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

Overview of attention for article published in BMC Genomics, August 2016
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Title
Identification of favorable SNP alleles and candidate genes for traits related to early maturity via GWAS in upland cotton
Published in
BMC Genomics, August 2016
DOI 10.1186/s12864-016-2875-z
Pubmed ID
Authors

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, Shuxun Yu

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.

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Mendeley readers

The data shown below were compiled from readership statistics for 46 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
China 1 2%
Unknown 45 98%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 16 35%
Student > Master 8 17%
Student > Doctoral Student 5 11%
Researcher 4 9%
Professor > Associate Professor 2 4%
Other 3 7%
Unknown 8 17%
Readers by discipline Count As %
Agricultural and Biological Sciences 26 57%
Biochemistry, Genetics and Molecular Biology 8 17%
Environmental Science 1 2%
Nursing and Health Professions 1 2%
Computer Science 1 2%
Other 0 0%
Unknown 9 20%

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 01 September 2016.
All research outputs
#7,188,738
of 8,314,034 outputs
Outputs from BMC Genomics
#5,185
of 5,866 outputs
Outputs of similar age
#211,327
of 251,801 outputs
Outputs of similar age from BMC Genomics
#239
of 278 outputs
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