The RUMIGEN EpiChip: a versatile, medium density DNA methylation Beadchip for large scale population studies in cattle

Abstract Background DNA methylation contributes to the elaboration of phenotypes and is hypothesized to account for interindividual variations in farm animals. Currently, methodologies available to investigate DNA methylation in cattle rely on high throughput sequencing, which cannot be applied to large cohorts. To enable large scale DNA methylation analysis, we developed the RUMIGEN EpiChip, the first DNA methylation array specifically designed for cattle. Results Manufactured by Illumina, the EpiChip contains 43,317 CpG markers allowing analysis of phenotypes of agronomical interest as well as the study of regulatory processes. The assay design drew on data from numerous studies achieved by the scientific community, and includes CpGs where methylation varies with health status, physiological stage, fertility, and environmental challenges, as well as CpGs located in functional genomic elements (promoters, CTCF binding sites, expression quantitative trait loci). The technical performances of the EpiChip were tested on several semen and blood DNA samples and in two laboratories, showing excellent repeatability, accuracy and interoperability. Methylation values were also concordant with those obtained by reduced representation bisulfite sequencing. The EpiChip has demonstrated a good ability to explore biological processes such as genomic imprinting and differences between cell types, opening the possibility of inferring blood cell composition. Finally, analysis of longitudinal ear biopsies allowed accurate age prediction, suggesting the potential of the array to refine epigenetic clocks. Conclusions The RUMIGEN EpiChip is a cost-effective and versatile resource that opens new opportunities for the study of regulatory mechanisms underlying phenotypic variation and for large-scale association analyses in cattle.

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Journal
bioRxiv (Cold Spring Harbor Laboratory)
Published
2025-12-22
DOI
https://doi.org/10.64898/2025.12.19.695474
Citations
1
Primary Topic
Epigenetics and DNA Methylation
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article
Field-Weighted Citation Impact
0.81

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article

The RUMIGEN EpiChip: a versatile, medium density DNA methylation Beadchip for large scale population studies in cattle

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1 citations
bioRxiv (Cold Spring Harbor Laboratory)
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article

The RUMIGEN EpiChip: a versatile, medium density DNA methylation Beadchip for large scale population studies in cattle

Gilles Foucras, M Boussaha, Shannon Clarke, J. C. Powell, Ananth N. Shankar, Javier López Viana, Alex Caulton, Valentin Costes, D.E. Rico, Laurent Schibler, Pau Navarro, Chrystelle Le Danvic, Goutam Sahana, Carmen García Alba, Óscar González-Recio, Christine Couldrey, Nathalie Bissonnette, Francesca Ali, Gabriel Costa Monteiro Moreira, Kumiko Takeda, Clotilde Patry, Eiji Kobayashi, Zexi Cai, Ludivine Lietar, Sophie Martel, Aurelie Chaulot-Talmon, Helene Jammes, Sebastien Fritz, Evelyne M. Ibeagha-Awemu, Helene Kiefer, Adrian Lopez-Catalina
article en
1 citations

Abstract

Abstract Background DNA methylation contributes to the elaboration of phenotypes and is hypothesized to account for interindividual variations in farm animals. Currently, methodologies available to investigate DNA methylation in cattle rely on high throughput sequencing, which cannot be applied to large cohorts. To enable large scale DNA methylation analysis, we developed the RUMIGEN EpiChip, the first DNA methylation array specifically designed for cattle. Results Manufactured by Illumina, the EpiChip contains 43,317 CpG markers allowing analysis of phenotypes of agronomical interest as well as the study of regulatory processes. The assay design drew on data from numerous studies achieved by the scientific community, and includes CpGs where methylation varies with health status, physiological stage, fertility, and environmental challenges, as well as CpGs located in functional genomic elements (promoters, CTCF binding sites, expression quantitative trait loci). The technical performances of the EpiChip were tested on several semen and blood DNA samples and in two laboratories, showing excellent repeatability, accuracy and interoperability. Methylation values were also concordant with those obtained by reduced representation bisulfite sequencing. The EpiChip has demonstrated a good ability to explore biological processes such as genomic imprinting and differences between cell types, opening the possibility of inferring blood cell composition. Finally, analysis of longitudinal ear biopsies allowed accurate age prediction, suggesting the potential of the array to refine epigenetic clocks. Conclusions The RUMIGEN EpiChip is a cost-effective and versatile resource that opens new opportunities for the study of regulatory mechanisms underlying phenotypic variation and for large-scale association analyses in cattle.

bioRxiv (Cold Spring Harbor Laboratory)
Agriculture and Agri-Food Canada (CA), Roslin Institute (GB), Consejo Superior de Investigaciones Científicas (ES), École Nationale Vétérinaire de Toulouse (FR), Université de Versailles Saint-Quentin-en-Yvelines (FR), Aarhus University (DK), AgroParisTech (FR), Université Paris-Saclay (FR), AgResearch (NZ), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (FR), Institute of Livestock and Grassland Science (JP), Laboratory of Molecular Genetics (PL), Centre de Recherche en Sciences Animales de Deschambault (CA), Biotech Park (IN), Interactions hôtes-agents pathogènes (FR), ElSohly Laboratories (United States) (US), Genomics (United Kingdom) (GB)
APIS-GENE, European Commission, Javna Agencija za Raziskovalno Dejavnost RS, Région Occitanie Pyrénées-Méditerranée, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
Zero hunger
Openalex Percentile: Top 20%
Epigenetics and DNA Methylation
0.81
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