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The Rice Paradox: Multiple Origins but Single Domestication in Asian Rice

Choi, JY; Platts, AE; Fuller, DQ; Hsing, Y-L; Wing, RA; Purugganan, MD; (2017) The Rice Paradox: Multiple Origins but Single Domestication in Asian Rice. Molecular Biology and Evolution , 34 (4) pp. 969-979. 10.1093/molbev/msx049. Green open access

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Abstract

The origin of domesticated Asian rice (Oryza sativa) has been a contentious topic, with conflicting evidence for either single or multiple domestication of this key crop species. We examined the evolutionary history of domesticated rice by analyzing de novo assembled genomes from domesticated rice and its wild progenitors. Our results indicate multiple origins, where each domesticated rice subpopulation (japonica, indica, and aus) arose separately from progenitor O. rufipogon and/or O. nivara. Coalescence-based modeling of demographic parameters estimate that the first domesticated rice population to split off from O. rufipogon was O. sativa ssp. japonica, occurring at ∼13.1–24.1 ka, which is an order of magnitude older then the earliest archeological date of domestication. This date is consistent, however, with the expansion of O. rufipogon populations after the Last Glacial Maximum ∼18 ka and archeological evidence for early wild rice management in China. We also show that there is significant gene flow from japonica to both indica (∼17%) and aus (∼15%), which led to the transfer of domestication alleles from early-domesticated japonica to proto-indica and proto-aus populations. Our results provide support for a model in which different rice subspecies had separate origins, but that de novo domestication occurred only once, in O. sativa ssp. japonica, and introgressive hybridization from early japonica to proto-indica and proto-aus led to domesticated indica and aus rice.

Type: Article
Title: The Rice Paradox: Multiple Origins but Single Domestication in Asian Rice
Open access status: An open access version is available from UCL Discovery
DOI: 10.1093/molbev/msx049
Publisher version: http://doi.org/10.1093/molbev/msx049
Language: English
Additional information: Copyright © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
Keywords: crop species, adaptation, introgressive hybridization, gene flow
UCL classification: UCL
UCL > Provost and Vice Provost Offices > UCL SLASH
UCL > Provost and Vice Provost Offices > UCL SLASH > Faculty of S&HS
UCL > Provost and Vice Provost Offices > UCL SLASH > Faculty of S&HS > Institute of Archaeology
UCL > Provost and Vice Provost Offices > UCL SLASH > Faculty of S&HS > Institute of Archaeology > Institute of Archaeology Gordon Square
URI: https://discovery.ucl.ac.uk/id/eprint/1549558
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