Influence of epistasis on response to genomic selection using complete sequence data

Autores
Forneris, Natalia Soledad; Vitezica, Zulma Gladis; Legarra, Andres; Pérez Enciso, Miguel
Año de publicación
2017
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Fil: Forneris, Natalia Soledad. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal. Buenos Aires, Argentina.
Background: The effect of epistasis on response to selection is a highly debated topic. Here, we investigated the impact of epistasis on response to sequence-based selection via genomic best linear prediction (GBLUP) in a regime of strong non-symmetrical epistasis under divergent selection, using real Drosophila sequence data. We also explored the possible advantage of including epistasis in the evaluation model and/or of knowing the causal mutations. Results: Response to selection was almost exclusively due to changes in allele frequency at a few loci with a large effect. Response was highly asymmetric (about four phenotypic standard deviations higher for upward than downward selection) due to the highly skewed site frequency spectrum. Epistasis accentuated this asymmetry and affected response to selection by modulating the additive genetic variance, which was sustained for longer under upward selection whereas it eroded rapidly under downward selection. Response to selection was quite insensitive to the evaluation model, especially under an additive scenario. Nevertheless, including epistasis in the model when there was none eventually led to lower accuracies as selection proceeded. Accounting for epistasis in the model, if it existed, was beneficial but only in the medium term. There was not much gain in response if causal mutations were known, compared to using sequence data, which is likely due to strong linkage disequilibrium, high heritability and availability of phenotypes on candidates. Conclusions: Epistatic interactions affect the response to genomic selection by modulating the additive genetic variance used for selection. Epistasis releases additive variance that may increase response to selection compared to a pure additive genetic action. Furthermore, genomic evaluation models and, in particular, GBLUP are robust, i.e. adding complexity to the model did not modify substantially the response (for a given architecture).
grafs.
Fuente
Genetics selection evolution
Vol.47, no.66
14
http://www.biomedcentral.com/
Materia
ANIMAL
BIOLOGICAL MODEL
DROSOPHILA
EPISTASIS
GENETIC DATABASE
GENETIC SELECTION
GENETICS
GENOME
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:2017forneris

id FAUBA_0ecc7a48287c0070837fdce882a97f9a
oai_identifier_str snrd:2017forneris
network_acronym_str FAUBA
repository_id_str 2729
network_name_str FAUBA Digital (UBA-FAUBA)
spelling Influence of epistasis on response to genomic selection using complete sequence dataForneris, Natalia SoledadVitezica, Zulma GladisLegarra, AndresPérez Enciso, MiguelANIMALBIOLOGICAL MODELDROSOPHILAEPISTASISGENETIC DATABASEGENETIC SELECTIONGENETICSGENOMEFil: Forneris, Natalia Soledad. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal. Buenos Aires, Argentina.Background: The effect of epistasis on response to selection is a highly debated topic. Here, we investigated the impact of epistasis on response to sequence-based selection via genomic best linear prediction (GBLUP) in a regime of strong non-symmetrical epistasis under divergent selection, using real Drosophila sequence data. We also explored the possible advantage of including epistasis in the evaluation model and/or of knowing the causal mutations. Results: Response to selection was almost exclusively due to changes in allele frequency at a few loci with a large effect. Response was highly asymmetric (about four phenotypic standard deviations higher for upward than downward selection) due to the highly skewed site frequency spectrum. Epistasis accentuated this asymmetry and affected response to selection by modulating the additive genetic variance, which was sustained for longer under upward selection whereas it eroded rapidly under downward selection. Response to selection was quite insensitive to the evaluation model, especially under an additive scenario. Nevertheless, including epistasis in the model when there was none eventually led to lower accuracies as selection proceeded. Accounting for epistasis in the model, if it existed, was beneficial but only in the medium term. There was not much gain in response if causal mutations were known, compared to using sequence data, which is likely due to strong linkage disequilibrium, high heritability and availability of phenotypes on candidates. Conclusions: Epistatic interactions affect the response to genomic selection by modulating the additive genetic variance used for selection. Epistasis releases additive variance that may increase response to selection compared to a pure additive genetic action. Furthermore, genomic evaluation models and, in particular, GBLUP are robust, i.e. adding complexity to the model did not modify substantially the response (for a given architecture).grafs.2017info:eu-repo/semantics/articlepublishedVersioninfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfdoi:10.1186/s12711-017-0340-3issn:0999-193Xhttp://ri.agro.uba.ar/greenstone3/library/collection/arti/document/2017fornerisGenetics selection evolutionVol.47, no.6614http://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#section42025-09-29T13:41:08Zsnrd:2017fornerisinstacron: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 13:41:09.597FAUBA Digital (UBA-FAUBA) - Universidad de Buenos Aires. Facultad de Agronomíafalse
dc.title.none.fl_str_mv Influence of epistasis on response to genomic selection using complete sequence data
title Influence of epistasis on response to genomic selection using complete sequence data
spellingShingle Influence of epistasis on response to genomic selection using complete sequence data
Forneris, Natalia Soledad
ANIMAL
BIOLOGICAL MODEL
DROSOPHILA
EPISTASIS
GENETIC DATABASE
GENETIC SELECTION
GENETICS
GENOME
title_short Influence of epistasis on response to genomic selection using complete sequence data
title_full Influence of epistasis on response to genomic selection using complete sequence data
title_fullStr Influence of epistasis on response to genomic selection using complete sequence data
title_full_unstemmed Influence of epistasis on response to genomic selection using complete sequence data
title_sort Influence of epistasis on response to genomic selection using complete sequence data
dc.creator.none.fl_str_mv Forneris, Natalia Soledad
Vitezica, Zulma Gladis
Legarra, Andres
Pérez Enciso, Miguel
author Forneris, Natalia Soledad
author_facet Forneris, Natalia Soledad
Vitezica, Zulma Gladis
Legarra, Andres
Pérez Enciso, Miguel
author_role author
author2 Vitezica, Zulma Gladis
Legarra, Andres
Pérez Enciso, Miguel
author2_role author
author
author
dc.subject.none.fl_str_mv ANIMAL
BIOLOGICAL MODEL
DROSOPHILA
EPISTASIS
GENETIC DATABASE
GENETIC SELECTION
GENETICS
GENOME
topic ANIMAL
BIOLOGICAL MODEL
DROSOPHILA
EPISTASIS
GENETIC DATABASE
GENETIC SELECTION
GENETICS
GENOME
dc.description.none.fl_txt_mv Fil: Forneris, Natalia Soledad. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal. Buenos Aires, Argentina.
Background: The effect of epistasis on response to selection is a highly debated topic. Here, we investigated the impact of epistasis on response to sequence-based selection via genomic best linear prediction (GBLUP) in a regime of strong non-symmetrical epistasis under divergent selection, using real Drosophila sequence data. We also explored the possible advantage of including epistasis in the evaluation model and/or of knowing the causal mutations. Results: Response to selection was almost exclusively due to changes in allele frequency at a few loci with a large effect. Response was highly asymmetric (about four phenotypic standard deviations higher for upward than downward selection) due to the highly skewed site frequency spectrum. Epistasis accentuated this asymmetry and affected response to selection by modulating the additive genetic variance, which was sustained for longer under upward selection whereas it eroded rapidly under downward selection. Response to selection was quite insensitive to the evaluation model, especially under an additive scenario. Nevertheless, including epistasis in the model when there was none eventually led to lower accuracies as selection proceeded. Accounting for epistasis in the model, if it existed, was beneficial but only in the medium term. There was not much gain in response if causal mutations were known, compared to using sequence data, which is likely due to strong linkage disequilibrium, high heritability and availability of phenotypes on candidates. Conclusions: Epistatic interactions affect the response to genomic selection by modulating the additive genetic variance used for selection. Epistasis releases additive variance that may increase response to selection compared to a pure additive genetic action. Furthermore, genomic evaluation models and, in particular, GBLUP are robust, i.e. adding complexity to the model did not modify substantially the response (for a given architecture).
grafs.
description Fil: Forneris, Natalia Soledad. 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/s12711-017-0340-3
issn:0999-193X
http://ri.agro.uba.ar/greenstone3/library/collection/arti/document/2017forneris
identifier_str_mv doi:10.1186/s12711-017-0340-3
issn:0999-193X
url http://ri.agro.uba.ar/greenstone3/library/collection/arti/document/2017forneris
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.47, no.66
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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