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

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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 re...

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Autores principales: Forneris, Natalia Soledad, Vitezica, Zulma Gladis, Legarra, Andres, Pérez Enciso, Miguel
Formato: Artículo publishedVersion
Lenguaje:Inglés
Publicado: 2017
Materias:
ANIMAL
BIOLOGICAL MODEL
DROSOPHILA
EPISTASIS
GENETIC DATABASE
GENETIC SELECTION
GENETICS
GENOME
Acceso en línea:http://ri.agro.uba.ar/greenstone3/library/collection/arti/document/2017forneris
Aporte de:
FAUBA Digital - Facultad de Agronomía (UBA) de Universidad de Buenos Aires
id snrd:2017forneris
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spelling snrd:2017forneris2021-10-15T16:56:07Z Forneris, Natalia Soledad Vitezica, Zulma Gladis Legarra, Andres Pérez Enciso, Miguel 2017 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. application/pdf 10.1186/s12711-017-0340-3 0999-193X http://ri.agro.uba.ar/greenstone3/library/collection/arti/document/2017forneris eng info:eu-repo/semantics/openAccess openAccess http://ri.agro.uba.ar/greenstone3/library/page/biblioteca#section4 Genetics selection evolution Vol.47, no.66 14 http://www.biomedcentral.com/ ANIMAL BIOLOGICAL MODEL DROSOPHILA EPISTASIS GENETIC DATABASE GENETIC SELECTION GENETICS GENOME Influence of epistasis on response to genomic selection using complete sequence data info:eu-repo/semantics/article info:ar-repo/semantics/artículo publishedVersion info:eu-repo/semantics/publishedVersion
institution Universidad de Buenos Aires
institution_str I-28
repository_str R-140
collection FAUBA Digital - Facultad de Agronomía (UBA)
language Inglés
orig_language_str_mv eng
topic ANIMAL
BIOLOGICAL MODEL
DROSOPHILA
EPISTASIS
GENETIC DATABASE
GENETIC SELECTION
GENETICS
GENOME
spellingShingle ANIMAL
BIOLOGICAL MODEL
DROSOPHILA
EPISTASIS
GENETIC DATABASE
GENETIC SELECTION
GENETICS
GENOME
Forneris, Natalia Soledad
Vitezica, Zulma Gladis
Legarra, Andres
Pérez Enciso, Miguel
Influence of epistasis on response to genomic selection using complete sequence data
topic_facet ANIMAL
BIOLOGICAL MODEL
DROSOPHILA
EPISTASIS
GENETIC DATABASE
GENETIC SELECTION
GENETICS
GENOME
description 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).
format Artículo
Artículo
publishedVersion
publishedVersion
author Forneris, Natalia Soledad
Vitezica, Zulma Gladis
Legarra, Andres
Pérez Enciso, Miguel
author_facet Forneris, Natalia Soledad
Vitezica, Zulma Gladis
Legarra, Andres
Pérez Enciso, Miguel
author_sort Forneris, Natalia Soledad
title Influence of epistasis on response to genomic selection using complete sequence data
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
publishDate 2017
url http://ri.agro.uba.ar/greenstone3/library/collection/arti/document/2017forneris
work_keys_str_mv AT fornerisnataliasoledad influenceofepistasisonresponsetogenomicselectionusingcompletesequencedata
AT vitezicazulmagladis influenceofepistasisonresponsetogenomicselectionusingcompletesequencedata
AT legarraandres influenceofepistasisonresponsetogenomicselectionusingcompletesequencedata
AT perezencisomiguel influenceofepistasisonresponsetogenomicselectionusingcompletesequencedata
_version_ 1790355031716790272

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