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Genome analysis traces regional dispersal of rice in Taiwan and Southeast Asia

Alam, O; Gutaker, RM; Wu, C-C; Hicks, KA; Bocinsky, K; Castillo, CC; Acabado, S; ... Purugganan, MD; + view all (2021) Genome analysis traces regional dispersal of rice in Taiwan and Southeast Asia. Molecular Biology and Evolution 10.1093/molbev/msab209. (In press). Green open access

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Abstract

The dispersal of rice (Oryza sativa) following domestication influenced massive social and cultural changes across South, East, and Southeast Asia. The history of dispersal across islands of Southeast Asia, and the role of Taiwan and the Austronesian expansion in this process remain largely unresolved. Here, we reconstructed the routes of dispersal of O. sativa ssp. japonica rice through Taiwan and the northern Philippines using whole-genome re-sequencing of indigenous rice landraces coupled with archaeological and paleoclimate data. Our results indicate that japonica rice found in the northern Philippines diverged from Indonesian landraces as early as 3500 BP. In contrast, rice cultivated by the indigenous peoples of the Taiwanese mountains has complex origins. It comprises two distinct populations, each best explained as a result of admixture between temperate japonica that presumably came from northeast Asia, and tropical japonica from the northern Philippines and mainland Southeast Asia respectively. We find that the temperate japonica component of these indigenous Taiwan populations diverged from northeast Asia subpopulations at about 2600 BP, while gene flow from the northern Philippines occurred before ∼1300 years BP. This coincides with a period of intensified trade established across the South China Sea. Finally, we find evidence for positive selection acting on distinct genomic regions in different rice subpopulations, indicating local adaptation associated with the spread of japonica rice.

Type: Article
Title: Genome analysis traces regional dispersal of rice in Taiwan and Southeast Asia
Location: United States
Open access status: An open access version is available from UCL Discovery
DOI: 10.1093/molbev/msab209
Publisher version: https://doi.org/10.1093/molbev/msab209
Language: English
Additional information: © The Author(s) 2021. 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/).
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/10131084
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