Analysis of genetic diversity and population structure in Pyricularia oryzae collected from western Japan using SSR markers.

Abstract

We selected 12 simple sequence repeat (SSR) markers useful for differentiating Japanese isolates of the rice blast fungus, Pyricularia oryzae, and developed three multiplex sets, each containing four SSRs, for fluorescence detection. Genetic diversity and population structure of P. oryzae field isolates in western Japan were studied based on these markers. For a total of 293 isolates collected from 16 prefectures in 2001, a high level of genetic diversity was observed, with 265 different haplotypes and an average of 14.3 (range 2-36) alleles per locus. Estimates of population differentiation varied greatly among 10 prefectures, with pairwise F_ST ranging from 0.002 to 0.275. A Mantel test revealed significant positive correlation (r²=0.224, P=0.004) between geographical distance (69-539 km) and pairwise F_ST, suggesting that the level of gene flow is remarkably high between neighboring prefectures, probably occurring via dispersal of spores and movement of infected rice seed. In contrast, a relatively high level of genetic differentiation was observed between prefectures located in geographically distant regions, suggesting that spore dispersal and seed movement over a relatively long distance is restricted. The SSR markers selected in this study should be useful for studying the population genetics of the rice blast fungus.