Article | Published:

Three geographically separate domestications of Asian rice

Nature Plants volume 1, Article number: 15164 (2015) | Download Citation


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.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.


  1. 1.

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

  2. 2.

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

  3. 3.

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

  4. 4.

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

  5. 5.

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

  6. 6.

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

  7. 7.

    , , , & Genomic paleontology provides evidence for two distinct origins of Asian rice (Oryza sativa L.). Mol. Genet. Genomics 272, 504–511 (2004).

  8. 8.

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

  9. 9.

    , , , & 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).

  10. 10.

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

  11. 11.

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

  12. 12.

    , , , & Genetic structure and diversity in Oryza sativa L. Genetics 169, 1631–1638 (2005).

  13. 13.

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

  14. 14.

    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).

  15. 15.

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

  16. 16.

    , , & Genetic differentiation of wild relatives of rice as assessed by RFLP analysis. Theor. Appl. Genet. 106, 101–106 (2002).

  17. 17.

    & 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).

  18. 18.

    Gene trees in species trees. Syst. Biol. 46, 523–536 (1997).

  19. 19.

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

  20. 20.

    , & Rice domestication by reducing shattering. Science 311, 1936–1939 (2006).

  21. 21.

    & AFLP data and the origins of domesticated crops. Genome 46, 448–453 (2003).

  22. 22.

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

  23. 23.

    , & Genome-wide DNA polymorphism analyses using VariScan. BMC Bioinf. 7, 409 (2006).

  24. 24.

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

  25. 25.

    , & Population structure and Eigenanalysis. PLoS Genet. 2, e190 (2006).

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


  1. Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester M1 7DN, Manchester, UK

    • Peter Civáň
    • , Hayley Craig
    •  & Terence A. Brown
  2. Centro de Ciências do Mar, Universidade do Algarve, Gambelas, 8005-139 Faro, Portugal

    • Cymon J. Cox


  1. Search for Peter Civáň in:

  2. Search for Hayley Craig in:

  3. Search for Cymon J. Cox in:

  4. Search for Terence A. Brown in:


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.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Terence A. Brown.

Supplementary information

About this article

Publication history





Further reading