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Evolutionary and functional genomics of DNA methylation in maize domestication and improvement

文献类型：期刊论文

作者Xu, Gen8; Lyu, Jing8; Li, Qing7; Liu, Han6; Wang, Dafang5; Zhang, Mei6; Springer, Nathan M.; Ross-Ibarra, Jeffrey; Yang, Jinliang8
刊名NATURE COMMUNICATIONS
出版日期2020
卷号11期号:1
ISSN号2041-1723
DOI10.1038/s41467-020-19333-4
文献子类Article
英文摘要DNA methylation is a ubiquitous chromatin feature, present in 25% of cytosines in the maize genome, but variation and evolution of the methylation landscape during maize domestication remain largely unknown. Here, we leverage whole-genome sequencing (WGS) and whole-genome bisulfite sequencing (WGBS) data on populations of modern maize, landrace, and teosinte (Zea mays ssp. parviglumis) to estimate epimutation rates and selection coefficients. We find weak evidence for direct selection on DNA methylation in any context, but thousands of differentially methylated regions (DMRs) are identified population-wide that are correlated with recent selection. For two trait-associated DMRs, vgt1-DMR and tb1-DMR, HiChIP data indicate that the interactive loops between DMRs and respective downstream genes are present in B73, a modern maize line, but absent in teosinte. Our results enable a better understanding of the evolutionary forces acting on patterns of DNA methylation and suggest a role of methylation variation in adaptive evolution.
学科主题Multidisciplinary Sciences
出版地BERLIN
WOS研究方向Science & Technology - Other Topics
语种英语
WOS记录号WOS:000627757000001
出版者NATURE RESEARCH
资助机构Agriculture and Food Research Initiative from the USDA National Institute of Food and Agriculture [201967013-29167] ; National Science FoundationNational Science Foundation (NSF) [OIA-1557417] ; Institutional Development Award (IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health [P20GM103476] ; University of Nebraska-Lincoln Start-up fund ; Layman seed award ; NSF grantNational Science Foundation (NSF) [1546719] ; USDA Hatch project [CA-D-PLS-2066-H] ; Nebraska Research Initiative
源URL[http://ir.ibcas.ac.cn/handle/2S10CLM1/21463]  
专题中科院植物分子生理学重点实验室
作者单位1.Univ Nebraska, Ctr Plant Sci Innovat, Lincoln, NE 68583 USA
2.Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA
3.Univ Calif Davis, Ctr Populat Biol, Dept Ecol & Evolut, Davis, CA 95616 USA
4.Delta State Univ, Div Math & Sci, Cleveland, MS 38733 USA
5.Chinese Acad Sci, Inst Bot, Key Lab Plant Mol Physiol, Nanxincun 20,Fragrant Hill, Beijing 100093, Peoples R China
6.Huazhong Agr Univ, Natl Key Lab Crop Genet Improvement, Wuhan 430070, Peoples R China
7.Li, Qing; Springer, Nathan M.] Univ Minnesota, Microbial & Plant Genom Inst, Dept Plant Biol, St Paul, MN 55108 USA
8.Univ Nebraska, Dept Agron & Hort, Lincoln, NE 68583 USA
推荐引用方式
GB/T 7714		 Xu, Gen,Lyu, Jing,Li, Qing,et al. Evolutionary and functional genomics of DNA methylation in maize domestication and improvement[J]. NATURE COMMUNICATIONS,2020,11(1).
APA Xu, Gen.,Lyu, Jing.,Li, Qing.,Liu, Han.,Wang, Dafang.,...&Yang, Jinliang.(2020).Evolutionary and functional genomics of DNA methylation in maize domestication and improvement.NATURE COMMUNICATIONS,11(1).
MLA Xu, Gen,et al."Evolutionary and functional genomics of DNA methylation in maize domestication and improvement".NATURE COMMUNICATIONS 11.1(2020).

入库方式： OAI收割

来源：植物研究所

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