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

A. Ahmadpour, C. Castell-Miller, M. Javan-Nikkhah, M. R. Naghavi, F. P. Dehkaei, Y. Leng, K. D. Puri, S. Zhong

Research output: Contribution to journalArticlepeer-review

20 Scopus citations


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 (RST = 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.

Original languageEnglish (US)
Pages (from-to)181-192
Number of pages12
JournalPlant Pathology
Issue number1
StatePublished - Jan 2018

Bibliographical note

Funding Information:
A.A. thanks the Iranian Ministry of Science, Research and Technology (MSRT), which provided a grant (no. 7110022/6/30) for a research assistantship during his PhD study at the University of Tehran and fellowship support during his visiting research at North Dakota State University. The authors would like to thank Drs C. M. Vera Cruz, T. Tsukiboshi and I. Hossain, for providing the Philippine, Japanese and Bangladeshi isolates of B. oryzae, respectively and to Dr B. G. Turgeon, Cornell University, USA for providing the sequences of the MAT1-1 and MAT1-2 idiomorph primers.

Publisher Copyright:
© 2017 British Society for Plant Pathology


  • Cochliobolus miyabeanus
  • gene and genotypic diversity
  • microsatellites
  • population differentiation
  • random mating


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