November 16, 2012

Some genetic support for South China origin of rice

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I really miss Vietnam and other parts of Indochina (Cambodia, Thailand...) in this oh-so-Chinese study. Draw a line on a map and go to sleep...

Xin Wei et al., Origin of Oryza sativa in China Inferred by Nucleotide Polymorphisms of Organelle DNA. PLoS ONE 2012. Open access ··> LINK [doi]


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.

The main interest of the study is to compare Oryza sativa (domestic rice) with O. rufipogon (wild rice and the ancestor of the former). It soon becomes obvious that both are the same species and that all O. sativa cluster with specific subpopulations of O. rufipogon (red rice, considered a weed):

Figure 3. Population structuring of O. sativa and O.rufipogon.

Complementarily a haploid phylogeny is studied and mapped by geography:

Figure 4. A map showing the sampled populations of O. rufipogon and the distribution of haplotypes.

From fig.2 we know that H1 corresponds to the haplotype found in O. sativa var. japonica (temperate climate variant) and that H2 and H3 correspond with the haplotypes found in O. sativa var. indica (tropical variant).

However notice how rare is the indica cluster in Tropical China O. rufipogon and that the exact combo only seems to show up in Hainan. For this reason, I would suggest future researchers to study the ancestor species also in Indochina, so we can understand better the origins of rice and particularly the indica variant, especially associated to Austroasiatic speakers now living almost exclusively in Indochina and parts of India.

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