Bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae is one of the epidemic diseases in rice. Rapid changes in the pathogenicity of the X. oryzae pv. oryzae pathogen demand the identification and characterization of novel BB resistance genes. Here, we report the transfer and mapping of a new BB resistance gene from Oryza rufipogon acc. CR100098A. Inheritance studies on the BC2F2 population, BC2F3 progenies, and backcross-derived recombinant inbred lines derived from a cross between Pusa44/O. rufipogon acc. CR100098A//2*PR114 showed that a single recessive gene confers resistance in O. rufipogon acc. CR100098A. Bulked segregant analysis using 203 simple sequence repeat (SSR) markers localized the BB resistance gene on chromosome 11 bracketed between two SSR markers, RM27235 and RM2136. Using PR114 and O. rufipogon acc. CR100098A genotyping by sequencing data, 86 KASP markers within the bracketed region were designed and tested for bulked segregant analysis. Only five KASP markers showed polymorphism between parents, and three were associated with the target gene. Seventy-seven new SSR markers were designed from the same interval. A total of 33 polymorphic markers were analyzed on the whole population and mapped the BB gene in an interval of 2.8 cM flanked by SSR markers PAU11_65 and PAU11_44 within a physical distance of 376.3 kb. The BB resistance gene mapped in this study is putatively new and designated as xa49(t). Fourteen putative candidate genes were identified within the xa49(t) region having a role in biotic stress resistance. The linked markers to the xa49(t) gene were validated in other rice cultivars for its successful deployment in BB resistance breeding.
Keywords: KASP markers; SSR markers; Xanthomonas oryzae pv. oryzae; bacterial blight; durable resistance; introgression; marker-assisted selection; wild species; xa49(t).