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

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.

Linkage and association mapping reveals the genetic basis of brown fibre (Gossypium hirsutum)

“…In total, 19 QTLs for fibre quality and 10 QTLs for fibre yield were identified (Figures S12–S25; Table S17). Compared with the published GWAS results for cotton ( G. hirsutum ) (Huang et al ., ; Sun et al ., ; Wang et al ., ), many new QTLs responsible for fibre quality and yield were discovered in this new panel including 100 brown fibre accessions.…”

“…A population structure mostly results from geographic isolation and gene exchange isolation, and it is an important factor in genome‐wide association analysis (Huang et al ., ). In this study, a distinctive population structure was found between the brown and white fibre accessions (Figure ); furthermore, a genome‐wide analysis of selection signatures showed that many SNPs ( F ST > 0.5) were significantly differentiated between the brown and white fibre cotton groups (Tables S14 and S15).…”

“…Compared with other association analysis of fibre traits (Huang et al ., ; Wang et al ., ), some new QTLs related to fibre quality and yield were discovered in this study, and favourable alleles have been enriched in the elite cultivars (Table S18). Due to the pleiotropy of QTLs, some QTLs overlapped within a given region of a chromosome, such as qFU‐A02‐2 , qSF‐A02‐2 and qFL‐A02‐1 ; and the Gh_A02G0758 gene has been identified as the candidate gene for these three QTLs (Figure ).…”

“…The pedigree of 51 accessions introduced from breeding institutes in China was unknown due to the old age of breeding of these accessions. Additionally, 109 white fibre cotton (G. hirsutum) accessions that were previously used in association mapping in our laboratory were selected for the population structure and selection signature analyses (Huang et al, 2017;Nie et al, 2016;Wang et al, 2017). The 100 brown fibre accessions and 21 white fibre accessions selected from the 109 white fibre accessions based on different cultivation areas and genetic diversity of SSR markers (Nie et al, 2016) were phenotyped for the colour, yield and fibre quality traits (Tables S3 and S4).…”

Genetic Mapping in Cotton

“…Association analysis conducted for fiber quality using CottonSNP63K in a germplasm collection of 503 genotypes at genome-wide level [154]. The populations were differentiated into three subgroups on the basis of 11975 SNPs and found that genetic structure is not based on geographic based.…”