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Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication.

Wang, M. and Tu, L. and Lin, M. and Lin, Z. and Wang, P. and Yang, Q. and Ye, Z. and Shen, C. and Zhou, X. and Zhang, L. and Li, J. and Nie, X. and Li, Z. and Guo, K. and Ma, Y. and Jin, S. and Zhu, L. and Yang, X. and Min, L. and Zhang, Q. and Lindsey, K. and Zhang, X. (2017) 'Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication.', Nature genetics., 49 (4). pp. 579-587.


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.

Item Type:Article
Full text:(AM) Accepted Manuscript
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Date accepted:10 February 2017
Date deposited:07 March 2017
Date of first online publication:06 March 2017
Date first made open access:06 September 2017

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