Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Three geographically separate domestications of Asian rice


Domesticated rice (Oryza sativa L.) accompanied the dawn of Asian civilization1 and has become one of world's staple crops. From archaeological and genetic evidence various contradictory scenarios for the origin of different varieties of cultivated rice have been proposed, the most recent based on a single domestication2,3. By examining the footprints of selection in the genomes of different cultivated rice types, we show that there were three independent domestications in different parts of Asia. We identify wild populations in southern China and the Yangtze valley as the source of the japonica gene pool, and populations in Indochina and the Brahmaputra valley as the source of the indica gene pool. We reveal a hitherto unrecognized origin for the aus variety in central India or Bangladesh. We also conclude that aromatic rice is a result of a hybridization between japonica and aus, and that the tropical and temperate versions of japonica are later adaptations of one crop. Our conclusions are in accord with archaeological evidence that suggests widespread origins of rice cultivation1,4. We therefore anticipate that our results will stimulate a more productive collaboration between genetic and archaeological studies of rice domestication, and guide utilization of genetic resources in breeding programmes aimed at crop improvement.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Selection landscapes for the three groups of cultivated rice on each of the 12 rice chromosomes.
Figure 2: Population structure analysis of low-variation regions in cultivated rice genomes.
Figure 3: Scheme for the origins of domesticated rice derived from phylogeographic analysis of 31 CLDGR trees.

Similar content being viewed by others


  1. Fuller, D. Q. Pathways to Asian civilizations: tracing the origins and spread of rice and rice cultures. Rice 4, 78–92 (2011).

    Article  Google Scholar 

  2. Molina, J. et al. Molecular evidence for a single evolutionary origin of domesticated rice. Proc. Natl Acad. Sci. USA 108, 8351–8356 (2011).

    Article  CAS  Google Scholar 

  3. Huang, X. et al. A map of rice genome variation reveals the origin of cultivated rice. Nature 490, 497–503 (2012).

    Article  CAS  Google Scholar 

  4. Gross, B. L. & Zhao, Z. Archaeological and genetic insights into the origins of domesticated rice. Proc. Natl Acad. Sci. USA 111, 6190–6197 (2014).

    Article  CAS  Google Scholar 

  5. Goff, S. A. et al. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296, 92–100 (2002).

    Article  CAS  Google Scholar 

  6. Yu, J. et al. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296, 79–92 (2002).

    Article  CAS  Google Scholar 

  7. Vitte, C., Ishii, T., Lamy, F., Brar, D. & Panaud, O. Genomic paleontology provides evidence for two distinct origins of Asian rice (Oryza sativa L.). Mol. Genet. Genomics 272, 504–511 (2004).

    Article  CAS  Google Scholar 

  8. Zhu, Q. & Ge, S. Phylogenetic relationships among A-genome species of the genus Oryza revealed by intron sequences of four nuclear genes. New Phytol. 167, 249–265 (2005).

    Article  CAS  Google Scholar 

  9. Londo, J. P., Chiang, Y.-C., Hung, K.-H., Chiang, T.-Y. & Schaal, B. A. Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, Oryza sativa. Proc. Natl Acad. Sci. USA 103, 9578–9583 (2006).

    Article  CAS  Google Scholar 

  10. Yang, C.-C. et al. Independent domestication of Asian rice followed by gene flow from japonica to indica. Mol. Biol. Evol. 29, 1471–1479 (2012).

    Article  CAS  Google Scholar 

  11. Ma, J. & Bennetzen, J. L. Rapid recent growth and divergence of rice nuclear genomes. Proc. Natl Acad. Sci. USA 101, 12404–12410 (2004).

    Article  CAS  Google Scholar 

  12. Garris, A. J., Tai, T. H., Coburn, J., Kresovich, S. & McCouch, S. Genetic structure and diversity in Oryza sativa L. Genetics 169, 1631–1638 (2005).

    Article  CAS  Google Scholar 

  13. Zhao, K. et al. Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nature Commun. 2, 467 (2011).

    Article  Google Scholar 

  14. Schatz, M. C. et al. Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica. Genome Biol. 15, 506 (2014).

    PubMed  PubMed Central  Google Scholar 

  15. Gao, L.-Z. & Innan, H. Nonindependent domestication of the two rice subspecies, Oryza sativa ssp. indica and ssp. japonica, demonstrated by multilocus microsatellites. Genetics 179, 965–976 (2008).

    Article  CAS  Google Scholar 

  16. Lu, B.-R., Zheng, K. L., Qian, H. R. & Zhuang, J. Y. Genetic differentiation of wild relatives of rice as assessed by RFLP analysis. Theor. Appl. Genet. 106, 101–106 (2002).

    Article  CAS  Google Scholar 

  17. Oka, H.-I. & Morishima, H. Phylogenetic differentiation of cultivated rice, XXIII: potentiality of wild progenitors to evolve the indica and japonica types of rice cultivars. Euphytica 31, 41–50 (1982).

    Article  Google Scholar 

  18. Maddison, W. P. Gene trees in species trees. Syst. Biol. 46, 523–536 (1997).

    Article  Google Scholar 

  19. Tan, L. et al. Control of a key transition from prostrate to erect growth in rice domestication. Nature Genet. 40, 1360–1364 (2008).

    Article  CAS  Google Scholar 

  20. Li, C., Zhou, A. & Sang, T. Rice domestication by reducing shattering. Science 311, 1936–1939 (2006).

    Article  CAS  Google Scholar 

  21. Allaby, R. G. & Brown, T. A. AFLP data and the origins of domesticated crops. Genome 46, 448–453 (2003).

    Article  CAS  Google Scholar 

  22. Felsenstein, J. PHYLIP (Phylogeny Inference Package) v.3.6 (Department of Genome Sciences, Univ. Washington, 2005).

  23. Hutter, S., Vilella, A. J. & Rozas, A. J. Genome-wide DNA polymorphism analyses using VariScan. BMC Bioinf. 7, 409 (2006).

    Article  Google Scholar 

  24. He, Z. et al. Two evolutionary histories in the genome of rice: the roles of domestication genes. PLoS Genet. 7, e1002100 (2011).

    Article  CAS  Google Scholar 

  25. Patterson, N., Price, A. L. & Reich, D. Population structure and Eigenanalysis. PLoS Genet. 2, e190 (2006).

    Article  Google Scholar 

Download references


This work was supported by European Research Council grant 339941 awarded to T.A.B. We thank E. Karimi for sparking interest in the origin of aromatic rice. We also thank J. Ross-Ibarra for constructive comments on an earlier draft of this paper.

Author information

Authors and Affiliations



P.C. conceived the project and led the data analysis. H.C. contributed the geographical data analysis. C.F.C. and T.A.B. contributed conceptual development and data interpretation. P.C. and T.A.B. wrote the manuscript and all co-authors contributed manuscript editing.

Corresponding author

Correspondence to Terence A. Brown.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Civáň, P., Craig, H., Cox, C. et al. Three geographically separate domestications of Asian rice. Nature Plants 1, 15164 (2015).

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI:

This article is cited by


Quick links

Nature Briefing: Translational Research

Sign up for the Nature Briefing: Translational Research newsletter — top stories in biotechnology, drug discovery and pharma.

Get what matters in translational research, free to your inbox weekly. Sign up for Nature Briefing: Translational Research