Unravelling novel and closely linked association signals for fat-related traits in pigs using prioritised variants from whole-genome sequence data

For most production traits, the largest proportions of genetic variance remain unmapped. Dense whole-genome sequence (WGS) data enable the possibility of discovering novel associations as well as unravelling closely linked association signals with a resolution that marker arrays cannot reach. Howeve...

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Autores: Molinero García, Eduard, Pena i Subirà, Ramona Natacha, Estany Illa, Joan, Ros Freixedes, Roger
Formato: artículo
Estado:Versión publicada
Fecha de publicación:2025
País:España
Recursos:Universitat de Lleida (UdL)
Repositorio:Repositori Obert UdL
OAI Identifier:oai:repositori.udl.cat:10459.1/467858
Acesso em linha:https://doi.org/10.1016/j.animal.2025.101496
https://hdl.handle.net/10459.1/467858
Access Level:acceso abierto
Palavra-chave:Fatty acid
Fine-mapping
Genome-wide association study
Linkage disequilibrium
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spelling Unravelling novel and closely linked association signals for fat-related traits in pigs using prioritised variants from whole-genome sequence dataMolinero García, Eduard Pena i Subirà, Ramona NatachaEstany Illa, JoanRos Freixedes, RogerFatty acidFine-mappingGenome-wide association studyLinkage disequilibriumFor most production traits, the largest proportions of genetic variance remain unmapped. Dense whole-genome sequence (WGS) data enable the possibility of discovering novel associations as well as unravelling closely linked association signals with a resolution that marker arrays cannot reach. However, the identification of variants from WGS data that are causal of the variation of complex traits is hindered by the high dimensionality and linkage disequilibrium. Thus, at best, we can narrow the circle around the causal variants to prioritise a set of variants for their posterior validation. In this study, we assessed the utility of WGS data for uncovering associations of weaker effects using, as a model, fat content and composition traits in a Duroc pig population where we previously described major effects of the LEPR and SCD genes. We genotyped 971 pigs for a set of 182 variants from 154 candidate genes that were prioritised from amongst the WGS variants discovered in 205 sequenced individuals. These variants were prioritised conditional to LEPR and SCD. The association of the prioritised variants with the target traits was then tested in the confirmation set of 971 pigs. A total of 17 potentially independent quantitative trait loci (8.4% of the total number of studied genes) were significantly associated (q-value < 0.05) with at least one of the studied traits. We identified novel associations attributable to genes such as ABCC2, MOGAT2, or PLPP1 for backfat thickness, myristic acid content, and monounsaturated fatty acid content, respectively. Our results also revealed a finer granularity of weaker genetic effects in loci such as those around the DGAT2 and FADS2 genes, which may mask the effects of closely located genes like MOGAT2 and DAGLA, respectively. To refine the prioritisation of variants for validation studies, especially when targeting those of weaker effects, we recommend larger and more diverse discovery sets, more precise and complete functional gene annotation, and the integration of other omics data.We acknowledge Josep Reixach and the personnel at Selecci\u00F3n Batall\u00E9 for their cooperation with farm data and sample collection. This research was supported by the Spanish Ministry of Science, Innovation & Universities and the EU Regional Development Funds (grants RTI2018-101346-B-I00 and PID2021-125689OB-I00). EM is recipient of a UdL-Santander Predoc scholarship.Elsevier2025info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttps://doi.org/10.1016/j.animal.2025.101496https://hdl.handle.net/10459.1/467858reponame:Repositori Obert UdL instname:Universitat de Lleida (UdL)Inglésinfo:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/RTI2018-101346-B-I00info: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.animal.2025.101496Animal, 2025, vol. 19, núm. 5, p. 1-15cc-by-nc-nd (c) Molinero et al., 2025Attribution-NonCommercial-NoDerivatives 4.0 Internationalinfo:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by-nc-nd/4.0/oai:repositori.udl.cat:10459.1/4678582026-06-24T12:42:17Z
dc.title.none.fl_str_mv Unravelling novel and closely linked association signals for fat-related traits in pigs using prioritised variants from whole-genome sequence data
title Unravelling novel and closely linked association signals for fat-related traits in pigs using prioritised variants from whole-genome sequence data
spellingShingle Unravelling novel and closely linked association signals for fat-related traits in pigs using prioritised variants from whole-genome sequence data
Molinero García, Eduard
Fatty acid
Fine-mapping
Genome-wide association study
Linkage disequilibrium
title_short Unravelling novel and closely linked association signals for fat-related traits in pigs using prioritised variants from whole-genome sequence data
title_full Unravelling novel and closely linked association signals for fat-related traits in pigs using prioritised variants from whole-genome sequence data
title_fullStr Unravelling novel and closely linked association signals for fat-related traits in pigs using prioritised variants from whole-genome sequence data
title_full_unstemmed Unravelling novel and closely linked association signals for fat-related traits in pigs using prioritised variants from whole-genome sequence data
title_sort Unravelling novel and closely linked association signals for fat-related traits in pigs using prioritised variants from whole-genome sequence data
dc.creator.none.fl_str_mv Molinero García, Eduard
Pena i Subirà, Ramona Natacha
Estany Illa, Joan
Ros Freixedes, Roger
author Molinero García, Eduard
author_facet Molinero García, Eduard
Pena i Subirà, Ramona Natacha
Estany Illa, Joan
Ros Freixedes, Roger
author_role author
author2 Pena i Subirà, Ramona Natacha
Estany Illa, Joan
Ros Freixedes, Roger
author2_role author
author
author
dc.subject.none.fl_str_mv Fatty acid
Fine-mapping
Genome-wide association study
Linkage disequilibrium
topic Fatty acid
Fine-mapping
Genome-wide association study
Linkage disequilibrium
description For most production traits, the largest proportions of genetic variance remain unmapped. Dense whole-genome sequence (WGS) data enable the possibility of discovering novel associations as well as unravelling closely linked association signals with a resolution that marker arrays cannot reach. However, the identification of variants from WGS data that are causal of the variation of complex traits is hindered by the high dimensionality and linkage disequilibrium. Thus, at best, we can narrow the circle around the causal variants to prioritise a set of variants for their posterior validation. In this study, we assessed the utility of WGS data for uncovering associations of weaker effects using, as a model, fat content and composition traits in a Duroc pig population where we previously described major effects of the LEPR and SCD genes. We genotyped 971 pigs for a set of 182 variants from 154 candidate genes that were prioritised from amongst the WGS variants discovered in 205 sequenced individuals. These variants were prioritised conditional to LEPR and SCD. The association of the prioritised variants with the target traits was then tested in the confirmation set of 971 pigs. A total of 17 potentially independent quantitative trait loci (8.4% of the total number of studied genes) were significantly associated (q-value < 0.05) with at least one of the studied traits. We identified novel associations attributable to genes such as ABCC2, MOGAT2, or PLPP1 for backfat thickness, myristic acid content, and monounsaturated fatty acid content, respectively. Our results also revealed a finer granularity of weaker genetic effects in loci such as those around the DGAT2 and FADS2 genes, which may mask the effects of closely located genes like MOGAT2 and DAGLA, respectively. To refine the prioritisation of variants for validation studies, especially when targeting those of weaker effects, we recommend larger and more diverse discovery sets, more precise and complete functional gene annotation, and the integration of other omics data.
publishDate 2025
dc.date.none.fl_str_mv 2025
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.animal.2025.101496
https://hdl.handle.net/10459.1/467858
url https://doi.org/10.1016/j.animal.2025.101496
https://hdl.handle.net/10459.1/467858
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 2017-2020/RTI2018-101346-B-I00
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.animal.2025.101496
Animal, 2025, vol. 19, núm. 5, p. 1-15
dc.rights.none.fl_str_mv cc-by-nc-nd (c) Molinero et al., 2025
Attribution-NonCommercial-NoDerivatives 4.0 International
info:eu-repo/semantics/openAccess
http://creativecommons.org/licenses/by-nc-nd/4.0/
rights_invalid_str_mv cc-by-nc-nd (c) Molinero et al., 2025
Attribution-NonCommercial-NoDerivatives 4.0 International
http://creativecommons.org/licenses/by-nc-nd/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
repository.name.fl_str_mv
repository.mail.fl_str_mv
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