Mapping of bacterial blight resistance gene Xa11 on rice chromosome 3

The bacterial blight (BB) resistance gene Xa11 confers resistance in rice to Japanese races IB, II, IIIA, and V of the BB pathogen Xanthomonas oryzae pv. oryzae (Xoo). Here, we report the mapping of Xa11 by using randomly amplified polymorphic DNA (RAPD), cleaved amplified polymorphic sequence (CAPS), and simple sequence repeat (SSR) markers. To detect DNA markers linked to Xa11, we used an Xa11 near-isogenic line, IR-BB11 (in genetic background of IR24), and the susceptible cultivar IR24. The RAPD fragment L19₁₂₀₀, putatively linked to Xa11, was identified. Cloning and sequencing of the L19₁₂₀₀ product indicated that it was held in the Rice Genome Program database as accession number AC097277, and that it occurs on chromosome 3. On the basis of the sequences of L19₁₂₀₀ and the flanking genomic region, we designed CAPS marker KUX11 and selected two SSR markers, RM347 and RM1350, for mapping Xa11. To confirm the putative linkage among Xa11 and the three markers, we conducted linkage analysis using the F₂ population of a cross between IR24 and IR-BB11. Each F₂ plant was inoculated with strain T7156 (race IB) and genotyped with KUX11, RM347, and RM1350. Segregation in the F₂ located Xa11 between the loci of RM347 (2.0 cM) and KUX11 (1.0 cM) on the long arm of chromosome 3. These results should be useful for the marker-assisted selection of Xa11 in breeding programs and for cloning Xa11 by map-based cloning.