Dissection of the genetic variation and candidate genes of lint percentage by a genome-wide association study in upland cotton

文献类型： 外文期刊

第一作者： Chengxiang Song

作者： Chengxiang Song;Wei Li;Xiaoyu Pei;Yangai Liu;Zhongying Ren;Kunlun He;Fei Zhang;Kuan Sun;Xiaojian Zhou;Xiongfeng Ma;Daigang Yang

作者机构：

期刊名称：THEORETICAL AND APPLIED GENETICS （ 影响因子：5.699； 五年影响因子：5.565 ）

ISSN： 0040-5752

年卷期： 2019 年 132 卷 7 期

页码：

收录情况： SCI

摘要： Key messageA genome-wide associated study identified six novel QTLs for lint percentage. Two candidate genes underlying this trait were also detected.AbstractIncreasing lint percentage (LP) is a core goal of cotton breeding. To better understand the genetic basis of LP, a genome-wide association study (GWAS) was conducted using 276 upland cotton accessions planted in multiple environments and genotyped with a CottonSNP63K array. After filtering, 10,660 high-quality single-nucleotide polymorphisms (SNPs) were retained. Population structure, principal component and neighbor-joining phylogenetic tree analyses divided the accessions into two subpopulations. These results along with linkage disequilibrium decay indicated accessions were not highly structured and exhibited weak relatedness. GWAS uncovered 23 polymorphic SNPs and 15 QTLs significantly associated with LP, with six new QTLs identified. Two candidate genes, Gh_D05G0313 and Gh_D05G1124, both contained one significant SNP, highly expressed during ovule and fiber development stages, implying that the two genes may act as the most promising regulators of LP. Furthermore, the phenotypic value of LP was found to be positively correlated with the number of favorable SNP alleles. These favorable alleles for LP identified in the study may be useful for improving lint yield.

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