Epigenome-wide association analysis of DNA methylation with phenotypic and environmental traits in French Holstein dairy cows using the RUMIGEN EpiChip
- Alexandre Asset (International Livestock Research Institute (ILRI))
- Valentin Costes (Université de Versailles Saint-Quentin-en-Yvelines)
- Gwendoline Potier (Université Paris-Saclay)
- Marie-Pierre Sanchez (Université Paris-Saclay)
- Florian Besnard (Eliance)
- Corentin Fouere (Eliance)
- Sébastien Fritz (Eliance)
- Clotilde Patry (Valogene)
- Gilles Foucras (French National Institute for Agricultural Research (INRAE))
- Helene Jammes (Université de Versailles Saint-Quentin-en-Yvelines)
- Christophe Richard (Université Paris-Saclay)
- Valerie Gelin (Université Paris-Saclay)
- Laurène Le Berre (Eliance)
- Alline De Paula Reis (Université Paris-Saclay)
- Didier Boichard (Université Paris-Saclay)
- Chrystelle Le Danvic (Eliance)
- Gabriel Costa Monteiro Moreira (Université de Versailles Saint-Quentin-en-Yvelines)
- David Makowski (Université Paris-Saclay)
- Hélène Kiefer (Université de Versailles Saint-Quentin-en-Yvelines)
Abstract
The goal of our study was to investigate the associations between DNA methylation patterns and various agronomic traits and environmental factors in French Holstein dairy cows. Blood samples were collected from 4,608 cows originating from 261 French herds. Phenotypic records included 33 traits related to milk production and composition, immunity, fertility, and morphology. DNA methylation profiles were obtained at 44,053 CpG sites using the cattle-specific EpiChip array, covering all annotated genes across the genome. Data were quality-controlled and normalized to remove low-quality probes and correct for batch effects. Associations between DNA methylation and phenotypic traits were evaluated using linear mixed models including fixed environmental effects (such as age and herd-related factors), while accounting for blood leukocyte composition. The first five principal components, derived from the genotypes obtained using the EuroGMD SNP array, were also considered to account for population structure. Multiple testing correction was applied using Bonferroni adjustment (adjusted p-value This project has received funding from the European Union's Horizon 2020 Programme for Research & Innovation under grant agreement n°101000226 (RUMIGEN), from APIS-GENE (PolyPheme) and the DIGIT-BIO INRAE Metaprogram EPINUM
Keywords: 2026
How to Cite:
Asset, A., Costes, V., Potier, G., Sanchez, M., Besnard, F., Fouere, C., Fritz, S., Patry, C., Foucras, G., Jammes, H., Richard, C., Gelin, V., Le Berre, L., De Paula Reis, A., Boichard, D., Le Danvic, C., Costa Monteiro Moreira, G., Makowski, D. & Kiefer, H., (2026) “Epigenome-wide association analysis of DNA methylation with phenotypic and environmental traits in French Holstein dairy cows using the RUMIGEN EpiChip”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286501. doi: https://doi.org/10.31274/wcgalp.24032
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