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

BMC Genomics

Research Article

Dandan Geng¹  Long Huang¹  Chengshe Wang²  Xiaoyun Jia³  Shuxun Yu³  Junji Su⁴  Shuli Fan⁵  Shuqi Zhao⁵  Caixiang Wang⁵  Libei Li⁵  Bing Liang⁵  Hengling Wei⁵  Meizhen Song⁵  Guangzhi Mao⁵  Hantao Wang⁵  Chaoyou Pang⁵ 

[1] Bioinformatics Division, Biomarker Technologies Corporation, Beijing, China;College of Agronomy, Northwest A&F University, Yangling, 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;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;

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

DOI  :  10.1186/s12864-016-2875-z

 received in 2016-02-23, accepted in 2016-07-05,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundEarly 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).ResultsA 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 Dt3 and a potential candidate gene (CotAD_01947) for early maturity were detected.ConclusionsThis 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.

【 授权许可】

CC BY   
© The Author(s). 2016