Origin of rice gametophytic cytoplasmic male sterility genes in Chinese populations of Oryza rufipogon through sequence features of B-atp6-orfH79

Abstract

Abstract Background: The cytoplasmic male sterility (CMS) of rice is caused by chimeric mitochondrial DNA (mtDNA) that is maternally inherited in the majority of multicellular organisms. Wild rice (Oryza rufipogon Griff.) has been regarded as an ancestral progenitor of Asian rice (Oryza sativa). To identify additional CMS sources, and explore the origin of gametophytic CMS gene, a total of 427 individuals with 17 representative populations of O. rufipogon were collected in from Dongxiang of Jiangxi Province to Sanya of Hainan Province, China, for the PCR amplification of atp6, orfH79 and B-atp6-orfH79, respectively. Results: Among 17 populations, the B-atp6-orfH79 and its variants (B-atp6-GSV) were detected in five populations (i.e. HK, GZ, PS, TL and YJ) through PCR amplification, which were divided into three haplotypes, i.e., BH1, BH2, and BH3. The BH2 haplotype was identical to B-atp6-orfH79, while the BH1 and BH3 were the novel haplotypes of B-atp6-orfH79. Combined with the high-homology sequences in GenBank, a total of 18 haplotypes have been revealed, which only could be divided into 10 haplotypes in orfH79 and its variants (GSV) section.thatbelong to 3 species (i.e. O. rufipogon, Oryza nivara and Oryza sativa) Enough haplotypes clearly demonstrate the structural characteristics of the B-atp6-orfH79 as follows: Except for the conserved sequence (671 bp) composed of B-atp6 (619 bp) and the downstream followed the B-atp6 (52 bp, DS), and GSV sequence, a rich variable sequence (VS, 176 bp) lies between the DS and GSV with 5 insertion or deletion and more than 30 single nucleotide polymorphism. Maximum likelihood analysis showed that 18 haplotypes formed three clades with high support rate. The hierarchical analysis of molecular variance (AMOVA) indicated the occurrence of variation among all populations (FST = 1; P < 0.001), which implied that the chimeric structure occurred independently. All 17 haplotypes of the orfH79 was statisticsed based on our results and the existing references, which belong to 6 species, but their genetic relationship can not be reflected through systematic analysis. 7 existed single nucleotide polymorphism in GSV section can be translated into 11 various amino acid sequences. Conclusions: In this study, the relevant populations provide diverse CMS primary sources. B-atp6 and the GSV simultaneous existence in the plant. The sequence characteristics of B-atp6-orfH79 and Maximum Likelihood analysis indicated the chimerise occur independently with consistent chimeric sites, which might help to explore the origin of rice gametophytic CMS genes in O. rufipogon.