Chinese Science Bulletin

, 56:3108 | Cite as

Ancient DNA sequences of rice from the low Yangtze reveal significant genotypic divergence

  • LongJiang FanEmail author
  • YiJie Gui
  • YunFei Zheng
  • Yu Wang
  • DaGuang Cai
  • XiuLing You
Open Access
Article Crop Genetics


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.


Oryza sativa ancient DNA sequence Hemudu Neolithic culture rice domestication 


  1. 1.
    Vaughan D A, Lu B, Tomooka N. The evolving story of rice evolution. Plant Sci, 2008, 174: 394–408Google Scholar
  2. 2.
    Londo J P, Chiang Y C, Hung K H, et al. Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, Oryza sativa. Proc Natl Acad Sci USA, 2006, 103: 9578–9583CrossRefGoogle Scholar
  3. 3.
    You X L. A Global Chinese History (the primitive society volume) (in Chinese). Beijing: China Agricultural Press, 2008. 175–198Google Scholar
  4. 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. 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
  6. 6.
    Fuller D Q, Qin L, Zheng Y F, et al. The domestication process and domestication rate in rice: Spikelet bases from the lower Yangtze. Science, 2009, 323: 1607–1610CrossRefGoogle Scholar
  7. 7.
    Goloubinoff P, Pääbo S, Wilson A. Evolution of maize inferred from sequence diversity of an Adh2 gene segment from archaeological specimens. Proc Natl Acad Sci USA, 1993, 90: 1997–2001CrossRefGoogle Scholar
  8. 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
  9. 9.
    Rollo F, Ubaldi M, Ermini L, et al. Otzi’s last meals: DNA analysis of the intestinal content of the Neolithic glacier mummy from the Apls. Proc Natl Acad Sci USA, 2002, 99: 12594–12599CrossRefGoogle Scholar
  10. 10.
    Jaenicke-Despres V, Buckler E S, Smith B D, et al. Early allelic selection in maize as revealed by ancient DNA. Science, 2003, 302: 1206–1208CrossRefGoogle Scholar
  11. 11.
    Erickson D L, Smith B D, Clarke A C, et al. An Asian origin for a 10000-year-old domesticated plant in the Americas. Proc Natl Acad Sci USA, 2005, 102: 18315–18320CrossRefGoogle Scholar
  12. 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
  13. 13.
    Huang X H, Wei X H, Sang T, et al. Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet, 2010, 42: 961–976CrossRefGoogle Scholar
  14. 14.
    Levison P R, Badger S E, Dennis J, et al. Recent developments of magnetic beads for use in nucleic acid purification. J Chromatography A, 1998, 816: 107–111CrossRefGoogle Scholar
  15. 15.
    Yang D Y. Contamination controls and detection in ancient DNA studies. Acta Anthropol Sin, 2003, 22: 163–173Google Scholar
  16. 16.
    Ge S, Sang T, Lu B R, et al. Phylogeny of rice genomes with emphasis on origins of allotetraploid species. Proc Natl Acad Sci USA, 1999, 96: 14400–14405CrossRefGoogle Scholar
  17. 17.
    Doebley J F, Gaut B S, Smith B D. The molecular genetics of crop domestication. Cell, 2006, 127: 1309–1321CrossRefGoogle Scholar
  18. 18.
    Zhu Q, Zheng X, Luo J, et al. Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: Severe bottleneck during domestication of rice. Mol Biol Evol, 2007, 24: 875–888CrossRefGoogle Scholar
  19. 19.
    Zeng X S. Double-harvest rice in the Song Dynasty (in Chinese). Studies History Nat Sci, 2002, 21: 255–268Google Scholar
  20. 20.
    You X L. On Champa rice (in Chinese). Agri Archaeol, 1983, (1): 25–31Google Scholar

Copyright information

© The Author(s) 2011

Open Access This article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution and reproduction in any medium, provided the original author(s) and source are credited.

Authors and Affiliations

  • LongJiang Fan
    • 1
    Email author
  • YiJie Gui
    • 1
  • YunFei Zheng
    • 2
  • Yu Wang
    • 1
  • DaGuang Cai
    • 3
  • XiuLing You
    • 4
  1. 1.Department of AgronomyZhejiang UniversityHangzhouChina
  2. 2.Zhejiang Provincial Institute of Archaeology and Cultural RelicsHangzhouChina
  3. 3.Department of Molekulare PhytopathologieChristian-Albrechts-Universität zu KielKielGermany
  4. 4.School of HumanitiesZhejiang UniversityHangzhouChina

Personalised recommendations