Summary
Gossypium hirsutum L. represents the largest source of textile fibre, and China is
one of the largest cotton producing and consuming countries in the world. To
investigate the genetic architecture of the agronomic traits of upland cotton
in China, a diverse and nation-wide 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 3 subpopulations based on 11,975 quantified polymorphic
single-nucleotide polymorphisms (SNPs). By comparing the genetic structure and
phenotypic variation among 3 genetic subpopulations, 7 geographic distributions
and 4 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 3 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
multi-effects in QTLs and inter-associations 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.
DOI: 10.1111/pbi.12722 IF=6.09