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.