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Crown rust fungus, Puccinia coronata f.sp. lolii is an obligate biotrophic pathogen of ryegrasses which causes significant reductions of herbage yield, palatability and digestibility. Genetic diversity in virulence has been reported in all the major temperate regions of the world and is therefore a major problem for pasture and turf breeders developing varieties with durable resistance for crown rust. Knowledge of the genetic variation present both within and between Australasian crown rust populations is essential for the efficient production of resistant varieties. A total of 11 efficient simple sequence repeat (SSR) markers developed from a urediniospore-derived expressed sequence tag (EST) resource have been used for Australasian intraspecific genetic diversity analysis. Seventy-two single pustule samples comprising three main populations from both North and South Islands of New Zealand and from south-eastern Australia were genotyped. The analysis identified 59 distinct genotypes, high levels of genetic diversity being detected both within and between populations. All methods of analysis detected no significant difference between isolates from the North and South Islands of New Zealand (p > 0.05), and high intrapopulation diversity between Victorian isolates. However high population differentiation (p < 0.001) was detected between Victorian isolates and those from the South Island (PhiPT [estimate of genetic variability = 0.101) and especially the North Islands (PhiPT = 0.162) of New Zealand. Genetic dissection of crown rust population structure within Australasia will inform the magnitude of gene pyramiding required for the development of varieties with durable resistance.

Development of accurate high-throughput molecular marker systems such as SNPs permits evaluation and selection of favourable gene variants to accelerate elite varietal production. SNP discovery in perennial ryegrass has been based on PCR amplification and sequencing of multiple amplicons designed to scan all components of the transcriptional unit.