Abstract
BackgroundFiber quality is an important economic trait of cotton, and its improvement is a major goal of cotton breeding. To better understand the genetic mechanisms responsible for fiber quality traits, we conducted a genome-wide association study to identify and mine fiber-quality-related quantitative trait loci (QTLs) and genes.ResultsIn total, 42 single nucleotide polymorphisms (SNPs) and 31 QTLs were identified as being significantly associated with five fiber quality traits. Twenty-five QTLs were identified in previous studies, and six novel QTLs were firstly identified in this study. In the QTL regions, 822 genes were identified and divided into four clusters based on their expression profiles. We also identified two pleiotropic SNPs. The SNP locus i52359Gb was associated with fiber elongation, strength, length and uniformity, while i11316Gh was associated with fiber strength and length. Moreover, these two SNPs were nonsynonymous and located in genes Gh_D09G2376 and Gh_D06G1908, respectively. RT-qPCR analysis revealed that these two genes were preferentially expressed at one or more stages of cotton fiber development, which was consistent with the RNA-seq data. Thus, Gh_D09G2376 and Gh_D06G1908 may be involved in fiber developmental processes.ConclusionsThe findings of this study provide insights into the genetic bases of fiber quality traits, and the identified QTLs or genes may be applicable in cotton breeding to improve fiber quality.
Highlights
Fiber quality is an important economic trait of cotton, and its improvement is a major goal of cotton breeding
Phenotypic characterization of fiber quality traits The 276 diverse upland cotton accessions were obtained from different ecological zones, and the best linear unbiased predictions (BLUPs) of the phenotypic data exhibited abundant variation among accessions
Significant positive correlations were observed among the four traits fiber elongation (FE), fiber strength (FS), fiber length (FL) and fiber uniformity (FU), ranging from 0.51 to 0.84, whereas fiber micronaire (FM) was significantly negatively correlated with FS and FL
Summary
Fiber quality is an important economic trait of cotton, and its improvement is a major goal of cotton breeding. The fiber quality traits of cotton mainly include fiber elongation (FE), fiber micronaire (FM), fiber strength (FS), fiber length (FL) and fiber uniformity (FU) These are all complex quantitative traits that are substantially affected by environmental factors, even though they are mainly controlled by genetic factors [5]. Nearly 1000 quantitative trait loci (QTLs) associated with fiber quality traits and distributed across the 26 cotton chromosomes have been reported using this mapping method [6, 7]. These studies provided important information for fiber-related genetics and accelerated the development of cotton breeding for fiber quality
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