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Genome-wide association study reveals the genetic basis of fiber quality traits in upland cotton (Gossypium hirsutum L.).
BMC Plant Biology ( IF 5.3 ) Pub Date : 2020-08-27 , DOI: 10.1186/s12870-020-02611-0
Wei Liu 1 , Chengxiang Song 2 , Zhongying Ren 2 , Zhiqiang Zhang 2 , Xiaoyu Pei 2 , Yangai Liu 2 , Kunlun He 2 , Fei Zhang 2 , Junjie Zhao 2 , Jie Zhang 3 , Xingxing Wang 2, 3 , Daigang Yang 2, 3 , Wei Li 1, 2, 3
Affiliation  

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. 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. 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.

中文翻译:

全基因组关联研究揭示了陆地棉(Gossypium hirsutum L.)纤维品质性状的遗传基础。

纤维质量是棉花的重要经济特性,而提高纤维质量是棉花育种的主要目标。为了更好地了解造成纤维品质性状的遗传机制,我们进行了全基因组关联研究,以鉴定和挖掘与纤维品质有关的定量性状位点(QTL)和基因。总共鉴定出42个单核苷酸多态性(SNP)和31个QTL与5个纤维品质性状显着相关。在先前的研究中鉴定了25个QTL,在本研究中首次鉴定了6个新的QTL。在QTL区域中,鉴定了822个基因,并根据其表达谱将其分为四个簇。我们还确定了两个多效性SNP。SNP位点i52359Gb与纤维伸长率,强度,长度和均匀性有关,而i11316Gh与纤维强度和长度有关。而且,这两个SNP不是同义词,分别位于基因Gh_D09G2376和Gh_D06G1908中。RT-qPCR分析显示这两个基因在棉纤维发育的一个或多个阶段优先表达,这与RNA-seq数据一致。因此,Gh_D09G2376和Gh_D06G1908可能参与了纤​​维发育过程。这项研究的发现为纤维品质性状的遗传基础提供了见识,而且鉴定出的QTL或基因可能适用于棉花育种以提高纤维品质。RT-qPCR分析显示这两个基因在棉纤维发育的一个或多个阶段优先表达,这与RNA-seq数据一致。因此,Gh_D09G2376和Gh_D06G1908可能参与了纤​​维发育过程。这项研究的发现为纤维品质性状的遗传基础提供了见识,而且鉴定出的QTL或基因可能适用于棉花育种以提高纤维品质。RT-qPCR分析显示这两个基因在棉纤维发育的一个或多个阶段优先表达,这与RNA-seq数据一致。因此,Gh_D09G2376和Gh_D06G1908可能参与了纤​​维发育过程。这项研究的发现为纤维品质性状的遗传基础提供了见识,而且鉴定出的QTL或基因可能适用于棉花育种以提高纤维品质。
更新日期:2020-08-27
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