Open AccessGenome‐wide association study discovered genetic variation and candidate genes of fibre quality traits in Gossypium hirsutum L.
Author(s) -
Sun Zhengwen,
Wang Xingfen,
Liu Zhengwen,
Gu Qishen,
Zhang Yan,
Li Zhikun,
Ke Huifeng,
Yang Jun,
Wu Jinhua,
Wu Liqiang,
Zhang Guiyin,
Zhang Caiying,
Ma Zhiying
Publication year - 2017
Publication title -
plant biotechnology journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.525
H-Index - 115
eISSN - 1467-7652
pISSN - 1467-7644
DOI - 10.1111/pbi.12693
Subject(s) - biology , candidate gene , single nucleotide polymorphism , genome wide association study , genetics , genetic association , quantitative trait locus , gene , genetic variation , genome , gossypium , snp , snp array , genotype
Summary 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 SNP s distributed in 26 chromosomes were screened across the cotton germplasms, and forty‐six significant SNP s associated with five fibre quality traits were detected. These significant SNP s 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 SNP s and genes to accelerate the improvement of upland cotton.