Development and Mapping of Markers Linked to the Rice Bacterial Blight Resistance Gene Xa7

Abstract

Markers were generated that are linked to the rice bacterial blight resistance gene Xa7 Amplified restriction fragment length polymorphism (AFLP) analysis of a segregating, near‐isogenic F3 population of IR24 × IRBB7 revealed one polymorphic fragment, M1, which was mapped to position 107.3 centimorgans (cM) on the Rice Genome Research Program (RGP) map. Sequence comparisons of resistant and susceptible lines near M1 were used to develop additional markers. A sequence tagged site (STS) named M2 was mapped proximal to M1 and farther from Xa7, indicating that Xa7 lies distal to M1. On the distal side of M1, two simple sequence repeats (SSRs), M3 and M4, were mapped 0.5 and 1.8 cM, respectively, from Xa7. The pattern of recombinants was consistent with the order of M1–Xa7–M3–M4, and the map distances indicated that Xa7 is located in the region corresponding to the ends of the physically mapped Clemson University Genomics Institute (CUGI) bacterial artificial chromosome (BAC) contigs 96 and 143. A complex repeat was identified in the DNA sequence from rice (Oryza sativa L.) cultivars 93‐11 and Nipponbare that matched the end of contig 96 and a previously mapped expressed sequence tag (EST) marker (C52865S). Amplification of the repeat and flanking sequences revealed the presence and absence of the repeat in IR24 and IRBB7, respectively. No recombinants were identified between Xa7 and the polymorphic repeat, which was named M5, in 277 F3 susceptible progeny of the IR24 × IRBB7 cross. Comparison of the physical and genetic maps of rice in this region indicates that Xa7 could lie within 40 kilobases (kb) of M5, a distance suitable for gene pyramiding efforts and Xa7 cloning strategies.