NZ547420A - Cellulase (CELL) from ryegrass ( lolium ), nucleic acids encoding them and related methods, constructs and plants - Google Patents

Abstract

A substantially purified or isolated nucleic acid encoding cellulase (CELL) protein and its polypeptide from a ryegrass (Lolium) species are described. Vectors and plant cells comprising the nucleic acid are described. The nucleic acid can be introduced into a plant to modify lignin biosynthesis and/or cellulose degradation in a plant, or can be used as a molecular marker, for QTL tagging to mapping, DNA fingerprinting and marker assisted selections to for a herbage quality trait such as dry matter digestibility, mechanical stress tolerance, disease resistance, insect pest resistance, plant stature and leaf and stem colour.

Description

005016644 5W2o 1 Manipulation of plant cell walls (3) This application is a divisional of New Zealand patent application 536802, which in turn is a divisional of New Zealand patent application 524586, the entire disclosures of which are incorporated herein by reference.

This application is the parent of a divisional application entitled "Manipulation of plant cell walls (4)".

The present invention relates to nucleic acid fragments encoding amino acid sequences for lignification and lignification-related enzymes, and for cellulases and cellulase-like enzymes in plants, and the use thereof for the modification of 10 lignin biosynthesis and cellulose degradation in plants to manipulate plant cell walls.

Lignins are complex phenolic polymers that strengthen plant cell walls against mechanical and chemical degradation. The process of lignification typically occurs during secondary thickening of the walls of cells with structural, conductive or 15 defensive roles. Three monolignol precursors, sinapyl, coniferyl and p-coumaryl alcohol combine by dehydrogenative polymerisation to produce respectively the syringyl (S), guaiacyl (G) and hydroxyl (H) subunits of the lignin polymer, which can also become linked to cell-wall polysaccharides through the action of peroxidases and other oxidative enzymes.

Biosynthesis of the monolignol precursors is a multistep process beginning with the aromatic amino-acids phenylalanine (and tyrosine in grasses). Lignin biosynthesis is initiated by the conversion of phenylalanine into cinnamate through the action of phenylalanine ammonia lyase (PAL). The second enzyme of the pathway is cinnamate-4-hydroxylase (C4H), responsible for the 25 conversion of cinnamate to p-coumarate. The second hydroxylation step in the pathway is catalyzed by p-coumarate-3-hydroxylase (C3H) producing caffeic acid. Caffeic acid is then O-methylated by caffeic acid O-methyltransferase (OMT) to form ferulic acid. Ferulic acid is subsequently converted into 5-hydroxyferulate through the last hydroxylation reaction of the general 30 phenylpropanoid pathway catalised by ferulate-5-hydroxylase (F5H). The 5- intellectual property office of n.z. 2 3 AUG 2007 1A hydroxyferulate produced by F5H is then O-methylated by OMT, the same enzyme that carries out the O-methylation of caffeic acid. The cinnamic acids are converted by action of the 4-coumarate:CoA ligase (4CL) and intellectual property office of nx 2 3 AUG 2007 caffeoyl-CoA 3-O-methyltransferase (CCoAMT) into the corresponding CoA derivatives. It is the final two reduction/dehydrogenation steps of the pathway, catalysed by cinnamoyi CoA reductase (CCR) and cinnamyl alcohol dehydrogenase (CAD) that are considered to be specific to lignin biosynthesis. The three monolignols, sinapyl, coniferyl and p-coumaryl alcohols, are then polymerised by extracellular peroxidases (PER) and laccases (LAC) to yield lignins. The proportions of monolignols incorporated into the lignin polymers vary depending on plant species, tissue, developmental stage and sub-cellular location.

Cellulose, a main component of plant cell wails, is degraded in maturing plant organs by the action of celluiases (CELL). Celiuiases play an important role in softening of plant organs and in fruit ripening.

Dry matter digestibility of forage grasses and legumes has been negatively correlated with lignin content. In addition, natural mutants of lignin biosynthetic enzymes in maize, sorghum and peari millet that have higher rumen digestibility have been characterised as having lower lignin content and altered S/G subunit ratio. Lignification of plant ceil wails is the major factor identified as responsible for lowering digestibility of forage tissues as they mature.

Furthermore, cellulose in forage grasses contributes significantly to the readily available energy in the feed for grazing ruminant animals. The fermentation processes in the rumen require considerable readily available energy. The improvement of the readily available energy in the rumen can increase the efficiency of rumen digestion. An increased efficiency in rumen digestion leads to an improved conversion of the forage protein fed to the ruminant animal into milk or meat, and to a reduction in nitrogenous waste as environmental pollutant. 3 Perennial ryegrass (Lolium perenrie L.) is a key pasture grass in temperate climates throughout the world. Perennial ryegrass is also an important turf grass.

It would be desirable to have methods of altering lignin biosynthesis 5 and/or cellulose degradation in plants, including grass species such as ryegrasses and fescues. For example it may be desirable to reduce the activity of key lignin biosynthetic enzymes in order to reduce lignin content and/or alter lignin composition and to increase cellulose degradation for enhancing dry matter digestibility and/or improving herbage quality. Cell wall 10 digestibility and feed (grazed, cut hay, silage) quality could thus be increased by the manipulation of enzymes involved in the biosynthesis of lignins and in the degradation of cellulose. For other applications it may be desirable to enhance lignin biosynthesis to increase lignin content and/or alter lignin composition and to reduce cellulose degradation, for example to increase 15 mechanical strength of wood, to increase mechanical strength of turf grasses, to reduce plant height, to reduce lodging, to improve disease resistance, to reduce fruit ripening and/or to reduce plant organ softening.

While nucleic acid sequences encoding some of the enzymes involved in the lignin biosynthetic pathway and in cellulose degradation have been 20 isolated for certain species of plants, there remains a need for materials useful in the modification of lignin biosynthesis and cellulose degradation in a wide range of plants, particularly in forage grasses and legumes including ryegrasses and fescues, and for methods for their use.

It is an object of the present invention to overcome, or at least alleviate, 25 one or more of the difficulties or deficiencies associated with the prior art.

In one aspect, the present invention provides substantially purified or isolated nucleic acids or nucleic acid fragments encoding amino acid sequences for the following enzymes from a ryegrass (Lolium) or fescue 4 (Festuca) species, or functionally active fragments or variants thereof: caffeoyl-CoA 3-O-methyitransferase (CCoAMT), cinnamyl alcohol dehydrogenase (CAD), caffeic acid O-methyltransferase (OMT), cinnamate-4-hydroxylase (C4H), cinnamoyl-CoA reductase (CCR), peroxidase (PER), 5 cellulase (CELL), ferulate-5-hydroxylase (F5H), phenylalanine ammonia lyase (PAL) and 4-coumarate:CoA ligase (4CL).

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 CCoAMT, CAD, OMT, C4H, CCR, PER, CELL, F5H, PAL and 4CL, or functionally active fragments or variants thereof. Such proteins are referred to herein as CCoAMT-like, CAD-like, OMT-like, C4H-like, CCR-like, PER-like, CELL-like, F5H-iike, PAL-like and 4CL-like, respectively.

The ryegrass (Lolium) or fescue (Festuca) species may be of any 15 suitable type, including Italian or annual ryegrass, perennial ryegrass, tall fescue, meadow fescue and red fescue. Preferably the species is a ryegrass, more preferably perennial ryegrass (L perenne).

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 25 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 005016644 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 5 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 10 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, the present invention provides a substantially purified or isolated nucleic acid or nucleic acid fragment encoding a cellulase 15 (CELL) from a Lolium species, or a functionally active fragment or variant thereof.

Preferably, the Lolium species is Lolium perenne or Lolium arundinaceum.

In a preferred embodiment, the present invention provides a substantially purified or isolated nucleic acid or nucleic acid fragment encoding a CELL, or complementary or antisense to a sequence encoding a CELL, and including a 20 nucleotide sequence selected from the group consisting of (a) sequences shown in Figures 56 and 58 hereto (Sequence ID Nos: 125 and 127 to 134, respectively); (b) complements of the sequences 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).

Preferably, the functionally active fragments and variants have at least approximately 90% identity to the relevant part of the sequences recited in (a), (b) and (c), respectively, and have a size of at least 20 nucleotides. intellectual property office of N.z. 2 3 AUG 2007 oPf.ElVED 5A In a preferred embodiment of this aspect of the invention, the substantially purified or isolated nucleic acid or nucleic acid fragment encoding a CCoAMT or CCoAMT-like protein includes a nucleotide sequence selected from the group consisting of (a) sequences shown in Figures 1, 3, 4, 6, 7, 82 and 87 hereto (Sequence ID Nos: 1, 3 to 11, 12, 14 to 20, 21, 168 and 170, respectively); (b) complements of the sequences shown in Figures 1, 3, 4, 6, 7, 82 and 87 hereto; (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 (o).

In a further preferred embodiment of this aspect of the invention, the substantially purified or isolated nucleic acid or nucleic acid fragment encoding a CAD or CAD-like protein includes a nucleotide sequence selected from the group consisting of (a) sequences shown in Figures 9, 11, 13, 15, 16, 18, 19, 21 and 22 hereto (Sequence ID Nos: 23, 25, 27, 29 to 33, 34, 36 to 40, 41, 43 to 44 and 45, respectively); (b) complements of the sequences shown in Figures 9, 11, 13, 15, 16,18,19, 21 and 22 hereto; (c) sequences 6 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 another preferred embodiment of this aspect of the invention, the substantially purified or isolated nucleic acid or nucleic acid fragment 5 encoding an OMT or OMT-like protein includes a nucleotide sequence selected from the group consisting of (a) sequences shown in Figures 24, 26, 27, 29, 30, 93 and 99 hereto (Sequence ID Nos: 47, 49 to 58, 59, 61 to 93, 94, 172 and 174, respectively): (b) complements of the sequences shown in Figures 24, 26, 27, 29, 30, 93 and 99 hereto; (c) sequences antisense to the 10 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 includes a nucleotide sequence selected 15 from the group consisting of (a) sequences shown in Figures 32, 34, 36 and 76 hereto (Sequence ID Nos: 96, 98, 100 and 166, respectively); (b) complements of the sequences shown in Figures 32, 34, 36 and 76 hereto; (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) 20 and (c).

In another preferred embodiment of this aspect of the invention, the substantially purified or isolated nucleic acid or nucleic acid fragment encoding a CCR or CCR-like protein includes a nucleotide sequence selected from the group consisting of (a) sequences shown in Figures 38, 40, 41, 43 25 and 44 hereto (Sequence ID Nos: 102, 104 to 106, 107, 109 to 110 and 111, respectively); (b) complements of the sequences shown in Figures 38, 40, 41, 43 and 44 hereto; (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). 7 In a further preferred embodiment of this aspect of the invention, the substantially purified or isolated nucleic acid or nucleic acid fragment encoding a PER or PER-like protein includes a nucleotide sequence selected from the group consisting of (a) sequences shown in Figures 46, 48, 49, 51, 5 52, 54 and 105 hereto (Sequence ID Nos: 113, 115 to 116, 117, 119 to 120, 121, 123 and 176, respectively); (b) complements of the sequences shown in Figures 46, 48, 49, 51, 52, 54 and 105 hereto; (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 another preferred embodiment of this aspect of the invention, the substantially purified or isolated nucleic acid or nucleic acid fragment - encoding a CELL or CELL-iike protein includes a nucleotide sequence selected from the group consisting of (a) sequences shown in Figures 56 and 58 hereto (Sequence ID Nos: 125 and 127 to 134, respectively); (b) 15 complements of the sequences shown in Figures 56 and 58 hereto; (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, 20 the substantially purified or isolated nucleic acid or nucleic acid fragment encoding a F5H or F5H-like protein includes a nucleotide sequence selected from the group consisting of (a) sequences shown in Figures 59 and 61 hereto (Sequence ID Nos: 135 and 137 to 139, respectively); (b) complements of the sequences shown in Figures 59 and 61 hereto; (c) sequences antisense to 25 the sequences recited in (a) and (b); and (d) functionally active fragments and variants of the sequences recited in (a), (b) and (c).

In another preferred embodiment of this aspect of the invention, the substantially purified or isolated nucleic acid or nucleic acid fragment encoding a PAL or PAL-like protein includes a nucleotide sequence selected 8 from a group consisting of (a) sequences shown in Figures 62, 64, 65 and 67 hereto (Sequence ID Nos: 140, 142 to 148, 149 and 151 to 153, respectively); (b) complements of the sequences shown in Figures 62, 64, 65 and 67 hereto; (c) sequences antisense to the sequences recited in (a) and (b); and (d) 5 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 4CL or 4CL-iike protein includes a nucleotide sequence selected 10 from the group consisting of (a) sequences shown in Figures 68, 70, 71 and 73 hereto (Sequence ID Nos: 154, 156 to 161, 162 and 164, respectively); (b) complements of the sequences shown in Figures 68, 70, 71 and 73 hereto; (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) 15 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 capable of modifying lignin biosynthesis and/or cellulose degradation in a plant. Such variants include naturally occurring allelic 20 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 80% identity to the relevant part of the 25 above mentioned nucleotide sequence, 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 9 sequence. Preferably the fragment has a size of at least 10 nucleotides, more preferably at least 15 nucleotides, most preferably at least 20 nucleotides.

The nucleic acids or nucleic acid fragments encoding at least a portion of several lignification and lignification-like enzymes and cellulase and 5 cellulase-like enzymes have been isolated and identified. The nucleic acids and 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 using sequence-dependent protocols is well known in the art. Examples of sequence-dependent protocols 10 include, but are not limited to, 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, iigase chain reaction).

For example, genes encoding other lignification or lignification-like 15 enzymes and other cellulase or cellulase-like enzymes, 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 employing the methodology well known to those skilled in the art. Specific oligonucleotide probes based 20 upon the nucleic acid sequences of the present invention may be designed and synthesized by methods known in the art. Moreover, the entire sequences may be used directly to synthesize DNA probes by methods known to the skilled artisan such as random primer DNA labelling, nick translation, or end-labelling techniques, or RNA probes using available in vitro transcription 25 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 30 stringency.

In addition, short segments of the nucleic acids or nucleic acid fragments of the present invention may be used in amplification protocols to amplify longer nucleic acids or nucleic acid fragments encoding homologous genes from DNA or RNA. For example, the polymerase chain reaction may 5 be performed on a library of cloned nucleic acid fragments wherein the sequence of one primer is derived from a nucleic acid or nucleic acid fragment 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 10 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' 15 end. Using commercially available 3' RACE and 5' RACE systems (BRL), specific 3' or 5' cDNA fragments may be isolated (Ohara et al. (1989j 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 20 full-length cDNAs.

In a second aspect of the present invention there is provided a substantially purified or isolated polypeptide from a ryegrass (Lolium) or fescue (Festuca) species, selected from the group consisting of CCoAMT and CCoAMT-like, CAD and CAD-like, OMT and OMT-like, C4H and C4H-like, 25 CCR and CCR-like, PER and PER-like, CELL and CELL-like, F5H and F5H-like, PAL and PAL-like, 4CL and 4CL-!ike, enzymes; and functionally active fragments and variants thereof.

The ryegrass (Lolium) or fescue (Festuca) species may be of any suitable type, including Italian or annual ryegrass, perennial ryegrass, tall 005016644 11 fescue, meadow fescue arid red fescue. Preferably the species is a ryegrass, more preferably perennial ryegrass (L. perenne).

In a preferred embodiment the present invention provides a substantially purified or isolated CELL polypeptide from a Lolium species; or a functionally 5 active fragment or variant thereof.

Preferably, the Lolium species is Lolium perenne or Lolium arundinaceum.

In a preferred embodiment, the present invention provides a substantially purified or isolated CELL polypeptide including an amino acid sequence shown in Figure 57 hereto (Sequence ID No: 126); or a functionally active fragment or 10 variant thereof.

Preferably, the functionally active fragments and variants have at least approximately 90% identity with the recited sequences and have a size of at least 20 amino acids.

In a preferred embodiment of this aspect of the invention, the substantially 15 purified or isolated CCoAMT or CCoAMT-like polypeptide includes an amino acid sequence selected from the group of sequences shown in Figures 2, 5, 8, 83 and 88 hereto (Sequence ID Nos: 2, 13, 22, 169 and 171, respectively); and functionally active fragments and variants thereof.

In a further preferred embodiment of this aspect of the invention, the 20 substantially purified or isolated CAD or CAD-like polypeptide includes an amino acid sequence selected from the group of sequences shown in Figures 10, 12, 14, 17, 20 and 23 hereto (Sequence ID Nos: 24, 26, 28, 35, 42 and 46, respectively); and functionally active fragments and variants thereof.

In another preferred embodiment of this aspect of the invention, the 25 substantially purified or isolated OMT or OMT-like polypeptide includes an amino acid sequence selected from the group of sequences shown in Figures 25, 28, 31, 94 and 100 hereto (Sequence ID Nos: 48, 60, 95, 173 and 175, respectively); and functionally active fragments and variants thereof. intellectual property office of n.z. 2 3 AUG 2087 RECEIVED 005016644 11A 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 of sequences shown in Figures 33, 35, 37 and 77 hereto (Sequence ID Nos: 97, 99, 101 and 167, respectively); and 5 functionally active fragments and variants thereof.

In another preferred embodiment of this aspect of the invention, the substantially purified or isolated CCR or CCR-like polypeptide includes an amino acid sequence selected from the group of sequences shown in Figures 39, 42 and 45 hereto (Sequence ID Nos: 103, 108 and 112, respectively); and functionally 10 active fragments and variants thereof. intellectual property office of n.z. 2 3 AUG 2007 RECEIVED 12 In a further preferred embodiment of this aspect of the invention, the substantially purified or isolated PER or PER-like polypeptide includes an amino acid sequence selected from the group of sequences shown in Figures 47, 50, 53, 55 and 106 hereto (Sequence ID Nos: 114, 118, 122, 124 and 5 177, respectively); and functionally active fragments and variants thereof.

In another preferred embodiment of this aspect of the invention, the substantially purified or isolated CELL or CELL-like polypeptide includes an amino acid sequence shown in Figure 57 hereto (Sequence ID No: 126); and functionally active fragments and variants thereof.

In another preferred embodiment of this aspect of the invention, the substantially purified or isolated F5H or F5H-like polypeptide includes an amino acid sequence shown in Figure 60 hereto (Sequence ID No: 136); and functionally active fragments and variants thereof.

In a further preferred embodiment of this aspect of the invention, the 15 substantially purified or isolated PAL or PAL-like polypeptide includes an amino acid sequence selected from the group of sequences shown in Figures 63 and 66 hereto (Sequence ID Nos: 141 and 150, respectively); and functionally active fragments and variants thereof.

In another preferred embodiment of this aspect of the invention, the 20 substantially purified or isolated 4CL or 4CL-like polypeptide includes an amino acid sequence selected from the group of sequences shown in Figures 69, 72 and 74 hereto (Sequence ID Nos: 155, 163 and 165, respectively); and functionally active fragments and variants thereof.

By "functionally active" in relation to polypeptides it is meant that the 25 fragment or variant has one or more of the biological properties of the enzymes CCoAMT, CCoAMT-like, CAD, CAD-like, OMT, OMT-like, C4H, C4H-like, CCR, CCR-like, PER, PER-like, CELL, CELL-like, F5H, F5H-like, 13 PAL, PAL-like, 4CL and 4CL-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 5 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 10 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 15 acid fragment according to the present invention. Techniques for recombinantiy producing polypeptides are well known to those skilled in the art.

Availability of the nucleotide sequences of the present invention and deduced amino acid sequences facilitates immunological screening of cDNA 20 expression libraries. Synthetic peptides representing portions of the instant amino acid sequences may be synthesized. These peptides can 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 25 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 14 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 5 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 10 single nucleotides between allelic forms of such nucleotide sequence, can be used as perfect markers or candidate genes for the given trait.

Applicants have identified a number of SNP's of the nucleic acids and nucleic acid fragments of the present invention. These are indicated (marked with grey on the black background) in the figures that show multiple 15 alignments of nucleotide sequences of nucleic acid fragments contributing to consensus contig sequences. See for example, Figures 3, 6, 15, 18, 26, 29, 40, 58, 61, 64, 67 and 70 (Sequence ID Nos: 3 to 11, 14 to 20, 29 to 33, 36 to 40, 49 to 58, 61 to 93, 104 to 106, 127 to 134, 137 to 139, 142 to 148, 151 to 153 and 156 to 161, respectively).

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, or complements or sequences antisense thereto, and functionally active 25 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 single nucleotide polymorphism (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 5 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 nucleic acids or nucleic acid fragments of the present invention including 10 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 according to the present invention, and/or nucleotide sequence information thereof, as a molecular genetic 15 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, 20 particularly in 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 forage and turf grass improvement, e.g. tagging QTLs for herbage quality traits, dry matter digestibility, mechanical stress tolerance, disease resistance, 25 insect pest resistance, plant stature, leaf and stem colour. Even more particularly, sequence information revealing SNPs in allelic variants of the nucleic acids or nucleic acid fragments of the present invention and/or 16 nucleotide sequence information thereof may be used as molecular genetic markers for QTL tagging and mapping and in marker assisted selection, particularly in ryegrasses and fescues.

In a still further aspect of the present invention there is provided a 5 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 10 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 15 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 includes both cloning and expression 20 vectors. Vectors are often recombinant molecules including 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; 25 said regulatory element, nucleic acid or nucleic acid fragment and term inator being operatively linked. 17 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 5 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 10 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 15 used as long as it is replicable or 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 20 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 25 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 18 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 poiyA and other terminators from the nopaline synthase (nos), the octopine synthase (ocs) and the rbcS 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 10 (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 15 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 20 known in the art, such as PGR (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 25 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. 19 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, com, oat, wheat and barley), dicotyledons (such as arabidopsis, tobacco, 5 white clover, red clover, subterranean clover, alfalfa, eucalyptus) 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.

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 15 embryos and high velocity projectile introduction to cells, tissues, caili, 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 20 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 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 5 ryegrass {Lolium species) or fescue (Festuca species), even more preferably a ryegrass, most preferably perennial ryegrass, including both forage- and turf-type cuitivars.

The present invention also provides a plant, plant seed or other plant part derived from a plant cell of the present invention.

The present invention also provides a plant, plant seed or other plant part derived from a plant of the present invention.

In a further aspect of the present invention there is provided a method of modifying lignin biosynthesis and/or cellulose degradation in a plant, said method including introducing into said plant an effective amount of a nucleic 15 acid or nucleic acid fragment construct and/or a vector according to the present invention.

By "an effective amount" 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 20 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, Coid Spring Harbor, the entire disclosure of which is incorporated 25 herein by reference.

Using the methods and materials of the present invention, plant lignin biosynthesis and/or cellulose degradation may be increased, decreased or 21 otherwise modified relative to an untransformed control plant. They may be increased or otherwise modified, 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 modified, for example, by 5 incorporating an antisense nucleic acid or nucleic acid fragment of the present invention. In addition, the number of copies of genes encoding different enzymes in the lignin biosynthetic pathway may be manipulated to modify the relative amount of each monolignol synthesized, thereby leading to the formation of lignin having altered composition.

In a still further aspect of the present invention there is provided a lignin or modified lignin or a cellulose or modified cellulose substantially or partially purified or isolated from a plant, plant seed or other plant part of the present invention.

Such lignins may be modified from naturally occurring lignins in terms 15 of, for example, their monomeric composition or ratios of individual monolignols, the presence of novel monolignols, the degree of linkage and/or nature of linkages between lignins and other plant cell wall components.

Such cellulose may be modified from naturally occurring cellulose in terms of, for example, the degree of polymerisation (number of units), and/or 20 degree of branching and/or nature of linkages between units and/or nature of linkages between cellulose and other plant cell wall components.

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 25 taken in any way as a restriction on the generality of the invention described above. 22 In the Figures Figure 1 shows the consensus contig nucleotide sequence of LpCCoAMTa (Sequence ID No: 1).

Figure 2 shows the deduced amino acid sequence of LpCCoAMTa (Sequence 5 ID No: 2).

Figure 3 shows the nucleotide sequences of the nucleic acid fragments contributing to the consensus contig sequence LpCCoAMTa (Sequence ID Nos: 3 to 11).

Figure 4 shows the consensus contig nucleotide sequence of LpCCoAMTb 10 (Sequence ID No: 12).

Figure 5 shows the deduced amino acid sequence of LpCCoAMTb (Sequence ID No: 13).

Figure 6 shows the nucleotide sequences of the nucleic acid fragments contributing to the consensus contig sequence LpCCoAMTb (Sequence ID 0 15 Nos: 14 to 20).

Figure 7 shows the nucleotide sequence of LpCCoAMTc (Sequence ID No: 21).

Figure 8 shows the deduced amino acid sequence of LpCCoAMTc (Sequence ID No: 22).

Figure 9 shows the nucleotide sequence of LpCADa (Sequence ID No: 23).

Figure 10 shows the deduced amino acid sequence of LpCADa (Sequence ID No: 24). 23 Figure 11 shows the nucleotide sequence of LpCADb (Sequence ID No: 25).

Figure 12 shows the deduced amino acid sequence of LpCADb (Sequence ID No: 26).

Figure 13 shows the consensus contig nucleotide sequence of LpCADc (Sequence ID No: 27).

Figure 14 shows the deduced amino acid sequence of LpCADc (Sequence ID No: 28).

Figure 15 shows the nucleotide sequences of the nucleic acid fragments contributing to the consensus contig sequence LpCADc (Sequence ID Nos: 10 29 to 33).

Figure 16 shows the consensus contig nucleotide sequence of LpCADd (Sequence ID No: 34).

Figure 17 shows the deduced amino acid sequence of LpCADd (Sequence ID No: 35).

Figure 18 shows the nucleotide sequences of the nucleic acid fragments contributing to the consensus contig sequence LpCADd (Sequence ID Nos: 36 to 40).

Figure 19 shows the consensus contig nucleotide sequence of LpCADe (Sequence ID No: 41).

Figure 20 shows the deduced amino acid sequence of LpCADe (Sequence ID No: 42). 24 Figure 21 shows the nucleotide sequences of the nucleic acid fragments contributing to the consensus contig sequence LpCADe (Sequence ID Nos: 43 and 44).

Figure 22 shows the nucleotide sequence of LpCADf (Sequence ID No: 45).

Figure 23 shows the deduced amino acid sequence of LpCADf (Sequence ID No: 46).

Figure 24 shows the consensus contig nucleotide sequence of LpOMTa (Sequence ID No: 47). & Figure 25 shows the deduced amino acid sequence of LpOMTa (Sequence ID 10 No: 48).

Figure 26 shows the nucleotide sequences of the nucleic acid fragments contributing to the consensus contig sequence LpOMTa (Sequence ID Nos: 49 to 58).

Figure 27 shows the consensus contig nucleotide sequence of LpOMTb 15 (Sequence ID No: 59).

Figure 28 shows the deduced amino acid sequence of LpOMTb (Sequence ID No: 60).

Figure 29 shows the nucleotide sequences of the nucleic acid fragments contributing to the consensus contig sequence LpOMTb (Sequence ID Nos: 20 61 to 93).

Figure 30 shows the nucleotide sequence of LpOMTc (Sequence ID No: 94).

Figure 31 shows the deduced amino acid sequence of LpOMTc (Sequence ID No: 95).

Figure 32 shows the nucleotide sequence of LpC4Ha (Sequence ID No: 96).

Figure 33 shows the deduced amino acid sequence of LpC4Ha (Sequence ID No: 97).

Figure 34 shows the nucleotide sequence of LpC4Hb (Sequence iD No: 98). 5 Figure 35 shows the deduced amino acid sequence of LpC4Hb (Sequence ID Figure 36 shows the nucleotide sequence of LpC4Hc (Sequence ID No: 100).

Figure 37 shows the deduced amino acid sequence of LpC4Hc (Sequence ID No: 101).

Figure 38 shows the consensus contig nucleotide sequence of LpCCRa (Sequence ID No: 102).

Figure 39 shows the deduced amino acid sequence of LpCCRa (Sequence ID No: 103).

Figure 40 shows the nucleotide sequences of the nucleic acid fragments 15 contributing to the consensus contig sequence LpCCRa (Sequence ID Nos: 104 to 106).

Figure 41 shows the consensus contig nucleotide sequence of LpCCRb (Sequence ID No: 107).

Figure 42 shows the deduced amino acid sequence of LpCCRb (Sequence ID 20 No: 108). 26 Figure 43 shows the nucleotide sequences of the nucleic acid fragments contributing to the consensus contig sequence LpCCRb (Sequence ID Nos: 109 and 110).

Figure 44 shows the nucleotide sequence of LpCCRc (Sequence ID No: 111).

Figure 45 shows the deduced amino acid sequence of LpCCRc (Sequence ID No: 112).

Figure 46 shows the consensus contig nucleotide sequence of LpPERa (Sequence ID No: 113).

Figure 47 shows the deduced amino acid sequence of LpPERa (Sequence ID 10 No: 114).

Figure 48 shows the nucleotide sequences of the nucleic acid fragments contributing to the consensus contig sequence LpPERa (Sequence ID No: 115 and 116).

Figure 49 shows the consensus contig nucleotide sequence of LpPERb 15 (Sequence ID No: 117).

Figure 50 shows the deduced amino acid sequence of LpPERb (Sequence ID No: 118).

Figure 51 shows the nucleotide sequences of the nucleic acid fragments contributing to the consensus contig sequence LpPERb (Sequence ID Nos: 20 119 and 120).

Figure 52 shows the nucleotide sequence of LpPERc (Sequence ID No: 121).

Figure 53 shows the deduced amino acid sequence of LpPERc (Sequence ID No: 122). 27 Figure 54 shows the nucleotide sequence of LpPERd (Sequence ID No: 123).

Figure 55 shows the deduced amino acid sequence of LpPERd (Sequence ID No: 124).

Figure 56 shows the consensus contig nucleotide sequence of LpCELL (Sequence ID No: 125).

Figure 57 shows the deduced amino acid sequence of LpCELL (Sequence ID No: 126).

Figure 58 shows the nucleotide sequences of the nucleic acid fragments contributing to the consensus contig sequence LpCELL (Sequence ID Nos: 10 127 to 134).

Figure 59 shows the consensus contig nucleotide sequence of LpF5Ha (Sequence ID No: 135).

Figure 60 shows the deduced amino acid sequence of LpF5Ha (Sequence ID No: 136).

Figure 61 shows the nucleotide sequences of the nucleic acid fragments contributing to the consensus contig sequence LpF5Ha (Sequence ID Nos: 137 to 139).

Figure 62 shows the consensus contig nucleotide sequence of LpPALa (Sequence ID No: 140).

Figure 63 shows the deduced amino acid sequence of LpPALa (Sequence ID No: 141). 28 Figure 64 shows the nucleotide sequences of the nucleic acid fragments contributing to the consensus contig sequence LpPALa (Sequence ID Nos: 142 to 148).

Figure 65 shows the consensus contig nucleotide sequence of LpPALb 5 (Sequence ID No: 149).

Figure 66 shows the deduced amino acid sequence of LpPALb (Sequence ID No: 150).

Figure 67 shows the nucleotide sequences of the nucleic acid fragments contributing to the consensus contig sequence LpPALb (Sequence ID Nos: 151 to 153).

Figure 68 shows the consensus contig nucleotide sequence of Lp4CLa (Sequence ID No: 154).

Figure 69 shows the deduced amino acid sequence of Lp4CLa (Sequence ID No: 155).

Figure 70 shows the nucleotide sequences of the nucleic acid fragments contributing to the consensus contig sequence Lp4CLa (Sequence ID Nos: 156 to 161).

Figure 71 shows the nucleotide sequence of Lp4CLb (Sequence ID No: 162).

Figure 72 shows the deduced amino acid sequence of Lp4CLb (Sequence ID 20 No: 163).

Figure 73 shows the nucleotide sequence of Lp4CLc (Sequence ID No: 164).

Figure 74 shows the deduced amino acid sequence of Lp4CLc (Sequence ID No: 165). 29 Figure 75 shows a plasmid map of the cDNA encoding perennial ryegrass C4H.

Figure 76 shows the nucleotide sequence of perennial ryegrass C4H cDNA (Sequence ID No: 166).

Figure 77 shows the deduced amino acid sequence of perennial ryegrass C4H cDNA (Sequence ID No: 167).

Figure 78 shows plasmid maps of sense and antisense constructs of LpC4H in pDH51 transformation vector.

Figure 79 shows plasmid maps of sense and antisense constructs of LpC4H 10 in pKYLX71:35S2 binary transformation vector.

Figure 80 shows screening by Southern hybridisation for RFLPs using LpC4H as a probe.

Figure 81 shows a plasmid map of the cDNA encoding perennial ryegrass CCoAOMT 1.

Figure 82 shows the nucleotide sequence of perennial ryegrass CCoAOMT 1 cDNA (Sequence ID No: 168).

Figure 83 shows the deduced amino acid sequence of perennial ryegrass CCoAOMT 1 cDNA (Sequence ID No: 169).

Figure 84 shows plasmid maps of sense and antisense constructs of 20 LpCCoAOMTI in pDH51 transformation vector.

Figure 85 shows screening by Southern hybridisation for RFLPs using LpCCoAOMT 1 as a probe.

Figure 86 shows a plasmid map of the cDNA encoding perennial ryegrass CCoAOMT2.

Figure 87 shows the nucleotide sequence of perennial ryegrass CC0AOMT2 cDNA (Sequence ID No: 170).

Figure 88 shows the deduced amino acid sequence of perennial ryegrass CCoAOMT2 cDNA (Sequence ID No: 171).

Figure 89 shows plasmid maps of sense and antisense constructs of LpCCoAOMT2 in pDH51 transformation vector.

Figure 90 shows plasmid maps of sense and antisense constructs of 10 LpCCoAOMT2 in pKYLX71:35S2 binary transformation vector.

Figure 91 shows screening by Southern hybridisation for RFLPs using LpCCoAOMT2 as a probe.

Figure 92 shows plasmid map of the cDNA encoding perennial ryegrass OMT2 cDNA.

Figure 93 shows the nucleotide sequence of perennial ryegrass OMT2 cDNA (Sequence ID No: 172).

Figure 94 shows the deduced amino acid sequence of perennial ryegrass OMT2 cDNA (Sequence ID No: 173).

Figure 95 shows plasmid maps of sense and antisense constructs of LpOMT2 20 in pDH51 transformation vector.

Figure 96 shows plasmid maps of sense and antisense constructs of LpOMT2 in pKYLX71:35S2 binary transformation vector. 31 Figure 97 shows screening by Southern hybridisation for RFLPs using LpOMT2 as a probe.

Figure 98 shows the plasmid map of the cDNA encoding perennial ryegrass OMT3.

Figure 99 shows the nucleotide sequence of perennial ryegrass OMT3 cDNA (Sequence ID No: 174).

Figure 100 shows the deduced amino acid sequence of perennial ryegrass OMT3 cDNA (Sequence ID No: 175).

Figure 101 shows Plasmid maps of sense and antisense constructs of 10 LpOMT3 in pDH51 transformation vector.

Figure 102 shows plasmid maps of sense and antisense constructs of LpOMT3 in pKYLX71:35S2 binary transformation vector.

Figure 103 shows screening by Southern hybridisation for RFLPs using LpOMT3 as a probe.

Figure 104 shows the plasmid map of the cDNA encoding perennial ryegrass Peroxidasel.

Figure 105 shows the nucleotide sequence of perennial ryegrass Peroxidasel cDNA (Sequence ID No: 176).

Figure 106 shows the deduced amino acid sequence of perennial ryegrass 20 Peroxidasel cDNA (Sequence ID No: 177).

Figure 107 shows plasmid maps of sense and antisense constructs of LpPeroxidasel in pDH51 transformation vector. 32 Figure 108 shows piasmid maps of sense and antisense constructs of LpPeroxidasel in pKYLX71:35S2 binary transformation vector.

Figure 109 shows screening by Southern hybridisation for RFLPs using LpPeroxidasel as a probe.

Figure 110 shows the regeneration of transgenic tobacco plants from direct gene transfer to protoplasts of chimeric ryegrass lignin biosynthesis genes.

Figure 111 shows a subgrid of a microarray for the expression profiling of perennial ryegrass lignin biosynthesis and cellulose degradation genes. Red represents up-regulated expression, green represents down-regulated 10 expression and yellow represents no change in expression. For example, an overlay of microarray images probed with 5LS tissues (red) and 5LR tissues (green). Expression level is relatively expressed as up-regulated in 5LS (red), down-regulated in 5LS (green) and no change in expression (yellow).

Figure 112 shows a genetic linkage map of perennial ryegrass NA6 showing 15 map location of ryegrass genes encoding enzymes involved in lignin biosynthesis and cellulose degradation.

EXAMPLE 1 Preparation of cDNA libraries, isolation and sequencing of cDNAs coding for CCoAMT, CAD, OMT, C4H, CCR, PER, CELL, F5H, PAL and 20 4CL from perennial ryegrass (Lolium perenne) cDNA libraries representing mRNAs from various organs and tissues of perennial ryegrass (Lolium perenne) were prepared. The characteristics of the libraries are described in Table 1. 33 TABLE 1 cDNA libraries from perennial ryegrass (Lolium perenne) Library Organ/Tissue 01 rg Roots from 3-4 day old light-grown seedlings 02 rg Leaves from 3-4 day old light-grown seedlings 03 rg Etiolated 3-4 day old dark-grown seedlings 04 rg Whole etiolated seedlings (1-5 day old and 17 days old) 05rg Senescing leaves from mature plants 06 rg Whole etiolated seedlings (1-5 day old and 17 days old) 07rg Roots from mature plants grown in hydroponic culture 08rg Senescent leaf tissue 09 rg Whole tillers and sliced leaves (0, 1, 3, 6, 12 and 24 h after harvesting) 10rg Embryogenic suspension-cultured cells 11 rg Non-embryogenic suspension-cultured cells 12rg Whole tillers and sliced leaves (0, 1, 3, 6, 12 and 24 h after harvesting) 13rg Shoot apices including vegetative apical meristems 14rg immature inflorescences including different stages of inflorescence meristem and inflorescence development 15rg Defatted pollen 16rg Leaf blades and leaf sheaths (rbcL, rbcS, cab, wir2A subtracted) 17rg Senescing leaves and tillers 18rg Drought-stressed tillers (pseudostems from plants subjected to PEG-simulated drought stress) 19rg Non-embryogenic suspension-cultured cells subjected to osmotic stress (grown in media with half-strength salts) (1, 2, 3, 4, 5, 6, 24 and 48 h after transfer) 20rg Non-embryogenic suspension-cultured cells subjected to osmotic 34 Library Organ/Tissue stress (grown in media with double-strength salts) (1, 2, 3, 4, 5, 6, 24 and 48 h after transfer) 21 rg Drought-stressed tillers (pseudostems from plants subjected to PEG-simulated drought stress) 22rg Spikelets with open and maturing florets 23rg Mature roots (specific subtraction with leaf tissue) 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 5 the manufacturers' instructions. cDNAs may be generated using the SMART PGR 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 10 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, CA, USA). The Uni-ZAP XR libraries are converted into plasmid libraries according to the protocol provided by Stratagene. Upon conversion, cDNA inserts will be 20 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 £=. coli DH10B cells according to the manufacturer's protocol (GIBCO BRL Products). , 35 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 5 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 10 an Applied Biosystems ABI 3700 sequence analyser.

EXAMPLE 2 DNA sequence analyses The cDNA clones encoding CCoAMT, CAD, OMT, C4H, CCR, PER, CELL, F5H, PAL and 4CL were identified by conducting BLAST (Basic Local 15 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 20 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 25 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 36 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 fuli-iength sequencing of perennial ryegrass C4H, CCoAOMT 1, CCoAOMT2, OMT2, OMT3 and Peroxidasel cDNAs encoding enzymes involved in cell wall modification To fully characterise for the purposes of the generation of probes for hybridisation experiments and the generation of transformation vectors, a set 10 of perennial ryegrass cDNAs encoding enzymes involved in cell wall modification was identified and fully sequenced.

Full-length 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 15 sequences using Sequencher (Gene Codes Corp., AnnArbor, Ml 48108, USA). The original plasmid was then used to transform chemically competent XL-1 cells (prepared in-house, CaCI2 protocol). After colony PCR (using HotStarTaq, Qiagen) a minimum of three PCR-positive colonies per transformation were picked for initial sequencing with M13F and M13R 20 primers. The resulting sequences were aligned with the original EST sequence using Sequencher to confirm identity and one of the three 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 25 primers were designed to the initial sequence and used for further sequencing. In most cases the sequencing could be done from both 5' and 3' end. The sequences of the oligonucleotide primers are shown in Table 2. In 37 some instances, however, an extended poiy-A tail necessitated the sequencing of the cDNA to be completed from the 5' end.

TABLE 2 List of primers used for sequencing of the full-length cDNAs gene name clone ID sequencing primer primer sequence (5'->3*) LpC4H 06rg1BsF03.3 06rg1BsF03.f1 TCAACCACCGCAACCTGATG 06rg1BsF03.r1 GAGTAATCGTCTCACTTCGC LpCCoAOMT 1 06rg1 JsF04.1 Q6rg1 JsF04.f1 CATCCCAGAAGACGGAAC LpCCoAOMT2 12rg1DsE01.1 12rg1DsE01.f1 TACGAGACCATCGGCAAG LpOMT2 06rg1SsG02.1 06rg1SsG02.f1 CGTTCGCTCTCCTCACCC 06rg1SsG02.r1 AAGTCGGCGAAGATGTAGG LpOMT3 06rg2QsG01.1 06rg2QsG01.f1 AAGTTCCTCACCCCCAAC 06rg2QsG01.f2 CGCTGCTCAAGAACTGCTAC 06rg2QsG01.r1 CTCATCTACTTGGTGAACTCG LpPeroxidasel 06rg20sG07.2 06rg20sG07.f1 CGCCAAGAAGAACCTCAAC 06rg20sG07.r1 ATTTTGAGCTGCACCACG Contigs were then assembled in Sequencher. The contigs include the sequences of the SMART primers used to generate the initial cDNA library as well as pGEM-T Easy vector sequence up to the EcoRI cut site both at the 5' and 3' end.

Plasmid maps and the full cDNA sequences of perennial ryegrass C4H, CCoAOMTI, CCoAOMT2, OMT2, OMT3 and Peroxidasel were obtained (Figures 75, 76, 81, 82, 86, 87, 92, 93, 98, 99, 104 and 105). 38 EXAMPLE 4 Development of transformation vectors containing chimeric genes with C4H, CCoAOMTi, CCoAOMT2, OMT2, OMT3 and Peroxidasel cDNA sequences from perennial ryegrass To alter the expression of the enzymes involved in lignin biosynthesis C4H, CCoAOMTi, CCoAOMT2, OMT2, OMT3 and Peroxidasel, through antisense and/or sense suppression technology and for over-expression of these key enzymes in transgenic plants, a set of sense and antisense 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 restriction sites for EcoRI and Xbal for directional and non-directional cloning into the target vector.

TABLE 3 List of primers used to PCR-amplify the open reading frames gene name clone ID primer primer sequence (5'->3') LpC4H 06rg1BsF03.3 06rg1BsF03.f GAATTCTAGACACAGTCACAGAAGCCACCTACC 06rg1BsF03.r GAATTCTAGACTCTCGGCACCAGCGTTCACG LpCCoAOMT 1 06rg1JsF04.1 LpCCoAOMT 1f GAATTCTAGAAAGACAGCCCAATCAT CC LpCCoAOMUr GAATTCTAGAGAAGAAAGCAACAACGGC LpCCoAOMT2 12rg1DsE01.1 12rg1DsE01.f GAATTCTAGAGTTCCTTCCTCCACCTAAACACC 12rg1DsE01.r GAATTCTAGAGCGAGCGTCATCAATCAGAC LpOMT2 06rg1SsG02.1 06rg1SsG02.f GAATTCTAGACTAGCAAGCAGCAACA-GGTAGC 06rg1SsG02.r GAATTCTAGAGGTGAGTTTAGCCTAC CAAAATG LpOMT3 06rg2QsG01.1 06rg2QsG01.f GAATTCTAGAGTCTCTCGCTCACACCAAAATCG 06rg2QsG01 .r GAATTCTAGATGTTGCCTGGATGCTTGGAGG LpPeroxidasel 06rg20sG07.2 06rg20sG07f GAATTCTAGAGACGCCGCAATATAGC TTGG 06rg20sG07r GAATTCTAGAGCTGAACTGCTAATAG TAGAGTGG 39 After PCR amplification and restriction digest with the appropriate restriction enzyme (usually Xbal), the cDNA fragments were cloned into the corresponding site in pDH51, a pUC18-based transformation vector containing a CaMV 35S expression cassette. The orientation of the constructs 5 (sense or antisense) was checked by DNA sequencing through the multi-cloning site of the vector. Transformation vectors containing chimeric genes using full-length open reading frame cDNAs of perennial ryegrass C4H, CCoAOMTi, CCoAOMT2, OMT2, OMT3 and Peroxidasel in sense and antisense orientations under the control of the CaMV 35S promoter were 10 generated (Figures 78, 84, 89, 95, 101 and 107).

EXAMPLE 5 Development of binary transformation vectors containing chimeric genes with C4H, CCoAOMT2, OMT2, OMT3 and Peroxidasel cDNA sequences from perennial ryegrass To alter the expression of the enzymes involved in lignin biosynthesis C4H, CCoAOMT2, OMT2, OMT3 and Peroxidasel, through antisense and/or sense suppression technology and for over-expression of these key enzymes in transgenic plants, a set of sense and antisense 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 restriction sites for EcoRI and Xbal for directional and non-directional cloning into the target vector. After PCR amplification and restriction digest with the appropriate restriction enzyme (usually Xbal), the 25 cDNA fragments were cloned into the corresponding site in pKYLX71:35S2, a binary transformation vector. The vector contains between the left and the right border the plant selectable marker gene nptll under the control of the nos promoter and nos terminator and an expression cassette with a CaMV 35S 40 promoter with a duplicated enhancer region and an rbcS terminator (An et al., 1985; Schardl et al., 1987). The orientation of the constructs (sense or antisense) was checked by restriction enzyme digest. Transformation vectors containing chimeric genes using full-length open reading frame cDNAs of perennial ryegrass C4H, CCoAOMT2, OMT2, OMT3 and Peroxidasel in sense and antisense orientations under the control of the CaMV 35S2 promoter were generated (Figures 79, 90, 96, 102 and 108).

EXAMPLE 6 Production of transgenic tobacco plants carrying chimeric C4H, CCoAOMTi, CCoAOMT2, OMT2, OMT3 and Peroxidasel genes from perennial ryegrass A set of transgenic tobacco plants carrying chimeric C4H, CCoAOMT 1, CCoAOMT2, OMT2, OMT3 and Peroxidasel cDNA genes from perennial ryegrass were produced. pDH51-based transformation vectors with LpC4H, LpCCoAOMT 1, LpCCoAOMT2, LpOMT2, LpOMT3 and LpPeroxidasel cDNAs comprising the full open reading frame sequences in sense and antisense orientations under the control of the CaMV 35S promoter were generated.

Direct gene transfer experiments to tobacco protoplasts were performed using these transformation vectors.

The production of transgenic tobacco plants carrying the perennial ryegrass C4H, CCoAOMTi, CCoAOMT2, OMT2, OMT3 and Peroxidasel cDNAs under the control of the constitutive CaMV 35S promoter is described here in detail. 41 Isolation of mesophyll protoplasts from tobacco shoot cultures 2 to 4 fully expanded leaves of a 6 week-old shoot culture were placed under sterile conditions (work in laminar flow hood, use sterilized forceps, scalpel and blades) in a 9 cm plastic culture dish containing 12 ml enzyme 5 solution [1.0% (w/v) cellulase "Onozuka" R10 and 1.0% (w/v) Macerozyme® R10]. The leaves were wetted thoroughly with enzyme solution and the midribs removed. The leaf halves were cut into small pieces and incubated overnight (14 to 18 h) at 25°C in the dark without shaking The protoplasts were released by gently pipetting up and down, and 10 the suspension poured through a 100 pm stainless steel mesh sieve on a 100 ml glass beaker. The protoplast suspension was mixed gently, distributed into two 14 ml sterile plastic centrifuge tubes and carefully overlayed with 1 ml W5 solution. After centrifugation for 5 min. at 70g (Clements Orbital 500 bench centrifuge, swing-out rotor, 400 rpm), the protoplasts were collected from the 15 interphase and transferred to one new 14 ml centrifuge tube. 10 ml W5 solution were added, the protoplasts resuspended by gentie tilting the capped tube and pelleted as before. The protoplasts were resuspended in 5 to 10 ml W5 solution and the yield determined by counting a 1:10 dilution in a haemocytometer.

Direct gene transfer to protoplasts using polyethylene glycol The protoplasts were pelleted [70g (Clements Orbital 500 bench centrifuge, 400 rpm) for 5 min.] and resuspended in transformation buffer to a density of 1.6 x 106 protoplasts/ml. Care should be taken to carry over as little as possible W5 solution into the transformation mix. 300 pi samples of the 25 protoplast suspension (ca. 5 x 105 protoplasts) were aliquotted in 14 ml sterile plastic centrifuge tubes, 30 pi of transforming DNA were added. After ca refully mixing, 300 pi of PEG solution were added and mixed again by careful shaking. The transformation mix was incubated for 15 min. at room temperature with occasional shaking. 10 ml W5 solution were gradually 42 added, the protoplasts pelleted [70g (Clements Orbital 500 bench centrifuge, 400 rpm) for 5 min.] and the supernatant removed. The protoplasts were resuspended in 0.5 ml K3 medium and ready for cultivation Culture of protoplasts, selection of transformed lines and regeneration 5 of transgenic tobacco plants Approximately 5 x 105 protoplasts were placed in a 6 cm petri dish. 4.5 ml of a pre-warmed (melted and kept in a water bath at 40 to 45°C) 1:1 mix of K3:H medium containing 0.6% SeaPlaque™ agarose were added and, after gentle mixing, allowed to set.

After 20 to 30 min the dishes were sealed with Parafilm® and the protoplasts were cultured for 24 h in darkness at 24°C, followed by 6 to 8 days in continuous dim light (5 pmol m"2 s'1, Osram L36 W/21 Lumilux white tubes), where first and multiple cell divisions occur. The agarose containing the dividing protoplasts was cut into quadrants and placed in 20 ml of A medium 15 in a 250 ml plastic culture vessel. The corresponding selection agent was added to the final concentration of 50 mg/i kanamycin sulphate (for npt2 expression) or 25 mg/l hygromycin B (for hph expression) or 20 mg/l phosphinotricin (for bar expression). Samples were incubated on a rotary shaker with 80 rpm and 1.25 cm throw at 24°C in continuous dim light.

Resistant colonies were first seen 3 to 4 weeks after protoplast plating, and after a total time of 6 to 8 weeks protoplast-derived resistant colonies (when 2 to 3 mm in diameter) were transferred onto MS morpho medium solidified with 0.6% (w/v) agarose in 12-weII plates and kept for the following 1 to 2 weeks at 24°C in continuous dim light (5 (jmol m"2 s"1, Osram L36 W/21 25 Lumilux white tubes), where calli proliferated, reached a size of 8 to 10 mm, differentiated shoots that were rooted on MS hormone free medium leading to the recovery of transgenic tobacco plants (Table 4 and Figure 110). 43 TABLE 4 Production of transgenic tobacco calli carrying chimeric ryegrass genes (in sense and antisense orientation) for enzymes involved in lignin biosynthesis and cellulose degradation from direct gene transfer to protoplasts construct transfected protoplasts transformed calli transformation efficiency pDH51LpC4H 2.3x10b 67 2.91x10"b pDH51LpC4H anti 2.3x10e 12 0.52x1 Q"5 pDH51 LpCCoAOMT 1 1.2x10b 113 9.42x10'b pDH51 LpCCoAOMT 1 anti 0.6x106 76 12.67x10"b pDH51 LpCCoAOMT2 2.3x106 41 1.78x10"b pDH51 LpCCoAOMT2 anti 2.3x106 61 2.65x10'5 pDH51LpOMT2 2.3x10B 115 .00x10'5 pDH51LpOMT2 anti 2.3x10^ 136 .91x10"b pDH51LpOMT3 2.3x10e 64 2.78x10-5 pDH51LpOMT3 anti 2.3x1 100 4.35x10^ pDH51 LpPeroxidasel 2.3x106 260 11.30x10"b pDH51 LpPeroxidasel anti 2.3x10e 250 .87x10"b EXAMPLE 7 Genetic mapping of perennial ryegrass genes involved in lignin biosynthesis and cellulose degradation The cDNAs representing genes involved in lignin biosynthesis and cellulose degradation were amplified by PCR from their respective plasmids, gel-purified and radio-labelled for use as probes to detect restriction fragment length polymorphisms (RFLPs). RFLPs were mapped in the Fi (first 44 generation) population, NA6 x AU6. This population was made by crossing an individual (NA6) from a North African ecotype with an individual (AU6) from the cultivar Aurora, which is derived from a Swiss ecotype. Genomic DNA of the 2 parents and 114 progeny was extracted using the 1 x CTAB method of Fulton 5 etal. (1995).

Probes were screened for their ability to detect polymorphism using the DNA (10 fag) of both parents and 5 Fi progeny restricted with the enzymes Dral, EcoRI, EcoRV or Hindlll. Hybridisations were carried out using the method of Sharp et al. (1988). Polymorphic probes were screened on a 10 progeny set of 114 individuals restricted with the appropriate enzyme (Figures 80, 85, 91, 97, 103 and 109).

RFLP bands segregating within the population were scored and the data was entered into an Excel spreadsheet. Alleles showing the expected 1:1 ratio were mapped using MAPMAKER 3.0 (Lander et al. 1987). Alleles 15 segregating from, and unique to, each parent, were mapped separately to give two different linkage maps. Markers were grouped into linkage groups at a LOD of 5.0 and ordered within each linkage group using a LOD threshold of 2.0.

Loci representing genes involved in lignin biosynthesis and cellulose 20 degradation mapped to the linkage groups as indicated in Table 5 and in Figure 112. These gene locations can now be used as candidate genes for quantitative trait loci for lignin biosynthesis-associated traits such as herbage quality, dry matter digestibility, mechanical stress tolerance, disease resistance, insect pest resistance, plant stature and leaf and stem colour. 45 TABLE 5 Map locations of ryegrass genes encoding enzymes for lignin biosynthesis and cellulose degradation across two genetic linkage maps of perennial ryegrass (NA6 and AU6) Probe Polymorphic Mapped with Locus Linkage group NA6 AU6 Lp4CLJa Y Hin6 Ili Lp4CLJa 4 4 Lp4CLJb Y Hind lil Lp4CUb 1 1 LpC4H Y EcoR 1 LpC4H 3 3 LpCADd Y Dra 1 LpCADd 3 LpCADc Y Dra 1 LpCADc 1 LpCCoAOMT1-1 Y EcoR V LpCCoAOMT1-1 7 LpCCRa Y Hind III LpCCRa 6 6 LpCCRb Y Dra I LpCCRb 7 7 LpCELL Y EcoR\ LpCELL 4 LpF5H Y EcoR V LpF5H.1 LpF5H.2 3 1 LpOMT2 Y Dra i LpOMT2 6 6 LpOMT3 Y Dra 1 LpOMT3 4 7 LpPALb Y EcoR i LpPALb 6 LpPeroxidasel Y Hind III LpPeroxidasel 2 2 46 EXAMPLE 8 Expression profiling of cDNAs encoding enzymes for iignin biosynthesis and cellulose degradation using microarray technology cDNAs encoding enzymes for lignin biosynthesis and cellulose degradation were PCR amplified and purified. The amplified products were spotted three times on each amino-silane coated glass slide (CMT-GAPS, Corning, USA) using a microarrayer MicroGrid (BioRobotics, UK). Spotting solution was also spotted in every subgrid of the microarray as negative and background controls. The duplicates were placed about 800 micron apart to prevent competitive hybridisation.

Table 6 gives details on the tissues used to extract total RNA.

TABLE 6 List of hybridization probes used in expression profiling of perennial ryegrass genes encoding enzymes for Signin biosynthesis and cellulose degradation using microarrays Hybridization probe for microarrays Organ specificity (3-month old plants grown hydroponically) Leaf blade Sheath Root Seedling grown under light condition -day old shoot (5LS) 7-day old shoot (7LS) -day old shoot (10LS) -day old root (5LR) 7-day old root (7LR) 47 -day old root (10LR) Seedling grown under dark condition -day old shoot (5DS) 7-day old shoot (7DS) -day old shoot (10DS) -day old root (5DR) 7-day old root (7DR) -day old root (10DR) Fluorescence labelled probes were synthesis by reversed transcribing RNA and incorporating Cyanine 3 or 5 labelled dCTP. The probes were hybridised onto microarrays. In each case the experiment was repeated on 5 two microarrays. After hybridisation for 16 hours (overnight), the microarrays were washed and scanned using a confocal laser scanner (ScanArray 3000, Packard, USA). The images obtained were quantified and analysed using Imagene 4.1 and GeneSight 2.1 (BioDiscovery, USA). Data were judged as not present (-), low expression (+), medium expression (++), high expression 10 (+++) and highly expression (++++) (Table 7).

TABLE 7 Results of expression profiling of ryegrass genes for lignin biosynthesis and cellulose degradation plate Row col Gene id clone id gene seq notes sheath leaf bade root 5LS 7LS 10LS 5LR 7LR 10LR 5DS 7DS 10DS 5DR 7DR 10DR Array2Urg A 1 NcwCAMT_POPTM7556 12rg1DsE01 LpCCoAOMTa (LpCCoAOMT2) full +++ ++ + + + + +++ ++ ++++ ++++ + Array2Urg A 2 NcwCAMT_POPTM7557 06rg1JsF04 LpCCoAOMTa (LpCCoAOMT 1 -1) full ++++ +++ + ++ +++ +++ + +++ ++++ ++++ ++++ Array2Urg A 3 NcwCAMT_POPTM7558 03rg1AsG11 LpCCoAOMTb partial ++++ ++++ ++++ +++ ++ ++++ -M-++ ++++ +++ ++++ ++++ ++++ ++++ ++++ Array2Urg A 4 NcwCAMT_PETCR7559 06rg1GsA09 LpCCoAOMTb full (likely) ++++ + ++ + + ++ + + ++ +++ ++ ++++ ++ + Array2Urg a NcwCAMT_P0PTM756() 06rg1CsC03 LpCCoAOMTb partial - - + - - - - - - - - - + - Array2Urg a 6 NcwCAMT_PET CR7561 06rg20sD10 LpCCoAOMTb partial ++++ ++++ - +++ ++++ ++++ - - - - ++++ - - - Array2Urg a 7 NcwCAMT_PETCR7562 06rg2RsH08 LpCCoAOMTb partial - .

- - - - - - - - - - - - Array2Urg a 8 NcwCAMT_P0PTM7563 07rg1XsG07 LpCCoAOMTb partial ++++ ++++ ++++ ++++ ++++ - ++++ ++++ ++++ ++++ ++++ - ++++ ++++ - Array2Urg a 9 NcwCAD2_ARATH7564 11rg1DsC02 LpCADc partial ~ - - + - - - - - - - Array2Urg a NcwCAD3_STYHU7565 19rg2HsG01 LpCADc partial - - - - - - - - - - - - Array2Urg a 11 NcwCADH_PICAB7566 19rg2TsD05 LpCADc partial + - + - - - - - - - - - - - Array2Urg a 12 NcwCADH_PICAB7567 20rg1DsG10 LpCADc full - - - - - - - - - - - - - - - Array2Urg b 1 XnsPSS_YEAST-7568 07rg1DsE08 LpCADd partial - - - - - - + - - - +++ +++ - Array2Urg D 2 NppDFRA_DIACA7569 11rg1VsE04 LpCADd partial + + 4-+ ++ ++ ++++ +++ +++ ++++ ++ ++++ ++++ ++++ Array2Urg b 3 NDFRA_CALCH~7570 16rg1HsE01 LpCADd partial - - - - - - ++ ++ + - +++ ♦ ++++ ++++ ++ Array 2Urg b 4 NDFRA_CALCH—7571 16rg1KsA12 LpCADd partial ++++ + ++ ++ +++ ++ ++++ +++ +++ +++ ++++ ++++ ++++ ++++ ++++ plate Row col Gene id clone id gene seq notes sheath leaf bade root 5LS 7LS 1GLS 5LR 7LR 10LR 5DS 7DS 10DS 5DR 7DR 10DR Array2Urg b NDFRA_CALCH~7572 14rg1 YsF03 LpCADe partial + - - - + - - - - - - - - Array2Urg b 6 XnsDFRA_SYNY37573 14rg2HsE09 LpCADe partial " ++ - - - - - - - - - - - - Array2Urg b 7 NcwCOMT_MAIZE7574 06rg1MsA04 LpOMT 1 full +++ + ++++ ++ ++ +++ ++++ + + + + ++++ ++ ++++ 4-4-4-4- ++++ ++++ ++++ Array2Urg b 8 NcwCOMT_MAIZE7575 01rg1lsG06 LpOMT 1 partial + - + + + + ++++ ++ + +++ + ++++ ++ ++++ ++ +++ Array2Urg b 9 NcwCOMT_MAIZE7576 01rgRsG06 LpOMTI partial ++ - ++++ ++ ++ - ++++ +++ + +++ ++ ++++ ++ ++++ ++++ ++++ Array2Urg b NcwCOMT_MAIZE7577 07rg1SsH02 LpOMTI partial ++ - ++ + ++ + ++++ +++ ++ ++ ++++ 4*4- ++++ ++ ++ Array2Urg b 11 NcwCOMT_MAIZE7578 07rg1YsF08 LpOMTI partial +++ + ++++ +++ ++ ++ ++++ + + + + ++++ +++ ++++ 4-4-4- ++++ ++++ ++++ Array2Urg b 12 NcwCOMT_MAIZE7579 17rg1WsD06 LpOMTI partial + - + + ++ * ++++ + - ++++ - +++ ++ - Array2Urg c 1 NcwCOMT_MAIZE7580 06rg1SsG02 LpOMT2 full ++ - - +++ ++ + + ++ + ++ ++++ ++ 4-4-++ +++ +++ +++ Array2Urg c 2 NcwCOMT_MAIZE7581 06rg2PsE02 LpOMT2 partial + - • ++ +++ + - + + + ++++ - ++++ +++ - ++ Array2Urg c 3 NcwTCMO_GLYEC7582 06rg1BsF03 LpC4H full ++++ ++ ++++ +++ ++++ +++ ++++ + + + + ++++ ++++ ++++ ++++ ++++ ++++ ++++ Array2Urg c 4 Xns10rg1 DsG087583 10rg1DsG08 LpCCRa partial " - - - - - - - - - - - - Array2Urg c XnsYCW 1_YEAST7584 10rg2RsD06 LpCCRa partial - - - - - - - - - - - - - - Array2Urg c 6 NppDFRA_HORVU7585 11rg1KsG07 LpCCRa partial " - - - - - - - - - " - - - Array2Urg c 7 NppDFRA_MAIZE7586 17rg1AsC12 LpCCRb partial + - + - - - - - - " - - - Array2Urg c 8 DdtPER1_HORVU7587 06rg1FsF09 LpPeroxidasel full + + ++ ++ +++ ++ ++++ +++ ++ + +4-++ ++++ ++++ ++++ ++++ Array2Urg c 9 NcwPERX_NICSY7588 06rg1TsG03 LpPeroxidasel partial - - ++ - - + ++ +++ ++ ++++ +++ + ++++ ++++ ++ Array2Urg c NcwPERX_NICSY7589 06rg2PsA06 LpPeroxidasel partial - + - - - +++ + + + ++++ ++++ - ++++ + + Array2Urg c 11 UioNTPE_ENTHR7590 06rg1MsG08 LpPeroxidase2 full +++ + + ++ + 4- ++ +++ ++ ++ 4-4-4-4- ++ ++ +++ ++ Array2Urg c 12 DdrPER1_ORYSA7591 08rg1SsF09 LpPeroxidase2 partial? - + ++ - + - - - + Array2Urg d 1 DdrPER1_ORYSA7592 08rg1TsE05 LpPeroxidase2 partial? - +++ - 4-+ ++++ ++ - " - - - - - - - Array2Urg d 2 BcwGUN1_PERAE7593 14rg1PsE01 LpCELL partial + - - - ++ - + ++ + - ++++ - ++ ++++ - + plate Row col Gene id clone id gene seq notes sheath leaf bade root 5LS 7LS 10LS 5LR 7LR 10LR 5DS 7DS 10DS 5DR 7DR 10DR Array2Urg d 3 NC7C4_MAIZE—7594 01rg1QsH09 LpF5H partial - - - • - - - - - - - - - - Array2Urg d 4 NC7C4_MAIZE~7595 06rg1PsE04 LpF5H partial - - - - - - + - - - - + + + Array2Urg d NC7D8_SOYBN—7596 08rg1DsE09 LpF5H partial - - - - - - - - - ++ - ++ +++ - Array2Urg d 6 N cwPALY_WH EAT7597 01rg1TsB03 LpPALa partial - " - - - - +++ + + - +++ - + ++ +++ Array2Urg d 7 NcwPALY_WHEAT7598 07rg2AsE04 LpPALa partial +++ +++ ++++ +++ ++ +++ ++++ ++++ ++++ ++++ ++++ ++++ ++++ ++++ ++++ Array2Urg d 8 NcwPALY_WHEAT7599 10rg1BsD02 LpPALa partial + +++ ++ ++ + ++++ ++++ ++++ ++++ ++++ +++ ++++ ++++ ++++ Array2Urg d 9 NcwPALY_WHEAT7600 16rg1CsD01 LpPALa partial - + +++ - - + ++++ ++++ ++++ ++++ ++++ +++ ++++ ++++ ++++ Array2Urg d N cwP ALY_W H E AT7601 16rg1DsF06 LpPALa partial - - +++ ++ ++ + ++++ ++++ ++++ ++++ ++++ ++++ ++++ ++++ ++++ Array2Urg d 11 N cwPALY_W H EAT7602 17rg1CsB01 LpPALa partial - ++ - - - ++ - ++ +++ ++++ - ++++ +++ ++ Array2Urg d 12 NcwP AL Y_W H E AT7603 18rg1BsA03 LpPALa partial + ++ - + +++ + ++ + ++++ ++ +++ ++++ +++ Array2Urg e 1 NcwPALY_WHEAT7604 06rg1 KsC02 LpPALb partial ++++ ++ ++++ ++++ +++ + 4*+++ ++++ ++++ +++ ++++ ++++ ++++ ++++ ++++ Array2Urg e 2 NcwPAL1_ORYSA7605 07rg20sG02 LpPALb partial ++ " +++ ++ +++ ++ +4-++ ++++ ++++ - ++++ ++++ ++++ ++++ ++++ Array2Urg e 3 NcwPALY_WHEAT7606 14rg2BsG03 LpPALb partial ++++ ++ ++++ ++++ ++++ ++++ ++4-4- ++++ ++++ +++ ++++ ++++ ++++ ++++ ++++ Array2Urg e 4 ZhyYDID_ECOLI7607 06rg1BsB04 Lp4CLJa partial - - - - - - - - - - - - Array2Urg e ZhyYDID_ECOLI7608 06rg2DsB06 Lp4CLJa partial - * - + - - - - - - - ++ - ++ + Array2Urg e 6 ZhyYDID_ECOLI7609 06rg2EsB06 Lp4CLJa partial " - - - - - - - - - - - Array2Urg e 7 DdtACSA_ALCEU7610 11rg2HsF03 Lp4CLJa partial/ shorter + + ++ ++ ++ ~ ++ +++ Array2Urg e 8 ZhyYDID_ECOLI7611 19rg10sA02 Lp4CLJa partial + - - - + - + - - - + - + - - Array2Urg e 9 MlsALKK_PSEOL7612 19rg1SsC08 Lp4CLJa partial? - - - - - - - - - + - Array2Urg e Ncw4CL_PI NT A-7 613 17rg1CsC09 Lp4CLJb partial - - - - - - - - - - - - - Array2Urg e 11 Ncw4CL1_SOLTU7614 08rg2GsE02 Lp4CLJc partial " - - - - - - - - - - - - - 003911105 51 REFERENCES An, G., Watson, B.D., Stachel, S., Gordon, M.P., Nester, E.W. (1985) New cloning vehicles for transformation of higher plants. The EMBO Journal 4, 227-284 Feinberg, A.P., Vogelstein, B. (1984). A technique for radiolabelling DNA 5 restriction endonuciease fragments to high specific activity. Anal. Biochem. 132: 6-13.

Frohman et al. (1988) Rapid production of full-length cDNAs from rare transcripts: amplification using a single gene-specific oligonucleotide primer. Proc. Natl. Acad Sci. USA 85:8998 Gish and States (1993) Identification of protein coding regions by database similarity serach. Nature Genetics 3:266-272 Lander, E.S., Green P., Abrahamson, J., Barlow, A., Daly, M.J., Lincoln, S.E., Newburg, L. (1987). MAPMAKER: an interactive computer package for constructing primary linkage maps of experimental and natural populations. 15 Genomics 1: 174-181.

^ Loh, E.Y., Elliott, J.F., Cwiria, S., Lanier, L.L., Davis, M.M. (1989).

Polymerase chain reaction with single-sided specificity: Analysis of T-cell receptor delta chain. Science 243:217-220 Ohara, O., Dorit, R.L., Gilbert, W. (1989). One-sided polymerase chain 20 reaction: The amplification of cDNA. Proc. Natl. Acad Sci USA 86:5673-5677 Sambrook, J., Fritsch, E.F., Maniatis, T. (1989). Molecular Cloning. A Laboratory Manual. Cold Spring Harbour Laboratory Press Schardl, C.L., Byrd, A.D., Benzion, G., Altschuler, M.A., Hildebrand, D.F., Hunt, A.G. (1987) Design and construction of a versatile system for the expression 25 of foreign genes in plants. Gene 61, 1-11 Sharp, P.J., Kreis, M., Shewry, P.R., Gale, M.D. (1988). Location of a-amylase sequences in wheat and its relatives. Theor. Appl. Genet. 75: 286-290.

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 an acknowledgment that they form part of the common general knowledge in the relevant art. 005016644

Claims (23)

53 CLAIMS

1. A substantially purified or isolated nucleic acid or nucleic acid fragment encoding a cellulase (CELL) from a Lolium species, or a functionally active fragment or variant thereof. 5

2. A nucleic acid or nucleic acid fragment according to Claim 1, wherein said Lolium species is Lolium perenne or Lolium arundinaceum.

3. A substantially purified or isolated nucleic acid or nucleic acid fragment encoding a CELL, or complementary or antisense to a sequence encoding a CELL, and including a nucleotide sequence selected from the group consisting of (a) sequences shown in 10 Figures 56 and 58 hereto (Sequence ID Nos: 125 and 127 to 134, respectively): (b) complements of the sequences 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).

4. A nucleic acid or nucleic acid fragment according to Claim 3, wherein said 15 functionally active fragments and variants have at least approximately 90% identity to the relevant part of the sequences recited in (a), (b) and (c), respectively, and have a size of at least 20 nucleotides.

5. A construct including a nucleic acid or nucleic acid fragment according to any one i of Claims 1-4. 20

6. A vector including a nucleic acid or nucleic acid fragment according to any one of Claims 1-4.

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, including a construct according 25 to Claim 5 or a vector according to Claim 6 or 7. intellectual property office of n.2. 23 AUG 2007 RECEIVED 005016644 54

9. A plant, plant seed or other plant part derived from a plant cell or plant according to Claim 8 and including a construct according to Claim 5 or a vector according to Claim 6 or 7.

10. A method of modifying lignin biosynthesis and/or cellulose degradation in a plant, 5 said method including introducing into said plant an effective amount of a nucleic acid or nucleic acid fragment according to any one of Claims 1-4, a construct according to Claim 5, and/or a vector according to Claim 6 or 7.

11. Use of a nucleic acid or nucleic acid fragment according to any one of Claims 1-4, and/or nucleotide sequence information thereof, and/or single nucleotide ^ 10 polymorphisms thereof as a molecular genetic marker.

12. The use according to claim 11 wherein the molecular genetic marker is for one or more quantative trait loci (QTL) tagging, QTL mapping, DNA fingerprinting or marker assisted selections.

13. The use according to claim 11 or 12 wherein the molecular marker is used in a 15 Lolium species.

14. The use according to any one of claims 11 to 13 wherein the molecular marker is used to select for a herbage quality trait selected from the group consisting of dry matter £ digestibility, mechanical stress tolerance, disease resistance, insect pest resistance, plant stature and leaf and stem colour. 20

15. A substantially purified or isolated nucleic acid or nucleic acid fragment including a single nucleotide polymorphism from a nucleic acid or nucleic acid fragment according to any one of claims 1 -4.

16. A substantially purified or isolated CELL polypeptide from a Lolium species; or a functionally active fragment or variant thereof. 25 17. A polypeptide according to Claim 16, wherein said Lolium species is Lolium perenne or Lolium arundinaceum. intellectual property office of n.z. 2 3 AUG 2007

RECEIVED 005016644 55

18. A substantially purified or isolated CELL polypeptide including an amino acid sequence shown in Figure 57 hereto (Sequence ID No: 126); or a functionally active fragment or variant thereof.

19. A polypeptide according to Claim 18 wherein said functionally active fragments 5 and variants have at least approximately 90% identity with the recited sequences and have a size of at least 20 amino acids.

20. A substantially purified or isolated nucleic acid or nucleic acid fragment encoding a polypeptide according to any one of Claims 16 to 19.

21. A lignin or modified lignin or a cellulose or modified cellulose substantially or 10 partially purified or isolated from a plant, plant seed or other plant part according to Claim 8 or 9.

22. A substantially purified or isolated nucleic acid or nucleic acid fragment according to claim 1, substantially as hereinbefore described with reference to any one of the figures or the examples. 15

23. A substantially purified or isolated polypeptide according to claim 16, substantially as hereinbefore described with reference to any one of the figures or the examples. intellectual property office of n.z. 2 3 AUG 2007 B c r. P i \/ FT)