Ancient DNA sequences of rice from the low Yangtze reveal significant genotypic divergence
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Rice (Oryza sativa) was first domesticated in the lower and middle Yangtze regions of China, and rice remains have been found in many Chinese archaeological sites. Until now, only phenotypic archeobotanical evidence, such as the spikelet bases of ancient grains, has been used to speculate on the domestication process and domestication rate of rice. In this study, we sequenced 4 genomic segments from rice remains in Tianluoshan, a site of the local Hemudu Neolithic culture in the low Yangtze and two other archaeological sites (∼2400 and 1200 BC, respectively). We compared our sequences with those of the current domesticated and wild rice (O. rufipogon) populations. At least two genotypes were found in the remains from each site, suggesting a heterozygotic state of the rice seeds. One ancient genotype was not found in the current domesticated population and might have been lost. The rice remains belonged to the japonica group, and most if not all were japonica-type, suggesting that the remains might be at an early stage of indica-japonica divergence or an indica-japonica mixture. We also identified sequences with significant similarity to those from species of Sapindales, Zygophyllales, and Brassicales, which is consistent with the identification of other plant remains in the Tianluoshan site and the common rice field weeds such as mustards in southern China.
KeywordsOryza sativa ancient DNA sequence Hemudu Neolithic culture rice domestication
- 1.Vaughan D A, Lu B, Tomooka N. The evolving story of rice evolution. Plant Sci, 2008, 174: 394–408Google Scholar
- 3.You X L. A Global Chinese History (the primitive society volume) (in Chinese). Beijing: China Agricultural Press, 2008. 175–198Google Scholar
- 4.You X L. Several view about rice and bone spade excavated from the 4th cultural layer in the Hemudu site (in Chinese). Cult Relics, 1976, (8): 20–23Google Scholar
- 5.Zheng Y F, Shun D G, Chen X G. Characteristics of the short rachillae of rice from archaeological sites dating to 7000 years ago. Chinese Sci Bull, 2007, 52: 1037–1041Google Scholar
- 8.Deakin W J, Rowley-Conwy P J, Shaw C H. Amplification and sequencing of DNA from preserved sorghum of up to 2800 years antiquity found at Qasr Ibrim. Ancient Biomol, 1998, 2: 27–41Google Scholar
- 12.Nakamura I, Sato Y I. Amplification of DNA fragments isolated form a single seed of ancient rice (AD 800) by polymerase chain reaction. Chinese J Rice Sci, 1991, 5: 175–179Google Scholar
- 15.Yang D Y. Contamination controls and detection in ancient DNA studies. Acta Anthropol Sin, 2003, 22: 163–173Google Scholar
- 19.Zeng X S. Double-harvest rice in the Song Dynasty (in Chinese). Studies History Nat Sci, 2002, 21: 255–268Google Scholar
- 20.You X L. On Champa rice (in Chinese). Agri Archaeol, 1983, (1): 25–31Google Scholar
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