title: Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication.
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.
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
authors.forename: Maojun
authors.initials: M
authors.lastname: Wang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
authors.forename: Lili
authors.initials: L
authors.lastname: Tu
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.|Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China.
authors.forename: Min
authors.initials: M
authors.lastname: Lin
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
authors.forename: Zhongxu
authors.initials: Z
authors.lastname: Lin
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
authors.forename: Pengcheng
authors.initials: P
authors.lastname: Wang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.|Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China.
authors.forename: Qingyong
authors.identifier: http://orcid.org/0000-0002-3510-8906
authors.initials: Q
authors.lastname: Yang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
authors.forename: Zhengxiu
authors.initials: Z
authors.lastname: Ye
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
authors.forename: Chao
authors.initials: C
authors.lastname: Shen
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
authors.forename: Jianying
authors.initials: J
authors.lastname: Li
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
authors.forename: Lin
authors.initials: L
authors.lastname: Zhang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
authors.forename: Xiaolin
authors.initials: X
authors.lastname: Zhou
authors.affiliation: Key Laboratory of Oasis Eco-agriculture of the Xinjiang Production and Construction Corps, College of Agronomy, Shihezi University, Shihezi, China.
authors.forename: Xinhui
authors.initials: X
authors.lastname: Nie
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
authors.forename: Zhonghua
authors.initials: Z
authors.lastname: Li
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
authors.forename: Kai
authors.initials: K
authors.lastname: Guo
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
authors.forename: Yizan
authors.initials: Y
authors.lastname: Ma
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
authors.forename: Cong
authors.initials: C
authors.lastname: Huang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
authors.forename: Shuangxia
authors.initials: S
authors.lastname: Jin
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
authors.forename: Longfu
authors.initials: L
authors.lastname: Zhu
authors.affiliation: College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.
authors.forename: Xiyan
authors.initials: X
authors.lastname: Yang
authors.affiliation: College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.
authors.forename: Ling
authors.initials: L
authors.lastname: Min
authors.affiliation: College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.
authors.forename: Daojun
authors.initials: D
authors.lastname: Yuan
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
authors.forename: Qinghua
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: Department of Biosciences, Durham University, Durham, UK.
authors.forename: Keith
authors.initials: K
authors.lastname: Lindsey
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
authors.forename: Xianlong
authors.initials: X
authors.lastname: Zhang
mesh_terms: D002874:Chromosome Mapping / Q000379:methods; D003850:Deoxyribonuclease I / Q000235:genetics; D000071278:Domestication; D018745:Genome, Plant / Q000235:genetics*; D055106:Genome-Wide Association Study / Q000379:methods; D003368:Gossypium / Q000235:genetics*; D012641:Selection, Genetic / Q000235:genetics*; D014158:Transcription, Genetic / Q000235:genetics
chemical_list: D003850:Deoxyribonuclease I