Molecular evolution of rice S5n and functional comparison among different sequences

Abstract

The wide compatibility gene, S5n, can overcome embryo sac sterility between indica and japonica subspecies of rice. Therefore, it is very important to characterize the features of the S5n sequence to reveal the origin and evolution of S5n. In this paper, 26 cultivated rice haplotypes and 22 wild rice accessions harboring S5n were used to sequence S5n. The results showed that 15 genotypes among the 48 materials were fully consistent with control cultivar 02428 (CK). The other 33 accessions had different degrees of variation in the S5n sequence. Variations in the coding region mainly occurred in the second exon and eight materials showed a 10-bp deletion at 1710-1719 bp, including wild (O. nivara) and cultivated rice, such as IRW501 and Yuetai B. S5n sequences were not biased and evolved neutrally. The 48 materials could be divided into 4 categories using a phylogenetic tree of the amino acid sequences. Most of the wild rice clustered together, and the cultivated rice clustered into another group. Eight cultivated rice and O. nivara (wild rice) clustered in another group, which were found to lack 10 consecutive bases in exon 2. Eight rice varieties with high numbers of differences in their S5n coding regions were crossed with testers (typically indica and japonica) to produced test cross F1 populations. The F1s were examined for their ability to overcome indica-japonica hybrid sterility. The result showed that the embryo sac fertility of S5n-containing hybrids increased significantly compared with control hybrids, but there were no differences among the materials with divergent sequences, indirectly proving that S5n is a non-functional gene. © 2011 Science China Press and Springer-Verlag Berlin Heidelberg.