DNA fingerprinting and virulence analysis of Xanthomonas oryzae pv. oryzae isolates from Punjab, northern India

DNAs of 693 isolates of bacterial blight pathogen of rice, Xanthomonas oryzae pv. oryzae (Xoo), were characterized using PCR-based primers pJEL1 and pJEL2. The pathogen populations were grouped into 97 haplotypes based on DNA-banding patterns. An un-weighted pair-group method using arithmetic averages (UPGMA) indicated a high level of diversity in the pathogen isolates (51 lineages of Xoo at a 70% similarity level). Among these, lineages 5, 7, 27, and 29 are widely distributed and others are localized in the northern region of India. The isolates represent lineage-27, were prevalent in the entire disease-prone area in the region except at Ferozepur. Pathotyping data of the representative isolates of each lineage also indicate 17 different reaction patterns on a set of isogenic lines. Resistance genes xa8 and Xa21 were the most effective followed by xa5, and Xa7 against Xoo isolates prevalent in northern India. Different genes in combinations (xa5+xa13, xa5+Xa21, xa13+Xa21, and xa5+xa13+Xa21) in IR24 genetic background provided better protection against all the pathogen isolates tested in this study than did the component genes.