Identification and fine mapping of the new bacterial blight resistance gene, Xa31(t), in rice

Zhachanglong (ZCL), a regional rice variety from Yunnan province in southwest China, has a high level of resistance to a broad spectrum of Xanthomones oryzae pv. oryzae (Xoo) isolates. In a previous study, a bacterial blight (BB) resistance (R) gene, Xa22(t), with resistance against Xoo strain Px061 on chromosome 11 was identified in ZCL. Here, we report another BB R-gene, tentatively named Xa31(t), with resistance against Xoo strain OS105 and susceptible to Px061 identified in ZCL. To determine the location of Xa31(t), 102 polymorphic RFLP markers on 12 rice chromosomes were selected for bulked segregation analysis (BSA). Twelve RFLP markers on chromosome 4 detected DNA polymorphisms between ZCL and Zhengzhu Ai (ZZA), as well as in the OS105-resistant and -susceptible bulks from F-2 populations derived from ZCL x ZZA. Genetic linkage analysis and fine mapping localised Xa31(t) within a genetic distance of 0.2 cM between two RFLP markers, G235 and C600, on the end of the long arm of chromosome 4, using two F-2 populations from the cross ZCL x ZZA and two F-3 populations, consisting of 3,311 plants with 301 F-3 random families and 3,333 plants with 303 F-3 Pxo61-susceptible families, derived from the same F-2 populations from the cross ZCL x ZZA. Using two flanking markers, G235 and C600, to screen the MH63 BAC library, the Xa31(t) locus was limited to one BAC clone with a length of about 100 kb.