Genomic variation associated with local adaptation of weedy rice during de-domestication

	Genomic variation associated with local adaptation of weedy rice during de-domestication
	Qiu, Jie 1; Zhou, Yongjun 2; Mao, Lingfeng 1; Ye, Chuyu 1; Wang, Weidi 1; Zhang, Jianping 2; Yu, Yongyi 1; Fu, Fei 1; Wang, Yunfei 3; Qian, Feijian 3; Qi, Ting 1; Wu, Sanling 4; Sultana, Most Humaira 1; Cao, Ya-Nan ; Wang, Yu 3; Timko, Michael P.; Ge, Song7 ; Fan, Longjiang 1; Lu, Yongliang 2
	2017
发表期刊	NATURE COMMUNICATIONS
ISSN	2041-1723
卷号	8
摘要	De-domestication is a unique evolutionary process by which domesticated crops are converted into 'wild predecessor like' forms. Weedy rice (Oryza sativa f. spontanea) is an excellent model to dissect the molecular processes underlying de-domestication. Here, we analyse the genomes of 155 weedy and 76 locally cultivated rice accessions from four representative regions in China that were sequenced to an average 18.2x coverage. Phylogenetic and demographic analyses indicate that Chinese weedy rice was de-domesticated independently from cultivated rice and experienced a strong genetic bottleneck. Although evolving from multiple origins, critical genes underlying convergent evolution of different weedy types can be found. Allele frequency analyses suggest that standing variations and new mutations contribute differently to japonica and indica weedy rice. We identify a Mb-scale genomic region present in weedy rice but not cultivated rice genomes that shows evidence of balancing selection, thereby suggesting that there might be more complexity inherent to the process of de-domestication.
学科领域	Plant Sciences
收录类别	SCI
语种	英语
WOS关键词	ORYZA-SATIVA ; EVOLUTION ; ORIGIN ; GENE ; POLYMORPHISM ; PATTERNS ; REVEALS ; FORMAT ; MAP
WOS记录号	WOS:000404235800007
出版者	NATURE RESEARCH
文献子类	Article
出版地	BERLIN
资助机构	China Agriculture Research System [CARS-01-02A] ; National Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [91435111] ; Jiangsu Collaborative Innovation Center for Modern Crop Production (JCIC-MCP) ; Rice Pest Management Research Group of the Agricultural Science and Technology Innovation Program of China Academy of Agricultural Science ; NSFNational Science Foundation (NSF) [IOS-1213059] ; IBM high performance computing cluster of Analysis Center of Agrobiology and Environmental Sciences, Zhejiang University
作者邮箱	fanlj@zju.edu.cn ; luyongliang@caas.cn
引用统计	被引频次：11[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.ibcas.ac.cn/handle/2S10CLM1/22294
专题	系统与进化植物学国家重点实验室
作者单位	1.Zhejiang Univ, Inst Crop Sci, Coll Agr & Biotechnol, Hangzhou 310058, Zhejiang, Peoples R China 2.Zhejiang Univ, Inst Bioinformat, Coll Agr & Biotechnol, Hangzhou 310058, Zhejiang, Peoples R China 3.Chinese Acad Agr Sci, China Natl Rice Res Inst, Hangzhou 310006, Zhejiang, Peoples R China 4.Zhejiang Sheng Ting Biotechnol Co Ltd, Taizhou 318020, Peoples R China 5.Zhejiang Univ, Anal Ctr Agrobiol & Environm Sci, Fac Agr Life & Environm Sci, Hangzhou 310058, Zhejiang, Peoples R China 6.Zhejiang Univ, Key Lab Conservat Biol Endangered Wildlife, Minist Educ, Hangzhou 310058, Zhejiang, Peoples R China 7.Wang, Yu; Timko, Michael P.] Univ Virginia, Dept Biol, Charlottesville, VA 22904 USA 8.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China
推荐引用方式 GB/T 7714	Qiu, Jie,Zhou, Yongjun,Mao, Lingfeng,et al. Genomic variation associated with local adaptation of weedy rice during de-domestication[J]. NATURE COMMUNICATIONS,2017,8.
APA	Qiu, Jie.,Zhou, Yongjun.,Mao, Lingfeng.,Ye, Chuyu.,Wang, Weidi.,...&Lu, Yongliang.(2017).Genomic variation associated with local adaptation of weedy rice during de-domestication.NATURE COMMUNICATIONS,8.
MLA	Qiu, Jie,et al."Genomic variation associated with local adaptation of weedy rice during de-domestication".NATURE COMMUNICATIONS 8(2017).

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