The contribution of whole-genome sequence data to genome-wide association studies in livestock: outcomes and perspectives

Genome-wide association studies (GWAS) in livestock are a powerful method for pursuing deeper insights into the biological mechanisms that control complex traits, often with sights set on the improvement of productive efficiency. There has been a wide uptake of whole-genome sequence (WGS) data for G...

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Autor: Ros Freixedes, Roger
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2024
País:España
Institución:Universitat de Lleida (UdL)
Repositorio:Repositori Obert UdL
OAI Identifier:oai:repositori.udl.cat:10459.1/465307
Acceso en línea:https://doi.org/10.1016/j.livsci.2024.105430
https://hdl.handle.net/10459.1/465307
Access Level:acceso abierto
Palabra clave:Complex trait
Fine-mapping
Genome-wide association study
GWAS
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spelling The contribution of whole-genome sequence data to genome-wide association studies in livestock: outcomes and perspectivesRos Freixedes, RogerComplex traitFine-mappingGenome-wide association studyGWASGenome-wide association studies (GWAS) in livestock are a powerful method for pursuing deeper insights into the biological mechanisms that control complex traits, often with sights set on the improvement of productive efficiency. There has been a wide uptake of whole-genome sequence (WGS) data for GWAS across the main livestock species. In this review, we aim to provide a critical survey of the contribution of WGS-based GWAS in livestock, by spotlighting the outcomes of some of the most representative efforts. First, we review the empirical results on the efficacy of WGS data for GWAS compared to marker arrays, and what strategies are currently being applied to increase the detection power of WGS-based GWAS. Then, we review the contribution of WGS-based GWAS to our understanding of the genetic architecture of complex traits, and how data structure but also our own practices hinder the fine-mapping of causal variants. We also provide a perspective on our own biases in identifying candidate genes and variants, the practical relevance of GWAS results, and data sharing. There is a need to apply better GWAS practices as the availability of WGS data continues to grow in the future.This research was supported by the Spanish Ministry of Science and Innovation MCIN, AEI, doi: 10.13039/501100011033 , and the European Regional Development Fund ERDF “A way of making Europe” (grant PID2021-125689OB-I00 ).Elsevier2024info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttps://doi.org/10.1016/j.livsci.2024.105430https://hdl.handle.net/10459.1/465307reponame:Repositori Obert UdL instname:Universitat de Lleida (UdL)Inglésinfo:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023/PID2021-125689OB-I00Reproducció del document publicat a https://doi.org/10.1016/j.livsci.2024.105430Livestock Science, 2024, vol. 281, núm. 105430, p. 1-12cc-by-nc, (c) Ros, 2024Attribution-NonCommercial 4.0 Internationalinfo:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by-nc/4.0/oai:repositori.udl.cat:10459.1/4653072026-06-24T12:42:17Z
dc.title.none.fl_str_mv The contribution of whole-genome sequence data to genome-wide association studies in livestock: outcomes and perspectives
title The contribution of whole-genome sequence data to genome-wide association studies in livestock: outcomes and perspectives
spellingShingle The contribution of whole-genome sequence data to genome-wide association studies in livestock: outcomes and perspectives
Ros Freixedes, Roger
Complex trait
Fine-mapping
Genome-wide association study
GWAS
title_short The contribution of whole-genome sequence data to genome-wide association studies in livestock: outcomes and perspectives
title_full The contribution of whole-genome sequence data to genome-wide association studies in livestock: outcomes and perspectives
title_fullStr The contribution of whole-genome sequence data to genome-wide association studies in livestock: outcomes and perspectives
title_full_unstemmed The contribution of whole-genome sequence data to genome-wide association studies in livestock: outcomes and perspectives
title_sort The contribution of whole-genome sequence data to genome-wide association studies in livestock: outcomes and perspectives
dc.creator.none.fl_str_mv Ros Freixedes, Roger
author Ros Freixedes, Roger
author_facet Ros Freixedes, Roger
author_role author
dc.subject.none.fl_str_mv Complex trait
Fine-mapping
Genome-wide association study
GWAS
topic Complex trait
Fine-mapping
Genome-wide association study
GWAS
description Genome-wide association studies (GWAS) in livestock are a powerful method for pursuing deeper insights into the biological mechanisms that control complex traits, often with sights set on the improvement of productive efficiency. There has been a wide uptake of whole-genome sequence (WGS) data for GWAS across the main livestock species. In this review, we aim to provide a critical survey of the contribution of WGS-based GWAS in livestock, by spotlighting the outcomes of some of the most representative efforts. First, we review the empirical results on the efficacy of WGS data for GWAS compared to marker arrays, and what strategies are currently being applied to increase the detection power of WGS-based GWAS. Then, we review the contribution of WGS-based GWAS to our understanding of the genetic architecture of complex traits, and how data structure but also our own practices hinder the fine-mapping of causal variants. We also provide a perspective on our own biases in identifying candidate genes and variants, the practical relevance of GWAS results, and data sharing. There is a need to apply better GWAS practices as the availability of WGS data continues to grow in the future.
publishDate 2024
dc.date.none.fl_str_mv 2024
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv https://doi.org/10.1016/j.livsci.2024.105430
https://hdl.handle.net/10459.1/465307
url https://doi.org/10.1016/j.livsci.2024.105430
https://hdl.handle.net/10459.1/465307
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023/PID2021-125689OB-I00
Reproducció del document publicat a https://doi.org/10.1016/j.livsci.2024.105430
Livestock Science, 2024, vol. 281, núm. 105430, p. 1-12
dc.rights.none.fl_str_mv cc-by-nc, (c) Ros, 2024
Attribution-NonCommercial 4.0 International
info:eu-repo/semantics/openAccess
http://creativecommons.org/licenses/by-nc/4.0/
rights_invalid_str_mv cc-by-nc, (c) Ros, 2024
Attribution-NonCommercial 4.0 International
http://creativecommons.org/licenses/by-nc/4.0/
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Elsevier
publisher.none.fl_str_mv Elsevier
dc.source.none.fl_str_mv reponame:Repositori Obert UdL
instname:Universitat de Lleida (UdL)
instname_str Universitat de Lleida (UdL)
reponame_str Repositori Obert UdL
collection Repositori Obert UdL
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