Implementing meta-analysis from genome-wide association studies for pork quality traits

Autores
Bernal Rubio, Yeni Liliana; Gualdron Duarte, Jose Luis; Bates, R. O.; Ernst, C. W.; Nonneman, D.; Rohrer, G. A.; King, A.; Schackelford, S. D.; Wheeler, T. L.; Cantet, Rodolfo Juan Carlos; Steibel, J. P.
Año de publicación
2015
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Pork quality plays an important role in the meat processing industry. Thus, different methodologies have been implemented to elucidate the genetic architecture of traits affecting meat quality. One of the most common and widely used approaches is to perform genome-wide association (GWA) studies. However, a limitation of many GWA in animal breeding is thelimited power due to small sample sizes in animal populations. One alternative is to implement a metaanalysis of GWA (MA-GWA) combining results from independent association studies. The objective of this study was to identify significant genomic regions associated with meat quality traits by performing MA-GWA for 8 different traits in 3 independent pig populations.Results from MA-GWA were used to search for genes possibly associated with the set of evaluated traits. Data from 3 pig data sets (U.S. Meat Animal Research Center, commercial, and Michigan State University Pig Resource Population) were used. A MA was implementedby combining z-scores derived for each SNP in every population and then weighting them using the inverse of estimated variance of SNP effects. A search for annotated genes retrieved genes previously reported as candidates for shear force (calpain-1 catalytic subunit [CAPN1] and calpastatin [CAST]), as well as for ultimate pH, purge loss, and cook loss (protein kinase,AMP-activated, γ 3 noncatalytic subunit [PRKAG3]). In addition, novel candidate genes were identified for intramuscular fat and cook loss (acyl-CoA synthetase family member 3 mitochondrial [ACSF3]) and for the objective measure of muscle redness, CIE a* (glycogensynthase 1, muscle [GYS1] and ferritin, light polypeptide [FTL]). Thus, implementation of MA-GWA allowed integration of results for economically relevant traits and identified novel genes to be tested as candidates for meat quality traits in pig populations.
Fil: Bernal Rubio, Yeni Liliana. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal; Argentina. Michigan State University; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Gualdron Duarte, Jose Luis. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Bates, R. O.. Michigan State University; Estados Unidos
Fil: Ernst, C. W.. Michigan State University; Estados Unidos
Fil: Nonneman, D.. Clay Center; Estados Unidos
Fil: Rohrer, G. A.. Clay Center; Estados Unidos
Fil: King, A.. Clay Center; Estados Unidos
Fil: Schackelford, S. D.. Clay Center; Estados Unidos
Fil: Wheeler, T. L.. Clay Center; Estados Unidos
Fil: Cantet, Rodolfo Juan Carlos. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Steibel, J. P.. Michigan State University; Estados Unidos
Materia
CANDIDATE GENES
GENOME-WIDE ASSOCIATION
MEAT QUALITY
META-ANALYSIS
PIGS
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/85072
Acceder
id CONICETDig_419b4d107b9d7b942ded17277eb51ab9
oai_identifier_str oai:ri.conicet.gov.ar:11336/85072
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Implementing meta-analysis from genome-wide association studies for pork quality traitsBernal Rubio, Yeni LilianaGualdron Duarte, Jose LuisBates, R. O.Ernst, C. W.Nonneman, D.Rohrer, G. A.King, A.Schackelford, S. D.Wheeler, T. L.Cantet, Rodolfo Juan CarlosSteibel, J. P.CANDIDATE GENESGENOME-WIDE ASSOCIATIONMEAT QUALITYMETA-ANALYSISPIGShttps://purl.org/becyt/ford/4.2https://purl.org/becyt/ford/4Pork quality plays an important role in the meat processing industry. Thus, different methodologies have been implemented to elucidate the genetic architecture of traits affecting meat quality. One of the most common and widely used approaches is to perform genome-wide association (GWA) studies. However, a limitation of many GWA in animal breeding is thelimited power due to small sample sizes in animal populations. One alternative is to implement a metaanalysis of GWA (MA-GWA) combining results from independent association studies. The objective of this study was to identify significant genomic regions associated with meat quality traits by performing MA-GWA for 8 different traits in 3 independent pig populations.Results from MA-GWA were used to search for genes possibly associated with the set of evaluated traits. Data from 3 pig data sets (U.S. Meat Animal Research Center, commercial, and Michigan State University Pig Resource Population) were used. A MA was implementedby combining z-scores derived for each SNP in every population and then weighting them using the inverse of estimated variance of SNP effects. A search for annotated genes retrieved genes previously reported as candidates for shear force (calpain-1 catalytic subunit [CAPN1] and calpastatin [CAST]), as well as for ultimate pH, purge loss, and cook loss (protein kinase,AMP-activated, γ 3 noncatalytic subunit [PRKAG3]). In addition, novel candidate genes were identified for intramuscular fat and cook loss (acyl-CoA synthetase family member 3 mitochondrial [ACSF3]) and for the objective measure of muscle redness, CIE a* (glycogensynthase 1, muscle [GYS1] and ferritin, light polypeptide [FTL]). Thus, implementation of MA-GWA allowed integration of results for economically relevant traits and identified novel genes to be tested as candidates for meat quality traits in pig populations.Fil: Bernal Rubio, Yeni Liliana. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal; Argentina. Michigan State University; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Gualdron Duarte, Jose Luis. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Bates, R. O.. Michigan State University; Estados UnidosFil: Ernst, C. W.. Michigan State University; Estados UnidosFil: Nonneman, D.. Clay Center; Estados UnidosFil: Rohrer, G. A.. Clay Center; Estados UnidosFil: King, A.. Clay Center; Estados UnidosFil: Schackelford, S. D.. Clay Center; Estados UnidosFil: Wheeler, T. L.. Clay Center; Estados UnidosFil: Cantet, Rodolfo Juan Carlos. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Steibel, J. P.. Michigan State University; Estados UnidosAmerican Society of Animal Science2015-12info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/85072Bernal Rubio, Yeni Liliana; Gualdron Duarte, Jose Luis; Bates, R. O.; Ernst, C. W.; Nonneman, D.; et al.; Implementing meta-analysis from genome-wide association studies for pork quality traits; American Society of Animal Science; Journal of Animal Science; 93; 12-2015; 5607-56170021-8812CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://www.animalsciencepublications.org/publications/jas/abstracts/93/12/5607info:eu-repo/semantics/altIdentifier/doi/10.2527/jas2015-9502info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-10-15T15:09:22Zoai:ri.conicet.gov.ar:11336/85072instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-10-15 15:09:23.082CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Implementing meta-analysis from genome-wide association studies for pork quality traits
title Implementing meta-analysis from genome-wide association studies for pork quality traits
spellingShingle Implementing meta-analysis from genome-wide association studies for pork quality traits
Bernal Rubio, Yeni Liliana
CANDIDATE GENES
GENOME-WIDE ASSOCIATION
MEAT QUALITY
META-ANALYSIS
PIGS
title_short Implementing meta-analysis from genome-wide association studies for pork quality traits
title_full Implementing meta-analysis from genome-wide association studies for pork quality traits
title_fullStr Implementing meta-analysis from genome-wide association studies for pork quality traits
title_full_unstemmed Implementing meta-analysis from genome-wide association studies for pork quality traits
title_sort Implementing meta-analysis from genome-wide association studies for pork quality traits
dc.creator.none.fl_str_mv Bernal Rubio, Yeni Liliana
Gualdron Duarte, Jose Luis
Bates, R. O.
Ernst, C. W.
Nonneman, D.
Rohrer, G. A.
King, A.
Schackelford, S. D.
Wheeler, T. L.
Cantet, Rodolfo Juan Carlos
Steibel, J. P.
author Bernal Rubio, Yeni Liliana
author_facet Bernal Rubio, Yeni Liliana
Gualdron Duarte, Jose Luis
Bates, R. O.
Ernst, C. W.
Nonneman, D.
Rohrer, G. A.
King, A.
Schackelford, S. D.
Wheeler, T. L.
Cantet, Rodolfo Juan Carlos
Steibel, J. P.
author_role author
author2 Gualdron Duarte, Jose Luis
Bates, R. O.
Ernst, C. W.
Nonneman, D.
Rohrer, G. A.
King, A.
Schackelford, S. D.
Wheeler, T. L.
Cantet, Rodolfo Juan Carlos
Steibel, J. P.
author2_role author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv CANDIDATE GENES
GENOME-WIDE ASSOCIATION
MEAT QUALITY
META-ANALYSIS
PIGS
topic CANDIDATE GENES
GENOME-WIDE ASSOCIATION
MEAT QUALITY
META-ANALYSIS
PIGS
purl_subject.fl_str_mv https://purl.org/becyt/ford/4.2
https://purl.org/becyt/ford/4
dc.description.none.fl_txt_mv Pork quality plays an important role in the meat processing industry. Thus, different methodologies have been implemented to elucidate the genetic architecture of traits affecting meat quality. One of the most common and widely used approaches is to perform genome-wide association (GWA) studies. However, a limitation of many GWA in animal breeding is thelimited power due to small sample sizes in animal populations. One alternative is to implement a metaanalysis of GWA (MA-GWA) combining results from independent association studies. The objective of this study was to identify significant genomic regions associated with meat quality traits by performing MA-GWA for 8 different traits in 3 independent pig populations.Results from MA-GWA were used to search for genes possibly associated with the set of evaluated traits. Data from 3 pig data sets (U.S. Meat Animal Research Center, commercial, and Michigan State University Pig Resource Population) were used. A MA was implementedby combining z-scores derived for each SNP in every population and then weighting them using the inverse of estimated variance of SNP effects. A search for annotated genes retrieved genes previously reported as candidates for shear force (calpain-1 catalytic subunit [CAPN1] and calpastatin [CAST]), as well as for ultimate pH, purge loss, and cook loss (protein kinase,AMP-activated, γ 3 noncatalytic subunit [PRKAG3]). In addition, novel candidate genes were identified for intramuscular fat and cook loss (acyl-CoA synthetase family member 3 mitochondrial [ACSF3]) and for the objective measure of muscle redness, CIE a* (glycogensynthase 1, muscle [GYS1] and ferritin, light polypeptide [FTL]). Thus, implementation of MA-GWA allowed integration of results for economically relevant traits and identified novel genes to be tested as candidates for meat quality traits in pig populations.
Fil: Bernal Rubio, Yeni Liliana. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal; Argentina. Michigan State University; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Gualdron Duarte, Jose Luis. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Bates, R. O.. Michigan State University; Estados Unidos
Fil: Ernst, C. W.. Michigan State University; Estados Unidos
Fil: Nonneman, D.. Clay Center; Estados Unidos
Fil: Rohrer, G. A.. Clay Center; Estados Unidos
Fil: King, A.. Clay Center; Estados Unidos
Fil: Schackelford, S. D.. Clay Center; Estados Unidos
Fil: Wheeler, T. L.. Clay Center; Estados Unidos
Fil: Cantet, Rodolfo Juan Carlos. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Steibel, J. P.. Michigan State University; Estados Unidos
description Pork quality plays an important role in the meat processing industry. Thus, different methodologies have been implemented to elucidate the genetic architecture of traits affecting meat quality. One of the most common and widely used approaches is to perform genome-wide association (GWA) studies. However, a limitation of many GWA in animal breeding is thelimited power due to small sample sizes in animal populations. One alternative is to implement a metaanalysis of GWA (MA-GWA) combining results from independent association studies. The objective of this study was to identify significant genomic regions associated with meat quality traits by performing MA-GWA for 8 different traits in 3 independent pig populations.Results from MA-GWA were used to search for genes possibly associated with the set of evaluated traits. Data from 3 pig data sets (U.S. Meat Animal Research Center, commercial, and Michigan State University Pig Resource Population) were used. A MA was implementedby combining z-scores derived for each SNP in every population and then weighting them using the inverse of estimated variance of SNP effects. A search for annotated genes retrieved genes previously reported as candidates for shear force (calpain-1 catalytic subunit [CAPN1] and calpastatin [CAST]), as well as for ultimate pH, purge loss, and cook loss (protein kinase,AMP-activated, γ 3 noncatalytic subunit [PRKAG3]). In addition, novel candidate genes were identified for intramuscular fat and cook loss (acyl-CoA synthetase family member 3 mitochondrial [ACSF3]) and for the objective measure of muscle redness, CIE a* (glycogensynthase 1, muscle [GYS1] and ferritin, light polypeptide [FTL]). Thus, implementation of MA-GWA allowed integration of results for economically relevant traits and identified novel genes to be tested as candidates for meat quality traits in pig populations.
publishDate 2015
dc.date.none.fl_str_mv 2015-12
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/85072
Bernal Rubio, Yeni Liliana; Gualdron Duarte, Jose Luis; Bates, R. O.; Ernst, C. W.; Nonneman, D.; et al.; Implementing meta-analysis from genome-wide association studies for pork quality traits; American Society of Animal Science; Journal of Animal Science; 93; 12-2015; 5607-5617
0021-8812
CONICET Digital
CONICET
url http://hdl.handle.net/11336/85072
identifier_str_mv Bernal Rubio, Yeni Liliana; Gualdron Duarte, Jose Luis; Bates, R. O.; Ernst, C. W.; Nonneman, D.; et al.; Implementing meta-analysis from genome-wide association studies for pork quality traits; American Society of Animal Science; Journal of Animal Science; 93; 12-2015; 5607-5617
0021-8812
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://www.animalsciencepublications.org/publications/jas/abstracts/93/12/5607
info:eu-repo/semantics/altIdentifier/doi/10.2527/jas2015-9502
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv American Society of Animal Science
publisher.none.fl_str_mv American Society of Animal Science
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score 13.22299

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