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Identification of genes related to intramuscular fat content of pigs using genome-wide association study
OBJECTIVE: The aim of this study is to identify single nucleotide polymorphisms (SNPs) and genes related to pig IMF and estimate the heritability of intramuscular fat content (IMF). METHODS: Genome-wide association study (GWAS) on 704 inbred Berkshires was performed for IMF. To consider the inbreedi...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Asian-Australasian Association of Animal Production Societies (AAAP) and Korean Society of Animal Science and Technology (KSAST)
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5767496/ https://www.ncbi.nlm.nih.gov/pubmed/28728355 http://dx.doi.org/10.5713/ajas.17.0218 |
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author | Won, Sohyoung Jung, Jaehoon Park, Eungwoo Kim, Heebal |
author_facet | Won, Sohyoung Jung, Jaehoon Park, Eungwoo Kim, Heebal |
author_sort | Won, Sohyoung |
collection | PubMed |
description | OBJECTIVE: The aim of this study is to identify single nucleotide polymorphisms (SNPs) and genes related to pig IMF and estimate the heritability of intramuscular fat content (IMF). METHODS: Genome-wide association study (GWAS) on 704 inbred Berkshires was performed for IMF. To consider the inbreeding among samples, associations of the SNPs with IMF were tested as random effects in a mixed linear model using the genetic relationship matrix by GEMMA. Significant genes were compared with reported pig IMF quantitative trait loci (QTL) regions and functional classification of the identified genes were also performed. Heritability of IMF was estimated by GCTA tool. RESULTS: Total 365 SNPs were found to be significant from a cutoff of p-value <0.01 and the 365 significant SNPs were annotated across 120 genes. Twenty five genes were on pig IMF QTL regions. Bone morphogenetic protein-binding endothelial cell precursor-derived regulator, forkhead box protein O1, ectodysplasin A receptor, ring finger protein 149, cluster of differentiation, tyrosine-protein phosphatase non-receptor type 1, SRY (sex determining region Y)-box 9 (SOX9), MYC proto-oncogene, and macrophage migration inhibitory factor were related to mitogen-activated protein kinase pathway, which regulates the differentiation to adipocytes. These genes and the genes mapped on QTLs could be the candidate genes affecting IMF. Heritability of IMF was estimated as 0.52, which was relatively high, suggesting that a considerable portion of the total variance of IMF is explained by the SNP information. CONCLUSION: Our results can contribute to breeding pigs with better IMF and therefore, producing pork with better sensory qualities. |
format | Online Article Text |
id | pubmed-5767496 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Asian-Australasian Association of Animal Production Societies (AAAP) and Korean Society of Animal Science and Technology (KSAST) |
record_format | MEDLINE/PubMed |
spelling | pubmed-57674962018-02-01 Identification of genes related to intramuscular fat content of pigs using genome-wide association study Won, Sohyoung Jung, Jaehoon Park, Eungwoo Kim, Heebal Asian-Australas J Anim Sci Article OBJECTIVE: The aim of this study is to identify single nucleotide polymorphisms (SNPs) and genes related to pig IMF and estimate the heritability of intramuscular fat content (IMF). METHODS: Genome-wide association study (GWAS) on 704 inbred Berkshires was performed for IMF. To consider the inbreeding among samples, associations of the SNPs with IMF were tested as random effects in a mixed linear model using the genetic relationship matrix by GEMMA. Significant genes were compared with reported pig IMF quantitative trait loci (QTL) regions and functional classification of the identified genes were also performed. Heritability of IMF was estimated by GCTA tool. RESULTS: Total 365 SNPs were found to be significant from a cutoff of p-value <0.01 and the 365 significant SNPs were annotated across 120 genes. Twenty five genes were on pig IMF QTL regions. Bone morphogenetic protein-binding endothelial cell precursor-derived regulator, forkhead box protein O1, ectodysplasin A receptor, ring finger protein 149, cluster of differentiation, tyrosine-protein phosphatase non-receptor type 1, SRY (sex determining region Y)-box 9 (SOX9), MYC proto-oncogene, and macrophage migration inhibitory factor were related to mitogen-activated protein kinase pathway, which regulates the differentiation to adipocytes. These genes and the genes mapped on QTLs could be the candidate genes affecting IMF. Heritability of IMF was estimated as 0.52, which was relatively high, suggesting that a considerable portion of the total variance of IMF is explained by the SNP information. CONCLUSION: Our results can contribute to breeding pigs with better IMF and therefore, producing pork with better sensory qualities. Asian-Australasian Association of Animal Production Societies (AAAP) and Korean Society of Animal Science and Technology (KSAST) 2018-02 2017-06-27 /pmc/articles/PMC5767496/ /pubmed/28728355 http://dx.doi.org/10.5713/ajas.17.0218 Text en Copyright © 2018 by Asian-Australasian Journal of Animal Sciences This is an open-access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Article Won, Sohyoung Jung, Jaehoon Park, Eungwoo Kim, Heebal Identification of genes related to intramuscular fat content of pigs using genome-wide association study |
title | Identification of genes related to intramuscular fat content of pigs using genome-wide association study |
title_full | Identification of genes related to intramuscular fat content of pigs using genome-wide association study |
title_fullStr | Identification of genes related to intramuscular fat content of pigs using genome-wide association study |
title_full_unstemmed | Identification of genes related to intramuscular fat content of pigs using genome-wide association study |
title_short | Identification of genes related to intramuscular fat content of pigs using genome-wide association study |
title_sort | identification of genes related to intramuscular fat content of pigs using genome-wide association study |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5767496/ https://www.ncbi.nlm.nih.gov/pubmed/28728355 http://dx.doi.org/10.5713/ajas.17.0218 |
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