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Three geographically separate domestications of Asian rice

Nature Plants volume 1, Article number: 15164 (2015) Cite this article

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Abstract

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.

Although genome sequences for Oryza sativa subsp. indica and subsp. japonica have been available for more than a decade5,6, the phylogenetic, geographic and temporal origins of these domesticated groups remain unresolved. The earliest archaeological evidence for human exploitation of rice dates to 9,000–10,000 years ago in India (Ganges plain) and China (middle and lower Yangtze valley) and suggests that there were independent origins of rice cultivation in these regions4. However, much of this work depends on the classification of archaeobotanical remains, which is problematic at the subspecies level. Moreover, large regions of southern and southeast Asia remain archaeologically unexplored1. Genetic studies of extant rice varieties aimed at resolving the questions of the origin of cultivated groups have resulted in diverse and often contradictory hypotheses. Genetic support for independent origins of domesticated rice7–11 includes the estimated divergence time for the two subspecies, indica and japonica, which at 200,000–440,000 years ago7,8,11 is much earlier than the beginning of agriculture in southeast Asia. Based on ecology, genetics and culinary properties, indica and japonica are subdivided into indica and aus, and temperate japonica, tropical japonica and aromatic, respectively12,13. Within long-grained indica, the aus group consists of drought-tolerant, early-maturing cultivars. Increasing evidence suggests that indica and aus could have separate origins that are obscured by their morphological similarities12–14, but a unique wild sister population of aus has not been identified so far. Within the japonica subspecies, typically giving sticky rice after cooking, the temperate and tropical japonica groups are adapted to distinct climatic conditions, whereas aromatic includes rice with specific flavours popular in Pakistan and northern India (basmati) and Iran (sadri).

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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.

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Acknowledgements

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.

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Authors and Affiliations

  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

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  1. Peter Civáň
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  2. Hayley Craig
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  3. Cymon J. Cox
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  4. Terence A. Brown
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Contributions

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.

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Correspondence to Terence A. Brown.

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Civáň, P., Craig, H., Cox, C. et al. Three geographically separate domestications of Asian rice. Nature Plants 1, 15164 (2015). https://doi.org/10.1038/nplants.2015.164

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