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Asexual fungal endophytes of the genus Epichloë form mutually beneficial associations with cool-season pasture grasses such as ryegrasses (Lolium spp.). Alkaloid production by the fungus confers both beneficial (deterrence of invertebrate herbivory) and detrimental (toxicity to mammalian livestock) attributes. A few novel strains with desirable metabolite profiles have been advanced into commercial production by inoculation of perennial ryegrass cultivars. In the present study, an integrated process for discovery of novel endophytes based on exploitation of genotypic information has been designed and implemented. A survey of genetic diversity was performed on a large-scale, customised germplasm collection (containing 244 accessions) in order to identify previously uncharacterised endophyte genotypes. Preliminary qualitative metabolic profiling in the endogenous genetic background permitted elimination of undesirable combinations, and definition of a subset of priority candidates. A novel method was developed for inoculation of endophytes into meristem-culture-derived callus tissue of single genotypes from multiple perennial ryegrass cultivars, in order to allow isogenic comparisons with respect to both host and endophyte genotype. Beneficial toxin profiles were confirmed for associations formed with the grass genotypic panel, and semi-quantitative metabolite analysis provided evidence for genotype-specific effects of both host and genotype on levels of alkaloid production. Vegetative stability was also assessed over both shorter and longer terms. A final set of three prioritised candidates was obtained, two of which (belonging to the known taxa E. festucae var. lolii and LpTG-2) produce the alkaloids ergovaline and peramine. The third candidate endophyte, belonging to a putative novel taxon, solely produces representatives of an additional alkaloid class, the epoxy-janthitrems.

Due to the complex genetic architecture of perennial ryegrass, based on an obligate outbreeding reproductive habit, association-mapping approaches to genetic dissection offer the potential for effective identification of genetic marker–trait linkages. Associations with genes for agronomic characters, such as components of herbage nutritive quality, may then be utilised for accelerated cultivar improvement using advanced molecular breeding practices. The objective of the present study was to evaluate the presence of such associations for a broad range of candidate genes involved in pathways of cell wall biosynthesis and carbohydrate metabolism. An association-mapping panel composed from a broad range of non-domesticated and varietal sources was assembled and assessed for genome-wide sequence polymorphism. Removal of significant population structure obtained a diverse meta-population (220 genotypes) suitable for association studies. The meta-population was established with replication as a spaced-plant field trial. All plants were genotyped with a cohort of candidate gene-derived single nucleotide polymorphism (SNP) markers. Herbage samples were harvested at both vegetative and reproductive stages and were measured for a range of herbage quality traits using near infrared reflectance spectroscopy. Significant associations were identified for ~50% of the genes, accounting for small but significant components of phenotypic variance. The identities of genes with associated SNPs were largely consistent with detailed knowledge of ryegrass biology, and they are interpreted in terms of known biochemical and physiological processes. Magnitudes of effect of observed marker–trait gene association were small, indicating that future activities should focus on genome-wide association studies in order to identify the majority of causal mutations for complex traits such as forage quality.

Australian canola (Brassica napus L.) has been relatively isolated from the global gene pool and limited knowledge is available for genetic variability based on DNA profiling. In the present study, genetic diversity of recent Australian canola cultivars was determined by simple sequence repeat (SSR) marker analysis. In total, 405 individuals from 48 varieties were genotyped with 18 primer pairs, resulting in 112 polymorphic features. The number of polymorphic features amplified by each SSR primer pair varied from 3 to 16. Analysis of molecular variance (AMOVA) detected 53.7% and 46.3% within- and between-cultivar variation, respectively. Intra-cultivar genetic variability differed according to cultivar. The number of polymorphic features per cultivar varied from 35 (Ag-Spectrum) to 72 (Ag-Insignia), while mean sum of squares (MSS) varied from 6.29 (Tornado TT) to 24.76 (Ag-Emblem). Genetic differentiation of cultivars generally reflected pedigree structure and origin by breeding organisation. Clustering and principal coordinate analysis (PCoA) indicated that the individuals were separated into 4 major groups. The genetic diversity information from this study will be useful for future Australian canola breeding programs.