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

• Published in: BMC plant biology 2023-02, Vol.23 (1), p.81-81, Article 81
• Main Authors: Zhang, Xuemei, Chen, Shuying, Zhao, Zixian, Ma, Cunqiang, Liu, Yating
• Format: Article
• Language: English
• Subjects: Amino acids; Amplification; Analysis; Chimeras (Organisms); Chimeric gene; Conserved sequence; Cultivation; Cytoplasm; Cytoplasmic male sterility; Deoxyribonucleic acid; DNA; DNA, Mitochondrial - genetics; DNA, Mitochondrial - metabolism; Gene deletion; Gene polymorphism; Genes; Genetic aspects; Grain cultivation; Haplotypes; Homology; Hybrid rice; Hybridization; Investigations; Male sterility; Mitochondria - metabolism; Mitochondrial DNA; Nucleotides; Oryza - genetics; Oryza rufipogon; Oryza sativa; Plant Breeding; Polymerase chain reaction; Polymorphism; Populations; Recombination; Rice; Sequence feature; Single nucleotide polymorphisms; Single-nucleotide polymorphism; Structure; Variance analysis; Varieties
• ISSN: 1471-2229; 1471-2229
• DOI: 10.1186/s12870-023-04082-5

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 the ancestral progenitor of Asian cultivated rice (Oryza sativa L.). 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 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. The B-atp6-orfH79 and 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 in orfH79 and its variants (GSV) that belong to three species (i.e. O. rufipogon, Oryza nivara and Oryza sativa). Enough haplotypes clearly demonstrated the uniform 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 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 (F  = 1; P