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
- Institución
- Universidad de Buenos Aires. Facultad de Agronomía
- OAI Identificador
- snrd:2017forneris
Ver los metadatos del registro completo
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snrd:2017forneris |
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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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