Genome-wide association study reveals the genetic basis of fiber quality traits in upland cotton ( Gossypium hirsutum L.
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RESEARCH ARTICLE
Open Access
Genome-wide association study reveals the genetic basis of fiber quality traits in upland cotton (Gossypium hirsutum L.) Wei Liu1†, Chengxiang Song2†, Zhongying Ren2, Zhiqiang Zhang2, Xiaoyu Pei2, Yangai Liu2, Kunlun He2, Fei Zhang2, Junjie Zhao2, Jie Zhang3, Xingxing Wang2,3, Daigang Yang2,3 and Wei Li1,2,3*
Abstract Background: Fiber 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. Results: In 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. Conclusions: The 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. Keywords: Upland cotton, Fiber quality, Genome-wide association study, Single nucleotide polymorphism, Quantitative trait locus
Background Cotton (Gossypium spp.) is an important economic crop, and the major source of natural fibers for the textile industry worldwide [1]. Upland cotton (Gossypium hirsutum L.), an allotetraploid species, has the advantages of wide adaptability and high production. Consequently, it * Correspondence: [email protected] † Wei Liu and Chengxiang Song contributed equally to this work. 1 Collaborative Innovation Center of Henan Grain Crops, Agronomy College, Henan Agricultural University, Zhengzhou 450002, China 2 State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China Full list of author information is available at the end of the article
is used to produce approximately 95% of the world’s cotton fiber [2]. In the past few decades, cotton breeders have been mainly focused on improving cotton yield. At present, with improvements in the quality of consumers’ lives and in textile technology, the demand for highquality fiber is increasing [3, 4]. Thus, improving fiber quality has become a new target of cotton breeding. Howeve
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