Two sequence alterations, a 136 bp InDel and an A/C polymorphic site, in the S5 locus are associated with spikelet fertility of indica-japonica hybrid in rice.

The rice indica/japonica hybrid shows strong heterosis. However, such inter-subspecific hybrid can't be directly used in rice production due to its low spikelet fertility. The S5 locus was proved to be associated with fertility of indica/japonica hybrid and its S5n allele from wide-compatibility variety (WCV) is capable to overcome fertility barrier. In the present study, we reported the causal sites in the S5 locus responsible for compatibility of indica/japonica hybrid. Fine-mapping of the S5 locus using the 11 test-cross families pinpoints a candidate S5 locus encoding aspartic protease (Asp). Intragenic recombination within the Asp gene happened in a number of recombinants, resulting in chimeric S5j-S5n alleles. Just like S5n, the chimeric S5j-S5n allele displayed higher spikelet fertility when combined with the S5i allele. In the complementary test, however, the S5n allele from WCVs failed to enhance fertilities of the indica/japonica hybrids. Compared to both indica and japonica varieties, all nine WCVs from different resources are characterized with a 136 bp deletion in the Asp N-terminus, which probably renders the S5n allele non-functional. Furthermore, an A/C polymorphic site is detected 1,233 bp downstream of the Asp start codon. The heterozygous A/C site of the Asp gene in indica/japonica hybrid is believed to be the casual factor to cause partial sterility. The functional makers based on the two polymorphic sites will be broadly used in developing wide-compatibility rice varieties.