A comparison of methods to estimate genomic relationships using pedigree and markers in livestock populations

Autores
Forneris, Natalia Soledad; Steibel, J. P.; Legarra, Andres; Vitezica, Zulma G.; Bates, R. O.; Ernst, C. W.; Basso Abraham, Alicia Leonor Rufina; Cantet, Rodolfo Juan Carlos
Año de publicación
2016
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Accurate prediction of breeding values depends on capturing the variability in genome sharing of relatives with the same pedigree relationship. Here, we compare two approaches to set up genomic relationship matrices for precision of genomic relationships (GR) and accuracy of estimated breeding values (GEBV). Real and simulated data (pigs, 60k SNP) were analysed, and GR were estimated using two approaches: (i) identity by state, corrected with either the observed (GVR -O) or the base population (GVR -B) allele frequencies and (ii) identity by descent using linkage analysis (GIBD -L). Estimators were evaluated for precision and empirical bias with respect to true pedigree IBD GR. All three estimators had very low bias. GIBD -L displayed the lowest sampling error and the highest correlation with true genome-shared values. GVR -B approximated GIBD -L's correlation and had lower error than GVR -O. Accuracy of GEBV for selection candidates was significantly higher when GIBD -L was used and identical between GVR -O and GVR -B. In real data, GIBD -L's sampling standard deviation was the closest to the theoretical value for each pedigree relationship. Use of pedigree to calculate GR improved the precision of estimates and the accuracy of GEBV.
Fil: Forneris, Natalia Soledad. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Unidad Ejecutora de Investigaciones en Producción Animal. Universidad de Buenos Aires. Facultad de Ciencias Veterinarias. Unidad Ejecutora de Investigaciones en Producción Animal; Argentina. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal; Argentina
Fil: Steibel, J. P.. Michigan State University; Estados Unidos
Fil: Legarra, Andres. Institut National de la Recherche Agronomique; Francia
Fil: Vitezica, Zulma G.. Institut National de la Recherche Agronomique; Francia. Instituto Polytechnique de Toulouse; Francia
Fil: Bates, R. O.. Michigan State University; Estados Unidos
Fil: Ernst, C. W.. Michigan State University; Estados Unidos
Fil: Basso Abraham, Alicia Leonor Rufina. Universidad de Buenos Aires. Facultad de Agronomia. Departamento de Biología Aplicada y Alimentos; Argentina
Fil: Cantet, Rodolfo Juan Carlos. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Unidad Ejecutora de Investigaciones en Producción Animal. Universidad de Buenos Aires. Facultad de Ciencias Veterinarias. Unidad Ejecutora de Investigaciones en Producción Animal; Argentina. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal; Argentina
Materia
Accuracy
Genomic Prediction
Genome Sharing
Identity by Descent
Snp
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:11336/51073
Acceder
id CONICETDig_34c8a6babada8eafe96b155937246fbe
oai_identifier_str oai:ri.conicet.gov.ar:11336/51073
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling A comparison of methods to estimate genomic relationships using pedigree and markers in livestock populationsForneris, Natalia SoledadSteibel, J. P.Legarra, AndresVitezica, Zulma G.Bates, R. O.Ernst, C. W.Basso Abraham, Alicia Leonor RufinaCantet, Rodolfo Juan CarlosAccuracyGenomic PredictionGenome SharingIdentity by DescentSnphttps://purl.org/becyt/ford/4.2https://purl.org/becyt/ford/4Accurate prediction of breeding values depends on capturing the variability in genome sharing of relatives with the same pedigree relationship. Here, we compare two approaches to set up genomic relationship matrices for precision of genomic relationships (GR) and accuracy of estimated breeding values (GEBV). Real and simulated data (pigs, 60k SNP) were analysed, and GR were estimated using two approaches: (i) identity by state, corrected with either the observed (GVR -O) or the base population (GVR -B) allele frequencies and (ii) identity by descent using linkage analysis (GIBD -L). Estimators were evaluated for precision and empirical bias with respect to true pedigree IBD GR. All three estimators had very low bias. GIBD -L displayed the lowest sampling error and the highest correlation with true genome-shared values. GVR -B approximated GIBD -L's correlation and had lower error than GVR -O. Accuracy of GEBV for selection candidates was significantly higher when GIBD -L was used and identical between GVR -O and GVR -B. In real data, GIBD -L's sampling standard deviation was the closest to the theoretical value for each pedigree relationship. Use of pedigree to calculate GR improved the precision of estimates and the accuracy of GEBV.Fil: Forneris, Natalia Soledad. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Unidad Ejecutora de Investigaciones en Producción Animal. Universidad de Buenos Aires. Facultad de Ciencias Veterinarias. Unidad Ejecutora de Investigaciones en Producción Animal; Argentina. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal; ArgentinaFil: Steibel, J. P.. Michigan State University; Estados UnidosFil: Legarra, Andres. Institut National de la Recherche Agronomique; FranciaFil: Vitezica, Zulma G.. Institut National de la Recherche Agronomique; Francia. Instituto Polytechnique de Toulouse; FranciaFil: Bates, R. O.. Michigan State University; Estados UnidosFil: Ernst, C. W.. Michigan State University; Estados UnidosFil: Basso Abraham, Alicia Leonor Rufina. Universidad de Buenos Aires. Facultad de Agronomia. Departamento de Biología Aplicada y Alimentos; ArgentinaFil: Cantet, Rodolfo Juan Carlos. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Unidad Ejecutora de Investigaciones en Producción Animal. Universidad de Buenos Aires. Facultad de Ciencias Veterinarias. Unidad Ejecutora de Investigaciones en Producción Animal; Argentina. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal; ArgentinaWiley Blackwell Publishing, Inc2016-12info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/51073Forneris, Natalia Soledad; Steibel, J. P.; Legarra, Andres; Vitezica, Zulma G.; Bates, R. O.; et al.; A comparison of methods to estimate genomic relationships using pedigree and markers in livestock populations; Wiley Blackwell Publishing, Inc; Journal Of Animal Breeding And Genetics-zeitschrift Fur Tierzuchtung Und Zuchtungsbiologie; 133; 6; 12-2016; 452-4620931-26681439-0388CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1111/jbg.12217info:eu-repo/semantics/altIdentifier/url/https://onlinelibrary.wiley.com/doi/abs/10.1111/jbg.12217info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-10-22T11:02:45Zoai:ri.conicet.gov.ar:11336/51073instacron: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:34982025-10-22 11:02:45.564CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv A comparison of methods to estimate genomic relationships using pedigree and markers in livestock populations
title A comparison of methods to estimate genomic relationships using pedigree and markers in livestock populations
spellingShingle A comparison of methods to estimate genomic relationships using pedigree and markers in livestock populations
Forneris, Natalia Soledad
Accuracy
Genomic Prediction
Genome Sharing
Identity by Descent
Snp
title_short A comparison of methods to estimate genomic relationships using pedigree and markers in livestock populations
title_full A comparison of methods to estimate genomic relationships using pedigree and markers in livestock populations
title_fullStr A comparison of methods to estimate genomic relationships using pedigree and markers in livestock populations
title_full_unstemmed A comparison of methods to estimate genomic relationships using pedigree and markers in livestock populations
title_sort A comparison of methods to estimate genomic relationships using pedigree and markers in livestock populations
dc.creator.none.fl_str_mv Forneris, Natalia Soledad
Steibel, J. P.
Legarra, Andres
Vitezica, Zulma G.
Bates, R. O.
Ernst, C. W.
Basso Abraham, Alicia Leonor Rufina
Cantet, Rodolfo Juan Carlos
author Forneris, Natalia Soledad
author_facet Forneris, Natalia Soledad
Steibel, J. P.
Legarra, Andres
Vitezica, Zulma G.
Bates, R. O.
Ernst, C. W.
Basso Abraham, Alicia Leonor Rufina
Cantet, Rodolfo Juan Carlos
author_role author
author2 Steibel, J. P.
Legarra, Andres
Vitezica, Zulma G.
Bates, R. O.
Ernst, C. W.
Basso Abraham, Alicia Leonor Rufina
Cantet, Rodolfo Juan Carlos
author2_role author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Accuracy
Genomic Prediction
Genome Sharing
Identity by Descent
Snp
topic Accuracy
Genomic Prediction
Genome Sharing
Identity by Descent
Snp
purl_subject.fl_str_mv https://purl.org/becyt/ford/4.2
https://purl.org/becyt/ford/4
dc.description.none.fl_txt_mv Accurate prediction of breeding values depends on capturing the variability in genome sharing of relatives with the same pedigree relationship. Here, we compare two approaches to set up genomic relationship matrices for precision of genomic relationships (GR) and accuracy of estimated breeding values (GEBV). Real and simulated data (pigs, 60k SNP) were analysed, and GR were estimated using two approaches: (i) identity by state, corrected with either the observed (GVR -O) or the base population (GVR -B) allele frequencies and (ii) identity by descent using linkage analysis (GIBD -L). Estimators were evaluated for precision and empirical bias with respect to true pedigree IBD GR. All three estimators had very low bias. GIBD -L displayed the lowest sampling error and the highest correlation with true genome-shared values. GVR -B approximated GIBD -L's correlation and had lower error than GVR -O. Accuracy of GEBV for selection candidates was significantly higher when GIBD -L was used and identical between GVR -O and GVR -B. In real data, GIBD -L's sampling standard deviation was the closest to the theoretical value for each pedigree relationship. Use of pedigree to calculate GR improved the precision of estimates and the accuracy of GEBV.
Fil: Forneris, Natalia Soledad. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Unidad Ejecutora de Investigaciones en Producción Animal. Universidad de Buenos Aires. Facultad de Ciencias Veterinarias. Unidad Ejecutora de Investigaciones en Producción Animal; Argentina. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal; Argentina
Fil: Steibel, J. P.. Michigan State University; Estados Unidos
Fil: Legarra, Andres. Institut National de la Recherche Agronomique; Francia
Fil: Vitezica, Zulma G.. Institut National de la Recherche Agronomique; Francia. Instituto Polytechnique de Toulouse; Francia
Fil: Bates, R. O.. Michigan State University; Estados Unidos
Fil: Ernst, C. W.. Michigan State University; Estados Unidos
Fil: Basso Abraham, Alicia Leonor Rufina. Universidad de Buenos Aires. Facultad de Agronomia. Departamento de Biología Aplicada y Alimentos; Argentina
Fil: Cantet, Rodolfo Juan Carlos. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Unidad Ejecutora de Investigaciones en Producción Animal. Universidad de Buenos Aires. Facultad de Ciencias Veterinarias. Unidad Ejecutora de Investigaciones en Producción Animal; Argentina. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal; Argentina
description Accurate prediction of breeding values depends on capturing the variability in genome sharing of relatives with the same pedigree relationship. Here, we compare two approaches to set up genomic relationship matrices for precision of genomic relationships (GR) and accuracy of estimated breeding values (GEBV). Real and simulated data (pigs, 60k SNP) were analysed, and GR were estimated using two approaches: (i) identity by state, corrected with either the observed (GVR -O) or the base population (GVR -B) allele frequencies and (ii) identity by descent using linkage analysis (GIBD -L). Estimators were evaluated for precision and empirical bias with respect to true pedigree IBD GR. All three estimators had very low bias. GIBD -L displayed the lowest sampling error and the highest correlation with true genome-shared values. GVR -B approximated GIBD -L's correlation and had lower error than GVR -O. Accuracy of GEBV for selection candidates was significantly higher when GIBD -L was used and identical between GVR -O and GVR -B. In real data, GIBD -L's sampling standard deviation was the closest to the theoretical value for each pedigree relationship. Use of pedigree to calculate GR improved the precision of estimates and the accuracy of GEBV.
publishDate 2016
dc.date.none.fl_str_mv 2016-12
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/11336/51073
Forneris, Natalia Soledad; Steibel, J. P.; Legarra, Andres; Vitezica, Zulma G.; Bates, R. O.; et al.; A comparison of methods to estimate genomic relationships using pedigree and markers in livestock populations; Wiley Blackwell Publishing, Inc; Journal Of Animal Breeding And Genetics-zeitschrift Fur Tierzuchtung Und Zuchtungsbiologie; 133; 6; 12-2016; 452-462
0931-2668
1439-0388
CONICET Digital
CONICET
url http://hdl.handle.net/11336/51073
identifier_str_mv Forneris, Natalia Soledad; Steibel, J. P.; Legarra, Andres; Vitezica, Zulma G.; Bates, R. O.; et al.; A comparison of methods to estimate genomic relationships using pedigree and markers in livestock populations; Wiley Blackwell Publishing, Inc; Journal Of Animal Breeding And Genetics-zeitschrift Fur Tierzuchtung Und Zuchtungsbiologie; 133; 6; 12-2016; 452-462
0931-2668
1439-0388
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1111/jbg.12217
info:eu-repo/semantics/altIdentifier/url/https://onlinelibrary.wiley.com/doi/abs/10.1111/jbg.12217
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
application/pdf
dc.publisher.none.fl_str_mv Wiley Blackwell Publishing, Inc
publisher.none.fl_str_mv Wiley Blackwell Publishing, Inc
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 12.982451

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