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Genome-Wide Detection of Genetic Loci and Candidate Genes for Body Conformation Traits in Duroc × Landrace × Yorkshire Crossbred Pigs
The Duroc × (Landrace × Yorkshire) hybrid pigs (DLY) are the most popular commercial pigs, providing consumers with the largest source of pork. In order to gain more insights into the genetic architecture of economically important traits in pigs, we performed a genome-wide association study (GWAS) u...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Frontiers Media S.A.
2021
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8542986/ https://www.ncbi.nlm.nih.gov/pubmed/34707635 http://dx.doi.org/10.3389/fgene.2021.664343 |
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author | Zhang, Hui Zhuang, Zhanwei Yang, Ming Ding, Rongrong Quan, Jianping Zhou, Shenping Gu, Ting Xu, Zheng Zheng, Enqin Cai, Gengyuan Yang, Jie Wu, Zhenfang |
author_facet | Zhang, Hui Zhuang, Zhanwei Yang, Ming Ding, Rongrong Quan, Jianping Zhou, Shenping Gu, Ting Xu, Zheng Zheng, Enqin Cai, Gengyuan Yang, Jie Wu, Zhenfang |
author_sort | Zhang, Hui |
collection | PubMed |
description | The Duroc × (Landrace × Yorkshire) hybrid pigs (DLY) are the most popular commercial pigs, providing consumers with the largest source of pork. In order to gain more insights into the genetic architecture of economically important traits in pigs, we performed a genome-wide association study (GWAS) using the GeneSeek Porcine 50 K SNP Chip to map the genetic markers and genes associated with body conformation traits (BCT) in 311 DLY pigs. The quantitative traits analyzed included body weight (BW), carcass length (CL), body length (BL), body height (BH), and body mass index (BMI). BMI was defined as BMI(CL), BMI(BL), and BMI(BH), respectively, based on CL, BL, and BH phenotypic data. We identified 82 SNPs for the seven traits by GEMMA-based and FarmCPU-based GWASs. Both methods detected two quantitative trait loci (QTL) on SSC8 and SSC17 for body conformation traits. Several candidate genes (such as TNFAIP3, KDM4C, HSPG2, BMP2, PLCB4, and GRM5) were found to be associated with body weight and body conformation traits in pigs. Notably, the BMP2 gene had pleiotropic effects on CL, BL, BH, BMI(CL), and BMI(BL) and is proposed as a strong candidate gene for body size due to its involvement in growth and bone development. Furthermore, gene set enrichment analysis indicated that most of the pathway terms are associated with regulation of cell growth, negative regulation of cell population proliferation, and chondrocyte differentiation. We anticipate that these results further advance our understanding of the genetic architecture of body conformation traits in the popular commercial DLY pigs and provide new insights into the genetic architecture of BMI in pigs. |
format | Online Article Text |
id | pubmed-8542986 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-85429862021-10-26 Genome-Wide Detection of Genetic Loci and Candidate Genes for Body Conformation Traits in Duroc × Landrace × Yorkshire Crossbred Pigs Zhang, Hui Zhuang, Zhanwei Yang, Ming Ding, Rongrong Quan, Jianping Zhou, Shenping Gu, Ting Xu, Zheng Zheng, Enqin Cai, Gengyuan Yang, Jie Wu, Zhenfang Front Genet Genetics The Duroc × (Landrace × Yorkshire) hybrid pigs (DLY) are the most popular commercial pigs, providing consumers with the largest source of pork. In order to gain more insights into the genetic architecture of economically important traits in pigs, we performed a genome-wide association study (GWAS) using the GeneSeek Porcine 50 K SNP Chip to map the genetic markers and genes associated with body conformation traits (BCT) in 311 DLY pigs. The quantitative traits analyzed included body weight (BW), carcass length (CL), body length (BL), body height (BH), and body mass index (BMI). BMI was defined as BMI(CL), BMI(BL), and BMI(BH), respectively, based on CL, BL, and BH phenotypic data. We identified 82 SNPs for the seven traits by GEMMA-based and FarmCPU-based GWASs. Both methods detected two quantitative trait loci (QTL) on SSC8 and SSC17 for body conformation traits. Several candidate genes (such as TNFAIP3, KDM4C, HSPG2, BMP2, PLCB4, and GRM5) were found to be associated with body weight and body conformation traits in pigs. Notably, the BMP2 gene had pleiotropic effects on CL, BL, BH, BMI(CL), and BMI(BL) and is proposed as a strong candidate gene for body size due to its involvement in growth and bone development. Furthermore, gene set enrichment analysis indicated that most of the pathway terms are associated with regulation of cell growth, negative regulation of cell population proliferation, and chondrocyte differentiation. We anticipate that these results further advance our understanding of the genetic architecture of body conformation traits in the popular commercial DLY pigs and provide new insights into the genetic architecture of BMI in pigs. Frontiers Media S.A. 2021-10-11 /pmc/articles/PMC8542986/ /pubmed/34707635 http://dx.doi.org/10.3389/fgene.2021.664343 Text en Copyright © 2021 Zhang, Zhuang, Yang, Ding, Quan, Zhou, Gu, Xu, Zheng, Cai, Yang and Wu. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Genetics Zhang, Hui Zhuang, Zhanwei Yang, Ming Ding, Rongrong Quan, Jianping Zhou, Shenping Gu, Ting Xu, Zheng Zheng, Enqin Cai, Gengyuan Yang, Jie Wu, Zhenfang Genome-Wide Detection of Genetic Loci and Candidate Genes for Body Conformation Traits in Duroc × Landrace × Yorkshire Crossbred Pigs |
title | Genome-Wide Detection of Genetic Loci and Candidate Genes for Body Conformation Traits in Duroc × Landrace × Yorkshire Crossbred Pigs |
title_full | Genome-Wide Detection of Genetic Loci and Candidate Genes for Body Conformation Traits in Duroc × Landrace × Yorkshire Crossbred Pigs |
title_fullStr | Genome-Wide Detection of Genetic Loci and Candidate Genes for Body Conformation Traits in Duroc × Landrace × Yorkshire Crossbred Pigs |
title_full_unstemmed | Genome-Wide Detection of Genetic Loci and Candidate Genes for Body Conformation Traits in Duroc × Landrace × Yorkshire Crossbred Pigs |
title_short | Genome-Wide Detection of Genetic Loci and Candidate Genes for Body Conformation Traits in Duroc × Landrace × Yorkshire Crossbred Pigs |
title_sort | genome-wide detection of genetic loci and candidate genes for body conformation traits in duroc × landrace × yorkshire crossbred pigs |
topic | Genetics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8542986/ https://www.ncbi.nlm.nih.gov/pubmed/34707635 http://dx.doi.org/10.3389/fgene.2021.664343 |
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