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Targeted resequencing of GWAS loci reveals novel genetic variants for milk production traits

BACKGROUND: Genome wide association study (GWAS) has been proven to be a powerful tool for detecting genomic variants associated with complex traits. However, the specific genes and causal variants underlying these traits remain unclear. RESULTS: Here, we used target-enrichment strategy coupled with...

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Autores principales: Jiang, Li, Liu, Xuan, Yang, Jie, Wang, Haifei, Jiang, Jicai, Liu, Lili, He, Sang, Ding, Xiangdong, Liu, Jianfeng, Zhang, Qin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4377845/
https://www.ncbi.nlm.nih.gov/pubmed/25510969
http://dx.doi.org/10.1186/1471-2164-15-1105
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author Jiang, Li
Liu, Xuan
Yang, Jie
Wang, Haifei
Jiang, Jicai
Liu, Lili
He, Sang
Ding, Xiangdong
Liu, Jianfeng
Zhang, Qin
author_facet Jiang, Li
Liu, Xuan
Yang, Jie
Wang, Haifei
Jiang, Jicai
Liu, Lili
He, Sang
Ding, Xiangdong
Liu, Jianfeng
Zhang, Qin
author_sort Jiang, Li
collection PubMed
description BACKGROUND: Genome wide association study (GWAS) has been proven to be a powerful tool for detecting genomic variants associated with complex traits. However, the specific genes and causal variants underlying these traits remain unclear. RESULTS: Here, we used target-enrichment strategy coupled with next generation sequencing technique to study target regions which were found to be associated with milk production traits in dairy cattle in our previous GWAS. Among the large amount of novel variants detected by targeted resequencing, we selected 200 SNPs for further association study in a population consisting of 2634 cows. Sixty six SNPs distributed in 53 genes were identified to be associated significantly with on milk production traits. Of the 53 genes, 26 were consistent with our previous GWAS results. We further chose 20 significant genes to analyze their mRNA expression in different tissues of lactating cows, of which 15 were specificly highly expressed in mammary gland. CONCLUSIONS: Our study illustrates the potential for identifying causal mutations for milk production traits using target-enrichment resequencing and extends the results of GWAS by discovering new and potentially functional mutations. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-1105) contains supplementary material, which is available to authorized users.
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spelling pubmed-43778452015-03-31 Targeted resequencing of GWAS loci reveals novel genetic variants for milk production traits Jiang, Li Liu, Xuan Yang, Jie Wang, Haifei Jiang, Jicai Liu, Lili He, Sang Ding, Xiangdong Liu, Jianfeng Zhang, Qin BMC Genomics Research Article BACKGROUND: Genome wide association study (GWAS) has been proven to be a powerful tool for detecting genomic variants associated with complex traits. However, the specific genes and causal variants underlying these traits remain unclear. RESULTS: Here, we used target-enrichment strategy coupled with next generation sequencing technique to study target regions which were found to be associated with milk production traits in dairy cattle in our previous GWAS. Among the large amount of novel variants detected by targeted resequencing, we selected 200 SNPs for further association study in a population consisting of 2634 cows. Sixty six SNPs distributed in 53 genes were identified to be associated significantly with on milk production traits. Of the 53 genes, 26 were consistent with our previous GWAS results. We further chose 20 significant genes to analyze their mRNA expression in different tissues of lactating cows, of which 15 were specificly highly expressed in mammary gland. CONCLUSIONS: Our study illustrates the potential for identifying causal mutations for milk production traits using target-enrichment resequencing and extends the results of GWAS by discovering new and potentially functional mutations. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-1105) contains supplementary material, which is available to authorized users. BioMed Central 2014-12-15 /pmc/articles/PMC4377845/ /pubmed/25510969 http://dx.doi.org/10.1186/1471-2164-15-1105 Text en © Jiang et al.; licensee BioMed Central Ltd. 2014 This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Jiang, Li
Liu, Xuan
Yang, Jie
Wang, Haifei
Jiang, Jicai
Liu, Lili
He, Sang
Ding, Xiangdong
Liu, Jianfeng
Zhang, Qin
Targeted resequencing of GWAS loci reveals novel genetic variants for milk production traits
title Targeted resequencing of GWAS loci reveals novel genetic variants for milk production traits
title_full Targeted resequencing of GWAS loci reveals novel genetic variants for milk production traits
title_fullStr Targeted resequencing of GWAS loci reveals novel genetic variants for milk production traits
title_full_unstemmed Targeted resequencing of GWAS loci reveals novel genetic variants for milk production traits
title_short Targeted resequencing of GWAS loci reveals novel genetic variants for milk production traits
title_sort targeted resequencing of gwas loci reveals novel genetic variants for milk production traits
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4377845/
https://www.ncbi.nlm.nih.gov/pubmed/25510969
http://dx.doi.org/10.1186/1471-2164-15-1105
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