Delimiting a rice wide-compatibility gene S5n supercript stop to a 50 kb region

Wide-compatibility (WC) is one of the most important traits in rice, which can overcome the fertility barrier in the indica/japonica hybrids, and hence to make it possible to utilize the higher yield potential of inter-subspecific hybrids. The S-5(n) gene located on chromosome 6 has been previously reported to be responsible for the wide-compatibility in rice. Here we report the precise location of the S-5(n) gene. In the first-pass mapping, the S-5(n) gene was restricted within a 200 kb region by using a population of 242 isogenic lines in combination with high-density markers developed in the S-5 region. In the fine mapping, the S-5 region was further saturated with newly developed markers and more isogenic lines (549 in total) were investigated. Eventually, the S-5(n) gene was mapped within a 50 kb region delimited by the left marker J13 and the right marker J17. One BAC clone screened from the BAC library of the WC rice variety 02428 covered the whole S-5 region. Sequence analysis of the 50 kb region revealed two candidate genes, coding an aspartyl protease and a hypothetical protein. This result would greatly accelerate both cloning and marker-assisted selection of this important S-5(n) gene.