Microsatellite (SSR) diversity among Australian Rhynchosporium secalis isolates

Abstract

Genetic analysis of cereal pathogen populations is fundamental to understanding host-pathogen co-evolution. Molecular markers have been widely used to characterize fungal pathogens, in particular for the assessment of genetic variation and population structure. The fungus, Rhynchosporium secalis, is the causal agent of barley scald and a globally important agricultural pathogen. Previous research has shown a high level of variation in virulence in this fungus, and this has also been reflected in molecular diversity studies. However, the mechanisms responsible for generating this genetic variation within populations remain unclear. Microsatellites, or simple sequence repeats (SSRs), are locus-specific, multi-allelic, and highly informative molecular markers that are ideal for population genetic studies. Using the sequence tagged microsatellite profiling (STMP) technique, 168 SSRs were developed for R. secalis, of which 66 (52%) exhibited a high level of polymorphism among a diverse set of 16 Australian isolates held in the SARDI collection. Each isolate exhibited a unique genotype, with an average of four alleles revealed per locus, and a gene diversity measure of 0.54 was obtained. These findings support hypotheses for a sexual stage in the R. secalis life cycle, and have important implications for breeding resistant barley cultivars.