DNA typing and virulence determination of Xanthomonas oryzae pv. oryzae population for the management of bacterial leaf blight of rice in Udham Singh Nagar, India

Bacterial leaf blight caused (BLB) by Xanthomonas oryzae pv. oryzae (Xoo) is the most serious biotic constraint of rice in Udham Singh Nagar (U.S. Nagar), India. We have experienced severe BLB outbreaks, causing total crop failure during 2007-2010. The severity of losses incurred due to BLB in U.S. Nagar necessitates the development of an ecology-conscious, effective and durable management strategy. Our interests here were focused to obtain information on the haplotypic and pathogenic variability of Xoo to develop effective breeding strategy for BLB resistance. Our results indicate that the currently existing population of Xoo in U.S. Nagar is highly virulent and genetically diverse. Twenty one haplotypes were detected among a collection of 193 strains by each of the PCR technique used i.e. rep-PCR and IS-PCR. The high value of total haplotypic diversity (H-T (=)0.79) reflected the genetic heterogeneity of Xoo population infecting popular varieties. Strains responsible for severe BLB outbreaks were grouped into eight distinct lineages with significant bootstrap values (p > 75). Virulence assay revealed the presence of 11 pathotypes. The interaction of lines with strains was found significant (p < 0.01) confirming the pathogenic specialization of Xoo in U.S. Nagar. Most of the single major resistance genes used in rice breeding program at International Rice research Institute (IRRI) was defeated by Xoo strains, at the same time; effectiveness of Xa21 to all the pathotypes is encouraging. The potential of Xa21 alone or in combination with xa13 and xa5 could be exploited for pyramiding into well-adapted rice cultivars for the effective management of the pathogen in this region. This is the first report on the population structure of Xoo in U.S. Nagar, India.