Статья

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

Junji SuCollege of Agronomy, Northwest A&F University, Yangling, ChinaChaoyou PangState Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, ChinaHengling WeiState Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, ChinaLibei LiState Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, ChinaBing LiangState Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, ChinaCaixiang WangCollege of Agronomy, Northwest A&F University, Yangling, China. [email protected]Meizhen SongChinese Academy of Agricultural SciencesHantao WangState Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, ChinaShuqi ZhaoState Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, ChinaXiaoyun JiaCollege of Agronomy, Northwest A&F University, Yangling, ChinaGuangzhi MaoState Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, ChinaLong HuangBioinformatics Division, Biomarker Technologies Corporation, Beijing, ChinaDandan GengBioinformatics Division, Biomarker Technologies Corporation, Beijing, ChinaChengshe WangCollege of Agronomy, Northwest A&F University, Yangling, China. [email protected]Shuli FanState Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, China. [email protected]Shuxun YuCollege of Agronomy, Northwest A&F University, Yangling, China. [email protected]

2016en

ABI

Аннотация

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 Dt3 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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Идентификаторы

DOI: 10.1186/s12864-016-2875-z

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Цитирований: 2Использованных источников: 0

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