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Searching for new loci and candidate genes for economically important traits through gene-based association analysis of Simmental cattle

Single-marker genome-wide association study (GWAS) is a convenient strategy of genetic analysis that has been successful in detecting the association of a number of single-nucleotide polymorphisms (SNPs) with quantitative traits. However, analysis of individual SNPs can only account for a small prop...

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Autores principales: Xia, Jiangwei, Fan, Huizhong, Chang, Tianpeng, Xu, Lingyang, Zhang, Wengang, Song, Yuxin, Zhu, Bo, Zhang, Lupei, Gao, Xue, Chen, Yan, Li, Junya, Gao, Huijiang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5294460/
https://www.ncbi.nlm.nih.gov/pubmed/28169328
http://dx.doi.org/10.1038/srep42048
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author Xia, Jiangwei
Fan, Huizhong
Chang, Tianpeng
Xu, Lingyang
Zhang, Wengang
Song, Yuxin
Zhu, Bo
Zhang, Lupei
Gao, Xue
Chen, Yan
Li, Junya
Gao, Huijiang
author_facet Xia, Jiangwei
Fan, Huizhong
Chang, Tianpeng
Xu, Lingyang
Zhang, Wengang
Song, Yuxin
Zhu, Bo
Zhang, Lupei
Gao, Xue
Chen, Yan
Li, Junya
Gao, Huijiang
author_sort Xia, Jiangwei
collection PubMed
description Single-marker genome-wide association study (GWAS) is a convenient strategy of genetic analysis that has been successful in detecting the association of a number of single-nucleotide polymorphisms (SNPs) with quantitative traits. However, analysis of individual SNPs can only account for a small proportion of genetic variation and offers only limited knowledge of complex traits. This inadequacy may be overcome by employing a gene-based GWAS analytic approach, which can be considered complementary to the single-SNP association analysis. Here we performed an initial single-SNP GWAS for bone weight (BW) and meat pH value with a total of 770,000 SNPs in 1141 Simmental cattle. Additionally, 21836 cattle genes collected from the Ensembl Genes 83 database were analyzed to find supplementary evidence to support the importance of gene-based association study. Results of the single SNP-based association study showed that there were 11 SNPs significantly associated with bone weight (BW) and two SNPs associated with meat pH value. Interestingly, all of these SNPs were located in genes detected by the gene-based association study.
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spelling pubmed-52944602017-02-10 Searching for new loci and candidate genes for economically important traits through gene-based association analysis of Simmental cattle Xia, Jiangwei Fan, Huizhong Chang, Tianpeng Xu, Lingyang Zhang, Wengang Song, Yuxin Zhu, Bo Zhang, Lupei Gao, Xue Chen, Yan Li, Junya Gao, Huijiang Sci Rep Article Single-marker genome-wide association study (GWAS) is a convenient strategy of genetic analysis that has been successful in detecting the association of a number of single-nucleotide polymorphisms (SNPs) with quantitative traits. However, analysis of individual SNPs can only account for a small proportion of genetic variation and offers only limited knowledge of complex traits. This inadequacy may be overcome by employing a gene-based GWAS analytic approach, which can be considered complementary to the single-SNP association analysis. Here we performed an initial single-SNP GWAS for bone weight (BW) and meat pH value with a total of 770,000 SNPs in 1141 Simmental cattle. Additionally, 21836 cattle genes collected from the Ensembl Genes 83 database were analyzed to find supplementary evidence to support the importance of gene-based association study. Results of the single SNP-based association study showed that there were 11 SNPs significantly associated with bone weight (BW) and two SNPs associated with meat pH value. Interestingly, all of these SNPs were located in genes detected by the gene-based association study. Nature Publishing Group 2017-02-07 /pmc/articles/PMC5294460/ /pubmed/28169328 http://dx.doi.org/10.1038/srep42048 Text en Copyright © 2017, The Author(s) http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
spellingShingle Article
Xia, Jiangwei
Fan, Huizhong
Chang, Tianpeng
Xu, Lingyang
Zhang, Wengang
Song, Yuxin
Zhu, Bo
Zhang, Lupei
Gao, Xue
Chen, Yan
Li, Junya
Gao, Huijiang
Searching for new loci and candidate genes for economically important traits through gene-based association analysis of Simmental cattle
title Searching for new loci and candidate genes for economically important traits through gene-based association analysis of Simmental cattle
title_full Searching for new loci and candidate genes for economically important traits through gene-based association analysis of Simmental cattle
title_fullStr Searching for new loci and candidate genes for economically important traits through gene-based association analysis of Simmental cattle
title_full_unstemmed Searching for new loci and candidate genes for economically important traits through gene-based association analysis of Simmental cattle
title_short Searching for new loci and candidate genes for economically important traits through gene-based association analysis of Simmental cattle
title_sort searching for new loci and candidate genes for economically important traits through gene-based association analysis of simmental cattle
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5294460/
https://www.ncbi.nlm.nih.gov/pubmed/28169328
http://dx.doi.org/10.1038/srep42048
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