Open AccessGenomic analyses reveal the genetic basis of early maturity and identification of loci and candidate genes in upland cotton ( Gossypium hirsutum L.)
Author(s) -
Li Libei,
Zhang Chi,
Huang Jianqin,
Liu Qibao,
Wei Hengling,
Wang Hantao,
Liu Guoyuan,
Gu Lijiao,
Yu Shuxun
Publication year - 2021
Publication title -
plant biotechnology journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.525
H-Index - 115
eISSN - 1467-7652
pISSN - 1467-7644
DOI - 10.1111/pbi.13446
Subject(s) - biology , gossypium hirsutum , identification (biology) , gene , gossypium , genetics , quantitative trait locus , candidate gene , maturity (psychological) , botany , psychology , developmental psychology
Summary Although upland cotton ( Gossypium hirsutism L.) originated in the tropics, this early maturity cotton can be planted as far north as 46°N in China due to the accumulation of numerous phenotypic and physiological adaptations during domestication. However, how the genome of early maturity cotton has been altered by strong human selection remains largely unknown. Herein, we report a cotton genome variation map generated by the resequencing of 436 cotton accessions. Whole‐genome scans for sweep regions identified 357 putative selection sweeps covering 4.94% (112 Mb) of the upland cotton genome, including 5184 genes. These genes were functionally related to flowering time control, hormone catabolism, ageing and defence response adaptations to environmental changes. A genome‐wide association study (GWAS) for seven early maturity traits identified 307 significant loci, 22.48% (69) of which overlapped with putative selection sweeps that occurred during the artificial selection of early maturity cotton. Several previously undescribed candidate genes associated with early maturity were identified by GWAS. This study provides insights into the genetic basis of early maturity in upland cotton as well as breeding resources for cotton improvement.