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
- Institución
- Consejo Nacional de Investigaciones Científicas y Técnicas
- OAI Identificador
- oai:ri.conicet.gov.ar:11336/51073
Ver los metadatos del registro completo
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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 Técnicas2025-09-29T09:34:43Zoai: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:34982025-09-29 09:34:43.918CONICET 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) |
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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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1844613076873117696 |
score |
13.070432 |