The origin of weedy rice Ludao in China deduced by genome wide analysis of its hybrid sterility genes

The authors report here a case of hybrid sterility between an indica cultivar, IR36 and a weedy strain, Ludao, which naturally grows in and around farms in Jiangsu province, China. A genome-wide analysis was performed with a backcross population of IR36/Ludao//IR36 using a total of 151 simple sequence repeat (SSR) markers covering the entire rice linkage map. As a result, two loci were found to induce independently the hybrid sterility via female gamete abortion. Of the two loci, the locus on chromosome 6 corresponded to S10 according to its chromosomal location, while the other one on chromosome 7 was different from all the previously reported hybrid sterility loci, and was designated as S30(t). Based on the allelic interaction which causes female gamete abortion, two alleles were identified: S30(t)-i in IR36 and S30(t)-j in Ludao. In the heterozygote, S30(t)-i/S30(t)-j, which was semi-sterile, female gametes carrying S30(t)-j were partially aborted. A javanica variety, Ketan Nangka, and an Aus variety, N22, carried the neutral allele, S30(t)-n. Thus, Ludao was found to harbor a hybrid sterility gene different from that of existing cultivars in China, as an evidence of its origin from an ancient wild rice variety.