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Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication

Wang, M.; Tu, L.; Lin, M.; Lin, Z.; Wang, P.; Yang, Q.; Ye, Z.; Shen, C.; Zhou, X.; Zhang, L.; Li, J.; Nie, X.; Li, Z.; Guo, K.; Ma, Y.; Jin, S.; Zhu, L.; Yang, X.; Min, L.; Zhang, Q.; Lindsey, K.; Zhang, X.

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


M. Wang

L. Tu

M. Lin

Z. Lin

P. Wang

Q. Yang

Z. Ye

C. Shen

X. Zhou

L. Zhang

J. Li

X. Nie

Z. Li

K. Guo

Y. Ma

S. Jin

L. Zhu

X. Yang

L. Min

Q. Zhang

X. Zhang


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.

Journal Article Type Article
Acceptance Date Feb 10, 2017
Online Publication Date Mar 6, 2017
Publication Date Apr 1, 2017
Deposit Date Mar 7, 2017
Publicly Available Date Sep 6, 2017
Journal Nature Genetics
Print ISSN 1061-4036
Electronic ISSN 1546-1718
Publisher Nature Research
Peer Reviewed Peer Reviewed
Volume 49
Issue 4
Pages 579-587
Public URL


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