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.

doi:10.1038/ng.3807

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.

Authors

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

Professor Keith Lindsey keith.lindsey@durham.ac.uk
Professor

X. Zhang

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.

Citation

Wang, M., Tu, L., Lin, M., Lin, Z., Wang, P., Yang, Q., …Zhang, X. (2017). Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication. Nature Genetics, 49(4), 579-587. https://doi.org/10.1038/ng.3807

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
DOI	https://doi.org/10.1038/ng.3807