NZ611224B2 - Novel endophytes - Google Patents

Abstract

substantially purified or isolated endophyte having a desired toxin profile, wherein the endophyte produces significantly less toxic alkaloids compared with a control endophyte and/or significantly more alkaloids conferring beneficial properties compared with a control endophyte, wherein said control endophyte is standard toxic endophyte; and wherein said endophyte is selected from the group consisting of NEA16, NEA17, NEA18, NEA19, NEA20, NEA21 and NEA23, as deposited at the National Measurement Institute with accession numbers V12/001413, V12/001414, V12/001415, V12/001416, V12/001417, V12/001418 and V12/001419, respectively.

Description

Patent No. # - Complete Specification No. Date: NOVEL ENDOPHYTES We, Agriculture Victoria Services Pty Ltd, of AgriBio Centre for AgriBioscience, 5 Ring Road, Bundoora VIC 3083, hereby declare the invention, for which we pray that a patent may be granted to us, and the method by which it is to be performed, to be particularly described in an by the following statement NOVEL ENDOPHYTES Field of the Invention The present invention relates to endophytic fungi (endophytes) and nucleic acids thereof, to plants infected with endophytes and to related methods, including methods of selecting, breeding and/or characterising endophytes.

Background of the Invention Important forage grasses perennial ryegrass and tall fescue are commonly found in association with fungal endophytes.

Both beneficial and detrimental agronomic properties result from the association, including improved tolerance to water and nutrient stress and resistance to insect pests.

Insect resistance is provided by specific metabolites produced by the endophyte, in particular loline alkaloids and peramine. Other metabolites produced by the endophyte, lolitrems and ergot alkaloids, are toxic to grazing animals and reduce herbivore feeding.

Considerable variation is known to exist in the metabolite profile of endophytes.

Endophyte strains that lack either or both of the animal toxins have been introduced into commercial cultivars.

Molecular genetic markers such as simple sequence repeat (SSR) markers have been developed as diagnostic tests to distinguish between endophyte taxa and detect genetic variation within taxa. The markers may be used to discriminate endophyte strains with different toxin profiles.

However, there remains a need for methods of identifying, isolating and/or characterising endophytes and a need for new endophyte strains having desired properties.

Neotyphodium endophytes are not only of interest in agriculture, as they are a potential source for bioactive molecules such as insecticides, fungicides, other biocides and bioprotectants, allelochemicals, medicines and nutraceuticals.

Difficulties in artificially breeding of these endophytes limit their usefulness. For example, many of the novel endophytes known to be beneficial to pasture-based agriculture exhibit low inoculation frequencies and are less stable in elite germplasm.

Thus, there remains a need for methods of molecular breeding of novel, highly compatible endophytes.

International patent application describes a method for identifying or characterising endophyte strains which involves subjecting multiple samples of endophytes to genetic and metabolic analyses, and optionally also assessing geographic origin. The application also identifies a number of endophytes which were isolated by this method, including E1, NEA10, NEA11, NEA12, NEA13 and NEA14.

However, there remains a need for more endophyte strains with desirable properties and for more detailed characterisation of their toxin and metabolic profiles, antifungal activity, stable host associations and their genomes.

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.

A large scale endophyte discovery program was undertaken to establish a ‘library’ of novel endophyte strains. A collection of perennial ryegrass and tall fescue accessions was established.

Genetic analysis of endophytes in these accessions has led to the identification of a number of novel endophyte strains. These novel endophyte strains are genetically distinct from known endophyte strains.

Metabolic profiling may be undertaken to determine the toxin profile of these strains grown in vitro and/or following inoculation in planta.

Specific detection of endophytes in planta with SSR markers may be used to confirm the presence and identity of endophyte strains artificially inoculated into, for example, grass plants, varieties and cultivars.

The endophytes may be subject to genetic analysis (genetically characterised) to demonstrate genetic distinction from known endophyte strains and to confirm the identity of endophyte strains artificially inoculated into, for example, grass plants, varieties and cultivars.

By ‘genetic analysis’ is meant analysing the nuclear and/or mitochondrial DNA of the endophyte.

This analysis may involve detecting the presence or absence of polymorphic markers, such as simple sequence repeats (SSRs) or mating-type markers. SSRs, also called microsatellites, are based on a 1-7 nucleotide core element, more typically a 1-4 nucleotide core element, that is tandemly repeated. The SSR array is embedded in complex flanking DNA sequences. Microsatellites are thought to arise due to the property of replication slippage, in which the DNA polymerase enzyme pauses and briefly slips in terms of its template, so that short adjacent sequences are repeated. Some sequence motifs are more slip-prone than others, giving rise to variations in the relative numbers of SSR loci based on different motif types. Once duplicated, the SSR array may further expand (or contract) due to further slippage and/or unequal sister chromatid exchange. The total number of SSR sites is high, such that in principle such loci are capable of providing tags for any linked gene.

SSRs are highly polymorphic due to variation in repeat number and are co- dominantly inherited. Their detection is based on the polymerase chain reaction (PCR), requiring only small amounts of DNA and suitable for automation. They are ubiquitous in eukaryotic genomes, including fungal and plant genomes, and have been found to occur every 21 to 65 kb in plant genomes. Consequently, SSRs are ideal markers for a broad range of applications such as genetic diversity analysis, genotypic identification, genome mapping, trait mapping and marker-assisted selection.

Known SSR markers which may be used to investigate endophyte diversity in perennial ryegrass are described in van Zijll de Jong et al (2003) Genome 46 (2): 277-290.

Alternatively, or in addition, the genetic analysis may involve sequencing genomic and/or mitochondrial DNA and performing sequence comparisons to assess genetic variation between endophytes.

The endophytes may be subject to metabolic analysis to identify the presence of desired metabolic traits.

By ‘metabolic analysis’ is meant analysing metabolites, in particular toxins, produced by the endophytes. Preferably, this is done by generation of inoculated plants for each of the endophytes and measurement of toxin levels in planta. More preferably, this is done by generation of isogenically inoculated plants for each of the endophytes and measurement of toxin levels in planta.

By a ‘desired genetic and metabolic profile’ is meant that the endophyte possesses genetic and/or metabolic characteristics that result in a beneficial phenotype in a plant harbouring, or otherwise associated with, the endophyte.

Such beneficial properties include improved tolerance to water and/or nutrient stress, improved resistance to pests and/or diseases, enhanced biotic stress tolerance, enhanced drought tolerance, enhanced water use efficiency, reduced toxicity and enhanced vigour in the plant with which the endophyte is associated, relative to a control endophyte such as standard toxic (ST) endophyte or to a no endophyte control plant.

For example, tolerance to water and/or nutrient stress may be increased by at least approximately 5%, more preferably at least approximately 10%, more preferably at least approximately 25%, more preferably at least approximately 50%, more preferably at least approximately 100%, relative to a control endophyte such as standard toxic (ST) endophyte or to no endophyte control plant. Preferably, tolerance to water and/or nutrient stress may be increased by between approximately 5% and approximately 50%, more preferably between approximately 10% and approximately %, relative to a control endophyte such as ST or to a no endophyte control plant.

Such beneficial properties also include reduced toxicity of the associated plant to grazing animals.

For example, toxicity may be reduced by at least approximately 5%, more preferably at least approximately 10%, more preferably at least approximately 25%, more preferably at least approximately 50%, more preferably at least approximately 100%, relative to a control endophyte such as ST endophyte. Preferably, toxicity may be reduced by between approximately 5% and approximately 100%, more preferably between approximately 50% and approximately 100% relative to a control endophyte such as ST endophyte.

In a preferred embodiment toxicity may be reduced to a negligible amount or substantially zero toxicity.

For example, water use efficiency and/or plant vigour may be increased by at least approximately 5%, more preferably at least approximately 10%, more preferably at least approximately 25%, more preferably at least approximately 50%, more preferably at least approximately 100%, relative to a control endophyte such as ST or to a no endophyte control plant. Preferably, tolerance to water and/or nutrient stress may be increased by between approximately 5% and approximately 50%, more preferably between approximately 10% and approximately 25%, relative to a control endophyte such as ST or to a no endophyte control plant.

In a first aspect the present invention provides a substantially purified or isolated endophyte having a desired toxin profile. Preferably the endophyte is isolated from a fescue species, preferably tall fescue. Preferably, the endophyte is of the genus Neotyphodium, more preferably it is from a species selected from the group consisting of N. uncinatum, N. coenophialum and N. lolii, most preferably N. coenophialum. The endophyte may also be from the genus Epichloe, including E. typhina, E. baconii and E. festucae. The endophyte may also be of the non-Epichloe out-group. The endophyte may also be from a species selected from the group consisting of FaTG-3 and FaTG-3 like, and FaTG-2 and FaTG-2 like.

In a preferred embodiment of this aspect of the invention, there is provided a substantially purified or isolated endophyte having a desired toxin profile, wherein the endophyte produces significantly less toxic alkaloids compared with a control endophyte and/or significantly more alkaloids conferring beneficial properties compared with a control endophyte, wherein said control endophyte is standard toxic endophyte; and wherein said endophyte is selected from the group consisting of NEA16, NEA17, NEA18, NEA19, NEA20, NEA21 and NEA23, as deposited at the National Measurement Institute with accession numbers V12/001413, V12/001414, V12/001415, V12/001416, V12/001417, V12/001418 and V12/001419, respectively.

By a ‘desired toxin profile’ is meant that the endophyte produces significantly less toxic alkaloids, such as ergovaline or Lolitrem B, compared with a plant inoculated with a control endophyte such as standard toxic (ST) endophyte; and/or significantly more alkaloids conferring beneficial properties such as improved tolerance to water and/or nutrient stress and improved resistance to pests and/or diseases in the plant with which the endophyte is associated, such as peramine, N-formylloline, N- acetylloline and norloline, again when compared with a plant inoculated with a control endophyte such as ST or with a no endophyte control plant.

For example, toxic alkaloids may be present in an amount less than approximately 1µg/g dry weight, for example between approximately 1 and 0.001 µg/g dry weight, preferably less than approximately 0.5 µg/g dry weight, for example between approximately 0.5 and 0.001 µg/g dry weight, more preferably less than approximately 0.2 µg/g dry weight, for example between approximately 0.2 and 0.001 µg/g dry weight.

In a particularly preferred embodiment the endophyte may not produce Lolitrem B toxins.

For example, said alkaloids conferring beneficial properties may be present in an amount of between approximately 5 and 100 µg/g dry weight, preferably between approximately 10 and 50 µg/g dry weight, more preferably between approximately 15 and 30 µg/g dry weight.

In a particularly preferred embodiment, the present invention provides a substantially purified or isolated endophyte selected from the group consisting of NEA16, NEA17, NEA18, NEA19, NEA20, NEA21 and NEA23, which were deposited at The National Measurement Institute on 3 April 2012 with accession numbers V12/001413, V12/001414, V12/001415, V12/001416, V12/001417, V12/001418 and V12/001419, respectively. Such endophytes may have a desired toxin profile as hereinbefore described.

By ‘substantially purified’ is meant that the endophyte is free of other organisms. The term therefore includes, for example, an endophyte in axenic culture. Preferably, the endophyte is at least approximately 90% pure, more preferably at least approximately 95% pure, even more preferably at least approximately 98% pure.

The term ‘isolated’ means that the endophyte is removed from its original environment (eg. the natural environment if it is naturally occurring). For example, a naturally occurring endophyte present in a living plant is not isolated, but the same endophyte separated from some or all of the coexisting materials in the natural system, is isolated.

On the basis of the deposits referred to above, the entire genome of an endophyte selected from the group consisting of NEA21, NEA23, NEA18, NEA19, NEA16 and NEA20, is incorporated herein by reference.

Thus, in a further aspect, the present invention includes identifying and/or cloning nucleic acids including genes encoding polypeptides or transcription factors from said genome.

Methods for identifying and/or cloning nucleic acids encoding such genes are known to those skilled in the art and include creating nucleic acid libraries, such as cDNA or genomic libraries, and screening such libraries, for example using probes for genes of the desired type; or mutating the genome of the endophyte of the present invention, for example using chemical or transposon mutagenesis, identifying changes in the production of polypeptides or transcription factors of interest, and thus identifying genes encoding such polypeptides or transcription factors.

Thus, in a further aspect of the present invention, there is provided a substantially purified or isolated nucleic acid encoding a polypeptide or transcription factor from the genome of an endophyte of the present invention.

By ‘nucleic acid’ is meant a chain of nucleotides capable of carrying genetic information. The term generally refers to genes or functionally active fragments or variants thereof and or other sequences in the genome of the organism that influence its phenotype. The term ‘nucleic acid’ includes DNA (such as cDNA or genomic DNA) and RNA (such as mRNA or microRNA) that is single- or double-stranded, optionally containing synthetic, non-natural or altered nucleotide bases, synthetic nucleic acids and combinations thereof.

By a ‘nucleic acid encoding a polypeptide or transcription factor’ is meant a nucleic acid encoding an enzyme or transcription factor normally present in an endophyte of the present invention.

The present invention encompasses functionally active fragments and variants of the nucleic acids of the present invention. By ‘functionally active’ in relation to the nucleic acid is meant that the fragment or variant (such as an analogue, derivative or mutant) is capable of manipulating the function of the encoded polypeptide, for example by being translated into an enzyme or transcription factor that is able to catalyse or regulate a step involved in the relevant pathway, or otherwise regulate the pathway in the endophyte. 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 80% identity to the relevant part of the above mentioned sequence to which the fragment or variant corresponds, more preferably at least approximately 90% identity, even more preferably at least approximately 95% identity, most preferably at least approximately 98% identity. Such functionally active variants and fragments include, for example, those having conservative nucleic acid changes.

Preferably the fragment has a size of at least 20 nucleotides, more preferably at least 50 nucleotides, more preferably at least 100 nucleotides.

Preferably, said fragments are able to produce the same activity as the original gene when expressed. Preferably, said fragments maintain conserved regions within consensus sequences of the original gene.

Preferably said variants are variants of the original sequences that provide either conserved substitution, or limited modifications in consensus sequences to a level, for example, of no more than approximately 5%, more preferably no more than 1%, relative to the original gene.

For example, fragments and variants of a sequence encoding X may include a wild type sequence from species Z that encodes X, a fragment of a wild type sequence wherein the fragment encodes X, and that retains conserved regions within consensus sequences from species Z, and variants of the wild type sequence or fragments which encode X activity and have only conservative substitutions, a variant X’ that encodes X activity and in which sequence differs only by substitutions found in one or more contributing sequences used in formulating the consensus sequence, or a variant X'' that encodes X activity in which the variant has not more than approximately 95% amino acid variation, more preferably not more than approximately 99% amino acid variation from the wild type sequence or fragment.

By ‘conservative nucleic acid changes’ or ‘conserved substitution’ is meant nucleic acid substitutions that result in conservation of the amino acid in the encoded protein, due to the degeneracy of the genetic code. Such functionally active variants and fragments also 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.

By ‘conservative amino acid substitutions’ is meant the substitution of an amino acid by another one of the same class, the classes being as follows: Nonpolar: Ala, Val, Leu, Ile, Pro, Met, Phe, Trp Uncharged polar: Gly, Ser, Thr, Cys, Tyr, Asn, Gln Acidic: Asp, Glu Basic: Lys, Arg, His Other conservative amino acid substitutions may also be made as follows: Aromatic: Phe, Tyr, His Proton Donor: Asn, Gln, Lys, Arg, His, Trp Proton Acceptor: Glu, Asp, Thr, Ser, Tyr, Asn, Gln In a further aspect of the present invention, there is provided a genetic construct including a nucleic acid according to the present invention.

By ‘genetic construct’ is meant a recombinant nucleic acid molecule.

In a preferred embodiment, the genetic construct according to the present invention may be a vector.

By a ‘vector’ is meant a genetic construct used to transfer genetic material to a target cell.

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 or integrative or viable in the target cell.

In a preferred embodiment of this aspect of the invention, the genetic construct may further include a promoter and a terminator; said promoter, gene and terminator being operatively linked.

By a ‘promoter’ is meant a nucleic acid sequence sufficient to direct transcription of an operatively linked nucleic acid sequence.

By ‘operatively linked’ is meant that the nucleic acid(s) and a regulatory sequence, such as a promoter, are linked in such a way as to permit expression of said nucleic acid under appropriate conditions, for example when appropriate molecules such as transcriptional activator proteins are bound to the regulatory sequence. Preferably an operatively linked promoter is upstream of the associated nucleic acid.

By ‘upstream’ is meant in the 3’->5’ direction along the nucleic acid.

The promoter and terminator may be of any suitable type and may be endogenous to the target cell or may be exogenous, provided that they are functional in the target cell.

A variety of terminators which may be employed in the genetic constructs 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 genetic construct, in addition to the promoter, the gene and the terminator, may include further elements necessary for expression of the nucleic acid, in different combinations, for example vector backbone, origin of replication (ori), multiple cloning sites, spacer sequences, enhancers, introns, antibiotic resistance genes and other selectable marker genes [such as the neomycin phosphotransferase (nptII) gene, the hygromycin phosphotransferase (hph) gene, the phosphinothricin acetyltransferase (bar or pat) gene], and reporter genes [such as beta-glucuronidase (GUS) gene (gusA) and the green fluorescent protein (GFP) gene (gfp)]. The genetic construct may also contain a ribosome binding site for translation initiation. The genetic construct may also include appropriate sequences for amplifying expression.

Those skilled in the art will appreciate that the various components of the genetic construct are operably linked, so as to result in expression of said nucleic acid.

Techniques for operably linking the components of the genetic construct 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.

Preferably, the genetic construct is substantially purified or isolated.

By ‘substantially purified’ is meant that the genetic construct is free of the genes, which, in the naturally-occurring genome of the organism from which the nucleic acid or promoter of the invention is derived, flank the nucleic acid or promoter. The term therefore includes, for example, a genetic construct which is incorporated into a vector; into an autonomously replicating plasmid or virus; or into the genomic DNA of a prokaryote or eukaryote; or which exists as a separate molecule (eg. a cDNA or a genomic or cDNA fragment produced by PCR or restriction endonuclease digestion) independent of other sequences. It also includes a genetic construct which is part of a hybrid gene encoding additional polypeptide sequence.

Preferably, the substantially purified genetic construct is at least approximately 90% pure, more preferably at least approximately 95% pure, even more preferably at least approximately 98% pure.

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.

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 genetic construct 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 assays (e.g. GUS assays), thin layer chromatography (TLC), northern and western blot hybridisation analyses.

The genetic constructs of the present invention may be introduced into plants or fungi by any suitable technique. Techniques for incorporating the genetic constructs of the present invention into plant cells or fungal cells (for example by transduction, transfection, transformation or gene targeting) are well known to those skilled in the art. Such techniques include Agrobacterium-mediated introduction, Rhizobium- 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, biolistic transformation, Whiskers transformation, and combinations thereof. The choice of technique will depend largely on the type of plant or fungus to be transformed, and may be readily determined by an appropriately skilled person. For transformation of protoplasts, PEG-mediated transformation is particularly preferred.

For transformation of fungi PEG-mediated transformation and electroporation of protoplasts and Agrobacterium-mediated transformation of hyphal explants are particularly preferred.

Cells incorporating the genetic constructs of the present invention may be selected, as described below, and then cultured in an appropriate medium to regenerate transformed plants or fungi, 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 or fungi may be reproduced, either sexually or asexually, using methods well known in the art, to produce successive generations of transformed plants or fungi.

In a further aspect, the present invention provides a plant inoculated with an endophyte as hereinbefore described, said plant comprising an endophyte-free host plant stably infected with said endophyte.

Preferably, the plant is infected with the endophyte by a method selected from the group consisting of inoculation, breeding, crossing, hybridization and combinations thereof.

In a preferred embodiment, the plant may be infected by isogenic inoculation. This has the advantage that phenotypic effects of endophytes may be assessed in the absence of host-specific genetic effects. More particularly, multiple inoculations of endophytes may be made in plant germplasm, and plantlets regenerated in culture before transfer to soil.

The identification of an endophyte of the opposite mating-type that is highly compatible and stable in planta provides a means for molecular breeding of endophytes for perennial ryegrass. Preferably the plant may be infected by hyper- inoculation.

Hyphal fusion between endophyte strains of the opposite mating-type provides a means for delivery of favourable traits into the host plant, preferably via hyper- inoculation. Such strains are preferably selected from the group including an endophyte strain that exhibits the favourable characteristics of high inoculation frequency and high compatibility with a wide range of germplasm, preferably elite perennial ryegrass and/or tall fescue host germplasm and an endophyte that exhibits a low inoculation frequency and low compatibility, but has a highly favourable alkaloid toxin profile.

It has generally been assumed that interactions between endophyte taxa and host grasses will be species specific. Applicants have surprisingly found that endophyte from tall fescue may be used to deliver favourable traits to ryegrasses, such as perennial ryegrass.

In a further aspect of the present invention there is provided a method of analysing metabolites in a plurality of endophytes, said method including: providing: a plurality of endophytes; and a plurality of isogenic plants; inoculating each isogenic plant with an endophyte; culturing the endophyte-infected plants; and analysing the metabolites produced by the endophyte-infected plants.

By ‘metabolites’ is meant chemical compounds, in particular toxins, produced by the endophyte-infected plant, including, but not limited to, lolines, peramine, ergovaline, lolitrem, and janthitrems, such as janthitrem I, janthitrem G and janthitem F.

By ‘isogenic plants’ is meant that the plants are genetically identical.

The endophyte-infected plants may be cultured by known techniques. The person skilled in the art can readily determine appropriate culture conditions depending on the plant to be cultured.

The metabolites may be analysed by known techniques such as chromatographic techniques or mass spectrometry, for example LCMS or HPLC. In a particularly preferred embodiment, endophyte-infected plants may be analysed by reverse phase liquid chromatography mass spectrometry (LCMS). This reverse phase method may allow analysis of specific metabolites (including lolines, peramine, ergovaline, lolitrem, and janthitrems, such as janthitrem I, janthitrem G and janthitem F) in one LCMS chromatographic run from a single endophyte-infected plant extract.

In a particularly preferred embodiment, the endophytes may be selected from the group consisting of NEA21, NEA23, NEA18, NEA19, NEA16 and NEA20.

In another particularly preferred embodiment, LCMS including EIC (extracted ion chromatogram) analysis may allow detection of the alkaloid metabolites from small quantities of endophyte-infected plant material. Metabolite identity may be confirmed by comparison of retention time with that of pure toxins or extracts of endophyte- infected plants with a known toxin profile analysed under substantially the same conditions and/or by comparison of mass fragmentation patterns, for example generated by MS2 analysis in a linear ion trap mass spectrometer.

In a further aspect, the present invention provides a plant, plant seed or other plant part derived from a plant of the present invention and stably infected with an endophyte of the present invention.

Preferably, the plant cell, plant, plant seed or other plant part is a grass, more preferably a forage, turf or bioenergy grass, such as those of the genera Lolium and Festuca, including L. perenne and L. arundinaceum.

By ‘plant cell’ is meant any self-propagating cell bounded by a semi-permeable membrane and containing plastid. Such a cell also required a cell wall if further propagation is desired. Plant cell, as used herein includes, without limitation, seeds suspension cultures, embryos, meristematic regions, callus tissue, leaves, roots, shoots, gametophytes, sporophytes, pollen and microspores.

In a further aspect, the present invention provides use of an endophyte as hereinbefore described to produce a plant stably infected with said endophyte.

In a still further aspect, the present invention provides a method of quantifying endophyte content of a plant, said method including measuring copies of a target sequence by quantitative PCR.

In a preferred embodiment, the method may be performed using an electronic device, such as a computer.

Preferably, quantitative PCR may be used to measure endophyte colonisation in planta, for example using a nucleic acid dye, such as SYBR Green chemistry, and qPCR-specific primer sets. The primer sets may be directed to a target sequence such as an endophyte gene, for example the peramine biosynthesis perA gene.

The development of a high-throughput PCR-based assay to measure endophyte biomass in planta may enable efficient screening of large numbers of plants to study endophyte–host plant biomass associations.

As used herein, except where the context requires otherwise, the term "comprise" and variations of the term, such as "comprising", "comprises" and "comprised", are not intended to exclude further additives, components, integers or steps.

Reference to any prior art in the specification is not, and should not be taken as, an acknowledgment or any form of suggestion that this prior art forms part of the common general knowledge in Australia or any other jurisdiction or that this prior art could reasonably be expected to be ascertained, understood and regarded as relevant by a person skilled in the art.

Detailed Description of the Embodiments In the figures: Figure 1 shows genotypic analysis of endophyte content in accessions from a targeted fescue germplasm collection.

Figure 2 shows genetic diversity analysis of tall fescue endophytes.

Figure 3 shows diversity analysis of host and endophyte.

Figure 4 shows selection of fescue-endophyte combinations for metabolic profiling, endophyte isolation and isogenic inoculation.

Figure 5 shows selection of fescue-endophyte combinations for metabolic profiling, endophyte isolation and isogenic inoculation.

Figure 6 shows a desired toxin profile of tall fescue endophytes.

Figure 6A shows an experimental design used for semi-quantitative metabolic profile analysis of tall fescue-endophyte associations for the detection of alkaloid production in the endogenous host background.

Figure 7 shows a metabolic profile analysis.

Figure 8 shows endophytes selected for semi-quantitative analysis of metabolites.

Figures 9 and 10 show metabolomics analyses of fescue endophytes.

Figure 11 shows a semi-quantitative analysis of metabolic profile under temperature/water stress.

Figure 12 shows endophytes selected for isogenic inoculation.

Figure 13 shows SSR-based genotyping of isolated endophytes cultures prior to isogenic inoculation.

Figure 14 shows endophyte vegetative stability in tall fescue and perennial ryegrass host genotypes (stability at 12 months post inoculation).

Figure 15 shows endophytes selected for isogenic inoculation.

Figures 16-19 show metabolic profiling of isogenic tall fescue-endophyte associations.

Figure 20 shows anti-fungal bioassays of fescue endophytes. Column 1 Colletotrichum graminicola, Column 2 Drechslera brizae, Column 3 Rhizoctonia cerealis.

Figure 21 shows sequencing of selected novel fescue endophytes.

Figure 22 shows peramine biosynthetic pathway.

Figures 23 A-C show presence of perA gene within non-Epichloe out-group endophytes (Fig 23A NEA17; Fig 23B NEA18; Fig 23C NEA19).

Figure 24 shows ergovaline biosynthetic pathway.

Figure 25 shows genes in the eas gene cluster.

Figures 26 A-D show presence of dmaW gene for ergovaline biosynthesis in endophyte strains (Fig 26A NEA17; Fig 26B NEA16; Fig 26C AR542; Fig 26D NEA20).

Figures 27 A-D show presence of eas gene cluster for ergovaline biosynthesis. Fig 27A FaTG-2 NEA17 (287819); Fig 27B non-Epichloe out-group NEA18 (FEtc6-75); Fig 27C FATG-3 NEA21 (231557); Fig 27D N. coenophialum NEA16 (FEtc7-342).

Figure 28 shows the Lolitrem B biosynthetic pathway.

Figure 29 shows genes in the Lolitrem B biosynthetic gene cluster.

Figures 30 A-D show presence of Lolitrem B biosynthetic gene cluster 1 (ltmG, ltmM and ltmK) in endophyte strains. Fig 30A FaTG-2 NEA17 (287819); Fig 30B non- Epichloe out-group NEA18 (FEtc6-75); Fig 30C FATG-3 NEA21 (231557); Fig 30D N. coenophialum NEA16 (FEtc7-342).

Figures 31 A-D show presence of Lolitrem B biosynthetic gene cluster 2 (ltmB, ltmQ, ltmP, ltmF and ltmC) in endophyte strains. Fig 31A FaTG-2 NEA17 (287819); Fig 31B non-Epichloe out-group NEA18 (FEtc6-75); Fig 31C FATG-3 NEA21 (231557); Fig 31D N. coenophialum NEA16 (FEtc7-342).

Figures 32 A-D show presence of Lolitrem B biosynthetic gene cluster 3 (ltmE and ltmJ) in endophyte strains. Fig 32A FaTG-2 NEA17 (287819); Fig 32B non-Epichloe out-group NEA18 (FEtc6-75); Fig 32C FATG-3 NEA21 (231557); Fig 32D N. coenophialum NEA16 (FEtc7-342).

Figure 33 shows the loline biosynthetic pathway.

Figure 34 shows the loline biosynthetic gene cluster.

Figures 35 A-D show presence of Loline biosynthetic gene cluster in endophyte strains. Fig 35A FaTG-2 NEA17 (287819); Fig 35B non-Epichloe out-group NEA18 (FEtc6-75); Fig 35C FATG-3 NEA21 (231557); Fig 35D N. coenophialum NEA16 (FEtc7-342).

Figures 36 A-F show alkaloid biosynthetic gene analysis for endophyte strain NEA23 (269850). Fig 36A Presence of loline gene cluster; Fig 36B Presence of peramine gene; Fig 36C Analysis of Lolitrem gene cluster 01; Fig 36D Analysis of Lolitrem gene clusters 02 and 03; Fig 36E Analysis of dmaW gene for ergovaline production; Fig 36F Analysis of eas gene cluster for ergovaline production.

Figure 37 shows genotypic analysis of NEA23 and NEA21.

Figure 38 shows genotypic analysis of NEA16 and NEA20.

The invention will now be described with reference to the following non-limiting examples.

Example 1 – Tall fescue endophyte discovery The objectives of this work on discovery and characterization of endophytes in tall fescue (Lolium arundinaceum) were: 1. Identification and characterisation of novel tall fescue endophytes for evaluation in germplasm. 2. Development and evaluation of optimised associations between novel endophytes and elite germplasm.

The endophyte discovery was based on screening 568 accessions to identify endophyte positive plants followed by genotyping 210 endophytes to identify novel endophytes in tall fescue.

The characterisation in planta of novel endophytes from tall fescue was based on the following steps: • Meristem cultures for tall fescue cultivars were established for isogenic host panel • Endogenous metabolic profiles were determined for 48 samples • Isolation of 38 endophytes was undertaken • Inoculation of 15-20 endophytes into isogenic host panel was undertaken • Isogenic host-endophyte associations were characterised Genotypic analysis of endophyte content in accessions from a targeted fescue germplasm collection Initially, 472 accessions from 30 countries were tested for endophyte incidence; with 2 replicates of 6-10 seeds in each bulk per accession used in the analysis and endophyte incidence assessed with 6 SSRs.

New accessions were included in the analysis from the under-represented geographic origins; with a total of 568 accessions from 40 countries tested for endophyte incidence.

Number of geographic Percentage positive origins accessions FEtc GRIN FEtc GRIN collection collection collection collection Incidence assessment 7 23 96% 30% Incidence assessment - 10 - 45% Table 1: Genotypic analysis of endophyte content in accessions from a targeted fescue germplasm collection Genotypic analysis of endophyte content in accessions from a targeted fescue germplasm collection is shown in Table 1. 233 endophyte positive accessions (41%) were detected. The geographical origins are represented in the endophyte incidence assessment.

A genetic diversity analysis of tall fescue endophytes is shown in Figure 2. A selected set of 210 accessions were used to assess genetic diversity of tall fescue endophytes. Genetic diversity was assessed with 38 SSR markers. Six different taxa were detected. The majority were N. coenophialum. Twenty were FaTG-2. Six were putative FaTG-3. Thirteen were FaTG-3 like.

Diversity of host and endophyte is shown in Figure 3.

Selection of fescue-endophyte combinations for metabolic profiling, endophyte isolation and isogenic inoculation is shown in Figure 4. 52 accessions were initially selected for metabolic profiling and endophyte isolation. Endophyte presence was consistently detected in 25 accessions (red). An additional 48 accessions from under- represented clusters were established in the glasshouse and screened for endophyte presence. 20 accessions were endophyte positive (blue) and were selected for further analysis.

Selection of fescue-endophyte combinations for metabolic profiling, endophyte isolation and isogenic inoculation is shown in Figure 5. Initial selections are shown in red. Additional selections are shown in blue.

The desired toxin profile of tall fescue endophytes is shown in Figure 6.

Example 2 – Metabolic profiling The experimental design used for semi-quantitative metabolic profile analysis of tall fescue-endophyte associations for the detection of alkaloid production in the endogenous host background is shown in Figure 6A.

A metabolic profile analysis for detection of ergovaline and peramine is shown in Figure 7.

Endophytes selected for semi-quantitative analysis of metabolites are shown in Figure 8.

Metabolic profile analysis for the detection of alkaloid production of different fescue endophytes A metabolic analysis of tall fescue-endophyte associations for the detection of alkaloid production including loline, loline formate, peramine, ergovaline and lolitrem B in the endogenous host background is shown in Figure 9. The alkaloid profile (i.e. lolines, peramine, ergovaline and lolitrem B) of tall fescue-endophyte associations in the endogenous host background for a range of endophyte strains belonging to different endophyte species is shown in Table 2.

Tall fescue accession details Alkaloid profile Endophyte Endophyte Lolitrem fescue Lolines Peramine Ergovaline* strain species B accession BE9301 E34 + + + - coenophialum 8PC NEA13 n.d + + n.d coenophialum FEtc7-180 NEA14 + + + - coenophialum FEtc7-58 NEA15 + + + - coenophialum FEtc7-342 NEA16 + + - - coenophialum FEtc7-343 NEA20 + + - - coenophialum 234746 NEA22 + + + - coenophialum FEtc6-83 NEA24 + + + - coenophialum FEtc7-289 NEA25 + - + - coenophialum FEtc6-68 NEA26 + + + - coenophialum FEtc6-85 NEA27 n.d + + n.d coenophialum FEtc6-87 NEA28 n.d + + n.d coenophialum FEtc7-127 NEA29 + + + - coenophialum FEtc6-128 NEA30 + + + - coenophialum FEtc6-129 NEA31 + + + - coenophialum 287819 NEA17 FaTG-2 - + - 231557 NEA21 FaTG-2 + + - - 269850 NEA23 FaTG-3 + + - - 231553 NEA19 Out group 1 - - - - FEtc6-75 NEA18 Out group 1 - - - - ST ST N. lolii - + + + AR542* AR542 + + - - coenophialum KY31* KY31 + + + - coenophialum E77* E77 + + + - coenophialum Table 2 Alkaloid profile (i.e. lolines, peramine, ergovaline and lolitrem B) of tall fescue-endophyte associations in the endogenous host background for a range of endophyte strains belonging to different endophyte species (* Published data; nd = not determined).

Further metabolic analysis of the fescue endophytes is shown in Figure 10.

Example 3 - Semi-quantitative Analysis of Metabolic Profile under Temperature/Water Stress In addition to the metabolic analysis of tall fescue-endophyte associations grown under standard conditions, for the detection of alkaloid production conferred by the endopohytes in the endogenous host background (Figures 7 – 10), a semi- quantitative analysis of metabolic profiles of tall fescue-endophyte associations grown under high temperature and water stress conditions was undertaken.

Corresponding tall fescue-endophyte associations were grown under 16h Light and C; 18h Dark and 20 C, and then sampled for alkaloid profile analysis as described below: • Harvest (control) ? freeze dry ? 50 mg pseudostem material ? 80% methanol extraction ? LCMS analysis • Recovery and water stress • Second harvest (stress) ? freeze dry ? SSR confirm all of the plant material again.

This was performed in a controlled (growth chamber) environment simulating summer conditions, with light watering as required. Nine copies per accession were planted in general potting mix. A Randomized Complete Block with subsampling was used.

Figure 11 shows a semi-quantitative analysis of metabolic profile of tall fescue- endophyte associations grown under high temperature and water stress conditions.

Example 4 – In planta isogenic inoculation in tall fescue with novel endophytes Summary: A total of 36 fescue endophytes have been isolated from a range of fescue accessions from different geographic origin as described in Table 3, and found to belong to different taxa as follows: 19 of them being N. coenophialum; 5 of them being FaTG-2; 3 of them being Outgroup; 3 of them being FaTG-3; 3 of them being FaTG-3 like; and 3 of them being N. uncinatum Fescue Endophyte Fescue Endophyte Origin Cluster Taxon Origin Cluster Taxon Accession Strain Accession Strain 1 8PC 8PC C01.1 N. coenophialum 23 231557 NEA21 Morocco C09 Fa TG-2 2 BE9301 E34 C01.1 N. coenophialum 24 287819 NEA17 Spain C09 Fa TG-2 3 E77 E77 C01.2 N. coenophialum 25 598834 Morocco C09 Fa TG-2 4 FEtc6-62 Catalunya (Spain) 4 C01.2 N. coenophialum 26 231559 Morocco C09 Fa TG-2 FEtc6-68 NEA26 Catalunya (Spain) 14 C01.2 N. coenophialum 27 598852 Morocco C09 Fa TG-2 6 FEtc7-127 NEA29 Aragon (Spain)14 C01.2 N. coenophialum 28 598934 Italy C10 Outgroup 7 FEtc7-289 NEA25 Aragon (Spain)14 C01.2 N. coenophialum 29 231553 NEA19 Algeria C10 Outgroup 8 FEtc7-58 NEA15 Aragon (Spain) 1 C01.2 N. coenophialum 30 FEtc6-75 NEA18 Sardegna (NW Italy) 5 C10 Outgroup 9 234746 NEA22 Spain C01.2 N. coenophialum 31 269850 NEA23 Tunisia C12 Fa TG-3 632582 Italy C02.1 N. coenophialum 32 610918 Tunisia C12 Fa TG-3 11 Kentucky 31 KY31 C02.1 N. coenophialum 33 610919 Tunisia C12 Fa TG-3 12 FEtc6-128 NEA30 Pyrenees13 C02.2 N. coenophialum 34 598829 Morocco C13 Fa TG-3 like 13 FEtc6-129 NEA31 Pyrenees17 C02.2 N. coenophialum 35 598863 Morocco C13 Fa TG-3 like 14 FEtc7-180 NEA14 PaySardegna (Basque (FrancC02.2 N. coenophialum 36 598870 Morocco C13 Fa TG-3 like 440364 Kazakhstan C03 N. coenophialum 37 M311046 Russion Federation C14 N. uncinatum 16 619005 China C03 N. coenophialum 38 M595026 United Kingdom C14 N. uncinatum 17 FEtc6-83 NEA24 Corsica (France)7 C04 N. coenophialum 39 M611046 Russion Federation C14 N. uncinatum 18 FEtc6-85 NEA27 Corsica (France) 15 C04 N. coenophialum 19 FEtc6-87 NEA28 Corsica (France) 17 C04 N. coenophialum AR542 AR542 Morocco C05 N. coenophialum 21 FEtc7-342 NEA16 Gaurda (Portugal) C06 N. coenophialum 22 FEtc7-343 NEA20 Gaurda (Portugal) C06 N. coenophialum Table 3 – Isolation of fungal endophyte cultures from endophyte-containing fescue accessions Establishment of Meristem Cultures for Diverse Host Panel for In Planta Inoculation of Fescue Endophytes Table 4 shows selected tall fescue and perennial ryegrass cultivars used to identify representative plant genotypes included in the diverse host panel for in planta inoculation of fescue endophytes. All the selected plant genotypes have a high regeneration frequency of >80%.

Cultivar Genotype Species Characteristics Soft leaved, later maturing, Bariane BARI 27 L. arundinaceum highly palatable High yielding, fast Dovey DOV 24 L. arundinaceum establishing Soft leaved with improved Quantum QUAN 17 L. arundinaceum rust resistance Cool season perennial Jesup JES 01 L. arundinaceum forage Standard perennial Bronsyn BRO 08 L. perenne ryegrass forage type Table 4 – Selected tall fescue and perennial ryegrass cultivars used to identify representative plant genotypes included in the diverse host panel for in planta inoculation of fescue endophytes Isolated fungal endophytes from endophyte-containing fescue accessions selected for in planta isogenic inoculation into the diverse host panel are shown in Figure 12.

Figure 13 shows SSR-based genotyping of isolated endophyte cultures prior to in planta isogenic inoculation to confirm their identity.

Results from the SSR genotyping indicating the allele number and sizes for different SSR markers for the different fescue endophyte strains are shown in Table 5.

Endophyte Tall Fescue NCESTA1DH04 (FAM) NLESTA1TA10 (FAM) NCESTA1HA02 (HEX) NCESTA1CC10 (HEX) Strain ID Accession ID Allele 1 Allele 2 Allele 3 Allele 1 Allele 2 Allele 3 Allele 1 Allele 2 Allele 3 Allele 1 Allele 2 Allele 3 AR542 - 212 218 227 165 175 322 327 330 198 201 211 E34 BE_9301 212 218 224 165 175 322 329 330 198 201 211 E77 - 212 218 224 165 175 308 322 330 197 201 211 NEA13 8PC 212 218 224 165 175 322 330 197 200 210 NEA14 FEtc7-180 215 218 229 165 175 322 329 330 198 201 NEA15 FEtc7-58 212 218 224 165 175 322 329 330 197 201 211 NEA16 FEtc7-342 215 227 165 175 309 322 330 198 201 211 NEA17 287819 215 221 227 171 175 322 201 203 NEA18 FEtc6-75 218 227 171 175 304 322 201 NEA19 231553 221 227 171 175 304 325 201 Table 5 – Presence of alleles in endophyte strains Results from the in planta isogenic inoculation into the diverse host panel of selected isolated fungal endophytes from endophyte-containing fescue accessions are shown in Table 6. Data on number of inoculations tested, number of successful inoculations and % of successful inoculations are provided in Table 6 to illustrate the inoculation ability of tall fescue endophytes in tall fescue and perennial ryegrass hosts.

A. Number of inoculations tested E77 E34 NEA13 NEA15 NEA14 AR542 NEA16 NEA17 NEA18 NEA19 E77 BE9301 8PC Fetc7-58 FEtc7-180 AR542 FEtc7-342 287819 FEtc6-75 231553 Total BARI 27 23 25 30 34 38 38 24 32 40 27 311 BRO 08 39 31 24 27 35 36 30 33 48 22 325 NI NI NI DOV 24 10 14 17 8 18 14 16 97 JESS 01 23 23 39 27 20 36 33 17 28 14 260 QUAN 17 8 31 20 15 17 21 18 16 15 8 169 Total 103 124 113 103 110 148 113 116 145 87 1162 B. Number of successful inoculations E77 E34 NEA13 NEA15 NEA14 AR542 NEA16 NEA17 NEA18 NEA19 E77 BE9301 8PC Fetc7-58 FEtc7-180 AR542 FEtc7-342 287819 FEtc6-75 231553 Total 3 3 4 0 1 11 3 17 18 2 62 BARI 27 BRO 08 0 0 2 0 2 0 0 4 2 5 15 DOV 24 3 0 NI NI NI 1 0 1 4 0 9 JESS 01 7 0 5 0 7 10 3 2 1 2 37 QUAN 17 3 0 1 0 0 0 0 6 5 3 18 Total 16 3 12 0 10 22 6 30 30 12 141 C. Percent of successful inoculations E77 E34 NEA13 NEA15 NEA14 AR542 NEA16 NEA17 NEA18 NEA19 E77 BE9301 8PC Fetc7-58 FEtc7-180 AR542 FEtc7-342 287819 FEtc6-75 231553 Total BARI 27 13.0 12.0 13.3 0.0 2.6 28.9 12.5 53.1 45.0 7.4 18.8 BRO 08 0.0 0.0 8.3 0.0 5.7 0.0 0.0 12.1 4.2 22.7 5.3 DOV 24 30.0 0.0 NI NI NI 5.9 0.0 5.6 28.6 0.0 10.0 JESS 01 30.4 0.0 12.8 0.0 35.0 27.8 9.1 11.8 3.6 14.3 14.5 QUAN 17 37.5 0.0 5.0 0.0 0.0 0.0 0.0 37.5 33.3 37.5 15.1 Total 22.2 2.4 9.9 0.0 10.8 12.5 4.3 24.0 22.9 16.4 12.7 Cluster 1 1 1 1 2 3 3 7 8 8 N. coenophialum Outgroup 1 Species Fa TG-2 NI Not inoculated Table 6 - Inoculation Ability of Tall Fescue Endophytes in Tall Fescue and Perennial Ryegrass Hosts Example 5 - Endophyte Vegetative Stability in Tall Fescue and Perennial Ryegrass Host Genotypes Following in planta isogenic inoculation with a range of selected isolated endophytes from fescue accessions, the endophyte vegetative stability of these endophytes in the different tall fescue and perennial host genotypes (i.e. BRO 08, BARI 27, DOV 24) was assessed, showing that: • Several tall fescue endophytes (e.g. NEA17, NEA18, NEA19) were stable in perennial ryegrass (BRO08).

• BARI27 formed stable associations with all endophytes except for NEA15.

• NEA15 failed to form stable associations with any of host genotypes tested.

• DOV24 formed few stable associations.

The stability of these associations of novel tall fescue endophytes inoculated in different tall fescue and perennial ryegrass genotypes from the diverse host panel was assessed 12 months post-inoculation. Corresponding results are shown in Table E7 NEA1 NEA1 NEA1 AR54 NEA1 NEA1 NEA1 NEA1 7 3 5 4 2 6 7 8 9 Plant Genotyp E7 BE930 Fetc7- FEtc7 AR54 FEtc7 28781 FEtc6 23155 7 1 58 -180 2 -342 9 -75 3 BARI 27 1/2 2/2 1/4 NA 1/1 7/7 1/1 1/2 8/10 1/1 BRO 08 NA NA 0/1 NA 0/2 NA NA 5/5 2/2 3/5 DOV 24 1/2 NA NI NI NI 0/1 NA 2/2 2/4 NA JESS 01 5/5 NA 4/6 NA 5/6 5/10 2/3 0/1 0/1 3/3 2/3 NA 0/1 NA NA NA NA 3/6 3/5 1/2 Table 7 – Stability of associations of novel tall fescue endophytes (e.g. NEA13, NEA14, NEA15, NEA16, NEA17, etc.) inoculated in different tall fescue and perennial ryegrass genotypes (BARI 27, BRO 08, DOV 24, JESS 01 and QUAN 17) from the diverse host panel assessed 12 months post-inoculation. NA – not applicable, NI – not inoculated, number of stable association/number of associations Figure 14 shows stability at 12 months post inoculation of selected endophytes in tall fescue and perennial ryegrass host genotypes from the diverse host panel.

The range of novel fescue endophytes selected for in planta isogenic inoculation is shown in Figure 15.

Table 8 shows additional novel tall fescue endophytes (e.g. NEA20, NEA21, NEA22, etc.) selected for in planta isogenic inoculations in tall fescue genotypes (i.e. BARI 27, JESS 01 and QUAN 17) from the diverse host panel, based on the following selection criteria: 1. Produce little or no ergovaline 2. Produce no lolitrem B 3. Produce lolines and/or peramine NEA20 NEA21 NEA22 NEA23 NEA24 NEA27 NEA30 FEtc7- FEtc6- FEtc6- FEtc6- 231557 234746 269850 343 83 85 128 Nco FaTG-3 Nco FaTG-3 Nco Nco Nco Lol/-/P/- Lol/-/P/- Lol/E/P/- Lol/-/P/- Lol/E/P/- ?/E/P/? ?/E/P/? 28 30 30 TBI 30 25 30 23 20 20 TBI 20 20 30 30 40 TBI 30 35 25 Table 8 – Additional novel tall fescue endophytes (e.g. NEA20, NEA21, NEA22, etc.) selected for in planta isogenic inoculations in tall fescue genotypes (i.e.

BARI 27, JESS 01 and QUAN 17) from the diverse host panel. Nco = N. coenophialum; ? = alkaloid profile not tested; TBI = To Be Inoculated.

Example 6 – Metabolic profiling of endophyte-tall fescue associations established following in planta isogenic inoculations of novel tall fescue endophytes in tall fescue genotypes from the diverse host panel Metabolic profiling of endophyte-tall fescue associations established following in planta isogenic inoculations of novel tall fescue endophytes in tall fescue genotypes from the diverse host panel is shown in Figures 16, 18 and 19. These figures: • Compare semi-quantitative alkaloid profiles of selected endophytes across different isogenic hosts • Compare semi-quantitative alkaloid profiles for diverse endophytes in an isogenic host • Compare semi-quantitative alkaloid profiles of tall fescue and perennial ryegrass endophytes in the perennial ryegrass genotype Bro08 Figure 17 shows the presence of peramine and ergovaline in endophyte-tall fescue associations established following in planta isogenic inoculations of novel tall fescue endophytes in tall fescue genotypes from the diverse host panel.

Table 9 shows metabolic profiling of endophyte-tall fescue associations established following in planta isogenic inoculations of novel tall fescue endophytes in tall fescue genotypes from the diverse host panel. Confirmed endophyte positive (E+) plants were split to 5 replicates and regularly trimmed to promote tillering. Four months later E+ plants were re-potted in 12 replicates. One month later E+ plants were re-potted if less than 9 positive copies were available at the time. Endophyte status was tested using SSR markers after each re- potting.

Table 9 – Endophyte-tall fescue associations established following in planta isogenic inoculations of novel tall fescue endophytes in tall fescue genotypes from the diverse host panel used for metabolic profiling.

A range of endophyte-tall fescue associations established following in planta isogenic inoculations of novel tall fescue endophytes in tall fescue genotypes from the diverse host panel were selected for metabolic profiling (Table 9). In total, 29 isogenic host- endophyte associations were subject to LCMS analysis, following the experimental design described below: Experimental design • Trim and re-pot plants • 16h Light, 30 C; 18h Dark, 20 C • Harvest (control) ? freeze dry ? 50 mg pseudostem material ? 80% methanol extraction ? LCMS analysis • Recovery and water stress • Second harvest (stressed) ? freeze dry ? 50mg pseudostem material ? 80% methanol extraction ? LCMS analysis.

This was performed in a controlled (growth chamber) environment simulating summer conditions, with light watering as required. Nine copies per accession were planted in general potting mix. A Randomized Complete Block with subsampling was used.

Example 7 – Bio-protective properties of fescue endophytes Three fungal pathogens (i.e. Colletrotrichum graminicola, Drechslera brizae and Rhizoctonia cerealis) - causing a range of fungal diseases and infecting a range of different plant hosts - were included in antifungal bioassays used to analyse the potential anti-fungal activities of isolated fescue endophytes. Figure 20 shows results from anti-fungal bioassays of isolated fescue endophytes. Results of anti-fungal bioassays are also shown in Table 10. A range of endophytes were found to have high (H) and medium (M) antifungal activity (Table 10).

Table 10 – Anti-fungal bioassays of isolated novel fescue endophytes Example 8 – Genome survey sequencing of novel tall fescue endophytes A range of novel tall fescue endophtyes were subjected to genome survey sequencing (GSS).

Figure 21 shows a strategy for GSS of selected novel fescue endophytes. The alkaloid profiles of novel fescue endophytes subjected to GSS analysis are shown in Table 11.

Tall fescue accession details Alkaloid profile in Endogenous Host Accession Endophyte Endophyte No/isolated Lolines Peramine Ergovaline Lolitrem B strain species E34 BE9301 N. coenophialum NEA13 8PC N. coenophialum NEA14 FEtc7-180 N. coenophialum NEA15 FEtc7-58 N. coenophialum NEA16 FEtc7-342 N. coenophialum NEA20 FEtc7-343 N. coenophialum NEA22 234746 N. coenophialum NEA24 FEtc6-83 N. coenophialum NEA17 287819 FaTG-2 NEA21 231557 FaTG-3 NEA23 269850 FaTG-3 non- Epichloë NEA19 231553 out-group non- Epichloë NEA18 FEtc6-75 out-group AR542* AR542* N. coenophialum E77* E77* N. coenophialum 598852 598852 FaTG-2 AR501* AR501* FaTG-3 598829 598829 FaTG-3 like E81 E81 N. uncinatum 9340 9340 E. typhina 9707 9707 E. baconii Table 11 – Alkaloid profiles of sequenced endophytes. Mid grey: alkaloid present, Light grey: Alkaloid absent, White: alkaloid profile not determined * Profiles are taken from published data Figure 22 shows the peramine biosynthetic pathway. PerA encodes a single multifunctional enzyme that catalyses all the biosynthetic steps. GenBank accession Number: AB205145. The presence of the perA gene in non-Epichloe out-group endophytes is shown in Figure 23.

Figure 24 shows the ergovaline biosynthetic pathway. Genes in the eas gene cluster which are involved in ergovaline biosynthesis are shown in Figure 25 and Table 12.

The dmaW gene encodes DMAT synthase enzyme, which catalyzes the first committed step in ergovaline biosynthesis. Presence of the dmaW gene in novel fescue endophytes is shown in Figure 26 and presence of the eas gene cluster in novel fescue endophytes is shown in Figure 27.

Gene Cluster Gene GenBank Accession No dmaW AY259838 easA EF125025 easE EF125025 easF EF125025 eas gene cluster easG EF125025 easH EF125025 lpsA AF368420 lpsB EF125025 Table 12 – Genes in the eas cluster Figure 28 shows the Lolitrem B biosynthetic pathway. Genes in the gene cluster which are involved in Lolitrem B biosynthesis are shown in Figure 29 and Table 13.

Presence of gene cluster 1 (ltmG, ltmM and ltmK) in endophytes is shown in Figure 30, presence of gene cluster 2 (ltmB, ltmQ, ltmP, ltmF and ltmC) is shown in Figure 31 and presence of gene cluster 3 (ltmE and ltmJ) is shown in Figure 32.

Gene Cluster Gene GenBank Accession No ltmG AY742903 gene cluster 01 ltmM AY742903 ltmK AY742903 ltmB DQ443465 ltmQ DQ443465 gene cluster 02 ltmP DQ443465 ltmF DQ443465 ltmC DQ443465 ltmJ DQ443465 gene cluster 03 ltmE DQ443465 Table 13 – Genes in the gene cluster involved in Lolitrem B biosynthesis Figure 33 shows the Loline biosynthetic pathway. Genes in the gene cluster which are involved in Loline biosynthesis are shown in Figure 34 and Table 14. Presence of Loline biosynthetic gene cluster in novel fescue endophytes is shown in Figure 35.

Gene Cluster Gene GenBank Accession No lolF EF012269 lolC EF012269 lolD EF012269 lolO EF012269 LOL gene cluster lolA EF012269 lolU EF012269 lolP EF012269 lolT EF012269 lolE EF012269 Table 14 – Genes in the Loline biosynthetic gene cluster Figure 36 shows an alkaloid biosynthetic gene analysis for endophyte strain NEA23.

Tables 15 and 16 show alkaloid biosynthetic gene analyses for various endophyte strains. Table 15 shows results from the assessment of alkaloid biosynthetic gene presence/absence for different endophytes by mapping genome survey sequence reads corresponding to the different alkaloid biosynthetic genes/gene clusters. non- Epichloë out- N. coenophialum FaTG-2 FaTG-3 group GenBank Gene BE9301 8PC NEA14 NEA15 NEA16 NEA20 AR542 NEA22 NEA17 NEA21 NEA23 AR501 NEA19 NEA18 Accession No Metabolite production in planta Lol nd Lol Lol Lol Lol Lol Lol - Lol Lol Lol - - Loline gene EF012269 alkaloids cluster Metabolite production in planta P P P P P P P P P P P P - - Peramine PerA AB205145 Metabolite production in planta E E E E - - - E E - - - - - dmaW AY259838 Ergot Alkaloids gene EF125025 cluster Metabolite production in planta - nd - - - - - - - - - - - - cluster AY742903 Lolitrems cluster DQ443465 cluster DQ443465 Gene/gene cluster present (-) No alkaloid detected Gene/gene cluster absent (nd) Not determined Gene/gene cluster partially present Table 15 – Assessment of alkaloid biosynthetic gene presence/absence for different endophytes by mapping genome survey sequence reads corresponding to the different alkaloid biosynthetic genes/gene clusters.

Table 16 shows results from the assessment of alkaloid biosynthetic gene presence/absence for different endophytes by mapping genome survey sequence reads corresponding to the different alkaloid biosynthetic genes/gene clusters as well as corresponding alkaloid profile observed for corresponding tall fescue-endophyte associations.

Tall fescue accession details Alkaloid profile and Gene presence Accession Endophyte Endophyte No/isolated Lolines Peramine Ergovaline* Lolitrem B strain species E34 BE9301 N. coenophialum G+ G+ G+ PG+ 8PC 8PC N. coenophialum G+ G+ G+ PG+ G+ G+ G+ PG+ NEA14 FEtc7-180 N. coenophialum G+ G+ G+ PG+ NEA15 FEtc7-58 N. coenophialum NEA16 FEtc7-342 N. coenophialum G+ G+ G- PG+ NEA20 FEtc7-343 N. coenophialum G+ G+ G- PG+ G+ G+ G+ PG+ NEA22 234746 N. coenophialum NEA24 FEtc6-83 N. coenophialum G- G+ G+ G+ NEA17 287819 FaTG-2 G+ G+ G- G- NEA21 231557 FaTG-3 NEA23 269850 FaTG-3 G+ G+ G- G- non- Epichloë G- G+ G- G- NEA19 231553 out-group non- Epichloë NEA18 FEtc6-75 G- G+ G- G- out-group G+ G+ G- PG+ AR542* AR542* N. coenophialum E77* E77* N. coenophialum 598852 598852 FaTG-2 G+ G+ G- G- AR501* AR501* FaTG-3 598829 598829 FaTG-3 like E81 E81 N. uncinatum 9340 9340 E. typhina G- PG+ G- G- 9707 9707 E. baconii Table 16 – Alkaloid biosynthetic gene and alkaloid production analysis. Mid Grey: alkaloid present, Light Grey: Alkaloid absent, White: alkaloid profile not determined, *Profiles are taken from published data, G+ = gene/gene cluster present, G- = gene/gene cluster absent, PG+ = gene/gene cluster partially present Table 17 shows novel fescue endophytes (NEA16, NEA18, NEA19, NEA20, NEA21 and NEA23) with favourable toxin profiles.

Tall fescue Alkaloid profile Taxon Antifungal accession (Lol/P/E/L) NEA21 FaTG-3 +/+/-/- High NEA23 FaTG-3 +/+/-/- Not tested AR501* FaTG-3 +/+/-/- - Non-Epichloë NEA18 -/-/-/- High Outgroup Non-Epichloë NEA19 -/-/-/- Not tested Outgroup NEA16 N. coenophialum +/+/-/- High NEA20 N. coenophialum +/+/-/- Not tested AR542* N. coenophialum +/+/-/- - Table 17 – Novel fescue endophytes (NEA16, NEA18, NEA19, NEA20, NEA21 and NEA23) with favourable toxin profiles and antifungal activities observed in bioassays. * Control commercial endophyte A genotypic analysis of the novel fescue endophytes NEA23 and NEA21 is shown in Figure 37.

Claims (12)

THE CLAIMS DEFINING THE INVENTION ARE AS FOLLOWS:

1. A substantially purified or isolated endophyte having a desired toxin profile, wherein the endophyte produces significantly less toxic alkaloids compared with a control endophyte and/or significantly more alkaloids conferring beneficial properties 5 compared with a control endophyte, wherein said control endophyte is standard toxic endophyte; and wherein said endophyte is selected from the group consisting of NEA16, NEA17, NEA18, NEA19, NEA20, NEA21 and NEA23, as deposited at the National Measurement Institute with accession numbers V12/001413, V12/001414, 10 V12/001415, V12/001416, V12/001417, V12/001418 and V12/001419, respectively.

2. An endophyte according to claim 1, wherein said beneficial properties include improved tolerance to water and/or nutrient stress and/or improved resistance to pests and/or diseases in the plant with which the endophyte is associated.

3. An endophyte according to claim 1 or 2, wherein said alkaloids conferring 15 beneficial properties are selected from the group consisting of peramine, N- formylloline, N-acetylloline and norloline.

4. An endophyte according to any one of claims 1 to 3, wherein said toxic alkaloids are selected from the group consisting of ergovaline and Lolitrem B.

5. An endophyte according to any one of claims 1 to 4, wherein said endophyte 20 is isolated from tall fescue.

6. An endophyte according to any one of claims 1 to 5, wherein said endophyte is from a species selected from the group consisting of N. coenophialum, FaTG-2, FaTG-3 and Non-Epichloë Outgroup.

7. An endophyte according to any one of claims 1 to 6, wherein said toxic 25 alkaloids are present in an amount less than approximately 1µg/g dry weight.

8. An endophyte according to any one of claims 1 to 7, wherein said alkaloids conferring beneficial properties are present in an amount of between approximately 5 and 100 µg/g dry weight.

9. A plant inoculated with an endophyte according to any one of claims 1 to 8, 5 said plant comprising an endophyte-free host plant stably infected with said endophyte.

10. A plant, plant seed or other plant part derived from a plant according to claim 9 and stably infected with an endophyte according to any one of claims 1 to 8.

11. Use of an endophyte according to any one of claims 1 to 8 to produce a plant 10 stably infected with said endophyte.

12. An endophyte according to claim 1, substantially as hereinbefore described with reference to any one of the figures or examples.