Fine location of the S-5 locus responsible for wide compatibility in rice using SSR markers

Partial abortion of gametes possessing S-5(j) in S-5(i)/S-5(j) genotype at locus S-5 is responsible for hybrid sterility between indica and japonica subspecies in rice (Otyza sativa L.), while a single wide compatibility (WC) allele S-5(n) can restore normal hybrid fertility between the two groups. In this study, Pei'ai 645, one of the most popular WC line widely used for subspecific hybrid rice breeding program in South China was studied for location of its S-5 locus. Twenty SSR (Simple Sequence Repeat) markers derived from Cornell SSR linkage map and 9 developed using sequences from GenBank database were employed to perform bulked segregant analysis of the mapping population derived from a three-way cross (Pei'ai 645/T8//Akihikari) to tag fine location of the hybrid sterility locus, S-5. This S-5 locus was mapped on chromosome 6 approximately 0.2 cM from GXR6 and RM276 SSR markers. This tight linkage of the markers and the S-5 locus would be very useful for efficient marker-assisted selection for WC varieties and for map-based cloning of the gene.