Genotypic and Pathotypic Diversity of Xanthomonas oryzae pv. oryzae, the Cause of Bacterial Blight of Rice in Punjab State of India

Abstract

AbstractBacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is a major biotic constraint in the intensive irrigated rice belt comprising Punjab and adjoining north‐western states of India. Development and deployment of host resistance is the only effective means of BB management. The pathogen is highly variable, and the current Xoo population from the state could be classified into seven distinct pathotypes (PbXo‐1 to PbXo‐7) by inducing differential reactions on a set of near‐isoganic lines in the background of IR24 and some international, national and regional cultivars. Known BB resistance genes (Xa1, Xa3, Xa10, Xa11, Xa14, Xa18) were ineffective, whereas xa13, Xa4 + xa13, xa5 + xa13, xa13 + Xa21, Xa4 + xa5 + xa13, Xa4 + xa5 + Xa21, Xa4 + xa13 + Xa21, xa5 + xa13 + Xa21 and Xa4 + xa5 + xa13 + Xa21 and rice line IET8585/Ajaya were effective against all the seven pathotypes analysed. Xa21 was effective against all the pathotypes except PbXo‐3 and PbXo‐4. PbXo‐7, the most dominant pathotype, was found to be virulent and induced susceptible/moderately susceptible reaction on 22 of the 40 test genotypes followed by PbXo‐1, PbXo‐5 and PbXo‐6; PbXo‐2 was the least virulent pathotype. Molecular profiling of these pathotypes using random amplified polymorphic DNA (RAPD) and IS1112‐based polymerase chain reaction (PCR) generated specific and reproducible fingerprint patterns. Primers S1117, S112, S109, S1106 and JEL are more informative in distinguishing pathotypes. At a similarity of 0.50, pathotypes PbXo‐1 and PbXo‐2 were grouped together, whereas other five pathotypes showed separate lineage. The data using RAPD‐PCR and IS1112‐based PCR approaches revealed their potential in generating unique DNA fragments specific for different pathotypes that may lead to the rapid assessment of genetic variation in the pathogen population. Pyramiding of two/more partially effective known Xa genes and/or search for new disease resistance genes effective against the wider Xoo population appears to be the most appropriate approach for BB management in the near future.