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

Autores
García Baccino, Carolina Andrea; Legarra, Andres; Christensen, Ole F.; Misztal, Ignacy; Pocrnic, Ivan; Vitezica, Zulma G.; Cantet, Rodolfo Juan Carlos
Año de publicación
2017
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Background: 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). Results: 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. Conclusions: 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.
Fil: García Baccino, Carolina Andrea. 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: Legarra, Andres. Institut National de la Recherche Agronomique; Francia. Instituto Polytechnique de Toulouse; Francia. École Nationale Vétérinaire de Toulouse; Francia
Fil: Christensen, Ole F.. University Aarhus; Dinamarca
Fil: Misztal, Ignacy. University of Georgia; Estados Unidos
Fil: Pocrnic, Ivan. University of Georgia; Estados Unidos
Fil: Vitezica, Zulma G.. Institut National de la Recherche Agronomique; Francia. Instituto Polytechnique de Toulouse; Francia. École Nationale Vétérinaire de Toulouse; Francia
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
METAFOUNDERS
GENETIC MERIT
ssGBLUP
BIAS
BASE POPULATION
GENOMIC PREDICTION
GENERALIZE LITTLE SQUARE
ESTIMATE BREEDING VALUE
GENOMIC RELATIONSHIP
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/51037

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repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Metafounders are related to Fst fixation indices and reduce bias in single-step genomic evaluationsGarcía Baccino, Carolina AndreaLegarra, AndresChristensen, Ole F.Misztal, IgnacyPocrnic, IvanVitezica, Zulma G.Cantet, Rodolfo Juan CarlosMETAFOUNDERSGENETIC MERITssGBLUPBIASBASE POPULATIONGENOMIC PREDICTIONGENERALIZE LITTLE SQUAREESTIMATE BREEDING VALUEGENOMIC RELATIONSHIPhttps://purl.org/becyt/ford/4.2https://purl.org/becyt/ford/4Background: 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). Results: 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. Conclusions: 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.Fil: García Baccino, Carolina Andrea. 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: Legarra, Andres. Institut National de la Recherche Agronomique; Francia. Instituto Polytechnique de Toulouse; Francia. École Nationale Vétérinaire de Toulouse; FranciaFil: Christensen, Ole F.. University Aarhus; DinamarcaFil: Misztal, Ignacy. University of Georgia; Estados UnidosFil: Pocrnic, Ivan. University of Georgia; Estados UnidosFil: Vitezica, Zulma G.. Institut National de la Recherche Agronomique; Francia. Instituto Polytechnique de Toulouse; Francia. École Nationale Vétérinaire de Toulouse; FranciaFil: 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; ArgentinaBioMed Central2017-03info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/51037García Baccino, Carolina Andrea; Legarra, Andres; Christensen, Ole F.; Misztal, Ignacy; Pocrnic, Ivan; et al.; Metafounders are related to Fst fixation indices and reduce bias in single-step genomic evaluations; BioMed Central; Genetics Selection Evolution; 49; 1; 3-2017; 1-140999-193X1297-9686CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1186/s12711-017-0309-2info:eu-repo/semantics/altIdentifier/url/https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5439149/info:eu-repo/semantics/altIdentifier/url/https://www.biorxiv.org/content/early/2016/10/26/083675info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:25:01Zoai:ri.conicet.gov.ar:11336/51037instacron: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 10:25:01.385CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
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
METAFOUNDERS
GENETIC MERIT
ssGBLUP
BIAS
BASE POPULATION
GENOMIC PREDICTION
GENERALIZE LITTLE SQUARE
ESTIMATE BREEDING VALUE
GENOMIC RELATIONSHIP
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, Ole F.
Misztal, Ignacy
Pocrnic, Ivan
Vitezica, Zulma G.
Cantet, Rodolfo Juan Carlos
author García Baccino, Carolina Andrea
author_facet García Baccino, Carolina Andrea
Legarra, Andres
Christensen, Ole F.
Misztal, Ignacy
Pocrnic, Ivan
Vitezica, Zulma G.
Cantet, Rodolfo Juan Carlos
author_role author
author2 Legarra, Andres
Christensen, Ole F.
Misztal, Ignacy
Pocrnic, Ivan
Vitezica, Zulma G.
Cantet, Rodolfo Juan Carlos
author2_role author
author
author
author
author
author
dc.subject.none.fl_str_mv METAFOUNDERS
GENETIC MERIT
ssGBLUP
BIAS
BASE POPULATION
GENOMIC PREDICTION
GENERALIZE LITTLE SQUARE
ESTIMATE BREEDING VALUE
GENOMIC RELATIONSHIP
topic METAFOUNDERS
GENETIC MERIT
ssGBLUP
BIAS
BASE POPULATION
GENOMIC PREDICTION
GENERALIZE LITTLE SQUARE
ESTIMATE BREEDING VALUE
GENOMIC RELATIONSHIP
purl_subject.fl_str_mv https://purl.org/becyt/ford/4.2
https://purl.org/becyt/ford/4
dc.description.none.fl_txt_mv Background: 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). Results: 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. Conclusions: 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.
Fil: García Baccino, Carolina Andrea. 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: Legarra, Andres. Institut National de la Recherche Agronomique; Francia. Instituto Polytechnique de Toulouse; Francia. École Nationale Vétérinaire de Toulouse; Francia
Fil: Christensen, Ole F.. University Aarhus; Dinamarca
Fil: Misztal, Ignacy. University of Georgia; Estados Unidos
Fil: Pocrnic, Ivan. University of Georgia; Estados Unidos
Fil: Vitezica, Zulma G.. Institut National de la Recherche Agronomique; Francia. Instituto Polytechnique de Toulouse; Francia. École Nationale Vétérinaire de Toulouse; Francia
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 Background: 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). Results: 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. Conclusions: 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.
publishDate 2017
dc.date.none.fl_str_mv 2017-03
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/11336/51037
García Baccino, Carolina Andrea; Legarra, Andres; Christensen, Ole F.; Misztal, Ignacy; Pocrnic, Ivan; et al.; Metafounders are related to Fst fixation indices and reduce bias in single-step genomic evaluations; BioMed Central; Genetics Selection Evolution; 49; 1; 3-2017; 1-14
0999-193X
1297-9686
CONICET Digital
CONICET
url http://hdl.handle.net/11336/51037
identifier_str_mv García Baccino, Carolina Andrea; Legarra, Andres; Christensen, Ole F.; Misztal, Ignacy; Pocrnic, Ivan; et al.; Metafounders are related to Fst fixation indices and reduce bias in single-step genomic evaluations; BioMed Central; Genetics Selection Evolution; 49; 1; 3-2017; 1-14
0999-193X
1297-9686
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1186/s12711-017-0309-2
info:eu-repo/semantics/altIdentifier/url/https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5439149/
info:eu-repo/semantics/altIdentifier/url/https://www.biorxiv.org/content/early/2016/10/26/083675
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by/2.5/ar/
dc.format.none.fl_str_mv application/pdf
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dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
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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