A combined GWAS approach reveals key loci for socially-affected traits in Yorkshire pigs

Socially affected traits in pigs are controlled by direct genetic effects and social genetic effects, which can make elucidation of their genetic architecture challenging. We evaluated the genetic basis of direct genetic effects and social genetic effects by combining single-locus and haplotype-base...

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Autores principales: Wu, Pingxian, Wang, Kai, Zhou, Jie, Chen, Dejuan, Jiang, Anan, Jiang, Yanzhi, Zhu, Li, Qiu, Xiaotian, Li, Xuewei, Tang, Guoqing
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2021
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Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8292486/
https://www.ncbi.nlm.nih.gov/pubmed/34285319
http://dx.doi.org/10.1038/s42003-021-02416-3
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author Wu, Pingxian
Wang, Kai
Zhou, Jie
Chen, Dejuan
Jiang, Anan
Jiang, Yanzhi
Zhu, Li
Qiu, Xiaotian
Li, Xuewei
Tang, Guoqing
author_facet Wu, Pingxian
Wang, Kai
Zhou, Jie
Chen, Dejuan
Jiang, Anan
Jiang, Yanzhi
Zhu, Li
Qiu, Xiaotian
Li, Xuewei
Tang, Guoqing
author_sort Wu, Pingxian
collection PubMed
description Socially affected traits in pigs are controlled by direct genetic effects and social genetic effects, which can make elucidation of their genetic architecture challenging. We evaluated the genetic basis of direct genetic effects and social genetic effects by combining single-locus and haplotype-based GWAS on imputed whole-genome sequences. Nineteen SNPs and 25 haplotype loci are identified for direct genetic effects on four traits: average daily feed intake, average daily gain, days to 100 kg and time in feeder per day. Nineteen SNPs and 11 haplotype loci are identified for social genetic effects on average daily feed intake, average daily gain, days to 100 kg and feeding speed. Two significant SNPs from single-locus GWAS (SSC6:18,635,874 and SSC6:18,635,895) are shared by a significant haplotype locus with haplotype alleles ‘GGG’ for both direct genetic effects and social genetic effects in average daily feed intake. A candidate gene, MT3, which is involved in growth, nervous, and immune processes, is identified. We demonstrate the genetic differences between direct genetic effects and social genetic effects and provide an anchor for investigating the genetic architecture underlying direct genetic effects and social genetic effects on socially affected traits in pigs.
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spelling pubmed-82924862021-07-23 A combined GWAS approach reveals key loci for socially-affected traits in Yorkshire pigs Wu, Pingxian Wang, Kai Zhou, Jie Chen, Dejuan Jiang, Anan Jiang, Yanzhi Zhu, Li Qiu, Xiaotian Li, Xuewei Tang, Guoqing Commun Biol Article Socially affected traits in pigs are controlled by direct genetic effects and social genetic effects, which can make elucidation of their genetic architecture challenging. We evaluated the genetic basis of direct genetic effects and social genetic effects by combining single-locus and haplotype-based GWAS on imputed whole-genome sequences. Nineteen SNPs and 25 haplotype loci are identified for direct genetic effects on four traits: average daily feed intake, average daily gain, days to 100 kg and time in feeder per day. Nineteen SNPs and 11 haplotype loci are identified for social genetic effects on average daily feed intake, average daily gain, days to 100 kg and feeding speed. Two significant SNPs from single-locus GWAS (SSC6:18,635,874 and SSC6:18,635,895) are shared by a significant haplotype locus with haplotype alleles ‘GGG’ for both direct genetic effects and social genetic effects in average daily feed intake. A candidate gene, MT3, which is involved in growth, nervous, and immune processes, is identified. We demonstrate the genetic differences between direct genetic effects and social genetic effects and provide an anchor for investigating the genetic architecture underlying direct genetic effects and social genetic effects on socially affected traits in pigs. Nature Publishing Group UK 2021-07-20 /pmc/articles/PMC8292486/ /pubmed/34285319 http://dx.doi.org/10.1038/s42003-021-02416-3 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Wu, Pingxian
Wang, Kai
Zhou, Jie
Chen, Dejuan
Jiang, Anan
Jiang, Yanzhi
Zhu, Li
Qiu, Xiaotian
Li, Xuewei
Tang, Guoqing
A combined GWAS approach reveals key loci for socially-affected traits in Yorkshire pigs
title A combined GWAS approach reveals key loci for socially-affected traits in Yorkshire pigs
title_full A combined GWAS approach reveals key loci for socially-affected traits in Yorkshire pigs
title_fullStr A combined GWAS approach reveals key loci for socially-affected traits in Yorkshire pigs
title_full_unstemmed A combined GWAS approach reveals key loci for socially-affected traits in Yorkshire pigs
title_short A combined GWAS approach reveals key loci for socially-affected traits in Yorkshire pigs
title_sort combined gwas approach reveals key loci for socially-affected traits in yorkshire pigs
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8292486/
https://www.ncbi.nlm.nih.gov/pubmed/34285319
http://dx.doi.org/10.1038/s42003-021-02416-3
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