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

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	Genomic variation associated with local adaptation of weedy rice during de-domestication
	Qiu, Jie 2; Zhou, Yongjun 1; Mao, Lingfeng 2; Ye, Chuyu 2; Wang, Weidi 2; Zhang, Jianping 1; Yu, Yongyi 2; Fu, Fei 2; Wang, Yunfei 3; Qian, Feijian 3
刊名	NATURE COMMUNICATIONS
	2017
卷号	8
ISSN号	2041-1723
文献子类	Article
英文摘要	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.
学科主题	Plant Sciences
出版地	BERLIN
WOS关键词	ORYZA-SATIVA ; EVOLUTION ; ORIGIN ; GENE ; POLYMORPHISM ; PATTERNS ; REVEALS ; FORMAT ; MAP
语种	英语
出版者	NATURE RESEARCH
WOS记录号	WOS:000404235800007
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
内容类型	期刊论文
源URL	[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 Bioinformat, Coll Agr & Biotechnol, Hangzhou 310058, Zhejiang, Peoples R China 2.Zhejiang Univ, Inst Crop Sci, 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).