Identification of favorable SNP alleles and candidate genes for traits related to early maturity via GWAS in upland cotton

文献类型： 外文期刊

第一作者： Junji Su

作者： Junji Su;Chaoyou Pang;Hengling Wei;Libei Li;Bing Liang;Caixiang Wang;Meizhen Song;Hantao Wang;Shuqi Zhao;Xiaoyun Jia;Guangzhi Mao;Long Huang;Dandan Geng;Chengshe Wang;Shuli Fan

作者机构： College of Agronomy, Northwest A&F University, Yangling, China;State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China;Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, Xinjiang, China;State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China;College of Agronomy, Northwest A&F University, Yangling, China;State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China;Bioinformatics Division, Biomarker Technologies Corporation, Beijing, China;College of Agronomy, Northwest A&F University, Yangling, China

关键词： Gossypium hirsutum L;GWAS;SLAF-seq;Early maturity traits;Candidate gene;SNP alleles

期刊名称：BMC GENOMICS （ 2020影响因子：3.969； 五年影响因子：4.478 ）

ISSN： 1471-2164

年卷期： 2016 年 17 卷

页码：

收录情况： SCI

摘要： Background: Early maturity is one of the most important and complex agronomic traits in upland cotton (Gossypium hirsutum L). To dissect the genetic architecture of this agronomically important trait, a population consisting of 355 upland cotton germplasm accessions was genotyped using the specific-locus amplified fragment sequencing (SLAF-seq) approach, of which a subset of 185 lines representative of the diversity among the accessions was phenotypically characterized for six early maturity traits in four environments. A genome-wide association study (GWAS) was conducted using the generalized linear model (GLM) and mixed linear model (MLM). Results: A total of 81,675 SNPs in 355 upland cotton accessions were discovered using SLAF-seq and were subsequently used in GWAS. Thirteen significant associations between eight SNP loci and five early maturity traits were successfully identified using the GLM and MLM; two of the 13 associations were common between the models. By computing phenotypic effect values for the associations detected at each locus, 11 highly favorable SNP alleles were identified for five early maturity traits. Moreover, dosage pyramiding effects of the highly favorable SNP alleles and significant linear correlations between the numbers of highly favorable alleles and the phenotypic values of the target traits were identified. Most importantly, a major locus (rs13562854) on chromosome D(t)3 and a potential candidate gene (CotAD_ 01947) for early maturity were detected. Conclusions: This study identified highly favorable SNP alleles and candidate genes associated with early maturity traits in upland cotton. The results demonstrate that GWAS is a powerful tool for dissecting complex traits and identifying candidate genes. The highly favorable SNP alleles and candidate genes for early maturity traits identified in this study should be show high potential for improvement of early maturity in future cotton breeding programs.

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