhance or otherwise alter flavonoid biosynthesis; may enhance or otherwise alter the plant capacity for protein binding, metal chelation, anti-oxidation, and UV-light absorption; may enhance or reduce or otherwise alter plant pigment production.
The individual or simultaneous enhancement or otherwise manipulation of the expression of C4H, 4CL, LDOX, TT12, TT2, TT8, TTG1 or -like polypeptides in plants has significant consequences for a range of applications in, for example, plant production and plant protection. For example, it has applications in increasing plant tolerance and plant defense to biotic stresses such as viruses, microorganisms, insects and fungal pathogens; in improving plant forage quality, for example by disrupting protein foam and in conferring protection from rumen pasture bloat; in reducing digestion rates in the rumen and reducing parasitic load; in the production of plant compounds leading to health benefits, such as isoflavonoids, which have been linked to anticancer benefits, and stilbenes that are believed to contribute to reduced heart disease.
White clover expresses multiple isoforms of 4CL and C4H. Co-ordinate expression of genes encoding isoforms of 4CL, PAL and C4H that are involved in the production of specific flavonoids, such as CTs, may allow the production of various flavonoids to be regulated independently by cell-specific factors and the circadian clock. Hence, the identification of CT-specific isoforms of enzymes located early in the phenylpropanoid pathway is an important step towards modification of this pathway in forage legumes.
Methods for the manipulation of C4H, 4CL, LDOX, TT12, TT2, TT8, TTG1 or like gene activities in plants, including legumes such as clovers (Trifolium species), lucerne (Medicago sativa) and grass species such as ryegrasses (Lolium species) and fescues (Festuca species) may facilitate the production of, for example, forage legumes and forage grasses and other crops with enhanced tolerance to biotic stresses such as viruses, microorganisms, insects and fungal pathogens; altered pigmentation in flowers; forage legumes with enhanced herbage quality and bloat-safety; crops with enhanced isoflavonoid content leading to health benefits.
The use of transcription factors to modify multiple product-specific enzymes in the flavonoid pathway may be a useful alternative strategy to cloning genes encoding many enzymes and modifying their expression in transgenic plants.
The clover (Trifolium), medic (Medicago), ryegrass (Lolium) or fescue (Festuca) species may be of any suitable type, including white clover (Trifolium repens), red clover (Trifolium pretense), subterranean clover (Trifolium subterraneum), alfalfa (Medicago sativa), Italian or annual ryegrass (Lolium multiflorum), perennial ryegrass (Lolium perenne), tall fescue (Festuca arundinacea), meadow fescue (Festuca pratensis) and red fescue (Festuca rubra). Preferably the species is a clover or a ryegrass, more preferably white clover (T. repens) or perennial ryegrass (L. perenne). White clover (Trifolium repens L.) and perennial ryegrass (Lolium perenne L.) are key pasture legumes and grasses, respectively, in temperate climates throughout the world. Perennial ryegrass is also an important turf grass.
Nucleic acids according to the invention may be full-length genes or part thereof, and are also referred to as “nucleic acid fragments” and “nucleotide sequences” in this specification. For convenience, the expression “nucleic acid or nucleic acid fragment” is used to cover all of these.
The nucleic acid or nucleic acid fragment may be of any suitable type and includes DNA (such as cDNA or genomic DNA) and RNA (such as mRNA) that is single- or double-stranded, optionally containing synthetic, non-natural or altered nucleotide bases, and combinations thereof.
The term “isolated” means that the material is removed from its original environment (eg. the natural environment if it is naturally occurring). For example, a naturally occurring nucleic acid present in a living plant is not isolated, but the same nucleic acid separated from some or all of the coexisting materials in the natural system, is isolated. Such nucleic acids could be part of a vector and/or such nucleic acids could be part of a composition, and still be isolated in that such a vector or composition is not part of its natural environment.
Such nucleic acids or nucleic acid fragments could be assembled to form a consensus contig. As used herein, the term “consensus contig” refers to a nucleotide sequence that is assembled from two or more constituent nucleotide sequences that share common or overlapping regions of sequence homology. For example, the nucleotide sequence of two or more nucleic acids or nucleic acid fragments can be compared and aligned in order to identify common or overlapping sequences. Where common or overlapping sequences exist between two or more nucleic acids or nucleic acid fragments, the sequences (and thus their corresponding nucleic acids or nucleic acid fragments) can be assembled into a single contiguous nucleotide sequence.
In a preferred embodiment of this aspect of the invention, the substantially purified or isolated nucleic acid or nucleic acid fragment encoding a TT12 or TT12-like protein or complementary or antisense to a sequence encoding a TT12 or TT12-like protein includes a nucleotide sequence selected from the group consisting of (a) the sequences shown in FIGS. 1 and 33 hereto; (b) the complement of the sequences recited in (a); (c) sequences antisense to the sequences recited in (a) and (b); and (d) functionally active fragments and variants of the sequences recited in (a), (b) and (c).
In a further preferred embodiment of this aspect of the invention, the substantially purified or isolated nucleic acid or nucleic acid fragment encoding a TTG1 or TTG1-like protein or complementary or antisense to a sequence encoding a TTG1 or TTG1-like protein includes a nucleotide sequence selected from the group consisting of (a) the sequences shown in FIGS. 4 and 37 hereto; (b) the complement of the sequences recited in (a); (c) the sequence antisense to the sequences recited in (a) and (b); and (d) functionally active fragments and variants of the sequences recited in (a), (b) and (c).
In a further preferred embodiment of this aspect of the invention, the substantially purified or isolated nucleic acid or nucleic acid fragment encoding an TT2 or TT2-like protein or complementary or antisense to a sequence encoding a TT2 or TT2-like protein includes a nucleotide sequence selected from the group consisting of (a) sequences shown in FIGS. 6, 9, 41 and 44 hereto; (b) complements of the sequences recited in (a); (c) sequences antisense to the sequences recited in (a) and (b); and (d) functionally active fragments and variants of the sequences recited in (a), (b) and (c).
In a further preferred embodiment of this aspect of the invention, the substantially purified or isolated nucleic acid or nucleic acid fragment encoding a TT8 or TT8-like protein or complementary or antisense to a sequence encoding a TT8 or TT8-like protein includes a nucleotide sequence selected from the group consisting of (a) the sequences shown in FIGS. 11 and 48 hereto; (b) the complement of the sequences recited in (a); (c) the sequences antisense to the sequences recited in (a) and (b); and (d) functionally active fragments and variants of the sequences recited in (a), (b) and (c).
In a further preferred embodiment of this aspect of the invention, the substantially purified or isolated nucleic acid or nucleic acid fragment encoding a LDOX or LDOX-like protein or complementary or antisense to a sequence encoding a LDOX or LDOX-like protein includes a nucleotide sequence selected from the group consisting of (a) the sequences shown in FIGS. 13 and 52 hereto; (b) the complement of the sequences recited in (a); (c) sequences antisense to the sequences recited in (a) and (b); and (d) functionally active fragments and variants of the sequences recited in (a), (b) and (c).
In a still further preferred embodiment of this aspect of the invention, the substantially purified or isolated nucleic acid or nucleic acid fragment encoding a 4CL or 4CL-like protein or complementary or antisense to a sequence encoding a 4CL or 4CL-like protein includes a nucleotide sequence selected from the group consisting of (a) sequences shown in FIGS. 16, 19, 21, 23, 56, 59, 62 and 65 hereto; (b) complements of the sequences recited in (a); (c) sequences antisense to the sequences recited in (a) and (b); and (d) functionally active fragments and variants of the sequences recited in (a), (b) and (c).
In a further preferred embodiment of this aspect of the invention, the substantially purified or isolated nucleic acid or nucleic acid fragment encoding a C4H or C4H-like protein or complementary or antisense to a sequence encoding a C4H or C4H-like protein includes a nucleotide sequence selected from the group consisting of (a) sequences shown in FIGS. 25, 28, 30, 70, 74 and 77 hereto; (b) complements of the sequences recited in (a); (c) sequences antisense to the sequences recited in (a) and (b); and (d) functionally active fragments and variants of the sequences recited in (a), (b) and (c).
By “functionally active” in relation to nucleic acids it is meant that the fragment or variant (such as an analogue, derivative or mutant) encodes a polypeptide, which is capable of modifying flavonoid biosynthesis; in a plant. Such variants include naturally occurring allelic variants and non-naturally occurring variants. Additions, deletions, substitutions and derivatizations of one or more of the nucleotides are contemplated so long as the modifications do not result in loss of functional activity of the fragment or variant. Preferably the functionally active fragment or variant has at least approximately 75% identity to the relevant part of the above mentioned nucleotide sequence, more preferably at least approximately 80% identity, more preferably at least approximately 90% identity, most preferably at least approximately 95% identity. Such functionally active variants and fragments include, for example, those having nucleic acid changes which result in conservative amino acid substitutions of one or more residues in the corresponding amino acid sequence. Preferably the fragment has a size of at least 30 nucleotides, more preferably at least 45 nucleotides, most preferably at least 60 nucleotides.
It will also be understood that the term “comprises” (or its grammatical variants) as used in this specification is equivalent to the term “includes” and should not be taken as excluding the presence of other elements or features.
Nucleic acids or nucleic acid fragments encoding at least a portion of several C4Hs, 4CLs, LDOXs, and candidate TT12, TT2, TT8 and TTG1 orthologs have been isolated and identified. The nucleic acids or nucleic acid fragments of the present invention may be used to isolate cDNAs and genes encoding homologous proteins from the same or other plant species. Isolation of homologous genes can be isolated using sequence-dependent protocols, such as methods of nucleic acid hybridisation, and methods of DNA and RNA amplification as exemplified by various uses of nucleic acid amplification technologies (e.g. polymerase chain reaction, ligase chain reaction).
For example, genes encoding other C4H or C4H-like, 4CL or 4CL-like, LDOX or LDOX-like, TT12-like, TT2-like, TT8-like, TTG1-like proteins, either as cDNAs or genomic DNAs, may be isolated directly by using all or a portion of the nucleic acids or nucleic acid fragments of the present invention as hybridisation probes to screen libraries from the desired plant. Specific oligonucleotide probes based upon the nucleic acid sequences of the present invention may be designed and synthesized. Moreover, the entire sequences may be used directly to synthesize DNA probes by methods such as random primer DNA labelling, nick translation, or end-labelling techniques, or RNA probes using available in vitro transcription systems. In addition, specific primers may be designed and used to amplify a part or all of the sequences of the present invention. The resulting amplification products may be labelled directly during amplification reactions or labelled after amplification reactions, and used as probes to isolate full-length cDNA or genomic fragments under conditions of appropriate stringency.
In addition, short segments of the nucleic acids or nucleic acid fragments of the present invention may be used in protocols to amplify longer nucleic acids or nucleic acid fragments encoding homologous genes from DNA or RNA. For example, polymerase chain reaction may be performed on a library of cloned nucleic acid fragments wherein the sequence of one primer is derived from the nucleic acid sequences of the present invention, and the sequence of the other primer takes advantage of the presence of the polyadenylic acid tracts to the 3′ end of the mRNA precursor encoding plant genes. Alternatively, the second primer sequence may be based upon sequences derived from the cloning vector. For example, those skilled in the art can follow the RACE protocol (Frohman et al. (1988) Proc. Natl. Acad. Sci. USA 85:8998, the entire disclosure of which is incorporated herein by reference) to generate cDNAs by using PCR to amplify copies of the region between a single point in the transcript and the 3′ or 5′ end. Using commercially available 3′ RACE and 5′ RACE systems (BRL), specific 3′ or 5′ cDNA fragments may be isolated (Ohara et al. (1989) Proc. Natl. Acad Sci USA 86:5673; Loh et al. (1989) Science 243:217, the entire disclosures of which are incorporated herein by reference). Products generated by the 3′ and 5′ RACE procedures may be combined to generate full-length cDNAs.
In a second aspect of the present invention there is provided a substantially purified or isolated polypeptide from a clover (Trifolium), medic (Medicago), ryegrass (Lolium) or fescue (Festuca) species, selected from the group consisting of C4H and C4H-like, 4CL and 4CL-like, LDOX and LDOX-like, TT12 and TT12-like, TT2 and TT2-like, TT8 and TT8-like and TTG1 and TTG1-like proteins; and functionally active fragments and variants thereof.
The clover (Trifolium), medic (Medicago), ryegrass (Lolium) or fescue (Festuca) species may be of any suitable type, including white clover (Trifolium repens), red clover (Trifolium pratense), subterranean clover (Trifolium subterraneum), alfalfa (Medicago sativa), Italian or annual ryegrass (Lolium multiflorum), perennial ryegrass (Lolium perenne), tall fescue (Festuca arundinacea), meadow fescue (Festuca pratensis) and red fescue (Festuca rubra). In particular, the species may be a clover or a ryegrass, more particularly white clover (T. repens) or perennial ryegrass (L. perenne).
In a preferred embodiment of this aspect of the invention, the substantially purified or isolated TT12 or TT12-like polypeptide includes an amino acid sequence selected from the group consisting of the sequences shown in FIGS. 2 and 34 hereto, and functionally active fragments and variants thereof.
In a further preferred embodiment of this aspect of the invention, the substantially purified or isolated TTG1 or TTG1-like polypeptide includes an amino acid sequence selected from the group consisting of the sequences shown in FIGS. 5 and 38 hereto, and functionally active fragments and variants thereof.
In a further preferred embodiment of this aspect of the invention, the substantially purified or isolated TT2 or TT2-like polypeptide includes an amino acid sequence selected from the group consisting of the sequences shown in FIGS. 7, 10, 42 and 45 hereto, and functionally active fragments and variants thereof.
In a still further preferred embodiment of this aspect of the invention, the substantially purified or isolated TT8 or TT8-like polypeptide includes an amino acid sequence selected from the group consisting of the sequences shown in FIGS. 12 and 49 hereto, and functionally active fragments and variants thereof.
In a still further preferred embodiment of this aspect of the invention, the substantially purified or isolated LDOX or LDOX-like polypeptide includes an amino acid sequence selected from the group consisting of the sequences shown in FIGS. 14 and 53 hereto, and functionally active fragments and variants thereof.
In a still further preferred embodiment of this aspect of the invention, the substantially purified or isolated 4CL or 4CL-like polypeptide includes an amino acid sequence selected from the group consisting of the sequences shown in FIGS. 17, 20, 22, 24, 57, 60, 63 and 66 hereto, and functionally active fragments and variants thereof.
In a still further preferred embodiment of this aspect of the invention, the substantially purified or isolated C4H or C4H-like polypeptide includes an amino acid sequence selected from the group consisting of the sequences shown in FIGS. 26, 29, 31, 71, 75 and 78 hereto, and functionally active fragments and variants thereof.
By “functionally active” in relation to polypeptides it is meant that the fragment or variant has one or more of the biological properties of the proteins TT12, TT12-like, TTG1, TTG1-like, TT2, TT2-like, TT8, TT8-like, LDOX, LDOX-like, 4CL, 4CL-like, C4H, C4H-like, respectively. Additions, deletions, substitutions and derivatizations of one or more of the amino acids are contemplated so long as the modifications do not result in loss of functional activity of the fragment or variant. Preferably the functionally active fragment or variant has at least approximately 60% identity to the relevant part of the above mentioned amino acid sequence, more preferably at least approximately 80% identity, most preferably at least approximately 90% identity. Such functionally active variants and fragments include, for example, those having conservative amino acid substitutions of one or more residues in the corresponding amino acid sequence. Preferably the fragment has a size of at least 10 amino acids, more preferably at least 15 amino acids, most preferably at least 20 amino acids.
In a further embodiment of this aspect of the invention, there is provided a polypeptide recombinantly produced from a nucleic acid or nucleic acid fragment according to the present invention.
Availability of the nucleotide sequences of the present invention and deduced amino acid sequences facilitates immunological screening of cDNA expression libraries. Synthetic peptides representing portions of the instant amino acid sequences may be synthesized. These peptides may be used to immunise animals to produce polyclonal or monoclonal antibodies with specificity for peptides and/or proteins including the amino acid sequences. These antibodies may be then used to screen cDNA expression libraries to isolate full-length cDNA clones of interest.
A genotype is the genetic constitution of an individual or group. Variations in genotype are important in commercial breeding programs, in determining parentage, in diagnostics and fingerprinting, and the like. Genotypes can be readily described in terms of genetic markers. A genetic marker identifies a specific region or locus in the genome. The more genetic markers, the finer defined is the genotype. A genetic marker becomes particularly useful when it is allelic between organisms because it then may serve to unambiguously identify an individual. Furthermore, a genetic marker becomes particularly useful when it is based on nucleic acid sequence information that can unambiguously establish a genotype of an individual and when the function encoded by such nucleic acid is known and is associated with a specific trait. Such nucleic acids and/or nucleotide sequence information including single nucleotide polymorphisms (SNPs), variations in single nucleotides between allelic forms of such nucleotide sequence, may be used as perfect markers or candidate genes for the given trait.
Applicants have identified a number of SNPs of the nucleic acids or nucleic acid fragments of the present invention. These are indicated (marked with grey on the black background) in the figures that show multiple alignments of nucleotide sequences of nucleic acid fragments contributing to consensus contig sequences. See for example, FIGS. 3, 15, 18 and 27 hereto.
Accordingly, in a further aspect of the present invention, there is provided a substantially purified or isolated nucleic acid or nucleic acid fragment including a single nucleotide polymorphism (SNP) from a nucleic acid or nucleic acid fragment according to the present invention, for example a SNP from a nucleic acid sequence shown in FIGS. 3, 15, 18 and 27 hereto; or complements or sequences antisense thereto, and functionally active fragments and variants thereof.
In a still further aspect of the present invention there is provided a method of isolating a nucleic acid or nucleic acid fragment of the present invention including a SNP, said method including sequencing nucleic acid fragments from a nucleic acid library.
The nucleic acid library may be of any suitable type and is preferably a cDNA library.
The nucleic acid or nucleic acid fragment may be isolated from a recombinant plasmid or may be amplified, for example using polymerase chain reaction.
The sequencing may be performed by techniques known to those skilled in the art.
In a still further aspect of the present invention, there is provided use of the nucleic acids or nucleic acid fragments of the present invention including SNPs, and/or nucleotide sequence information thereof, as molecular genetic markers.
In a still further aspect of the present invention there is provided use of a nucleic acid or nucleic acid fragment of the present invention, and/or nucleotide sequence information thereof, as a molecular genetic marker.
More particularly, nucleic acids or nucleic acid fragments according to the present invention and/or nucleotide sequence information thereof may be used as a molecular genetic marker for quantitative trait loci (QTL) tagging, QTL mapping, DNA fingerprinting and in marker assisted selection, particularly in clovers, alfalfa, ryegrasses and fescues.
Even more particularly, nucleic acids or nucleic acid fragments according to the present invention and/or nucleotide sequence information thereof may be used as molecular genetic markers in plant improvement in relation to plant tolerance to biotic stresses such as viruses, microorganisms, insects, fungal pathogens; in relation to forage quality; in relation to bloat safety; in relation to condensed tannin content; in relation to plant pigmentation. Even more particularly, sequence information revealing SNPs in allelic variants of the nucleic acids or nucleic acid fragments of the present invention and/or nucleotide sequence information thereof may be used as molecular genetic markers for QTL tagging and mapping and in marker assisted selection, particularly in clovers, alfalfa, ryegrasses and fescues.
In a still further aspect of the present invention there is provided a construct including a nucleic acid or nucleic acid fragment according to the present invention.
The term “construct” as used herein refers to an artificially assembled or isolated nucleic acid molecule, which includes the gene of interest. In general a construct may include the gene or genes of interest, a marker gene which in some cases can also be the gene of interest and appropriate regulatory sequences. It should be appreciated that the inclusion of regulatory sequences in a construct is optional, for example, such sequences may not be required in situations where the regulatory sequences of a host cell are to be used. The term construct includes vectors but should not be seen as being limited thereto.
In a still further aspect of the present invention there is provided a vector including a nucleic acid or nucleic acid fragment according to the present invention.
The term “vector” as used herein encompasses both cloning and expression vectors. Vectors are often recombinant molecules containing nucleic acid molecules from several sources.
In a preferred embodiment of this aspect of the invention, the vector may include a regulatory element such as a promoter, a nucleic acid or nucleic acid fragment according to the present invention and a terminator; said regulatory element, nucleic acid or nucleic acid fragment and terminator being operatively linked.
By “operatively linked” is meant that said regulatory element is capable of causing expression of said nucleic acid or nucleic acid fragment in a plant cell and said terminator is capable of terminating expression of said nucleic acid or nucleic acid fragment in a plant cell. Preferably, said regulatory element is upstream of said nucleic acid or nucleic acid fragment and said terminator is downstream of said nucleic acid or nucleic acid fragment.
The vector may be of any suitable type and may be viral or non-viral. The vector may be an expression vector. Such vectors include chromosomal, non-chromosomal and synthetic nucleic acid sequences, eg. derivatives of plant viruses; bacterial plasmids; derivatives of the Ti plasmid from Agrobacterium tumefaciens, derivatives of the Ri plasmid from Agrobacterium rhizogenes; phage DNA; yeast artificial chromosomes; bacterial artificial chromosomes; binary bacterial artificial chromosomes; vectors derived from combinations of plasmids and phage DNA. However, any other vector may be used as long as it is replicable, integrative or viable in the plant cell.
The regulatory element and terminator may be of any suitable type and may be endogenous to the target plant cell or may be exogenous, provided that they are functional in the target plant cell.
Preferably the regulatory element is a promoter. A variety of promoters which may be employed in the vectors of the present invention are well known to those skilled in the art. Factors influencing the choice of promoter include the desired tissue specificity of the vector, and whether constitutive or inducible expression is desired and the nature of the plant cell to be transformed (eg. monocotyledon or dicotyledon). Particularly suitable constitutive promoters include the Cauliflower Mosaic Virus 35S (CaMV 35S) promoter, the maize Ubiquitin promoter, and the rice Actin promoter.
A variety of terminators which may be employed in the vectors of the present invention are also well known to those skilled in the art. The terminator may be from the same gene as the promoter sequence or a different gene. Particularly suitable terminators are polyadenylation signals, such as the CaMV 35S polyA and other terminators from the nopaline synthase (nos) and the octopine synthase (ocs) genes.
The vector, in addition to the regulatory element, the nucleic acid or nucleic acid fragment of the present invention and the terminator, may include further elements necessary for expression of the nucleic acid or nucleic acid fragment, in different combinations, for example vector backbone, origin of replication (ori), multiple cloning sites, spacer sequences, enhancers, introns (such as the maize Ubiquitin Ubi intron), antibiotic resistance genes and other selectable marker genes [such as the neomycin phosphotransferase (npt2) gene, the hygromycin phosphotransferase (hph) gene, the phosphinothricin acetyltransferase (bar or pat) gene], and reporter genes (such as beta-glucuronidase (GUS) gene (gusA)]. The vector may also contain a ribosome binding site for translation initiation. The vector may also include appropriate sequences for amplifying expression.
As an alternative to use of a selectable marker gene to provide a phenotypic trait for selection of transformed host cells, the presence of the vector in transformed cells may be determined by other techniques well known in the art, such as PCR (polymerase chain reaction), Southern blot hybridisation analysis, histochemical GUS assays, northern and western blot hybridisation analyses.
Those skilled in the art will appreciate that the various components of the vector are operatively linked, so as to result in expression of said nucleic acid or nucleic acid fragment. Techniques for operatively linking the components of the vector of the present invention are well known to those skilled in the art. Such techniques include the use of linkers, such as synthetic linkers, for example including one or more restriction enzyme sites.
The vectors of the present invention may be incorporated into a variety of plants, including monocotyledons (such as grasses from the genera Lolium, Festuca, Paspalum, Pennisetum, Panicum and other forage and turfgrasses, corn, oat, sugarcane, wheat and barley), dicotyledons (such as arabidopsis, tobacco, clovers, medics, eucalyptus, potato, sugarbeet, canola, soybean, chickpea) and gymnosperms.
In a preferred embodiment, the vectors may be used to transform monocotyledons, preferably grass species such as ryegrasses (Lolium species) and fescues (Festuca species), more preferably perennial ryegrass, including forage- and turf-type cultivars. In an alternate preferred embodiment, the vectors may be used to transform dicotyledons, preferably forage legume species such as clovers (Trifolium species) and medics (Medicago species), more preferably white clover (Trifolium repens), red clover (Trifolium pratense), subterranean clover (Trifolium subterraneum) and alfalfa (Medicago sativa). Clovers, alfalfa and medics are key pasture legumes in temperate climates throughout the world.
Techniques for incorporating the vectors of the present invention into plant cells (for example by transduction, transfection or transformation) are well known to those skilled in the art. Such techniques include Agrobacterium mediated introduction, electroporation to tissues, cells and protoplasts, protoplast fusion, injection into reproductive organs, injection into immature embryos and high velocity projectile introduction to cells, tissues, calli, immature and mature embryos. The choice of technique will depend largely on the type of plant to be transformed.
Cells incorporating the vectors of the present invention may be selected, as described above, and then cultured in an appropriate medium to regenerate transformed plants, using techniques well known in the art. The culture conditions, such as temperature, pH and the like, will be apparent to the person skilled in the art. The resulting plants may be reproduced, either sexually or asexually, using methods well known in the art, to produce successive generations of transformed plants.
In a further aspect of the present invention there is provided a plant cell, plant, plant seed or other plant part, including, e.g. transformed with, a vector or construct, nucleic acid or nucleic acid fragment of the present invention.
The plant cell, plant, plant seed or other plant part may be from any suitable species, including monocotyledons, dicotyledons and gymnosperms. In a preferred embodiment the plant cell, plant, plant seed or other plant part may be from a monocotyledon, preferably a grass species, more preferably a ryegrass (Lolium species) or fescue (Festuca species), more preferably perennial ryegrass, including both forage- and turf-type cultivars. In an alternate preferred embodiment the plant cell, plant, plant seed or other plant part may be from a dicotyledon, preferably forage legume species such as clovers (Trifolium species) and medics (Medicago species), more preferably white clover (Trifolium repens), red clover (Trifolium pratense), subterranean clover (Trifolium subterraneum) and alfalfa (Medicago sativa).
The present invention also provides a plant, plant seed or other plant part, or a plant extract derived from a plant cell of the present invention.
The present invention also provides a plant, plant seed or other plant part, or a plant extract derived from a plant of the present invention.
Using the methods and materials of the present invention, flavonoid biosynthesis may be increased or decreased. It may be increased, for example by incorporating additional copies of a sense nucleic acid of the present invention. It may be decreased, for example, by incorporating an antisense nucleic acid or dsRNA or small interfering RNA (siRNA) derived from the nucleotide sequences of the present invention. In addition, the number of copies of genes encoding different enzymes involved in flavonoid biosynthesis may be manipulated to modify flavonoid biosynthesis, protein binding, metal chelation, anti oxidation, UV light absorption, plant pigment production, plant defense to biotic stresses and modifying forage quality.
In a further aspect of the present invention there is provided a method of modifying flavonoid biosynthesis; of modifying protein binding, metal chelation, anti-oxidation, and UV-light absorption; of modifying plant pigment production; of modifying plant defense to biotic stresses such as viruses, microorganisms, insects, fungal pathogens; of modifying forage quality by disrupting protein foam and conferring protection from rumen pasture bloat, said method including introducing into said plant an effective amount of a nucleic acid or nucleic acid fragment and/or a vector according to the present invention.
By “an effective amount” it is meant an amount sufficient to result in an identifiable phenotypic trait in said plant, or a plant, plant seed or other plant part derived therefrom. Such amounts can be readily determined by an appropriately skilled person, taking into account the type of plant, the route of administration and other relevant factors. Such a person will readily be able to determine a suitable amount and method of administration. See, for example, Maniatis et al, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, the entire disclosure of which is incorporated herein by reference.
Using the methods and materials of the present invention, flavonoid biosynthesis, protein binding, metal chelation, anti-oxidation, UV-light absorption, tolerance to biotic stresses such as viruses, microorganisms, insects and fungal pathogens; pigmentation in for example flowers and leaves; herbage quality and bloat-safety; isoflavonoid content leading to health benefits, may be increased or otherwise altered, for example by incorporating additional copies of a sense nucleic acid or nucleic acid fragment of the present invention. They may be decreased or otherwise altered, for example by incorporating an antisense nucleic acid or nucleic acid fragment of the present invention.
Documents cited in this specification are for reference purposes only and their inclusion is not acknowledgment that they form part of the common general knowledge in the relevant art.
The present invention will now be more fully described with reference to the accompanying Examples and drawings. It should be understood, however, that the description following is illustrative only and should not be taken in any way as a restriction on the generality of the invention described above.



IN THE FIGURES
FIG. 1 shows the consensus nucleotide sequence of WcCTa (TrTT12a) (SEQ ID No: 1).
FIG. 2 shows the deduced amino acid sequence of WcCTa (TrTT12a) (SEQ ID No: 2).
FIG. 3 shows the nucleotide sequences of nucleic acid fragments contributing to the consensus sequence of WcCTa (TrTT12a) (SEQ ID Nos: 3 to 6).
FIG. 4 shows the nucleotide sequence of WcCTb (TrTTG1a) (SEQ ID No: 7).
FIG. 5 shows the deduced amino acid sequence of WcCTb (TrTTG1a) (SEQ ID No: 8).
FIG. 6 shows the consensus nucleotide sequence of WcCTc (TrTT2a) (SEQ ID No: 9).
FIG. 7 shows the deduced amino acid sequence of WcCTc (TrTT2a) (SEQ ID No: 10).
FIG. 8 shows the nucleotide sequences of nucleic acid fragments contributing to the consensus sequence of WcCTc (TrTT2b) (SEQ ID Nos: 11 and 12).
FIG. 9 shows the nucleotide sequence of WcCTd (TrTT2b) (SEQ ID No: 13).
FIG. 10 shows the deduced amino acid sequence of WcCTd (TrTT2b) (SEQ ID No: 14).
FIG. 11 shows the nucleotide sequence of WcCTe (TrTT8a) (SEQ ID No: 15).
FIG. 12 shows the deduced amino acid sequence of WcCTe (TrTT8a) (SEQ ID No: 16).
FIG. 13 shows the consensus nucleotide sequence of WcCTf (TrLDOXa) (SEQ ID No: 17).
FIG. 14 shows the deduced amino acid sequence of WcCTf (TrLDOXa) (SEQ ID No: 18).
FIG. 15 shows the nucleotide sequences of nucleic acid fragments contributing to the consensus sequence of WcCTf (TrLDOXa) (SEQ ID Nos: 19 to 33).
FIG. 16 shows the consensus nucleotide sequence of WcCTg (Tr4CLa) (SEQ ID No: 34).
FIG. 17 shows the deduced amino acid sequence of WcCTg (Tr4CLa) (SEQ ID No: 35).
FIG. 18 shows the nucleotide sequences of nucleic acid fragments contributing to the consensus sequence of WcCTg (Tr4CLa) (SEQ ID Nos: 36 to 38).
FIG. 19 shows the nucleotide sequence of WcCTh (Tr4CLb) (SEQ ID No: 39).
FIG. 20 shows the deduced amino acid sequence of WcCTh (Tr4CLb) (SEQ ID No: 40).
FIG. 21 shows the nucleotide sequence of WcCTi (Tr4CLc) (SEQ ID No: 41).
FIG. 22 shows the deduced amino acid sequence of WcCTi (Tr4CLc) (SEQ ID No: 42).
FIG. 23 shows the nucleotide sequence of WcCTj (Tr4CLd) (SEQ ID No: 43).
FIG. 24 shows the deduced amino acid sequence of WcCTj (Tr4CLd) (SEQ ID No: 44).
FIG. 25 shows the consensus nucleotide sequence of WcCTk (TrC4Ha) (SEQ ID No: 45).
FIG. 26 shows the deduced amino acid sequence of WcCTk (TrC4Ha) (SEQ ID No: 46).
FIG. 27 shows the nucleotide sequences of nucleic acid fragments contributing to the consensus sequence of WcCTk (TrC4Ha) (SEQ ID Nos: 47 to 51).
FIG. 28 shows the nucleotide sequence of WcCTl (TrC4Hb) (SEQ ID No: 52).
FIG. 29 shows the deduced amino acid sequence of WcCTl (TrC4Hb) (SEQ ID No: 53).
FIG. 30 shows the nucleotide sequence of WcCTm (TrC4Hc) (SEQ ID No: 54).
FIG. 31 shows the deduced amino acid sequence of WcCTm (TrC4Hc) (SEQ ID No: 55).
FIG. 32 shows a plasmid map of the cDNA encoding white clover WcCTa (TrTT12a).
FIG. 33 shows the full nucleotide sequence of the white clover WcCTa (TrTT12a) cDNA (SEQ ID No: 56).
FIG. 34 shows the deduced amino acid sequence of white clover WcCTa (TrTT12a) cDNA (SEQ ID No: 57).
FIG. 35 shows plasmid maps of the cDNA encoding white clover WcCTa (TrTT12a) in the sense and antisense orientations in the pPZP221 binary transformation vector
FIG. 36 shows a plasmid map of the cDNA encoding white clover WcCTb (TrTTG1a).
FIG. 37 shows the full nucleotide sequence of the white clover WcCTb (TrTTG1a) cDNA (SEQ ID No: 58).
FIG. 38 shows the deduced amino acid sequence of the white clover WcCTb (TrTTG1a) cDNA (SEQ ID No: 59).
FIG. 39 shows plasmid maps of the cDNA encoding white clover WcCTb (TrTTG1a) in the sense and antisense orientations in the pPZP221 binary transformation vector
FIG. 40 shows a plasmid map of the cDNA encoding white clover WcCTc (TrTT2a).
FIG. 41 shows the full nucleotide sequence of the white clover WcCTc (TrTT2a) cDNA (SEQ ID No: 60).
FIG. 42 shows the deduced amino acid sequence of the white clover WcCTc (TrTT2a) cDNA (SEQ ID No: 61).
FIG. 43 shows a plasmid map of the cDNA encoding white clover WcCTd (TrTT2b).
FIG. 44 shows the full nucleotide sequence of the white clover WcCTd (TrTT2b) cDNA (SEQ ID No: 62).
FIG. 45 shows the deduced amino acid sequence of the white clover WcCTd (TrTT2b) cDNA (SEQ ID No: 63).
FIG. 46 shows plasmid maps of the cDNAs encoding white clover WcCTc (TrTT2a) and WcCTd (TrTT2b) in the sense and antisense orientations in the pPZP221 binary transformation vector
FIG. 47 shows a plasmid map of the cDNA encoding white clover WcCTe (TrTT8a).
FIG. 48 shows the full nucleotide sequence of the white clover WcCTe (TrTT8a) cDNA (SEQ ID No: 64).
FIG. 49 shows the deduced amino acid sequence of the white clover WcCTe (TrTT8a) cDNA (SEQ ID No: 65).
FIG. 50 shows a plasmid map of the cDNA encoding white clover WcCTe (TrTT8a) in the antisense orientation in the pPZP221 binary transformation vector
FIG. 51 shows a plasmid map of the cDNA encoding white clover WcCTf (TrLDOXa).
FIG. 52 shows the full nucleotide sequence of the white clover WcCTf (TrLDOXa) cDNA (SEQ ID No: 66).
FIG. 53 shows the deduced amino acid sequence of the white clover WcCTf (TrLDOXa) cDNA (SEQ ID No: 67).
FIG. 54 shows plasmid maps of the cDNA encoding white clover WcCTf (TrLDOXa) in the sense and antisense orientations in the pPZP221 binary transformation vector
FIG. 55 shows a plasmid map of the cDNA encoding white clover WcCTg (Tr4CLa).
FIG. 56 shows the full nucleotide sequence of the white clover WcCTg (Tr4CLa) cDNA (SEQ ID No: 68).
FIG. 57 shows the deduced amino acid sequence of the white clover WcCTg (Tr4CLa) cDNA (SEQ ID No: 69).
FIG. 58 shows a plasmid map of the cDNA encoding white clover WcCTh (Tr4CLb).
FIG. 59 shows the full nucleotide sequence of the white clover WcCTh (Tr4CLb) cDNA (SEQ ID No: 70).
FIG. 60 shows the deduced amino acid sequence of the white clover WcCTh (Tr4CLb) cDNA (SEQ ID No: 71).
FIG. 61 shows a plasmid map of the cDNA encoding white clover WcCTi (Tr4CLc).
FIG. 62 shows the full nucleotide sequence of the white clover WcCTi (Tr4CLc) cDNA (SEQ ID No: 72).
FIG. 63 shows the deduced amino acid sequence of the white clover WcCTi (Tr4CLc) cDNA (SEQ ID No: 73).
FIG. 64 shows a plasmid map of the cDNA encoding white clover WcCTj (Tr4CLd).
FIG. 65 shows the full nucleotide sequence of the white clover WcCTj (Tr4CLd) cDNA (SEQ ID No: 74).
FIG. 66 shows the deduced amino acid sequence of the white clover WcCTj (Tr4CLd) cDNA (SEQ ID No: 75).
FIG. 67 shows plasmid maps of the cDNAs encoding white clover WcCTg (Tr4CLa), WcCTh (Tr4CLb), WcCTi (Tr4CLc) and WcCTj (Tr4CLd) in the sense orientation in the pPZP221 binary transformation vector
FIG. 68 shows plasmid maps of the cDNAs encoding white WcCTg (Tr4CLa), WcCTh (Tr4CLb), WcCTi (Tr4CLc) and WcCTj (Tr4CLd) in the antisense orientation in the pPZP221 binary transformation vector
FIG. 69 shows a plasmid map of the cDNA encoding white clover WcCTk (TrC4Ha).
FIG. 70 shows the full nucleotide sequence of the white clover WcCTk (TrC4Ha) cDNA (SEQ ID No: 76).
FIG. 71 shows the deduced amino acid sequence of the white clover WcCTk (TrC4Ha) cDNA (SEQ ID No: 77).
FIG. 72 shows a plasmid map of the cDNA encoding white clover WcCTk (TrC4Ha) in the sense orientation in the pPZP221 binary transformation vector
FIG. 73 shows a plasmid map of the cDNA encoding white clover WcCTl (TrC4Hb).
FIG. 74 shows the full nucleotide sequence of the white clover WcCTl (TrC4Hb) cDNA (SEQ ID No: 78).
FIG. 75 shows the deduced amino acid sequence of the white clover WcCTl (TrC4Hb) cDNA (SEQ ID No: 79).
FIG. 76 shows a plasmid map of the cDNA encoding white clover WcCTm (TrC4Hc).
FIG. 77 shows the full nucleotide sequence of the white clover WcCTm (TrC4Hc) cDNA (SEQ ID No: 80).
FIG. 78 shows the deduced amino acid sequence of the white clover WcCTm (TrC4Hc) cDNA (SEQ ID No. 81)
FIG. 79 shows plasmid maps of the cDNAs encoding white clover WcCTk (TrC4Ha), WcCTl (TrC4Hb) and WcCTm (TrC4Hc) in the antisense orientation in the pPZP221 binary transformation vector
FIG. 80 shows a plasmid map of the pDONR221 GATEWAY entry vector (Invitrogen, Carlsbad, USA).
FIG. 81 shows the steps of selection during Agrobacterium-mediated transformation of white clover cotyledons. Cotyledonary explants are extracted from imbibed seeds (A), cocultivated with Agrobacterium tumefaciens strain containing the binary transformation vector and subjected to a series of 2-week selective steps on tissue culture plates (B, C and D). Shoots are excised and grown on root-inducing media in tissue culture vessels (E). Finally, transgenic white clover plantlets are transferred to glasshouse conditions (F and G), allowing molecular and phenotypic analyses to take place.
FIG. 82 shows 4-dimethylaminocinnemaldehyde (DMACA) staining patterns in Trifolium repens (cv ‘Mink’) leaf (A) and inflorescence (B) tissue and in Lotus corniculatus (cv ‘Draco’) leaf tissue (C).
FIG. 83 shows the results of real-time RT-PCR analysis of white clover homologues of TT12, TTG1, TT2, TT8, LDOX, 4CL and C4H in upper and lower halves of white clover (cv Mink) buds as well as whole buds. More particularly, FIG. 83 shows comparative expression of flavonoid-related genes relative to a histone control gene. Complementary DNA from white clover (cv Mink) upper, lower and whole buds was tested by real-time RT-PCT using SYBR Green chemistry, primer sets designed using cDNA clones of flavonoid-related genes (Table 3) and the δδCT method of analysis. TT12, TTG1, TT2b, TT8, LDOX, 4Cla, 4CLb, 4CLd, C4Ha, C4Hb and C4Hc correspond to WcCTa, WcCTb, WcCTd, WcCTe, WcCTf, WcCTg, WcCTh, WcCTj, WcCTK, WcCT1, and WcCTM respectively.



EXAMPLE 1
Preparation of cDNA Libraries, Isolation and Sequencing of cDNAs Coding for TT12-Like, TTG1-Like, TT2-Like, TT8-Like, LDOX, LDOX-Like, 4CL, 4CL-Like, C4H and C4H-Like Proteins from White Clover (Trifolium repens)
cDNA libraries representing mRNAs from various organs and tissues of white clover (Trifolium repens) were prepared. The characteristics of the white clover libraries, respectively, are described below (Tables 1 and 2).







TABLE 1







cDNA libraries from white clover (Trifolium repens)








Library
Organ/Tissue





01wc
Whole seedling, light grown


02wc
Nodulated root 3, 5, 10, 14, 21 &28 day old seedling


03wc
Nodules pinched off roots of 42 day old rhizobium inoculated



plants


04wc
Cut leaf and stem collected after 0, 1, 4, 6 &14 h after cutting


05wc
Inflorescences: <50% open, not fully open and fully open


06wc
Dark grown etiolated


07wc
Inflorescence - very early stages, stem elongation, <15 petals,



15-20 petals


08wc
seed frozen at −80° C., imbibed in dark overnight at 10° C.


09wc
Drought stressed plants


10wc
AMV infected leaf


11wc
WCMV infected leaf


12wc
Phophorus starved plants


13wc
Vegetative stolon tip


14wc
stolon root initials


15wc
Senescing stolon


16wc
Senescing leaf









The cDNA libraries may be prepared by any of many methods available. For example, total RNA may be isolated using the Trizol method (Gibco-BRL, USA) or the RNeasy Plant Mini kit (Qiagen, Germany), following the manufacturers' instructions. cDNAs may be generated using the SMART PCR cDNA synthesis kit (Clontech, USA), cDNAs may be amplified by long distance polymerase chain reaction using the Advantage 2 PCR Enzyme system (Clontech, USA), cDNAs may be cleaned using the GeneClean spin column (Bio 101, USA), tailed and size fractionated, according to the protocol provided by Clontech. The cDNAs may be introduced into the pGEM-T Easy Vector system 1 (Promega, USA) according to the protocol provided by Promega. The cDNAs in the pGEM-T Easy plasmid vector are transfected into Escherichia coli Epicurian coli XL10-Gold ultra competent cells (Stratagene, USA) according to the protocol provided by Stratagene.
Alternatively, the cDNAs may be introduced into plasmid vectors for first preparing the cDNA libraries in Uni-ZAP XR vectors according to the manufacturer's protocol (Stratagene Cloning Systems, La Jolla, Calif., USA). The Uni-ZAP XR libraries are converted into plasmid libraries according to the protocol provided by Stratagene. Upon conversion, cDNA inserts will be contained in the plasmid vector pBluescript. In addition, the cDNAs may be introduced directly into precut pBluescript II SK(+) vectors (Stratagene) using T4 DNA ligase (New England Biolabs), followed by transfection into E. coli DH10B cells according to the manufacturer's protocol (GIBCO BRL Products).
Once the cDNA inserts are in plasmid vectors, plasmid DNAs are prepared from randomly picked bacterial colonies containing recombinant plasmids, or the insert cDNA sequences are amplified via polymerase chain reaction using primers specific for vector sequences flanking the inserted cDNA sequences. Plasmid DNA preparation may be performed robotically using the Qiagen QiaPrep Turbo kit (Qiagen, Germany) according to the protocol provided by Qiagen. Amplified insert DNAs are sequenced in dye-terminator sequencing reactions to generate partial cDNA sequences (expressed sequence tags or “ESTs”). The resulting ESTs are analyzed using an Applied Biosystems ABI 3700 sequence analyser.
EXAMPLE 2
DNA Sequence Analyses
The cDNA clones encoding TT12, TT12-like, TTG1, TTG1-like, TT8, TT8-like, TT2, TT2-like, LDOX, LDOX-like, 4CL, 4CL-like, C4H and C4H-like proteins were identified by conducting BLAST (Basic Local Alignment Search Tool; Altschul et al. (1993) J. Mol. Biol. 215:403-410) searches. The cDNA sequences obtained were analysed for similarity to all publicly available DNA sequences contained in the eBioinformatics nucleotide database using the BLASTN algorithm provided by the National Center for Biotechnology Information (NCBI). The DNA sequences were translated in all reading frames and compared for similarity to all publicly available protein sequences contained in the SWISS-PROT protein sequence database using BLASTx algorithm (v 2.0.1) (Gish and States (1993) Nature Genetics 3:266-272) provided by the NCBI.
The cDNA sequences obtained and identified were then used to identify additional identical and/or overlapping cDNA sequences generated using the BLASTN algorithm. The identical and/or overlapping sequences were subjected to a multiple alignment using the CLUSTALw algorithm, and to generate a consensus contig sequence derived from this multiple sequence alignment. The consensus contig sequence was then used as a query for a search against the SWISS-PROT protein sequence database using the BLASTx algorithm to confirm the initial identification.
EXAMPLE 3
Identification and Full-Length Sequencing of cDNAs Encoding White Clover TT12, TTG1, TT2, TT8, LDOX, 4CL and C4H Proteins
To fully characterise for the purposes of the generation of probes for hybridisation experiments and the generation of transformation vectors, a set of cDNAs encoding white clover TT12, TTG1, TT2, TT8, LDOX, 4CL and C4H proteins was identified and fully sequenced.
Full-length or partial cDNAs were identified from our EST sequence database using relevant published sequences (NCBI databank) as queries for BLAST searches. Full-length cDNAs were identified by alignment of the query and hit sequences using Sequencher (Gene Codes Corp., Ann Arbor, Mich. 48108, USA). The original cDNA in the pGEM-T easy vector was then used to transform chemically competent DH5 alpha cells (Invitrogen, Carlsbad, USA). At least two colonies per transformation were picked for initial sequencing with M13F and M13R primers. The resulting sequences were aligned with the original EST sequence using Sequencher to confirm identity and one of the two clones was picked for full-length sequencing, usually the one with the best initial sequencing result.
Sequencing was completed by primer walking, i.e. oligonucleotide primers were designed to the initial sequence and used for further sequencing from the 5′ end. The sequences of the oligonucleotide primers are shown in Table 2. In most instances, an extended poly-A tail necessitated the sequencing of the cDNA to be completed from the 5′ end.
Contigs were then assembled in Sequencher. The contigs include at least the 5′ end of the original EST sequence and extend to at least the poly-A tail at the 3′ end of the cDNA.
Plasmid maps and the full or partial cDNA sequences of white clover TT12, TTG1, TT2, TT8, LDOX, 4CL and C4H genes in the pGEM-T Easy vector were obtained (FIGS. 32, 33, 36, 37, 40, 41, 43, 44, 47, 48, 51, 52, 55, 56, 58, 59, 61, 62, 64, 65, 69, 70, 73, 74, 76, 77).







TABLE 2







List of primers used for sequencing of the 


full-length cDNAs














primer 
Seq.




sequencing 
sequence
ID


gene name
clone ID
primer
(5′>3′)
No.














WcCTa
05wc1CsD12
05wc1CsD12.f
GCATTTGCATTGAG
82


(TrTT12a)


TTGTC





05wc1CsD12.f2
AGCCAGTGTGCGAG
83





TTAG





05wc1CsD12.f3
AATTGTCAGTCTTC
84





GTAGTG





05wc1CsD12.r1
ACAACGAAGTATGA
85





CAGAAG



 


WcCTb
10wc1CsD07
10wc1CsD07.f
GCATCGCTGTTGGT
86


(TrTTG1a)


AGTT





10wc1CsD07.r1
CAACGCCTCTTTCA
87





ATGTC





10wc1CsD07.f2
TACCCCTTTGCTTC
88





GTTTG



 


WcCTc
14wc1LsB05
14wc1LsB05.f1
CACACGCATTTGAA
89


(TrTT2a)


GAAG



 


WcCTd
04wc1EsE11
04wc1EsE11.f1
AACCAACAAGGCCA
90


(TrTT2b)


CAAC



 


WcCTe
06wc2DsD04
06wc2DsD04.f1
ATAGGTGAGACAAG
91


(TrTT8a)


GAGACAGA



 


WcCTf
07wc3GsD03
07wc3GsD03.f1
GCCTAAGACTCCAG
92


(TrLDOXa)


CTGA





07wc3GsD03.r1
TCCCATTCAAGTTG
93





ACCAC





07wc3GsD03.f2
AACAAGGGCCACAA
94





GTTC





07wc3GsD03.f3
TCTTGGGCAGTGTT
95





TTGTG



 


WcCTg
14wc2KsH10
14wc2KsH10.f1
CAGCAGCCAATCCT
96


(Tr4Cla)


TTCTTC





14wc2KsH10.f2
AGTCCAACAGGGTG
97





ATGT





14wc2KsH10.f3
GTAGTTCCTCCGAT
98





AGTGT





14wc2KsH10.f4
TCTGATGCTGCTGT
99





TGTC



 


WcCTh
13wc1DsH07
13wc1DsH07.f1
TTGGTAAGGAACTT
100


(Tr4CLb)


GAGGACA





13wc1DsH07.f2
CAAAAGCCTCCAAT
101





GCTAAG



 


WcCTi
16wc1NsB11
16wc1NsB11.f1
GAAGAGGCTGTAAA
102


(Tr4CLc)


GGAG



 


WcCTj
12wc1CsA11
12wc1CsA11.f1
ACTCATCGTAACTC
103


(Tr4CLd)


AATCC





12wc1CsA11.f2
GCGTTGGTAAAAAG
104





TGGTG





12wc1CsA11.f3
TTTCGATGCTGCTG
105





TTGT





12wc1CsA11.f4
GCCTATTCGTTCGC
106





TTCT



 


WcCTk
14wc2CsB09
14wc2CsB09.f1
TACGGTGAACATTG
107


(TrC4Ha)


GCGT





14wc2CsB09.f2
GATGCTCAAAAGAA
108





AGGAGAG





14wc2CsB09.f3
ATCGGGCGTCTTGT
109





TCAG



 


WcCTl
11wc1OsE04
11wc1OsE04.f1
AGGACCAGGACACC
110


(TrC4Hb)


AAGTA



 


WcCTm
06wc1OsE12
06wc1OsE12.f1 
TAACCCGGCTCTAT
111


(TrC4Hc)

(810)
GGAA









EXAMPLE 4
Development of Binary Transformation Vectors Containing Chimeric Genes with cDNA Sequences from White Clover TT12a, TrTTG1, TrTT2a, TrTT2b, TrTT8a, TrLDOXa, Tr4CLa, Tr4CLb, Tr4Clc Tr4CLd, TrC4Ha, TrC4Hb and TrC4Hc
To alter the expression of the proteins involved in flavonoid biosynthesis, protein binding, metal chelation, anti-oxidation, UV-light absorption, tolerance to biotic stresses such as viruses, micro-organisms, insects and fungal pathogens; pigmentation in for example flowers and leaves; herbage quality and bloat-safety and isoflavonoid content leading to health benefits, white clover TT12a, TTG1, TT2a, TT2b, TT8a, LDOXa, 4CLa, 4CLb, 4Clc 4CLd, C4Ha, C4Hb and C4Hc through antisense and/or sense suppression technology and for over-expression of these key proteins in transgenic plants, a set of sense and antisense binary transformation vectors was produced.
cDNA fragments were generated by high fidelity PCR using the original pGEM-T Easy plasmid cDNA as a template. The primers used (Table 3) contained attB1 and attB2 GATEWAY® recombination sites for directional cloning into the target vector. After PCR amplification and purification of the products, the cDNA fragments were cloned into the recombination site of the pDONR221TM vector (FIG. 80) using BP GATEWAY® technology (Invitrogen, Carlsbad, USA). vector The pPZP221 binary vector (Hajdukiewicz et al., 1994) was modified to contain the 35S2 cassette from pKYLX71:35 S2 as follows. pKYLX71:35 S2 was cut with Clal. The 5′ overhang was filled in using Klenow and the blunt end was A-tailed with Taq polymerase. After cutting with EcoRI, the 2 kb fragment with an EcoRI-compatible and a 3′-A tail was gel-purified. pPZP221 was cut with HindIII and the resulting 5′ overhang filled in and T-tailed with Taq polymerase. The remainder of the original pPZP221 multi-cloning site was removed by digestion with EcoRI, and the expression cassette cloned into the EcoRI site and the 3′ T overhang restoring the HindIII site. This binary vector contains between the left and right border the plant selectable marker gene aaaC1 under the control of the 35S promoter and 35S terminator and the pKYLX71:35 S2-derived expression cassette with a CaMV 35S promoter with a duplicated enhancer region and an rbcS terminator. This vector was GATEWAY®-enabled by digesting it with XbaI and blunt-ended using Klenow DNA polymerase, allowing the RfA recombination cassette to be cloned in the sense or antisense orientation between the enhanced 35S promoter and the rbcS terminator.
The orientation of the constructs (sense or antisense) was checked by restriction enzyme digestion and sequencing. Transformation vectors containing chimeric genes using full-length open reading frame cDNAs encoding white clover TT12a, TTG1, TT2a, TT2b, TT8a, LDOXa, 4CLa, Tr4CLb, 4Clc 4CLd, C4Ha, C4Hb and C4Hc proteins in sense and antisense orientations under the control of the CaMV 35S2 promoter were generated (FIGS. 35, 39, 46, 50, 54, 67, 68, 72 and 79).







TABLE 3







List of primers used to PCR-amplify the open reading frames of


flavonoid-related genes from white clover











gene name
clone ID
primer
primer sequence (5′->3′
SEQ. ID NO.














WcCTa
05wc1CsD12
05wc1CsD12GW.f
GGGGACAAGTTTGTACAAAAAAGCAGGCTT
112


(TrTT12a)


CATGAGCTCTATAGAAAACCAACC



 


WcCTa
05wc1CsD12
05wc1CsD12GW.r
GGGGACCACTTTGTACAAGAAAGCTGGGTC
113


(TrTT12a)


TCATATGTCGGCAACCAGTTGATCC



 


WcCTb
10wc1CsD07
10wc1CsD07GW.f
GGGGACAAGTTTGTACAAAAAAGCAGGCTT
114


(TrTTG1a)


CATGGAGAATTCAACTCAAGAATCACAC



 


WcCTb
10wc1CsD07
10wc1CsD07GW.r
GGGGACCACTTTGTACAAGAAAGCTGGGTC
115


(TrTT2a)


TCAAACCCGCAAAAGCTGCATCTTG



 


WcCTc
14wc1LsB05
14wc1LsBO5GW.f
GGGGACAAGTTTGTACAAAAAAGCAGGCTT
116


(TrTT2a)


CATGGTAAGAGCTCCTTGTTGTGA



 


WcCTc
14wc1LsB05
14wc1LsB05GW.r
GGGGACCACTTTGTACAAGAAAGCTGGGTC
117


(TrTT2a)


TTAGAACTCTGGCAATTCTATTTGATC



 


WcCTd
04wc1EsE11
04wc1EsE11GW.f
GGGGACAAGTTTGTACAAAAAAGCAGGCTT
118


(TrTT2b)


CATGGTGAGAGCTCCATGTTGTGA



 


WcCTd
04wc1EsE11
04wc1EsE11GW.r
GGGGACCACTTTGTACAAGAAAGCTGGGTC
119


(TrTT2b)


TCACAATTCAAGTAACTCAGTAATTTCC



 


WcCTe*
06wc2DsD04
06wc2DsD04GW.f
GGGGACAAGTTTGTACAAAAAAGCAGGCTT
120


(TrTT8a)


CATGAACCATGTTTTGTCAGAAAGAAGG



 


WcCTe*
06wc2DsD04
06wc2DsD04GW.r
GGGGACCACTTTGTACAAGAAAGCTGGGTC
121


(TrTT8a)


TCAAAACTTTGAAGCCACTTTTTGTAGG



 


WcCTf
07wc3GsD03
07wc3GsD03GW.f
GGGGACAAGTTTGTACAAAAAAGCAGGCTT
122


(TrLDOXa)


CATGGGAGCCGTGGCACAAAGAGTTG



 


WcCTf
07wc3GsD03
07wc3GsD03GW.r
GGGGACCACTTTGTACAAGAAAGCTGGGTC
123


(TrLDOXa)


TCATTTTTTAGGATCATCCTTCTTCTC



 


WcCTg
14wc2KsH10
14wc2KsH10GW.f
GGGGACAAGTTTGTACAAAAAAGCAGGCTT
124


(Tr4CLa)


CATGGCGGCCGCGGGAATTCGATTAAGC



 


WcCTg
14wc2KsH10
14wc2KsH10GW.r
GGGGACCACTTTGTACAAGAAAGCTGGGTC
125


(Tr4CLa)


TTATTCTGCTGCTAACTTTGCTCTGAG



 


WcCTh
13wc1DsH07
13wc1DsH07GW.f
GGGGACAAGTTTGTACAAAAAAGCAGGCTT
126


(Tr4CLb)


CATGGCGGCCGCGGGAATTCGATTAAGC



 


WcCTh
13wc1DsH07
13wc1DsH07GW.r
GGGGACCACTTTGTACAAGAAAGCTGGGTC
127


(Tr4CLb)


TTAATTTGTTGGAACACCAGCTGC



 


WcCTi
16wc1NsB11
16wc1NsB11GW.f
GGGGACAAGTTTGTACAAAAAAGCAGGCTT
128


(Tr4CLc)


CATGGCGGCCGCGGGAATTCGATTAAGC



 


WcCTi
16wc1NsB11
16wc1NsB11GW.r
GGGGACCACTTTGTACAAGAAAGCTGGGTC
129


(Tr4CLc)


TCAAGGCTTTTGGGTGGTACTTTCTAAC



 


WcCTj
12wc1CsA11
12wc1CsA11GW.f
GGGGACAAGTTTGTACAAAAAAGCAGGCTT
130


(Tr4CLd)


CATGTCACCATTTCCTCCACAGCAAG



 


WcCTj
12wc1CsA11
12wc1CsA11GW.r
GGGGACCACTTTGTACAAGAAAGCTGGGTC
131


(Tr4CLd)


TTAAGTGGCCACCACCAAACCTTCG



 


WcCTk
14wc2CsB09
14wc2CsB09GW.f
GGGGACAAGTTTGTACAAAAAAGCAGGCTT
132


(TrC4Ha)


CATGGATCTACTCCTTCTTGAAAAGACTC



 


WcCTk
14wc2CsB09
14wc2CsB09GW.r
GGGGACCACTTTGTACAAGAAAGCTGGGTC
133


(TrC4Ha)


TTAAAATGATCTTGGCTTAGCAACAATG



 


WcCTl*
11wc1OsE04
11wc1OsE04GW.f
GGGGACAAGTTTGTACAAAAAAGCAGGCTT
134


(TrC4Hb)


CGCAGTGGTAACAACGCAGAGTACGC



 


WcCTl*
11wc1OsE04
11wc1OsE04GW.r
GGGGACCACTTTGTACAAGAAAGCTGGGTC
135


(TrC4Hb)


TTAAAATGATCTTGGCTTAGCAACAATG



 


WcCTm*
06wc1OsE12
06wc1OsE12GW.f
GGGGACAAGTTTGTACAAAAAAGCAGGCTT
136


(TrC4Hc)


CCCGACGTCGCATGCTCCCGGC



 


WcCTm*
06wc1OsE12
06wc1OsE12GW.r
GGGGACCACTTTGTACAAGAAAGCTGGGTC
137


(TrC4Hc)


TTAAAATGATCTTGGCTTAGCAACAATG









EXAMPLE 5
Production and Analysis of Transgenic White Clover Plants Carrying Chimeric White Clover TT12a, TTG1, TT2a, TT2b, TT8a, LDOXa, 4CLa, 4CLb, 4Clc 4CLd, C4Ha, C4Hb and C4Hc Genes Involved in Flavonoid Biosynthesis
A set of transgenic white clover plants carrying white clover genes involved in flavonoid biosynthesis, protein binding, metal chelation, anti-oxidation, UV-light absorption, tolerance to biotic stresses such as viruses, micro-organisms, insects and fungal pathogens; pigmentation in for example flowers and leaves; herbage quality and bloat-safety and isoflavonoid content leading to health benefits, were produced.
pPZP221-based transformation vectors with WcCTa (TrTT12a), WcCTb (TrTTG1), WcCTc (TrTT2a), WcCTd (TrTT2b), WcCTe (TrTT8a), WcCTf (TrLDOXa), WcCTg (Tr4Cla), WcCTh (Tr4CLb), WcCTi (Tr4Clc) WcCTj (Tr4CLd), WcCTk (TrC4Ha), WcCTl (TrC4Hb) and WcCTm (TrC4Hc) cDNAs comprising the full open reading frame sequences in sense and antisense orientations under the control of the CaMV 35S promoter with duplicated enhancer region (35S2) were generated as detailed in Example 4.
Agrobacterium-mediated gene transfer experiments were performed using these transformation vectors.
The production of transgenic white clover plants carrying the white clover WcCTa (TrTT12a), WcCTb (TrTTG1), WcCTc (TrTT2a), WcCTd (TrTT2b), WcCTe (TrTT8a), WcCTf (TrLDOXa), WcCTg (Tr4Cla), WcCTh (Tr4CLb), WcCTi (Tr4Clc), WcCTj (Tr4CLd), WcCTk (TrC4Ha), WcCTl (TrC4Hb) and WcCTm (TrC4Hc) cDNAs under the control of the CaMV 35S promoter with duplicated enhancer region (35S2) is described here in detail. The selection process is shown in FIG. 81.
Preparation of White Clover Cotyledonary Explants
White clover (cv ‘Mink’) seeds were rinsed for 5 minutes in running tap water and incubated twice, for 5 minutes in 70% v/v ethanol in a 120 ml tissue culture container with gentle shaking. The same container was used to incubate the seeds for 2 minutes in 1% sodium hypochlorite (1:3 ratio of DomestosTM bleach in water) with gentle shaking. The seeds were then rinsed six times in sterile water in a laminar flow hood and incubated for 18 hours at 4° C. in the dark. Cotyledonary explant were extracted using 10 ml syringes attached to 21 G needles (Terumo, Japan) under a dissecting microscope in a laminar flow hood. Both layers of the seed coat were peeled away, the end of the hypocotyl was cut off and the cotyledons with approximately 4 mm of hypocotyl were separated and transferred to a 90×90×20 mm petri dish containing MGL medium.
Preparation of Agrobacterium 
Agrobacterium tumefaciens strain AGL-1 containing each PZP221-derived binary expression vector was streaked on LB medium containing 50 μg/ml rifampicin and 100 μg/ml spectinomycin and grown at 27° C. for 48 hours. A single colony was used to inoculate 5 ml of LB medium containing 50 μg/ml rifampicin and 100 μg/ml spectinomycin and grown over night at 27° C. and 250 rpm on an orbital shaker. The overnight culture was used as an inoculum for 40 ml of YEP medium containing 100 μg/ml spectinomycin and 40 mg/l acetosyringone. Incubation was over night at 27° C. and 250 rpm on an orbital shaker in a 250 ml Erlenmeyer flask.
The overnight cultures were centrifuged for 15 min at 5500×g and the supernatant discarded. The cells were resuspended in MGL media with 40 mg/l acetosyringone to a volume corresponding to an OD600 reading of 0.4. The cells were then incubated at 27° C. and 250 rpm until the OD600 reading reached 0.8.
Cocultivation and Selection of White Clover Transformants
The MGL medium was removed from the petri dish containing white clover cotyledonary explants and replaced with the prepared Agrobacterium suspension using a sterile serological pipette. The petri dish was sealed with laboratory film, covered with aluminium foil and incubated with gentle shaking for 45 min. The dish was opened in the laminar flow hood and the Agrobacterium suspension removed with a pipette. The explants were then transferred to plates containing RM73 media with 40 mg/l acetosyringone (Table 4) and incubated for 3 days in a plant tissue culture room at 22° C. with a 16 hour photoperiod. After this, the explants were transferred, with the hypocotyl end in the media, to plates containing RM73 media with 75 mg/l gentamicin and 250 mg/l cefotaxime. The explants were transferred to fresh plates every two weeks for 6-8 weeks. Shoots were then transferred to 120 ml tissue culture vessels containing RIM media (Table 5) with 75 mg/l gentamicin and 250 mg/l cefotaxime. When roots had developed, the plantlets were transferred to pots of soil and after 2 weeks of recovery in a misting bench, were grown under standard glasshouse conditions.
Preparation of Genomic DNA
1-2 leaflets of white clover plants recovered from the transformation process were harvested and freeze-dried. The tissue was homogenised on a Retsch MM300 mixer mill, then centrifuged for 10 min at 1700×g to collect cell debris. Genomic DNA was isolated from the supernatant using Wizard Magnetic 96 DNA Plant System kits (Promega) on a Biomek FX (Beckman Coulter). 5 μl of the sample (50 μl) were then analysed on an agarose gel to check the yield and the quality of the genomic DNA.
Analysis of DNA from Putative Transgenic Lines Using Real-Time PCR
Genomic DNA was analysed for the presence of the transgene by real-time PCR using SYBR Green chemistry. PCR primer pairs were designed to detect the aacC1 gentamycin resistance gene in the transferred T-DNA region using MacVector (Accelrys). The sequences of these primers are as follows:









SEQ ID No.: 138



pPZPaacC1-1.f 5′-TCAAGTATGGGCATCATTCGCAC-3′



 



SEQ ID No.: 139



pPZPaacC1-1.r 5′-TGCTCAAACCGGGCAGAACG-3′






2.5 μl of each genomic DNA sample was run in a 25 μl PCR reaction including SYBR Green on an ABI (Applied Biosystems) together with samples containing DNA isolated from wild type white clover plants (cv ‘Mink’, negative control), samples containing buffer instead of DNA (buffer control) and samples containing the plasmid used for transformation (positive plasmid control).







TABLE 4







Composition of RM73 tissue culture media, pH 5.75











Component
[Stock]
For 1 litre
















MS Macronutients
 10x
100
mL



MS Micronutrients
100x
10
mL



MS Vitamins
100x
10
mL



TDZ
100 mM
50
uL



NAA
 1 mM
0.5
mL



Sucrose (BDH Chemicals)
—
30
g



Agar
—
8
g

















TABLE 5







Composition of root-inducing tissue


culture media (RIM73), pH 5.75











Component
[Stock]
For 1 litre
















MS macronutrients
 10x
100
mL



MS micronutrients
100x
10
mL



MS vitamins
100x
10
mL



Indole-3-butyric acid
1 mM
1.2
mL



Sucrose (BDH Chemicals)
—
15
g



Agar (Becton-Dickinson)
—
8
g










EXAMPLE 6
Analysis of Condensed Tannins and Their Monomers in the Leaves of Transgenic White Clover Plants Carrying Chimeric White Clover TT12a, TTG1, TT2a, TT2b, TT8a, LDOXa, 4CLa, 4CLb, 4Clc 4CLd, C4Ha, C4Hb and C4Hc Genes Involved in Flavonoid Biosynthesis
Accumulation of condensed tannins and their monomers was analysed qualitatively in leaves of transgenic and wild type (cv ‘Mink’) white clover plants using 4-dimethylaminocinnemaldehyde (DMACA) staining. Two mature leaflets from each plant were decolourised in absolute ethanol in 6-well tissue culture plates for 3 hours with gentle shaking. The ethanol was removed and replaced with a 0.01% w/v solution of DMACA (Fluka), freshly made up in absolute ethanol with 2.4% v/v concentrated hydrochloric acid. After 1 hour of incubation with gentle shaking, the leaflets were rinsed with distilled water and mounted in 50% glycerol for analysis with a dissecting microscope. Wild type white clover plants show blue staining in epidermal cells in the floral organs and in trichomes. Lotus corniculatus (cv ‘Draco’), a forage legume with a ‘bloat-safe’ level of condensed tannins in the leaves, shows blue staining of approximately 50% of mesophyll cells in leaves (FIG. 82). Achieving a level of condensed tannins in white clover leaves that is comparable to the level seen in leaves of L. corniculatus by metabolic engineering would be agronomically valuable.
DMACA staining can detect economically significant levels of condensed tannins and their monomers in the leaves of established bloat-safe forage legumes. However, the condensation of catechin monomers to form condensed tannins and their transport from the cytoplasm to the vacuole is poorly understood. Hence, modifying the regulation of known enzymes and transcription factors in the flavonoid pathway may up-regulate catechin levels but not increase condensed tannin levels, and therefore, bloat-safety. The PVPP-butanol-HCl assay detects only condensed tannins, relying on the ability of condensed tannins, but not their monomers to bind to PVPP. The detailed method is as follows.
Clover leaf and inflorescence (positive control) tissue was snap-frozen and ground to a fine powder in a mortar and pestle under liquid nitrogen. After grinding, 0.75 g of the powder from each sample was transferred to a 14 ml screw-cap centrifuge tube (Falcon), vortex-mixed with 1.5 ml of extraction buffer containing 80% v/v methanol in distilled water with 5.3 mM sodium bisulfite. Samples were mixed for 5 hours on a mixing wheel before centrifugation at 3000×g for 10 minutes. A 1 ml aliquot of each supernatant was transferred to a 1.5 ml microcentrifuge tube and reduced to 0.25 ml in a vacuum centrifuge. Equal volumes of the sample were added to each of two 1.5 ml microcentrifuge tubes containing 25 mg of polyvinyl polypyrrolidone (PVPP). Each mixture was vortex-mixed intermittently for 15 min and centrifuged for 1 min at maximum speed in a microcentrifuge. After removal of the supernatant, the pellet was washed four times with 1 ml of methanol, with a 1 min centrifugation step at maximum speed in a microcentrifuge between each wash. A freshly-made 70:30 (v/v) solution of butanol and concentrated hydrochloric acid was added to each pellet and one tube of the mixture was incubated for 1 hour at 70° C., whereas the other tube was incubated at ambient temperature. The difference in the absorbance (530 nm) between the two tubes from each plant sample was proportional to the level of condensed tannins in the sample. This assay can be quantitated with a condensed tannin of known concentration, although only the relative levels of tannins were measured in this experiment.
EXAMPLE 7
Design of Real Time RT-PCR Primers Based on cDNA Sequences of Clover TT12, TTG1, TT2, TT8, LDOX, 4CL and C4H Genes
Real-time RT-PCR is a recently developed technique that allows more quantitative analyses of gene expression than Northern or conventional RT-PCR experiments. Essentially, real-time RT-PCR with SYBR Green chemistry and gene-specific primers involves the automatic measurement of the level of a fluorescent PCR product generated from a cDNA species over each cycle. The abundance of each template is proportional to the amplification rate. Therefore, a threshold corresponding to the start of the exponential phase of PCR allows the relative abundance of target genes to be standardised against a uniformly expressed ‘housekeeping’ gene in each tissue and compared to a negative control without a template. Real-time RT-PCR with SYBR Green chemistry has been used successfully by others in the field to quantify the expression of four flavonoid-related genes in Lotus corniculatus plants exposed to different light regimes (Paolocci et al., 2005)
A Real-Time RT-PCR strategy involving with SYBR Green chemistry and the δδCT method of analysis was used characterise the expression of TT12, TTG1, TT2, TT8, LDOX, 4CL and C4H homologues in white clover tissues containing high and low levels of condensed tannins. This approach aimed to determine which of the genes and isoforms were most likely to be involved in condensed tannin production, or in the production of other flavonoids, and could therefore be targeted for overexpression or downregulation in the metabolic engineering of bloat-safe white clover.
The full-length cDNA sequences of white clover of TT12, TTG1, TT2, TT8, LDOX, 4CL and C4H homologues were used as input data for the Primer Express (Applied Biosystems, Foster City, USA) primer design program, using the default settings, no 3′ GC clamp and a predicted amplicon size of 50-150 base pairs. Primers close to the 3′ ends of the input sequences were preferred, due to the likelihood of a large number of cDNA molecules derived from clover samples being incomplete at the 5′ end. The sequences of the chosen primers are shown in Table 6.
The specificity of the primer sets was tested using 1 ul of plasmid DNA (0.01 ng/ul) from the original cDNA cloned into pGEM-T Easy or autoclaved, purified water, 12.5 μl 2×SYBR Green Master Mix (Applied Biosystems), 0.5 ul each of the forward and reverse primers (10 uM) and 10.5 ul of autoclaved, purified water (Sartorius AG, Goettingen, Germany). Real-time PCR was performed in 96-well optical PCR plates (Applied Biosystems) using the Stratagene MX3000P cycler and the following cycling parameters: 95° C. for 10 min, 40 cycles of 95° C. for 30 sec and 60° C. for 1 min, followed by 55° C. for 1 min and 95° C. for 1 min. All of the primer sets except those designed to amplify clover TT2a amplified a satisfactory level of products from the corresponding cDNA templates with a cycle threshold cut-off of 24 cycles (Table 7). The primer sets were isoform-specific, with the exception of the two sets designed to amplify clover C4H homologues.
It was shown by DMACA staining that the lower half of Mink white clover buds are enriched for condensed tannins. Therefore a preliminary experiment was carried out to test for the expression of clover TT12, TTG1, TT2, TT8, LDOX, 4CL and C4H genes in the buds of white clover (cv Mink), relative to expression of a clover histone control gene. Total RNA was extracted from upper and lower halves of buds as well as whole buds using the RNeasy kit (QIAGEN GmbH, Hilden, Germany) and contaminating genomic DNA was digested on the column using the optional on-column DNAse digestion according to the manufacturers' instructions. Complementary DNA (cDNA) was synthesised from 0.5 ug of total RNA using the Quantitect Reverse Transcriptase Kit (QIAGEN GmbH). Real-time RT-PCR reactions were set up and run as described earlier using 1 ul of cDNA, plasmid control DNA or autoclaved, purified water as the template. The experiment showed that expression of clover LDOX correlated well with condensed tannin production in the lower half of white clover buds (FIG. 83).







TABLE 6 







List of primers designed for Real-time RT-PCR analysis of condensed


tannin-rich organs of white clover, based on cDNA sequences of


clover TT12, TTG1, TT2, TT8, LDOX, 4CL and C4H genes










Gene





name
Clone ID
primer 1 (forward)
primer 2 (reverse)





WcCTa
05wc1CsD12
GACAGAGAGCATAGCCGAGCA
GGTATAAGACCGCGAGCGAA


(TrTT12a)

SEQ. ID. NO. 140
SEQ. ID. NO. 141


 


WcCTb
10wc1CsD07
AACTCATGTTCCATCCCGCA
CGGAGGAGGTTTTCTGGAGAG


(TrTTG1a)

SEQ. ID. NO. 142
SEQ. ID. NO. 143


 


WcCTc
14wc1LsB05
GTAATGGCAACTGGCGTGCT
CACATCTTAACAAGCCTCGTAGCT


(TrTT2a)

SEQ. ID. NO. 144
SEQ. ID. NO. 145


 


WcCTd
04wc1EsE11
CCATTCTAATTGGCGTGCTCT
CCACACCTTAACAACCCAGCTT


(TrTT2b)

T SEQ. ID. NO. 146
SEQ. ID. NO. 147


 


WcCTe
06wc2DsD04
TGGGAGGCTTCATGTGATCA
GCATTAGCTGGTCCTTTGAACTTAG


(TrTT8a)

SEQ. ID. NO. 148
SEQ. ID. NO. 149


 


WcCTf
07wc3GsD03
GCTAGTGGTCAACTTGAATGG
TCAGGAAAAATACAATGAAAGAAATA


(TrLDOXa)

GA SEQ. ID. NO. 150
ATCT SEQ. ID. NO. 151


 


WcCTg
14wc2KsH10
GCACCCACCGGAAAAGTCTA
CCGAGAGGTGAGTTCGACGT


(Tr4Cla)

SEQ. ID. NO. 152
SEQ. ID. NO. 153


 


WcCTh
13wc1DsH07
TCATAGTGGATAGGCTTAAAG
TGGGATGTGAAAGAATAATGGCTT


(Tr4CLb)

AATTGAT 
SEQ. ID. NO. 155




SEQ. ID. NO. 154



 


WcCTi
16wc1NsB11
GTTGTCCCGCAAAAGGATGT
CACAAAGGCAACAGGAACTTCAC


(Tr4CLc)

SEQ. ID. NO. 156
SEQ. ID. NO. 157


 


WcCTj
12wc1CsA11
CTTTCCTCGGTGCCTCCTTC
AAGGATTTGCGGTGGTGATG


(Tr4CLd)

SEQ. ID. NO. 158
SEQ. ID. NO. 159


 


WcCTk
14wc2CsB09
CTTGCCGGTTATGACATCCC
CCACGCGTTGACCAATATCTT


(TrC4Ha)
06wc1OsEl2
SEQ. ID. NO. 160
SEQ. ID. NO. 161


WcCTm





(TrC4Hc)





 


WcCTl
11wc1OsE04
CGTTGATGAGAGAAAGAAACT
GAGCATCCAAAATGTGATCAATTG


(TrC4Hb)

TGAAA 
SEQ. ID. NO. 163




SEQ. ID. NO. 162
















TABLE 7







Results of testing real-time PCR primer sets on plasmids containing cDNA


sequences encoding clover TT12, TTG1, TT2, TT8, LDOX, 4CL and C4H genes









Primers



















Template
TT12a
TTG1a
TT2a
TT2b
TT8a
LDOXa
4CLa
4CLb
4CLc
4CLd
C4Hac
C4Hb






















WcCTa
26.7













(TrTT12)


WcCTb

19.6


(TrTTG1a)


WcCTc


27.7
0 Ct


(TrTT2a)


WcCTd


36.2
20.8


(TrTT2b)


WcCTe




20


(TrTT8)


WcCTf





21.13


(TrLDOX)


WcCTg






19.5
no Ct
37.7
no Ct


(Tr4CLa)


WcCTh






no Ct
19.3
39.7
no Ct


(Tr4CLb)


WcCTi






37.4
36.8
19.8
35.8


(Tr4CLc)


WcCTj






31.3
31.8
32.5
20.6


(Tr4CLd)


WcCTk










22.44
22.9


(TrC4ha)


WcCTI










22.05
17.55


(TrC4Hb)


WcCTm










20.2
37.13


(TrC4Hc)


ddH2O
37.2
0 Ct
0 Ct
38.8
35.3
0 Ct
37.6
0 Ct
32.5
31.1
37.2
0 Ct









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Finally, it is to be understood that various alterations, modifications and/or additions may be made without departing from the spirit of the present invention as outlined herein.
It will also be understood that the term “comprises” (or its grammatical variants) as used in this specification is equivalent to the term “includes” and should not be taken as excluding the presence of other elements or features.
Documents cited in this specification are for reference purposes only and their inclusion is not acknowledgment that they form part of the common general knowledge in the relevant art.

## Claims

1. A substantially purified or isolated nucleic acid, said nucleic acid being selected from the group consisting of:
(a) a nucleotide sequence encoding a TRANSPARENT TESTA 2 (TT2) selected from the group consisting of Seq ID Nos. 9, 11, 12, 13, 60, 62 and functionally active fragments thereof;
(b) a nucleotide sequence which is the full length complement to a sequence selected from the group consisting of Seq ID Nos. 9, 11, 12, 13, 60 and 62; and
(c) a variant nucleotide sequence encoding a TT2 or TT2-like protein which is a variant of a starting sequence, said starting sequence having a sequence as defined in paragraph (a), wherein the variant nucleotide sequence has at least 90% identity to the starting sequence.

2. The nucleic acid of claim 1, wherein the variant nucleotide sequence has at least 95% identity to the starting sequences.

3. The nucleic acid of claim 1, wherein the variant nucleotide sequence has at least 98% identity to the starting sequence.

4. The nucleic acid of claim 1, wherein the nucleotide sequence encoding a TT2 or TT2-like protein is selected from the group consisting of Seq ID Nos. 9, 11, 12, 13, 60 and 62.

5. A construct comprising a nucleic acid or nucleic acid fragment according to claim 1.

6. A vector comprising a nucleic acid or nucleic acid fragment according to claim 1.

7. A vector according to claim 6, further including a promoter and a terminator, said promoter, nucleic acid or nucleic acid fragment and terminator being operatively linked.

8. A plant cell, plant, plant seed or other plant part, comprising a nucleotide construct or a vector, said construct or vector comprising a nucleic acid or nucleic acid fragment according to claim 1.

9. A plant, plant seed or other plant part derived from a plant cell or plant according to claim 8.

10. A method of modifying a flavonoid-related biological property of a plant comprising introducing into said plant an effective amount of nucleic acid or nucleic fragment according to claim 1, wherein said nucleic acid or nucleic fragment is optionally introduced in a construct or vector.

11. A method according to claim 10 wherein the property of the plant that is modified is flavonoid biosynthesis in a plant, said method comprising introducing into said plant an effective flavonoid biosynthesis-modifying amount of the nucleic acid or nucleic acid fragment.

12. A method according to claim 10 wherein the property of the plant that is modified is protein binding, metal chelation, anti-oxidation, and/or UV-light absorption in a plant, said method comprising introducing into said plant an effective protein binding, metal chelation, anti-oxidation, and/or UV-light absorption modifying amount of the nucleic accord or nucleic acid fragment.

13. A method according to claim 10 wherein the property of the plant that is modified is pigment production in a plant, said method comprising introducing into said plant an effective pigment production-modifying amount of the nucleic acid or nucleic acid fragment.

14. A method according to claim 10 wherein the property of the plant that is modified is plant defense to a biotic stress, said method comprising introducing into said plant an effective defense to biotic stress-modifying amount of the nucleic acid or nucleic acid fragment.

15. A method according to claim 14 wherein said biotic stress is selected from the group consisting of viruses, microorganisms, insects and fungal pathogens.

16. A method according to claim 10 wherein the property of the plant that is modified is forage quality of a plant by disrupting protein foam and/or conferring protection from rumen pasture bloat, said method comprising introducing into said plant an effective forage quality-modifying amount of the nucleic acid or nucleic acid fragment.

17. A substantially purified or isolated polypeptide encoded by a nucleic acid or nucleic fragment according to claim 1.

18. A substantially purified or isolated polypeptide, said polypeptide being selected from the group consisting of:
(a) an amino acid sequence encoding a TT2 or TT2-like polypeptide selected from the group consisting of Seq ID Nos. 10, 14, 61, 63 and functionally active fragments thereof; and
(b) a variant amino acid sequence encoding a TT2 or TT2-like polypeptide which is a variant of a sequence recited in (a), wherein the variant sequence has at least 90% identity to the sequence recited in (a).