Genotypic and pathotypic diversity in Xanthomonas oryzae pv. oryzae in Nepal

Among the 171 strains of Xanthomonas oryzae pv. oryzae (the bacterial bligh t pathogen of rice) collected from eight rice-producing zones in Nepal, 31 molecular haplotypes were distinguished using two polymerase chain reaction -based assays. Six common haplotypes represented nearly 63% of the strains, and some haplotypes were geographically dispersed. Multiple correspondence analysis divided the collection into five putative genetic lineages. Linea ges 1, 2, and 4 were the most frequently detected and occurred in diverse g eographic populations. Twenty-six pathotypes (virulence phenotypes) of X. o ryzae pv. oryzae were identified using 11 near-isogenic rice lines, each co ntaining a single gene for resistance. The 26 pathotypes grouped into five clusters, and cluster 1 contained wide virulence spectrum strains from all geographic populations. Although molecular variation was greatest between s trains of different virulence phenotypes, some variation was observed among strains with identical virulence. There was a weak correlation (r = 0.52) between molecular haplotypes and virulence phenotypes. There are two major groups of X. oryzae pv. oryzae in Nepal. One group consists of strains with high molecular polymorphism and many pathotypes that are either virulent t o the 11 major resistance genes or avirulent only to Xa21. Strains in the s econd group have low molecular polymorphism and are avirulent to Xa4, xa5, Xa7, and Xa21.