Molecular evolution of S5 locus and large differences in its coding region revealed insignificant effect on indica × japonica embryo sac fertility

Abstract

Embryo sac sterility is one of the main reasons for infertility of indica–japonica hybrids and S5 is a major locus for embryo sac fertility. The present study was planned: (1) to sequence germplasm not carrying \({S_{\it{5}}}^{\it{n}}\) gene to ascertain their sequence diversity and domestication of Asian cultivated rice (indica–japonica), (2) to identify genotypes of ORF3 and ORF4 gene in materials with S5 gene coding region variation, and (3) to evaluate the effect of S5 gene coding region variation on embryo sac sterility. A total of 273 materials were sequenced, including 134 cultivars of Oryzasativa and 139 accessions of Oryzarufipogon. The results showed that 273 materials had different degrees of variation in S5 gene sequence compared with control cultivars. Coding region variation mainly occurred in exon 1 and exon 2, including 3 variable sites, of which 8 materials had 9 bp deletion at 177–185 bp, 1 materials had 12 bp deletion at 1,479–1,490 bp. Phylogenetic analysis suggested independent origin of indica and japonica subspecies from wild rice. Further, we found that all materials carrying S5 gene coding region variation were ORF3+, ORF4+, and ORF5+. Testcross hybrids were developed by crossing typical indica and japonica cultivars with lines carrying large differences in S5 coding region. Substantial evidence showed that ORF3+ is a major type for overcoming hybrid sterility, and S5 gene coding region variation had insignificant effect on embryo sac fertility. Genetic nucleotide diversity of \({S_{\it{5}}}^{\it{i}}\) and \({S_{\it{5}}}^{\it{j}}\) indicated that S5 is a very conservative gene. Further, it suggested that indica and japonica subspecies originated separately from ancestral wild rice.