Genome-wide Association Study for Carcass Primal Cut Yields Using Single-step Bayesian Approach in Hanwoo Cattle

The importance of meat and carcass quality is growing in beef cattle production to meet both producer and consumer demands. Primal cut yields, which reflect the body compositions of carcass, could determine the carcass grade and, consequently, command premium prices. Despite its importance, there ha...

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Autores principales:	Masoumeh Naserkheil, Hossein Mehrban, Deukmin Lee, Mi Na Park
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	candidate genes QTL carcass primal cut yield single-step GWAS hanwoo Genetics QH426-470
Acceso en línea:	https://doaj.org/article/d471c61f8fc54af98116ceb4922eba17
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spelling	oai:doaj.org-article:d471c61f8fc54af98116ceb4922eba172021-12-01T07:41:17ZGenome-wide Association Study for Carcass Primal Cut Yields Using Single-step Bayesian Approach in Hanwoo Cattle1664-802110.3389/fgene.2021.752424https://doaj.org/article/d471c61f8fc54af98116ceb4922eba172021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fgene.2021.752424/fullhttps://doaj.org/toc/1664-8021The importance of meat and carcass quality is growing in beef cattle production to meet both producer and consumer demands. Primal cut yields, which reflect the body compositions of carcass, could determine the carcass grade and, consequently, command premium prices. Despite its importance, there have been few genome-wide association studies on these traits. This study aimed to identify genomic regions and putative candidate genes related to 10 primal cut traits, including tenderloin, sirloin, striploin, chuck, brisket, top round, bottom round, shank, flank, and rib in Hanwoo cattle using a single-step Bayesian regression (ssBR) approach. After genomic data quality control, 43,987 SNPs from 3,745 genotyped animals were available, of which 3,467 had phenotypic records for the analyzed traits. A total of 16 significant genomic regions (1-Mb window) were identified, of which five large-effect quantitative trait loci (QTLs) located on chromosomes 6 at 38–39 Mb, 11 at 21–22 Mb, 14 at 6–7 Mb and 26–27 Mb, and 19 at 26–27 Mb were associated with more than one trait, while the remaining 11 QTLs were trait-specific. These significant regions were harbored by 154 genes, among which TOX, FAM184B, SPP1, IBSP, PKD2, SDCBP, PIGY, LCORL, NCAPG, and ABCG2 were noteworthy. Enrichment analysis revealed biological processes and functional terms involved in growth and lipid metabolism, such as growth (GO:0040007), muscle structure development (GO:0061061), skeletal system development (GO:0001501), animal organ development (GO:0048513), lipid metabolic process (GO:0006629), response to lipid (GO:0033993), metabolic pathways (bta01100), focal adhesion (bta04510), ECM–receptor interaction (bta04512), fat digestion and absorption (bta04975), and Rap1 signaling pathway (bta04015) being the most significant for the carcass primal cut traits. Thus, identification of quantitative trait loci regions and plausible candidate genes will aid in a better understanding of the genetic and biological mechanisms regulating carcass primal cut yields.Masoumeh NaserkheilHossein MehrbanDeukmin LeeMi Na ParkFrontiers Media S.A.articlecandidate genesQTLcarcass primal cut yieldsingle-step GWAShanwooGeneticsQH426-470ENFrontiers in Genetics, Vol 12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	candidate genes QTL carcass primal cut yield single-step GWAS hanwoo Genetics QH426-470
spellingShingle	candidate genes QTL carcass primal cut yield single-step GWAS hanwoo Genetics QH426-470 Masoumeh Naserkheil Hossein Mehrban Deukmin Lee Mi Na Park Genome-wide Association Study for Carcass Primal Cut Yields Using Single-step Bayesian Approach in Hanwoo Cattle
description	The importance of meat and carcass quality is growing in beef cattle production to meet both producer and consumer demands. Primal cut yields, which reflect the body compositions of carcass, could determine the carcass grade and, consequently, command premium prices. Despite its importance, there have been few genome-wide association studies on these traits. This study aimed to identify genomic regions and putative candidate genes related to 10 primal cut traits, including tenderloin, sirloin, striploin, chuck, brisket, top round, bottom round, shank, flank, and rib in Hanwoo cattle using a single-step Bayesian regression (ssBR) approach. After genomic data quality control, 43,987 SNPs from 3,745 genotyped animals were available, of which 3,467 had phenotypic records for the analyzed traits. A total of 16 significant genomic regions (1-Mb window) were identified, of which five large-effect quantitative trait loci (QTLs) located on chromosomes 6 at 38–39 Mb, 11 at 21–22 Mb, 14 at 6–7 Mb and 26–27 Mb, and 19 at 26–27 Mb were associated with more than one trait, while the remaining 11 QTLs were trait-specific. These significant regions were harbored by 154 genes, among which TOX, FAM184B, SPP1, IBSP, PKD2, SDCBP, PIGY, LCORL, NCAPG, and ABCG2 were noteworthy. Enrichment analysis revealed biological processes and functional terms involved in growth and lipid metabolism, such as growth (GO:0040007), muscle structure development (GO:0061061), skeletal system development (GO:0001501), animal organ development (GO:0048513), lipid metabolic process (GO:0006629), response to lipid (GO:0033993), metabolic pathways (bta01100), focal adhesion (bta04510), ECM–receptor interaction (bta04512), fat digestion and absorption (bta04975), and Rap1 signaling pathway (bta04015) being the most significant for the carcass primal cut traits. Thus, identification of quantitative trait loci regions and plausible candidate genes will aid in a better understanding of the genetic and biological mechanisms regulating carcass primal cut yields.
format	article
author	Masoumeh Naserkheil Hossein Mehrban Deukmin Lee Mi Na Park
author_facet	Masoumeh Naserkheil Hossein Mehrban Deukmin Lee Mi Na Park
author_sort	Masoumeh Naserkheil
title	Genome-wide Association Study for Carcass Primal Cut Yields Using Single-step Bayesian Approach in Hanwoo Cattle
title_short	Genome-wide Association Study for Carcass Primal Cut Yields Using Single-step Bayesian Approach in Hanwoo Cattle
title_full	Genome-wide Association Study for Carcass Primal Cut Yields Using Single-step Bayesian Approach in Hanwoo Cattle
title_fullStr	Genome-wide Association Study for Carcass Primal Cut Yields Using Single-step Bayesian Approach in Hanwoo Cattle
title_full_unstemmed	Genome-wide Association Study for Carcass Primal Cut Yields Using Single-step Bayesian Approach in Hanwoo Cattle
title_sort	genome-wide association study for carcass primal cut yields using single-step bayesian approach in hanwoo cattle
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/d471c61f8fc54af98116ceb4922eba17
work_keys_str_mv	AT masoumehnaserkheil genomewideassociationstudyforcarcassprimalcutyieldsusingsinglestepbayesianapproachinhanwoocattle AT hosseinmehrban genomewideassociationstudyforcarcassprimalcutyieldsusingsinglestepbayesianapproachinhanwoocattle AT deukminlee genomewideassociationstudyforcarcassprimalcutyieldsusingsinglestepbayesianapproachinhanwoocattle AT minapark genomewideassociationstudyforcarcassprimalcutyieldsusingsinglestepbayesianapproachinhanwoocattle
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Genome-wide Association Study for Carcass Primal Cut Yields Using Single-step Bayesian Approach in Hanwoo Cattle

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