Study on the Origin of CMS Gene and DNA Barcode for Oryza Based on Rice Mitochondrial atp6 Gene

Purpose To explore the origin of CMS gene in Oryza sativa and the application of the rice mitochondrial rice atp6 specific primer as Oryza DNA barcode markers.

Method The atp6 specific primer were used to detect 4 kinds of rice produced in China by PCR, a total of 720 individuals, and 111 individuals were sequenced.

Result Conserved sequence of atp6 was detected in O. rufipogon and O. sativa. No amplification products were detected in O. officinalis. A total of 17 variation locus between the five haplotypes were detected in O. meyeriana. Lancang, Pu'er, Menghai population shared H1. Haplotype H2, H3, H4 and H5 were unique to Xinping, Mojiang, Baoting and Yacheng population respectively.Yunnan group and Hainan group, average genetic distance within the group were all 0, and between groups was 0.02. The genetic differentiation coefficient F_st of between groups was 92.08%. Number of variant sites (S), number of haplotypes (h) and nucleotide diversity (P_i) showed that the genetic diversity of Yunnan group (4, 3, 0.002 01) was greater than that in Hainan group (1, 2, 0.001 31). The haplotype diversity H_d of the Yunnan group was 0.6, and that in Hainan was 1. The similarity between 5 haplotypes and the rice atp6 conserved sequence was up to 45.19%. Maximum likelihood (ML) evolutionary tree displayed: the Lancang, Pu’er, Menghai area might be the origin of the O. meyeriana and Hainan O. meyeriana might originate from the mainland.

Conclusion Rice atp6 specific primers can be used as barcode markers within O. meyeriana species. The marker can also distinguish between O. rufipogon, O. officinalis, and O. meyeriana. O. sativa CMS gene is derived from O. rufipogon from the perspective of mitochondrial DNA.