| Rice is the staple food in China and it has been cultivated for more than 7000 years. At present, both yield and cultivated area of rice in China are on the top level in the world. The Common Wild Rice (Oryza rufipogon) which has been regarded as the ancestor of cultivated rice (Oryza sativa) distributed widely in China and has rich genetic diversity. Generally, China has been recognized to be one of the origin regions of Oryza sativa but where it is origin from and how it is evoluted from Oryza rufipogon have been debated for a long time and are still in controversy. Furthermore, how the subspecies of Indica-Japonica of Oryza sativa differentiated is also in discussion. The purpose of this study was to find some evidences at molecular level to get some conclusions for the evolution and origin of Oryza sativa in China.Chloroplast DNA is a circular DNA with full length 134,525bp, which is inherited in maternal pathway. So it has fewer gene recombination and lower gene mutation rate. Previous studies showed that the mutation rate of chloroplast DNA is only one tenth of nuclear genome and has a slow evolution process. But compared with mitochondria DNA, it has relatively higher mutation rate and is recognized to be more suitable for studying genetic evolution.In this research, we used 98 accessions of cultivated rice and 125 accessions of common wild rice collected from the micro-core collection established before. From related reference, we selected five high mutation rate sequences from chloroplast genome to analyze polymorphisms of these sequences. The selected sequences are: ATP synthetaseαsubunit coding sequence, ribosome S16 subunit intron sequence, the intergenic spacer of tRNA-Pro and ribosome L33, the intergenic spacer of tRNA-Thr and tRNA-Leu, and a high mutation rate sequence including tRNA-Gly and tRNA-fMet. Through analysis on sequences from each accession, the gene diversity in chloroplast DNA in rice was obtained and the haplotype network and the phylogenetic tree were constructed. The results are showed as below:First, common wild rice has more gene diversity than cultivated rice, similar with results from nuclear DNA, indicated that wild rice suffered less selective pressure in long term's evolution. Its SNPs and Indels rates are 0.25% and 0.21%, less than the rates in nuclear, illustrated that it's feasible to use chloroplast DNA for the evolution research because of its slow evolution rate.Second, all cultivated rice accessions could be divided into two parts from the polymorphisms in chloroplast DNA, which were similar with the Indica rice and Japonica rice distinguished by phenotype classification. Similarly, the common wild rice accessions were also divided into two groups and inferred that Indica-Japonica differentiation also exists in Common Wild Rice, and the cultivated rice may has two origin pathways, one from Indica-like wild rice and the other from Japanica-like wild rice.Third, there are more Japonica-like rice in common wild rice which distribute mainly in Guangdong and Guangxi provinces, and they have a close relationship with Japonica cultivated rice. Though Indica-like wild rice accessions are not closely related with Indica cultivated rice, they have closer relationship with Indica cultivated rice than Japonica cultivated rice and they mainly distributed in Guangxi and Hainan provinces. The results could be explained that the main kind of Chinese common wild rice is Japonica-like, and the origin place of cultivated rice is in South China, support the theory of South China origin. |
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