Genome and haplotype provide insights into the population differentiation and breeding improvement of Gossypium barbadense

Nian Wang; Yuanxue Li; Qingying Meng; Meilin Chen; Mi Wu; Ruiting Zhang; Zhiyong Xu; Jie Sun; Xianlong Zhang; Xinhui Nie; Daojun Yuan; Zhongxu Lin

doi:10.1016/j.jare.2023.02.002

Genome and haplotype provide insights into the population differentiation and breeding improvement of Gossypium barbadense

J Adv Res. 2023 Dec:54:15-27. doi: 10.1016/j.jare.2023.02.002. Epub 2023 Feb 10.

Authors

Nian Wang¹, Yuanxue Li², Qingying Meng³, Meilin Chen⁴, Mi Wu⁵, Ruiting Zhang⁶, Zhiyong Xu⁷, Jie Sun⁸, Xianlong Zhang⁹, Xinhui Nie¹⁰, Daojun Yuan¹¹, Zhongxu Lin¹²

Affiliations

¹ National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China. Electronic address: wangnian@webmail.hzau.edu.cn.
² National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China. Electronic address: liyx1124@163.com.
³ National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China. Electronic address: qymeng1996@foxmail.com.
⁴ National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China. Electronic address: 1204514079@qq.com.
⁵ National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China. Electronic address: wumi@webmail.hzau.edu.cn.
⁶ National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China. Electronic address: 934520453@qq.com.
⁷ National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China. Electronic address: 17097462507@163.com.
⁸ Key Laboratory of Oasis Ecology Agricultural of Xinjiang Bingtuan, College of Agriculture, Shihezi University, Shihezi 832000, Xinjiang, China. Electronic address: sunjie@shzu.edu.cn.
⁹ National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China. Electronic address: xlzhang@mail.hzau.edu.cn.
¹⁰ Key Laboratory of Oasis Ecology Agricultural of Xinjiang Bingtuan, College of Agriculture, Shihezi University, Shihezi 832000, Xinjiang, China. Electronic address: xjnxh2004130@126.com.
¹¹ National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China. Electronic address: robert@mail.hzau.edu.cn.
¹² National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Hubei Hongshan Laboratory, Wuhan 430070, China; Key Laboratory of Oasis Ecology Agricultural of Xinjiang Bingtuan, College of Agriculture, Shihezi University, Shihezi 832000, Xinjiang, China. Electronic address: linzhongxu@mail.hzau.edu.cn.

Abstract

Introduction: Sea-island cotton (Gossypium barbadense, Gb) is one of the major sources of high-grade natural fiber. Besides the common annual Gb cotton, perennial Gb cotton is also cultivated, but studies on perennial Gb cotton are rare.

Objectives: We aimed to make a systematic analysis of perennial sea-island cotton and lay a foundation for its utilization in breeding, and try to identify the representative structural variations (SVs) in sea-island cotton, and to reveal the population differentiation and adaptive improvement of sea-island cotton.

Methods: Through genome assembly of one perennial Gb cotton accession (named Gb_M210936) and comparative genome analysis, variations during Gb cotton domestication were identified by comparing Gb_M210936 with annual Gb accession 3-79 and with wild allotetraploid cotton G. darwinii. Six perennial Gb accessions combining with the resequenced 1,129 cotton accessions were used to conduct population and genetic analysis. Large haplotype blocks (haploblocks), generated from interspecific introgressions and intraspecific inversions, were identified and were used to analyze their effects on population differentiation and agronomic traits of sea-island cotton.

Results: One reference genome of perennial sea-island cotton was assembled. Representative SVs in sea-island cotton were identified, and 31 SVs were found to be associated with agronomic traits. Perennial Gb cotton had a closer kinship with the wild-to-landrace continuum Gb cotton from south America where Gb cotton is originally domesticated. Haploblocks were associated with agronomic traits improvement of sea-island cotton, promoted sea-island cotton differentiation into three subgroups, were suffered from breeding selection, and may drive Gb cotton to be adapted to central Asian.

Conclusion: Our study made up the lack of perennial Gb cotton genome, and clarified that exotic introgressions improved the traits of sea-island cotton, promoted the population differentiation, and drove sea-island cotton adaptive to central Asia, which will provide new insights for the genetic breeding improvement of sea-island cottons.

Keywords: Gossypium barbadense; Haplotype; Perennial accession; Population structure; Selection and domestication; Structural variation.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Genome, Plant / genetics
Gossypium* / genetics
Haplotypes
Phenotype
Plant Breeding*