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Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication

信息来源:作物遗传改良国家重点实验室    发布时间:2017-05-08
Maojun Wang,1,
  • Lili Tu,1,
  • Min Lin,1, 2,
  • Zhongxu Lin,1,
  • Pengcheng Wang,1,
  • Qingyong Yang,1, 2,
  • Zhengxiu Ye,1,
  • Chao Shen,1,
  • Jianying Li,1,
  • Lin Zhang,1,
  • Xiaolin Zhou,1,
  • Xinhui Nie,3,
  • Zhonghua Li,1,
  • Kai Guo,1,
  • Yizan Ma,1,
  • Cong Huang,1,
  • Shuangxia Jin,1,
  • Longfu Zhu,1,
  • Xiyan Yang,4,
  • Ling Min,4,
  • Daojun Yuan,4,
  • Qinghua Zhang,1,
  • Keith Lindsey5,
  • & Xianlong Zhang1,
  •  

    Journal name:Nature GeneticsVolume:49,Pages:579–587Year published:(2017)DOI:doi:10.1038/ng.3807Received04 August 2016Accepted10 February 2017Published online06 March 2017

    Abstract

      Comparative population genomics offers an excellent opportunity for unraveling the genetic history of crop domestication. Upland cotton (Gossypium hirsutum) has long been an important economic crop, but a genome-wide and evolutionary understanding of the effects of human selection is lacking. Here, we describe a variation map for 352 wild and domesticated cotton accessions. We scanned 93 domestication sweeps occupying 74 Mb of the A subgenome and 104 Mb of the D subgenome, and identified 19 candidate loci for fiber-quality-related traits through a genome-wide association study. We provide evidence showing asymmetric subgenome domestication for directional selection of long fibers. Global analyses of DNase I–hypersensitive sites and 3D genome architecture, linking functional variants to gene transcription, demonstrate the effects of domestication on cis-regulatory divergence. This study provides new insights into the evolution of gene organization, regulation and adaptation in a major crop, and should serve as a rich resource for genome-based cotton improvement.
     Full Paper: http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3807.html

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