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Genetic Structure of Populations of the Rice-Infecting Pathogen Rhizoctonia solani AG-1 IA from China

First, second, third, eighth, and ninth authors: Plant Pathology, Institute of Integrative Biology, ETH Zurich, Universitaetstr. 2, LFW B28, 8092, Zurich, Switzerland; fourth author: Plant Protection Institute, Anhui Academy of Agricultural Science, Hefei, 230031, Anhui, China; fifth author: College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China; sixth author: Soilborne Diseases Laboratory, State key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, The Chinese Academy of Agricultural Sciences, Beijing 100081, China; seventh author: Plant Protection Institute, Agricultural Academy of Zhejiang, Hangzhou, Zhejiang, China; and ninth author: UNESP, Campus de Ilha Solteira, Depto. de Fitossanidade, Engenharia Rural e Solos, 15385-000, Ilha Solteira, São Paulo, Brazil.

Sheath blight disease (SBD) on rice, caused by Rhizoctonia solani AG-1 IA, is one of the most devastating rice diseases on a global basis, including China (in Eastern Asia), the world's largest rice-growing country. We analyzed the population genetics of nine rice-infecting populations from China using nine microsatellite loci. One allopatric population from India (Southern Asia) was included in the analyses. In total, 300 different multilocus genotypes were found among 572 fungal isolates. Clonal fractions within rice fields were 16 to 95%, suggesting that sclerotia were a major source of primary inoculum in some fields. Global Φ_ST statistics (Φ_ST = 42.49; P ≤ 0.001) were consistent with a relatively high level of differentiation among populations overall; however, pairwise comparisons gave nonsignificant R_ST values, consistent with contemporary gene flow among five of the populations. Four of these populations were located along the Yangtze River tributary network. Gene flow followed an isolation-by-distance model consistent with restricted long-distance migration. Historical migration rates were reconstructed and yielded values that explained the current levels of population subdivision. Except for one population which appeared to be strictly clonal, all populations showed evidence of a mixed reproductive mode, including both asexual and sexual reproduction. One population had a strictly recombining structure (all loci were in Hardy-Weinberg equilibrium) but the remaining populations from China and the one from India exhibited varying degrees of sexual reproduction. Six populations showed significant F_IS values consistent with inbreeding.