Genotypic and Pathotypic Diversity in Xanthomonas oryzae pv. oryzae in Nepal

Abstract

Among the 171 strains of Xanthomonas oryzae pv. oryzae (the bacterial blight 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. Lineages 1, 2, and 4 were the most frequently detected and occurred in diverse geographic populations. Twenty-six pathotypes (virulence phenotypes) of X. oryzae pv. oryzae were identified using 11 near-iso-genic rice lines, each containing 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 strains 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 to the 11 major resistance genes or avirulent only to Xa21. Strains in the second group have low molecular polymorphism and are avirulent to Xa4, xa5, Xa7, and Xa21.

Genome Sequence of Xanthomonas oryzae pv. oryzae Suggests Contribution of Large Numbers of Effector Genes and Insertion Sequences to Its Race Diversity

“…The relationship between pathotypic and genetic diversity of Xoo strains has been studied mainly based on analyses of differential interactions with resistance genes and DNA fingerprinting using insertion sequences 1,23,26 . The results suggested that some phylogenetic lineages based on insertion sequences were related to pathotypes (races).…”

Diversity in Virulence of Xanthomonas oryzae pv. oryzae from Northern Vietnam

“…The transposable element used in these studies was assumed to be phenotypically neutral and suitable for phylogenetic analysis. Adhikari et al 2,3 and George et al 6 also found evidence of the geographic migration of Xoo using multicopy genetic markers. They suggested that the distribution might be through germplasm exchange.…”

“…Therefore, a breeding program should be initiated to transfer these resistant genes from differential varieties to high quality varieties of Vietnamese rice to control the disease effectively. Lee et al 9 and Adhikari et al 2 showed that strains virulent to Xa21 gene were widely distributed in Korea and Nepal. Several strains moderately virulent to Xa21 (of lesion length between 10 and 15 cm) were detected in our limited sample range from northern Vietnam.…”

“…Genomic diversity was evaluated by a PCR assay based on the amplification of sequences between copies of the endogenous Xoo insertion sequence (IS) elements, IS1112 and IS1113 2,3,6,12,13 . The repetitive primer sequences corresponding to JEL1 (5'-CTCAGGTCAGGTC-GCC-3') and JEL2 (5'-GCTCTACAATCGTCCGC-3'), and J3 (5'-GCTCAGGTCAGGTCGCCTGG-3') were used to determine whether they could reveal polymorphism in Xoo isolates in northern Vietnam.…”

Magnitude of genotype x environment interaction for bacterial leaf blight resistance in rice growing areas of Uganda

“…However, the durability of resistance depends upon the prevalence of pathogen races in time and space (Jagjeet et al, 2010). This is due to the fact that the pathogen Xoo is highly variable and more than 30 races of the bacterium have been reported worldwide (Adhikari et al, 1999;Noda et al, 2001).…”