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

Publication Overview
TitlePopulation structure and genetic basis of the agronomic traits of upland cotton in China revealed by a genome-wide association study using high-density SNPs
AuthorsHuang C, Nie X, Shen C, You C, Li W, Zhao W, Zhang X, Lin Z
TypeJournal Article
Journal NamePlant Biotechnology Journal
Volume15
Issue11
Year2017
Page(s)1374–1386
CitationHuang C, Nie X, Shen C, You C, Li W, Zhao W, Zhang X, Lin Z. 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. Plant Biotechnol J. 2017 Nov;15(11):1374-1386.

Abstract

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.
Features
This publication contains information about 160 features:
Feature NameUniquenameType
fiber strengthqFS.3T-F2_c19QTL
fiber strengthqFS.3T-F2_c20QTL
fiber strengthqFS.3T-F2_c26QTL
fiber uniformityqFU.3T-F2_c02QTL
fiber uniformityqFU.3T-F2_c03QTL
fiber uniformityqFU.3T-F2_c10.1QTL
fiber uniformityqFU.3T-F2_c10.2QTL
fiber uniformityqFU.3T-F2_c17QTL
fiber uniformityqFU.3T-F2_c19QTL
fiber uniformityqFU.3T-F2_c20QTL
fiber uniformityqFU.3T-F2_c23QTL
lint percentqLP.3T-F2_c05QTL
lint percentqLP.3T-F2_c07QTL
lint percentqLP.3T-F2_c08QTL
lint percentqLP.3T-F2_c09QTL
lint percentqLP.3T-F2_c10.1QTL
lint percentqLP.3T-F2_c10.2QTL
lint percentqLP.3T-F2_c13QTL
lint percentqLP.3T-F2_c19QTL
lint percentqLP.3T-F2_c22.1QTL
lint percentqLP.3T-F2_c22.2QTL
lint percentqLP.3T-F2_c23QTL
lint percentqLP.3T-F2_c24QTL
lint percentqLP.3T-F2_c26QTL
lint yieldqLY.3T-F2_c01QTL

Pages

Projects
This publication contains information about 1 projects:
Project NameDescription
3T-F2-2017
Properties
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URLhttp://onlinelibrary.wiley.com/doi/10.1111/pbi.12722/abstract
Elocation10.1111/pbi.12722