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A map of rice genome variation reveals the origin of cultivated rice

Crop domestications are long-term selection experiments that have greatly advanced human civilization. The domestication of cultivated rice (Oryza sativa L.) ranks as one of the most important developments in history. However, its origins and domestication processes are controversial and have long b...

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Autores principales: Huang, Xuehui, Kurata, Nori, Wei, Xinghua, Wang, Zi-Xuan, Wang, Ahong, Zhao, Qiang, Zhao, Yan, Liu, Kunyan, Lu, Hengyun, Li, Wenjun, Guo, Yunli, Lu, Yiqi, Zhou, Congcong, Fan, Danlin, Weng, Qijun, Zhu, Chuanrang, Huang, Tao, Zhang, Lei, Wang, Yongchun, Feng, Lei, Furuumi, Hiroyasu, Kubo, Takahiko, Miyabayashi, Toshie, Yuan, Xiaoping, Xu, Qun, Dong, Guojun, Zhan, Qilin, Li, Canyang, Fujiyama, Asao, Toyoda, Atsushi, Lu, Tingting, Feng, Qi, Qian, Qian, Li, Jiayang, Han, Bin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7518720/
https://www.ncbi.nlm.nih.gov/pubmed/23034647
http://dx.doi.org/10.1038/nature11532
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author Huang, Xuehui
Kurata, Nori
Wei, Xinghua
Wang, Zi-Xuan
Wang, Ahong
Zhao, Qiang
Zhao, Yan
Liu, Kunyan
Lu, Hengyun
Li, Wenjun
Guo, Yunli
Lu, Yiqi
Zhou, Congcong
Fan, Danlin
Weng, Qijun
Zhu, Chuanrang
Huang, Tao
Zhang, Lei
Wang, Yongchun
Feng, Lei
Furuumi, Hiroyasu
Kubo, Takahiko
Miyabayashi, Toshie
Yuan, Xiaoping
Xu, Qun
Dong, Guojun
Zhan, Qilin
Li, Canyang
Fujiyama, Asao
Toyoda, Atsushi
Lu, Tingting
Feng, Qi
Qian, Qian
Li, Jiayang
Han, Bin
author_facet Huang, Xuehui
Kurata, Nori
Wei, Xinghua
Wang, Zi-Xuan
Wang, Ahong
Zhao, Qiang
Zhao, Yan
Liu, Kunyan
Lu, Hengyun
Li, Wenjun
Guo, Yunli
Lu, Yiqi
Zhou, Congcong
Fan, Danlin
Weng, Qijun
Zhu, Chuanrang
Huang, Tao
Zhang, Lei
Wang, Yongchun
Feng, Lei
Furuumi, Hiroyasu
Kubo, Takahiko
Miyabayashi, Toshie
Yuan, Xiaoping
Xu, Qun
Dong, Guojun
Zhan, Qilin
Li, Canyang
Fujiyama, Asao
Toyoda, Atsushi
Lu, Tingting
Feng, Qi
Qian, Qian
Li, Jiayang
Han, Bin
author_sort Huang, Xuehui
collection PubMed
description Crop domestications are long-term selection experiments that have greatly advanced human civilization. The domestication of cultivated rice (Oryza sativa L.) ranks as one of the most important developments in history. However, its origins and domestication processes are controversial and have long been debated. Here we generate genome sequences from 446 geographically diverse accessions of the wild rice species Oryza rufipogon, the immediate ancestral progenitor of cultivated rice, and from 1,083 cultivated indica and japonica varieties to construct a comprehensive map of rice genome variation. In the search for signatures of selection, we identify 55 selective sweeps that have occurred during domestication. In-depth analyses of the domestication sweeps and genome-wide patterns reveal that Oryza sativa japonica rice was first domesticated from a specific population of O. rufipogon around the middle area of the Pearl River in southern China, and that Oryza sativa indica rice was subsequently developed from crosses between japonica rice and local wild rice as the initial cultivars spread into South East and South Asia. The domestication-associated traits are analysed through high-resolution genetic mapping. This study provides an important resource for rice breeding and an effective genomics approach for crop domestication research. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/nature11532) contains supplementary material, which is available to authorized users.
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spelling pubmed-75187202020-10-07 A map of rice genome variation reveals the origin of cultivated rice Huang, Xuehui Kurata, Nori Wei, Xinghua Wang, Zi-Xuan Wang, Ahong Zhao, Qiang Zhao, Yan Liu, Kunyan Lu, Hengyun Li, Wenjun Guo, Yunli Lu, Yiqi Zhou, Congcong Fan, Danlin Weng, Qijun Zhu, Chuanrang Huang, Tao Zhang, Lei Wang, Yongchun Feng, Lei Furuumi, Hiroyasu Kubo, Takahiko Miyabayashi, Toshie Yuan, Xiaoping Xu, Qun Dong, Guojun Zhan, Qilin Li, Canyang Fujiyama, Asao Toyoda, Atsushi Lu, Tingting Feng, Qi Qian, Qian Li, Jiayang Han, Bin Nature Article Crop domestications are long-term selection experiments that have greatly advanced human civilization. The domestication of cultivated rice (Oryza sativa L.) ranks as one of the most important developments in history. However, its origins and domestication processes are controversial and have long been debated. Here we generate genome sequences from 446 geographically diverse accessions of the wild rice species Oryza rufipogon, the immediate ancestral progenitor of cultivated rice, and from 1,083 cultivated indica and japonica varieties to construct a comprehensive map of rice genome variation. In the search for signatures of selection, we identify 55 selective sweeps that have occurred during domestication. In-depth analyses of the domestication sweeps and genome-wide patterns reveal that Oryza sativa japonica rice was first domesticated from a specific population of O. rufipogon around the middle area of the Pearl River in southern China, and that Oryza sativa indica rice was subsequently developed from crosses between japonica rice and local wild rice as the initial cultivars spread into South East and South Asia. The domestication-associated traits are analysed through high-resolution genetic mapping. This study provides an important resource for rice breeding and an effective genomics approach for crop domestication research. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/nature11532) contains supplementary material, which is available to authorized users. Nature Publishing Group UK 2012-10-03 2012 /pmc/articles/PMC7518720/ /pubmed/23034647 http://dx.doi.org/10.1038/nature11532 Text en © The Author(s) 2012 This article is distributed under the terms of the Creative Commons Attribution-Non-Commercial-Share Alike licence (http://creativecommons.org/licenses/by-nc-sa/3.0/), which permits distribution, and reproduction in any medium, provided the original author and source are credited. This licence does not permit commercial exploitation, and derivative works must be licensed under the same or similar licence.
spellingShingle Article
Huang, Xuehui
Kurata, Nori
Wei, Xinghua
Wang, Zi-Xuan
Wang, Ahong
Zhao, Qiang
Zhao, Yan
Liu, Kunyan
Lu, Hengyun
Li, Wenjun
Guo, Yunli
Lu, Yiqi
Zhou, Congcong
Fan, Danlin
Weng, Qijun
Zhu, Chuanrang
Huang, Tao
Zhang, Lei
Wang, Yongchun
Feng, Lei
Furuumi, Hiroyasu
Kubo, Takahiko
Miyabayashi, Toshie
Yuan, Xiaoping
Xu, Qun
Dong, Guojun
Zhan, Qilin
Li, Canyang
Fujiyama, Asao
Toyoda, Atsushi
Lu, Tingting
Feng, Qi
Qian, Qian
Li, Jiayang
Han, Bin
A map of rice genome variation reveals the origin of cultivated rice
title A map of rice genome variation reveals the origin of cultivated rice
title_full A map of rice genome variation reveals the origin of cultivated rice
title_fullStr A map of rice genome variation reveals the origin of cultivated rice
title_full_unstemmed A map of rice genome variation reveals the origin of cultivated rice
title_short A map of rice genome variation reveals the origin of cultivated rice
title_sort map of rice genome variation reveals the origin of cultivated rice
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7518720/
https://www.ncbi.nlm.nih.gov/pubmed/23034647
http://dx.doi.org/10.1038/nature11532
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