Open AccessResequencing core accessions of a pedigree identifies derivation of genomic segments and key agronomic trait loci during cotton improvement
Author(s) -
Ma Xiongfeng,
Wang Zhenyu,
Li Wei,
Zhang Yuzhou,
Zhou Xiaojian,
Liu Yangai,
Ren Zhongying,
Pei Xiaoyu,
Zhou Kehai,
Zhang Wensheng,
He Kunlun,
Zhang Fei,
Liu Junfang,
Ma Wenyu,
Xiao Guanghui,
Yang Daigang
Publication year - 2019
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.13013
Subject(s) - biology , lint , domestication , linkage disequilibrium , quantitative trait locus , trait , genetics , heterosis , genome , genomics , genetic diversity , microbiology and biotechnology , single nucleotide polymorphism , gene , agronomy , hybrid , genotype , population , computer science , programming language , demography , sociology
Summary Upland cotton ( Gossypium hirsutum ) is the world's largest source of natural fibre and dominates the global textile industry. Hybrid cotton varieties exhibit strong heterosis that confers high fibre yields, yet the genome‐wide effects of artificial selection that have influenced Upland cotton during its breeding history are poorly understood. Here, we resequenced Upland cotton genomes and constructed a variation map of an intact breeding pedigree comprising seven elite and 19 backbone parents. Compared to wild accessions, the 26 pedigree accessions underwent strong artificial selection during domestication that has resulted in reduced genetic diversity but stronger linkage disequilibrium and higher extents of selective sweeps. In contrast to the backbone parents, the elite parents have acquired significantly improved agronomic traits, with an especially pronounced increase in the lint percentage. Notably, identify by descent ( IBD ) tracking revealed that the elite parents inherited abundant beneficial trait segments and loci from the backbone parents and our combined analyses led to the identification of a core genomic segment which was inherited in the elite lines from the parents Zhong 7263 and Ejing 1 and that was strongly associated with lint percentage. Additionally, SNP correlation analysis of this core segment showed that a non‐synonymous SNP (A‐to‐G) site in a gene encoding the cell wall‐associated receptor‐like kinase 3 (Gh WAKL 3) protein was highly correlated with increased lint percentage. Our results substantially increase the valuable genomics resources available for future genetic and functional genomics studies of cotton and reveal insights that will facilitate yield increases in the molecular breeding of cotton.