Population structure, genetic diversity, and sexual state of the rice brown spot pathogen Bipolaris oryzae from three Asian countries

Bipolaris oryzae causes brown spot in rice (Oryza sativa) inflicting substantial grain yield losses worldwide. Knowledge of the population structure, genetic diversity and sexual recombination of the fungal pathogen can help to implement effective disease management strategies. In this study, B.oryzae isolates sampled from Iran, the Philippines and Japan were analysed with 12 simple-sequence repeat (SSR) markers, newly developed from the genome sequence of the fungus. Among the 288 B.oryzae isolates genotyped, 278 unique haplotypes were identified. High genotype numbers (richness) with even distribution (evenness) were found within the collection sites. Both mating types, MAT1-1 and MAT1-2, were present in each collection area, and the sexual state was induced under controlled conditions with production of viable ascospores. However, the tests of linkage disequilibrium rejected of the hypothesis of random mating. Discriminant analysis of principal components (DAPC) revealed that the B.oryzae collection formed three clusters, each consisting of isolates from different collection sites. Analysis of molecular variance (amova) showed that genetic variation among clusters was 18.7%, with the rest of the variation distributed within clusters (R-ST=0.187, P<0.001). Statistically significant pairwise genetic differentiation was found between the clusters. These results show that Asian B.oryzae isolates are genetically diverse, and, overall, distributed in three groups. These findings will be helpful in managing the disease and guide the use of representative isolates needed for selection of resistant rice varieties.