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China is rich of germplasm resources of common wild rice ( Oryza rufipogon  Griff.) and Asian cultivated rice ( O. sativa  L.) which consists of two subspecies, indica and japonica. Previous studies have shown that China is one of the domestication centers of  O .  sativa . However, the geographic origin and the domestication times of  O .  sativa  in China are still under debate. To settle these disputes, six chloroplast loci and four mitochondrial loci were selected to examine the relationships between 50 accessions of Asian cultivated rice and 119 accessions of common wild rice from China based on DNA sequence analysis in the present study. The results indicated that Southern China is the genetic diversity center of  O .  rufipogon  and it might be the primary domestication region of  O .  sativa . Molecular dating suggested that the two subspecies had diverged 0.1 million years ago, much earlier than the beginning of rice domestication. Genetic differentiations and phylogeography analyses indicated that indica was domesticated from tropical  O .  rufipogon  while japonica was domesticated from  O .  rufipogon  which located in higher latitude. These results provided molecular evidences for the hypotheses of (i) Southern China is the origin center of  O .  sativa  in China and (ii) the two subspecies of  O .  sativa  were domesticated multiple times.

Origin of Oryza sativa in China Inferred by Nucleotide Polymorphisms of Organelle DNA