2002. Development and mapping of markers linked to the rice bacterial leaf blight resistance gene Xa7

2002. Development and mapping of markers linked to the rice bacterial leaf blight resistance gene Xa7

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ABSTRACT

Markers were generated that are linked to the rice bacterial blight resistance gene Xa7. AFLP analysis of a segregating, near-isogenic F3 population of IR24 X IRBB7 revealed one polymorphic fragment, M1, which was mapped to position 107.3 centimorgans (cM) on the RGP map. Sequence comparisons of resistant and susceptible lines near M1 were used to develop additional markers. A STS named M2 was mapped proximal to M1 that indicated that Xa7 is on the distal side of M1. On the distal side of M1, two SSRs, M3 and M4, were mapped 0.5 cM 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 CUGI BAC contigs 96 and 143. A complex repeat was identified in the DNA sequence from rice cultivars '93-11' and 'Nipponbare' that matched the end of contig 96 and a previously mapped EST marker (C52865S). Amplification of the repeat and flanking sequences revealed the presence and absence of the repeat in IR24 and IRBB7, respectively. The polymorphic STS was named M5. No recombinants were identified between Xa7 and M5 in 277 F3 susceptible progeny of the IR24 X IRBB7 cross. Comparison of the physical and genetic maps of rice indicates that Xa7 could lie within 40 kb of M5, a distance suitable for gene pyramiding efforts and Xa7 cloning strategies .