Metafounders are related to Fst fixation indices and reduce bias in single - step genomic evaluations

Autores
García Baccino, Carolina Andrea; Legarra, Andres; Christensen, O. F.; Misztal, Ignacy; Pocrnic, I.; Vitezica, Zulma Gladis; Cantet, Rodolfo Juan Carlos
Año de publicación
2017
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Fil: García Baccino, Carolina Andrea. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal. Buenos Aires, Argentina.
Fil: Legarra, Andres. Université de Toulouse. GenPhySE, INRA, INPT, ENVT. Tolosan, France.
Fil: Christensen, O. F. Aarhus University. Department of Molecular Biology and Genetics. Center for Quantitative Genetics and Genomics. Tjele, Denmark.
Fil: Misztal, Ignacy. University of Georgia. Animal and Dairy Science. Athens, USA.
Fil: Pocrnic, I. University of Georgia. Animal and Dairy Science. Athens, USA.
Fil: Vitezica, Zulma Gladis. Université de Toulouse. GenPhySE, INRA, INPT, ENVT. Tolosan, France.
Fil: Cantet, Rodolfo Juan Carlos. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal. Buenos Aires, Argentina.
Metafounders are pseudo-individuals that encapsulate genetic heterozygosity and relationships within and across base pedigree populations, i.e. ancestral populations. This work addresses the estimation and usefulness of metafounder relationships in single-step genomic best linear unbiased prediction (ssGBLUP). We show that ancestral relationship parameters are proportional to standardized covariances of base allelic frequencies across populations, such as Fst fixation indexes. These covariances of base allelic frequencies can be estimated from marker genotypes of related recent individuals and pedigree. Simple methods for their estimation include naïve computation of allele frequencies from marker genotypes or a method of moments that equates average pedigree-based and marker-based relationships. Complex methods include generalized least squares (best linear unbiased estimator (BLUE) or maximum likelihood based on pedigree relationships. To our knowledge, methods to infer Fst coefficients from marker data have not been developed for related individuals. We derived a genomic relationship matrix, compatible with pedigree relationships, that is constructed as a cross-product of (−1,0,1)codes and that is equivalent (apart from scale factors) to an identity-by-state relationship matrix at genome-wide markers. Using a simulation with a single population under selection in which only males and youngest animals are genotyped, we observed that generalized least squares or maximum likelihood gave accurate and unbiased estimates of the ancestral relationship parameter (true value: 0.40) whereas the naïve method and the method of moments were biased (average estimates of 0.43 and 0.35). We also observed that genomic evaluation by ssGBLUP using metafounders was less biased in terms of estimates of genetic trend (bias of 0.01 instead of 0.12), resulted in less overdispersed (0.94 instead of 0.99) and as accurate (0.74) estimates of breeding values than ssGBLUP without metafounders and provided consistent estimates of heritability. Estimation of metafounder relationships can be achieved using BLUP-like methods with pedigree and markers. Inclusion of metafounder relationships reduces bias of genomic predictions with no loss in accuracy.
tbls., grafs.
Fuente
Genetics selection evolution
Vol.49, no.1
1-14
http://www.biomedcentral.com/
Nivel de accesibilidad
acceso abierto
Condiciones de uso
acceso abierto
Repositorio
FAUBA Digital (UBA-FAUBA)
Institución
Universidad de Buenos Aires. Facultad de Agronomía
OAI Identificador
snrd:2017garciabaccino1

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repository_id_str 2729
network_name_str FAUBA Digital (UBA-FAUBA)
spelling Metafounders are related to Fst fixation indices and reduce bias in single - step genomic evaluationsGarcía Baccino, Carolina AndreaLegarra, AndresChristensen, O. F.Misztal, IgnacyPocrnic, I.Vitezica, Zulma GladisCantet, Rodolfo Juan CarlosFil: García Baccino, Carolina Andrea. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal. Buenos Aires, Argentina.Fil: Legarra, Andres. Université de Toulouse. GenPhySE, INRA, INPT, ENVT. Tolosan, France.Fil: Christensen, O. F. Aarhus University. Department of Molecular Biology and Genetics. Center for Quantitative Genetics and Genomics. Tjele, Denmark.Fil: Misztal, Ignacy. University of Georgia. Animal and Dairy Science. Athens, USA.Fil: Pocrnic, I. University of Georgia. Animal and Dairy Science. Athens, USA.Fil: Vitezica, Zulma Gladis. Université de Toulouse. GenPhySE, INRA, INPT, ENVT. Tolosan, France.Fil: Cantet, Rodolfo Juan Carlos. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal. Buenos Aires, Argentina.Metafounders are pseudo-individuals that encapsulate genetic heterozygosity and relationships within and across base pedigree populations, i.e. ancestral populations. This work addresses the estimation and usefulness of metafounder relationships in single-step genomic best linear unbiased prediction (ssGBLUP). We show that ancestral relationship parameters are proportional to standardized covariances of base allelic frequencies across populations, such as Fst fixation indexes. These covariances of base allelic frequencies can be estimated from marker genotypes of related recent individuals and pedigree. Simple methods for their estimation include naïve computation of allele frequencies from marker genotypes or a method of moments that equates average pedigree-based and marker-based relationships. Complex methods include generalized least squares (best linear unbiased estimator (BLUE) or maximum likelihood based on pedigree relationships. To our knowledge, methods to infer Fst coefficients from marker data have not been developed for related individuals. We derived a genomic relationship matrix, compatible with pedigree relationships, that is constructed as a cross-product of (−1,0,1)codes and that is equivalent (apart from scale factors) to an identity-by-state relationship matrix at genome-wide markers. Using a simulation with a single population under selection in which only males and youngest animals are genotyped, we observed that generalized least squares or maximum likelihood gave accurate and unbiased estimates of the ancestral relationship parameter (true value: 0.40) whereas the naïve method and the method of moments were biased (average estimates of 0.43 and 0.35). We also observed that genomic evaluation by ssGBLUP using metafounders was less biased in terms of estimates of genetic trend (bias of 0.01 instead of 0.12), resulted in less overdispersed (0.94 instead of 0.99) and as accurate (0.74) estimates of breeding values than ssGBLUP without metafounders and provided consistent estimates of heritability. Estimation of metafounder relationships can be achieved using BLUP-like methods with pedigree and markers. Inclusion of metafounder relationships reduces bias of genomic predictions with no loss in accuracy.tbls., grafs.2017info:eu-repo/semantics/articlepublishedVersioninfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfdoi:10.1186/s12711-017-0309-2issn:0999-193Xhttp://ri.agro.uba.ar/greenstone3/library/collection/arti/document/2017garciabaccino1Genetics selection evolutionVol.49, no.11-14http://www.biomedcentral.com/reponame:FAUBA Digital (UBA-FAUBA)instname:Universidad de Buenos Aires. Facultad de Agronomíaenginfo:eu-repo/semantics/openAccessopenAccesshttp://ri.agro.uba.ar/greenstone3/library/page/biblioteca#section42025-09-29T13:41:05Zsnrd:2017garciabaccino1instacron:UBA-FAUBAInstitucionalhttp://ri.agro.uba.ar/Universidad públicaNo correspondehttp://ri.agro.uba.ar/greenstone3/oaiserver?verb=ListSetsmartino@agro.uba.ar;berasa@agro.uba.ar ArgentinaNo correspondeNo correspondeNo correspondeopendoar:27292025-09-29 13:41:05.802FAUBA Digital (UBA-FAUBA) - Universidad de Buenos Aires. Facultad de Agronomíafalse
dc.title.none.fl_str_mv Metafounders are related to Fst fixation indices and reduce bias in single - step genomic evaluations
title Metafounders are related to Fst fixation indices and reduce bias in single - step genomic evaluations
spellingShingle Metafounders are related to Fst fixation indices and reduce bias in single - step genomic evaluations
García Baccino, Carolina Andrea
title_short Metafounders are related to Fst fixation indices and reduce bias in single - step genomic evaluations
title_full Metafounders are related to Fst fixation indices and reduce bias in single - step genomic evaluations
title_fullStr Metafounders are related to Fst fixation indices and reduce bias in single - step genomic evaluations
title_full_unstemmed Metafounders are related to Fst fixation indices and reduce bias in single - step genomic evaluations
title_sort Metafounders are related to Fst fixation indices and reduce bias in single - step genomic evaluations
dc.creator.none.fl_str_mv García Baccino, Carolina Andrea
Legarra, Andres
Christensen, O. F.
Misztal, Ignacy
Pocrnic, I.
Vitezica, Zulma Gladis
Cantet, Rodolfo Juan Carlos
author García Baccino, Carolina Andrea
author_facet García Baccino, Carolina Andrea
Legarra, Andres
Christensen, O. F.
Misztal, Ignacy
Pocrnic, I.
Vitezica, Zulma Gladis
Cantet, Rodolfo Juan Carlos
author_role author
author2 Legarra, Andres
Christensen, O. F.
Misztal, Ignacy
Pocrnic, I.
Vitezica, Zulma Gladis
Cantet, Rodolfo Juan Carlos
author2_role author
author
author
author
author
author
dc.description.none.fl_txt_mv Fil: García Baccino, Carolina Andrea. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal. Buenos Aires, Argentina.
Fil: Legarra, Andres. Université de Toulouse. GenPhySE, INRA, INPT, ENVT. Tolosan, France.
Fil: Christensen, O. F. Aarhus University. Department of Molecular Biology and Genetics. Center for Quantitative Genetics and Genomics. Tjele, Denmark.
Fil: Misztal, Ignacy. University of Georgia. Animal and Dairy Science. Athens, USA.
Fil: Pocrnic, I. University of Georgia. Animal and Dairy Science. Athens, USA.
Fil: Vitezica, Zulma Gladis. Université de Toulouse. GenPhySE, INRA, INPT, ENVT. Tolosan, France.
Fil: Cantet, Rodolfo Juan Carlos. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal. Buenos Aires, Argentina.
Metafounders are pseudo-individuals that encapsulate genetic heterozygosity and relationships within and across base pedigree populations, i.e. ancestral populations. This work addresses the estimation and usefulness of metafounder relationships in single-step genomic best linear unbiased prediction (ssGBLUP). We show that ancestral relationship parameters are proportional to standardized covariances of base allelic frequencies across populations, such as Fst fixation indexes. These covariances of base allelic frequencies can be estimated from marker genotypes of related recent individuals and pedigree. Simple methods for their estimation include naïve computation of allele frequencies from marker genotypes or a method of moments that equates average pedigree-based and marker-based relationships. Complex methods include generalized least squares (best linear unbiased estimator (BLUE) or maximum likelihood based on pedigree relationships. To our knowledge, methods to infer Fst coefficients from marker data have not been developed for related individuals. We derived a genomic relationship matrix, compatible with pedigree relationships, that is constructed as a cross-product of (−1,0,1)codes and that is equivalent (apart from scale factors) to an identity-by-state relationship matrix at genome-wide markers. Using a simulation with a single population under selection in which only males and youngest animals are genotyped, we observed that generalized least squares or maximum likelihood gave accurate and unbiased estimates of the ancestral relationship parameter (true value: 0.40) whereas the naïve method and the method of moments were biased (average estimates of 0.43 and 0.35). We also observed that genomic evaluation by ssGBLUP using metafounders was less biased in terms of estimates of genetic trend (bias of 0.01 instead of 0.12), resulted in less overdispersed (0.94 instead of 0.99) and as accurate (0.74) estimates of breeding values than ssGBLUP without metafounders and provided consistent estimates of heritability. Estimation of metafounder relationships can be achieved using BLUP-like methods with pedigree and markers. Inclusion of metafounder relationships reduces bias of genomic predictions with no loss in accuracy.
tbls., grafs.
description Fil: García Baccino, Carolina Andrea. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal. Buenos Aires, Argentina.
publishDate 2017
dc.date.none.fl_str_mv 2017
dc.type.none.fl_str_mv info:eu-repo/semantics/article
publishedVersion
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 doi:10.1186/s12711-017-0309-2
issn:0999-193X
http://ri.agro.uba.ar/greenstone3/library/collection/arti/document/2017garciabaccino1
identifier_str_mv doi:10.1186/s12711-017-0309-2
issn:0999-193X
url http://ri.agro.uba.ar/greenstone3/library/collection/arti/document/2017garciabaccino1
dc.language.none.fl_str_mv eng
language eng
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
openAccess
http://ri.agro.uba.ar/greenstone3/library/page/biblioteca#section4
eu_rights_str_mv openAccess
rights_invalid_str_mv openAccess
http://ri.agro.uba.ar/greenstone3/library/page/biblioteca#section4
dc.format.none.fl_str_mv application/pdf
dc.source.none.fl_str_mv Genetics selection evolution
Vol.49, no.1
1-14
http://www.biomedcentral.com/
reponame:FAUBA Digital (UBA-FAUBA)
instname:Universidad de Buenos Aires. Facultad de Agronomía
reponame_str FAUBA Digital (UBA-FAUBA)
collection FAUBA Digital (UBA-FAUBA)
instname_str Universidad de Buenos Aires. Facultad de Agronomía
repository.name.fl_str_mv FAUBA Digital (UBA-FAUBA) - Universidad de Buenos Aires. Facultad de Agronomía
repository.mail.fl_str_mv martino@agro.uba.ar;berasa@agro.uba.ar
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