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Genome–wide association study of carcass weight in commercial Hanwoo cattle

OBJECTIVE: The objective of the present study was to validate genes and genomic regions associated with carcass weight using a low-density single nucleotide polymorphism (SNP) Chip in Hanwoo cattle breed. METHODS: Commercial Hanwoo steers (n = 220) were genotyped with 20K GeneSeek genomic profiler B...

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Autores principales: Edea, Zewdu, Jeoung, Yeong Ho, Shin, Sung-Sub, Ku, Jaeul, Seo, Sungbo, Kim, Il-Hoi, Kim, Sang-Wook, Kim, Kwan-Suk
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
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5838337/
https://www.ncbi.nlm.nih.gov/pubmed/29103288
http://dx.doi.org/10.5713/ajas.17.0276
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author Edea, Zewdu
Jeoung, Yeong Ho
Shin, Sung-Sub
Ku, Jaeul
Seo, Sungbo
Kim, Il-Hoi
Kim, Sang-Wook
Kim, Kwan-Suk
author_facet Edea, Zewdu
Jeoung, Yeong Ho
Shin, Sung-Sub
Ku, Jaeul
Seo, Sungbo
Kim, Il-Hoi
Kim, Sang-Wook
Kim, Kwan-Suk
author_sort Edea, Zewdu
collection PubMed
description OBJECTIVE: The objective of the present study was to validate genes and genomic regions associated with carcass weight using a low-density single nucleotide polymorphism (SNP) Chip in Hanwoo cattle breed. METHODS: Commercial Hanwoo steers (n = 220) were genotyped with 20K GeneSeek genomic profiler BeadChip. After applying the quality control of criteria of a call rate ≥90% and minor allele frequency (MAF) ≥0.01, a total of 15,235 autosomal SNPs were left for genome-wide association (GWA) analysis. The GWA tests were performed using single-locus mixed linear model. Age at slaughter was fitted as fixed effect and sire included as a covariate. The level of genome-wide significance was set at 3.28×10(−6) (0.05/15,235), corresponding to Bonferroni correction for 15,235 multiple independent tests. RESULTS: By employing EMMAX approach which is based on a mixed linear model and accounts for population stratification and relatedness, we identified 17 and 16 loci significantly (p<0.001) associated with carcass weight for the additive and dominant models, respectively. The second most significant (p = 0.000049) SNP (ARS-BFGL-NGS-28234) on bovine chromosome 4 (BTA4) at 21 Mb had an allele substitution effect of 43.45 kg. Some of the identified regions on BTA2, 6, 14, 22, and 24 were previously reported to be associated with quantitative trait loci for carcass weight in several beef cattle breeds. CONCLUSION: This is the first genome-wide association study using SNP chips on commercial Hanwoo steers, and some of the loci newly identified in this study may help to better DNA markers that determine increased beef production in commercial Hanwoo cattle. Further studies using a larger sample size will allow confirmation of the candidates identified in this study.
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spelling pubmed-58383372018-03-21 Genome–wide association study of carcass weight in commercial Hanwoo cattle Edea, Zewdu Jeoung, Yeong Ho Shin, Sung-Sub Ku, Jaeul Seo, Sungbo Kim, Il-Hoi Kim, Sang-Wook Kim, Kwan-Suk Asian-Australas J Anim Sci Article OBJECTIVE: The objective of the present study was to validate genes and genomic regions associated with carcass weight using a low-density single nucleotide polymorphism (SNP) Chip in Hanwoo cattle breed. METHODS: Commercial Hanwoo steers (n = 220) were genotyped with 20K GeneSeek genomic profiler BeadChip. After applying the quality control of criteria of a call rate ≥90% and minor allele frequency (MAF) ≥0.01, a total of 15,235 autosomal SNPs were left for genome-wide association (GWA) analysis. The GWA tests were performed using single-locus mixed linear model. Age at slaughter was fitted as fixed effect and sire included as a covariate. The level of genome-wide significance was set at 3.28×10(−6) (0.05/15,235), corresponding to Bonferroni correction for 15,235 multiple independent tests. RESULTS: By employing EMMAX approach which is based on a mixed linear model and accounts for population stratification and relatedness, we identified 17 and 16 loci significantly (p<0.001) associated with carcass weight for the additive and dominant models, respectively. The second most significant (p = 0.000049) SNP (ARS-BFGL-NGS-28234) on bovine chromosome 4 (BTA4) at 21 Mb had an allele substitution effect of 43.45 kg. Some of the identified regions on BTA2, 6, 14, 22, and 24 were previously reported to be associated with quantitative trait loci for carcass weight in several beef cattle breeds. CONCLUSION: This is the first genome-wide association study using SNP chips on commercial Hanwoo steers, and some of the loci newly identified in this study may help to better DNA markers that determine increased beef production in commercial Hanwoo cattle. Further studies using a larger sample size will allow confirmation of the candidates identified in this study. Asian-Australasian Association of Animal Production Societies (AAAP) and Korean Society of Animal Science and Technology (KSAST) 2018-03 2017-11-03 /pmc/articles/PMC5838337/ /pubmed/29103288 http://dx.doi.org/10.5713/ajas.17.0276 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
Edea, Zewdu
Jeoung, Yeong Ho
Shin, Sung-Sub
Ku, Jaeul
Seo, Sungbo
Kim, Il-Hoi
Kim, Sang-Wook
Kim, Kwan-Suk
Genome–wide association study of carcass weight in commercial Hanwoo cattle
title Genome–wide association study of carcass weight in commercial Hanwoo cattle
title_full Genome–wide association study of carcass weight in commercial Hanwoo cattle
title_fullStr Genome–wide association study of carcass weight in commercial Hanwoo cattle
title_full_unstemmed Genome–wide association study of carcass weight in commercial Hanwoo cattle
title_short Genome–wide association study of carcass weight in commercial Hanwoo cattle
title_sort genome–wide association study of carcass weight in commercial hanwoo cattle
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5838337/
https://www.ncbi.nlm.nih.gov/pubmed/29103288
http://dx.doi.org/10.5713/ajas.17.0276
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