Genetic and physical mapping of xa13, a recessive bacterial blight resistance gene in rice

The recessive gene, xal3, confers resistance to Philippine race 6 (PXO99) o f the bacterial blight pathogen Xanthomonas oryzae pv oryzae. Fine genetic mapping and physical mapping were conducted as initial steps in an effort t o isolate the gene. Using nine selected DNA markers and two F-2 populations of 132 and 230 plants, xal3 was fine-mapped to a genomic region < 4 cM on the long arm of rice chromosome 8, flanked by two RFLP markers, RG136 and R 2027. Four DNA markers. RG136, R2027, S14003, and G1149, in the target regi on were used to identify bacterial artificial chromosome (BAC) clones poten tially harboring the xal3 locus from a rice BAC library. A total of 11 BACs were identified. forming four separate contigs including a single-clone co ntig, 29I3, associated with the RG136 STS marker, the S14003 contig consist ing of four clones (44F8, 41O2, 12A16, and 12F20). the G1149 contig with tw o clones, 23D11 and 21H18, and the R2027 contig consisting of four overlapp ing clones, 42C23, 30B5, 6B7 and 21H14. Genetic mapping indicated that the xa13 locus was contained in the R2027 contig, Chromosomal walking on the R2 027 contig resulted in two more clones, 33C7 and 14L3. DNA fingerprinting s howed that the six clones of the R2027 contig were overlapping. Clone 44F8 hybridized with a single fragment from the clone 14L3, integrating the R202 7 and S14003 contigs into a single contig consisting of ten BAC clones with a total size of approximately 330 kb, The physical presence of the xa13 lo cus in the contig was determined by mapping the ends of the BAC inserts gen erated by TAIL-PCR. In an F2 Population of 230 plants, the BAG-end markers 42C23R and 6B7F flanked the xa13 locus, The probes 21H14F and 21H14R derive d from BAC clone 21H14 were found to Rank xa13 at a distance of 0.5 cM on e ither side, using a second F2 population of 132 plants. Thus, genetic mappi ng indicated that the contig and the 96-kb clone, 21H14, contained the xa13 locus.