Microsatellite and sequence-tagged site markers diagnostic for the rice bacterial leaf blight resistance gene xa-5

Microsatellite and sequence-tagged site (STS) markers tightly linked to the bacterial leaf blight (BLB) resistance gene xa-5 were identified in this study. A survey was conducted to find molecular markers that detected polymorphisms between the resistant (IRBB5) and susceptible ('IR24') nearly isogenic lines for xa-5, and between Chinsurah Bore II (CBII), an alternative source of xa-5, and a widely planted variety ('IR64') that lacks xa-5. Two F-2 populations, from the crosses 'IR24' x IRBB5 and CBII x 'IR64', were used to estimate linkage based on marker genotype and reaction to disease inoculation with Xanthomonas oryzae pv. oryzae. Two RFLP clones, RZ390 and RG556, were found to co-segregate with xa-5 and were converted into STS markers, A microsatellite marker, RM390, was developed based on a simple sequence repeat in the 5' untranslated region of the cDNA probe, RZ390, and found to co-segregate with resistance. Two other microsatellites. RM122 and RM13, were located 0.3 cM and 14.1 cM away from xa-5. A germplasm survey of diverse lines containing BLB resistance genes using automated fluorescent detection indicated the range of allelic diversity for each of the microsatellite loci linked to xa-5 and confirmed their usefulness in following genes through the narrow crosses typical of a breeding program. The limited number of alleles observed at the microsatellite loci linked to the resistance gene in 35 xa-5-containing accessions suggested either a single ancestral origin or a few independent origins of the xa-5 gene. PCR-based markers, like the ones developed in this study, are economical and easy to use, and have applicability in efforts to pyramid the recessive xa-5 gene with other BLB resistance genes.