Investigation of B-atp6-orfH79 distributing in Chinese populations of Oryza rufipogon and analysis of its chimeric structure

Abstract

AbstractBackgroundThe 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 rufipogonGriff.) has been regarded as the ancestral progenitor of Asian cultivated rice (Oryza sativaL.). To investigate the distribution of original CMS source, and explore the origin of gametophytic CMS gene, a total of 427 individuals with seventeen representative populations ofO. rufipogonwere collected in from Dongxiang of Jiangxi Province to Sanya of Hainan Province, China, for the PCR amplification ofatp6, orfH79and B-atp6-orfH79, respectively.ResultsThe B-atp6-orfH79and its variants (B-atp6-GSV) were detected in five among seventeen populations (i.e. HK, GZ, PS, TL and YJ) through PCR amplification, which could be 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-GSV. Combined with the high-homology sequences in GenBank, a total of eighteen haplotypes have been revealed, only with ten haplotypes inorfH79and its variants (GSV) that belong to three species (i.e.O. rufipogon,Oryza nivaraandOryza sativa). Enough haplotypes clearly demonstrated the uniform structural characteristics of the B-atp6-orfH79as 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 five insertion or deletion and more than 30 single nucleotide polymorphism. Maximum likelihood analysis showed that eighteen 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. Three haplotypes (i.e., H1, H2 and H3) were detected by the primer oforfH79, which were identical to the GVS in B-atp6-GVS structure, respectively. All seventeen haplotypes of theorfH79,belonged to six species based on our results and the existing references. Seven existed single nucleotide polymorphism in GSV section can be translated into eleven various amino acid sequences.ConclusionsGenerally, this study, indicating thatorfH79was always accompanied by the B-atp6, not only provide two original CMS sources for rice breeding, but also confirm the uniform structure of B-atp-orfH79,which contribute to revealing the origin of rice gametophytic CMS genes, and the reason about frequent recombination of mitochondrial DNA.