title: Identification of favorable SNP alleles and candidate genes for traits related to early maturity via GWAS in upland cotton.
abstract: 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).
  
  
  
  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 Dt3 and a potential candidate gene (CotAD_01947) for early maturity were detected.
  
  
  
  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.
authors: 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.
authors: Junji
authors: J
authors: Su
authors: State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
authors: Chaoyou
authors: C
authors: Pang
authors: State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
authors: Hengling
authors: H
authors: Wei
authors: State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
authors: Libei
authors: L
authors: Li
authors: State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
authors: Bing
authors: B
authors: Liang
authors: State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
authors: Caixiang
authors: C
authors: Wang
authors: State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
authors: Meizhen
authors: M
authors: Song
authors: State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
authors: Hantao
authors: H
authors: Wang
authors: State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
authors: Shuqi
authors: S
authors: Zhao
authors: 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.
authors: Xiaoyun
authors: X
authors: Jia
authors: State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China.
authors: Guangzhi
authors: G
authors: Mao
authors: Bioinformatics Division, Biomarker Technologies Corporation, Beijing, China.
authors: Long
authors: L
authors: Huang
authors: Bioinformatics Division, Biomarker Technologies Corporation, Beijing, China.
authors: Dandan
authors: D
authors: Geng
authors: College of Agronomy, Northwest A&F University, Yangling, China. wangcs2008@126.com.
authors: Chengshe
authors: C
authors: Wang
authors: State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China. fsl427@126.com.
authors: Shuli
authors: S
authors: Fan
authors: College of Agronomy, Northwest A&F University, Yangling, China. ysx195311@163.com.|State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China. ysx195311@163.com.
authors: Shuxun
authors: S
authors: Yu
mesh_terms: D001947:Breeding; D002874:Chromosome Mapping; D032561:Cotton Fiber; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D005838:Genotype; D003368:Gossypium / Q000235:genetics*; D015810:Linkage Disequilibrium; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D040641:Quantitative Trait Loci / Q000235:genetics*
keywords: Candidate gene; Early maturity traits; GWAS; Gossypium hirsutum L; SLAF-seq; SNP alleles