title: Genome-wide association study discovered genetic variation and candidate genes of fibre quality traits in Gossypium hirsutum L.
abstract: Genetic improvement of fibre quality is one of the main breeding goals for the upland cotton, Gossypium hirsutum, but there are difficulties with precise selection of traits. Therefore, it is important to improve the understanding of the genetic basis of phenotypic variation. In this study, we conducted phenotyping and genetic variation analyses of 719 diverse accessions of upland cotton based on multiple environment tests and a recently developed Cotton 63K Illumina Infinium SNP array and performed a genome-wide association study (GWAS) of fibre quality traits. A total of 10 511 polymorphic SNPs distributed in 26 chromosomes were screened across the cotton germplasms, and forty-six significant SNPs associated with five fibre quality traits were detected. These significant SNPs were scattered over 15 chromosomes and were involved in 612 unique candidate genes, many related to polysaccharide biosynthesis, signal transduction and protein translocation. Two major haplotypes for fibre length and strength were identified on chromosomes Dt11 and At07. Furthermore, by combining GWAS and transcriptome analysis, we identified 163 and 120 fibre developmental genes related to length and strength, respectively, of which a number of novel genes and 19 promising genes were screened. These results provide new insight into the genetic basis of fibre quality in G. hirsutum and provide candidate SNPs and genes to accelerate the improvement of upland cotton.
authors.affiliation: North China Key Laboratory for Crop Germplasm Resources of Education Ministry/Key Laboratory for Crop Germplasm Resources of Hebei Province, Hebei Agricultural University, Baoding, China.
authors.forename: Zhengwen
authors.initials: Z
authors.lastname: Sun
authors.affiliation: North China Key Laboratory for Crop Germplasm Resources of Education Ministry/Key Laboratory for Crop Germplasm Resources of Hebei Province, Hebei Agricultural University, Baoding, China.
authors.forename: Xingfen
authors.initials: X
authors.lastname: Wang
authors.affiliation: North China Key Laboratory for Crop Germplasm Resources of Education Ministry/Key Laboratory for Crop Germplasm Resources of Hebei Province, Hebei Agricultural University, Baoding, China.
authors.forename: Zhengwen
authors.initials: Z
authors.lastname: Liu
authors.affiliation: North China Key Laboratory for Crop Germplasm Resources of Education Ministry/Key Laboratory for Crop Germplasm Resources of Hebei Province, Hebei Agricultural University, Baoding, China.
authors.forename: Qishen
authors.initials: Q
authors.lastname: Gu
authors.affiliation: North China Key Laboratory for Crop Germplasm Resources of Education Ministry/Key Laboratory for Crop Germplasm Resources of Hebei Province, Hebei Agricultural University, Baoding, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: North China Key Laboratory for Crop Germplasm Resources of Education Ministry/Key Laboratory for Crop Germplasm Resources of Hebei Province, Hebei Agricultural University, Baoding, China.
authors.forename: Zhikun
authors.initials: Z
authors.lastname: Li
authors.affiliation: North China Key Laboratory for Crop Germplasm Resources of Education Ministry/Key Laboratory for Crop Germplasm Resources of Hebei Province, Hebei Agricultural University, Baoding, China.
authors.forename: Huifeng
authors.initials: H
authors.lastname: Ke
authors.affiliation: North China Key Laboratory for Crop Germplasm Resources of Education Ministry/Key Laboratory for Crop Germplasm Resources of Hebei Province, Hebei Agricultural University, Baoding, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Yang
authors.affiliation: North China Key Laboratory for Crop Germplasm Resources of Education Ministry/Key Laboratory for Crop Germplasm Resources of Hebei Province, Hebei Agricultural University, Baoding, China.
authors.forename: Jinhua
authors.initials: J
authors.lastname: Wu
authors.affiliation: North China Key Laboratory for Crop Germplasm Resources of Education Ministry/Key Laboratory for Crop Germplasm Resources of Hebei Province, Hebei Agricultural University, Baoding, China.
authors.forename: Liqiang
authors.initials: L
authors.lastname: Wu
authors.affiliation: North China Key Laboratory for Crop Germplasm Resources of Education Ministry/Key Laboratory for Crop Germplasm Resources of Hebei Province, Hebei Agricultural University, Baoding, China.
authors.forename: Guiyin
authors.initials: G
authors.lastname: Zhang
authors.affiliation: North China Key Laboratory for Crop Germplasm Resources of Education Ministry/Key Laboratory for Crop Germplasm Resources of Hebei Province, Hebei Agricultural University, Baoding, China.
authors.forename: Caiying
authors.initials: C
authors.lastname: Zhang
authors.affiliation: North China Key Laboratory for Crop Germplasm Resources of Education Ministry/Key Laboratory for Crop Germplasm Resources of Hebei Province, Hebei Agricultural University, Baoding, China.
authors.forename: Zhiying
authors.initials: Z
authors.lastname: Ma
mesh_terms: D002874:Chromosome Mapping; D014644:Genetic Variation / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics; D055106:Genome-Wide Association Study / Q000379:methods*; D005838:Genotype; D003368:Gossypium / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D040641:Quantitative Trait Loci / Q000235:genetics
keywords: 
  Gossypium hirsutum
  ; Genome-wide association study; RNA-sequencing; fibre quality; single nucleotide polymorphism