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
- Institución
- Universidad de Buenos Aires. Facultad de Agronomía
- OAI Identificador
- snrd:2017garciabaccino1
Ver los metadatos del registro completo
id |
FAUBA_4e405b3cc867924f6d3a21f1a44761dc |
---|---|
oai_identifier_str |
snrd:2017garciabaccino1 |
network_acronym_str |
FAUBA |
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 |
_version_ |
1844618852610080769 |
score |
13.070432 |