Genetic diversity and pathotype profiling of Xanthomonas oryzae pv. oryzae isolates from diverse rice growing ecosystems of Karnataka state of India

Bacterial leaf blight (BLB) disease of rice caused by Xanthomonas oryzae pv. (Xoo) is one the significant constraints for production. A study was carried out to analyze virulence, genetic diversity, and population structure Xoo isolates collected from different ecosystems Karnataka, India. The taxonomic identity all 54 confirmed using a Xoo-specific PCR assay. virulence assay on set twenty-eight near-isogenic differentials identified nine pathotype groups (KPthX-1 KPthX-9). Among them, KPthX-6 highly virulent, whereas KPthx-2 less virulent. Differentials with four five resistance (R) genes (Xa4+xa5+xa13+Xa21, Xa4+Xa7+xa13+Xa21, Xa4+xa5+Xa7+xa13+Xa21) were effective against pathotypes. Further, diversity deduced universal marker set, JEL-1, JEL-2, complementary conserved repetitive sequence IS1112. amplicon size numbers varied 100 bp 3 Kb 1 25. Based counts, Jaccard’s co-efficient phylogenetic analyses categorized into three clusters (I III). Cluster-II contains maximum number (27), followed cluster-I (23 isolates) cluster-III (one isolate). analysis subgroups, viz. SG1, SG2, SG3, SG4, SG5 indicate existence subpopulations. present has reported R gene/s ecosystems, which can be used in breeding program eco-specific management BLB rice.