Guiding eQTL mapping and genomic prediction of gene expression in three pig breeds with tissue-specific epigenetic annotations from early development
Gene expression is a dynamic phenotype influenced by tissue-specific regulatory mechanisms, which can modulate expression directly or indirectly through cis or trans factors. Identifying genetic variants in these regulatory regions can improve both expression quantitative trait locus (eQTL) mapping and gene expression prediction. Whole genome sequences offer the possibility for enhanced eQTL mapping accuracy, but detecting causal variants remains challenging. Here, we evaluate the potential added-value of integrating tissue-specific epigenetic annotations, such as chromatin accessibility and methylation status, into within-breed genomic predictions of expression for three pig breeds. Functional annotations from early developmental stages improved eQTL mapping interpretability as shown by the enrichment of trait-relevant QTLs. However, despite the use of functional annotations, predictions across breeds remain challenging due to differences in genetic architectures. Our work contributes to the understanding of gene expression regulation in livestock and highlights the value of functional annotations, despite continued challenges for predictions across breeds.
Authors
- Elisabetta Giuffra (ORCID: https://orcid.org/0000-0001-9568-2056)
- Andréa Rau (ORCID: https://orcid.org/0000-0001-6469-488X)
- Sylvain Foissac (ORCID: https://orcid.org/0000-0002-2631-5356)
- M.P.L. Calus (ORCID: https://orcid.org/0000-0002-3213-704X)
- Fanny Mollandin (ORCID: https://orcid.org/0000-0003-0806-1062)
- Pascal Croiseau (ORCID: https://orcid.org/0000-0001-6493-2892)
- B.C. Perez (ORCID: https://orcid.org/0000-0002-7062-5263)
- Hervé Acloque (ORCID: https://orcid.org/0000-0003-4761-1055)
- Hélène Gilbert (ORCID: https://orcid.org/0000-0002-4385-3228)
- Sarah Djebali (ORCID: https://orcid.org/0000-0002-0599-1267)
- Cervin Guyomar (ORCID: https://orcid.org/0000-0003-2707-2541)
- M.C.A.M. Bink (ORCID: https://orcid.org/0000-0002-1278-2092)
- Daniel Crespo‐Piazuelo (ORCID: https://orcid.org/0000-0001-7896-2507)
- Jani de Vos (ORCID: https://orcid.org/0000-0001-9507-5969)
- Marie-José Mercat (ORCID: https://orcid.org/0000-0002-3087-082X)
- Ole Madsen (ORCID: https://orcid.org/0000-0001-8082-7881)
- María Ballester (ORCID: https://orcid.org/0000-0002-5413-4640)
Institutions
- Université Toulouse III - Paul Sabatier (FR)
- Inserm (FR)
- École Nationale Vétérinaire de Toulouse (FR)
- Université Fédérale de Toulouse Midi-Pyrénées (FR)
- AgroParisTech (FR)
- Université Paris-Saclay (FR)
- Microbiologie de l’alimentation au service de la santé (FR)
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (FR)
- Institute of Agrifood Research and Technology (ES)
- Hendrix Genetics (Netherlands) (NL)
- Institut de Recherche en Santé Digestive (FR)
- Génétique Animale et Biologie Intégrative (FR)
- Institut du Porc (FR)
- Génétique Physiologie et Systèmes d'Elevage (FR)
- Wageningen University & Research (NL)
Publication Details
- Journal
- Genomics
- Published
- 2025-11-26
- DOI
- https://doi.org/10.1016/j.ygeno.2025.111158
- Primary Topic
- Genetic Mapping and Diversity in Plants and Animals
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- European Commission
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement