Population structure and genetic basis of the agronomic traits of upland cotton in China revealed by a genome‐wide association study using high‐density SNPs

Cong Huang,Wenxia Zhao,Wu Li,Chao Shen,Chunyuan You,Xianlong Zhang,Zhongxu Lin,Xinhui Nie

doi:10.1111/pbi.12722

Abstract

Summary Gossypium hirsutum L. represents the largest source of textile fibre, and China is one of the largest cotton‐producing and cotton‐consuming countries in the world. To investigate the genetic architecture of the agronomic traits of upland cotton in China, a diverse and nationwide population containing 503 G. hirsutum accessions was collected for a genome‐wide association study (GWAS) on 16 agronomic traits. The accessions were planted in four places from 2012 to 2013 for phenotyping. The CottonSNP63K array and a published high‐density map based on this array were used for genotyping. The 503 G. hirsutum accessions were divided into three subpopulations based on 11 975 quantified polymorphic single‐nucleotide polymorphisms (SNPs). By comparing the genetic structure and phenotypic variation among three genetic subpopulations, seven geographic distributions and four breeding periods, we found that geographic distribution and breeding period were not the determinants of genetic structure. In addition, no obvious phenotypic differentiations were found among the three subpopulations, even though they had different genetic backgrounds. A total of 324 SNPs and 160 candidate quantitative trait loci (QTL) regions were identified as significantly associated with the 16 agronomic traits. A network was established for multieffects in QTLs and interassociations among traits. Thirty‐eight associated regions had pleiotropic effects controlling more than one trait. One candidate gene, Gh_D08G2376, was speculated to control the lint percentage (LP). This GWAS is the first report using high‐resolution SNPs in upland cotton in China to comprehensively investigate agronomic traits, and it provides a fundamental resource for cotton genetic research and breeding.

Highlights

Cotton (Gossypium spp.) is an economically important crop around the world, providing the most natural fibre for the manufacture of textiles
A few accessions were introduced from the Soviet Union (SU) and the United States (USA), such as Deltapine, Coker and Stoneville, which are the founder accessions for cotton breeding in China and have made significant contributions to Chinese cotton production
The relatively larger sample size ensured sufficient genetic variation, and the sample size was similar to the genome-wide association study (GWAS) population sizes used for Arabidopsis thaliana (Zhao et al, 2005), Oryza sativa (Crowell et al, 2016; Famoso et al, 2011), Zea mays (Li et al, 2013a; Wen et al, 2014) and Brassica napus (Xu et al, 2016)

Summary

Introduction

Cotton (Gossypium spp.) is an economically important crop around the world, providing the most natural fibre for the manufacture of textiles. Gossypium contains more than 50 recognized species belonging to eight genome groups (Wendel and Grover, 2015). G. herbaceum (A1), G. arboreum (A2), G. hirsutum (AD1) and G. barbadense (AD2), have been domesticated and cultivated. (2n = 4x = 52, genome size: 2.5 Gb; Li et al, 2014a, 2015; Wendel and Grover, 2015), called upland cotton, is cultivated worldwide and accounts for more than 95% of cotton production (Chen et al, 2007; Zhang et al, 2008). High-end textile products using natural fibre have become increasingly popular. Extensive studies have focused on forward and reverse genetics molecular biology methods to reveal genes for traits in upland cotton

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