Multi-omics analysis

The RUMIGEN EpiChip: a new tool for integrating epigenetics into dairy cow selection

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Abstract

The DNA methylation BeadChip (EpiChip), developed in the H2020 RUMIGEN project, offers a powerful approach to understanding the epigenetic factors influencing dairy cow performance. This study used the RUMIGEN EpiChip on blood samples from 4,679 Holstein cows to evaluate the extent to which DNA methylation may help predict cow phenotypes. A total of 35 traits related to milk production, fertility, udder health, and morphology were analyzed using mixed models that included random genetic and/or epigenetic effects. Genetic covariance structure was computed from SNP genotypes obtained from the EuroGMD chip, while epigenome covariance structure was derived from methylation similarity between individuals, estimated from EpiChip data adjusted for blood leukocyte composition. We compared: (1) a model including only the genetic component, and (2) a joint model including both genetic and epigenetic components, alongside fixed environmental effects. To evaluate predictive performance, cows were divided into training (80%) and validation (20%) sets, and the accuracy of estimated genomic breeding values (GEBVs) was assessed across models. For 14 traits, DNA methylation accounted for between 1% and 15% of the total phenotypic variance-specifically, 10 morphology traits (1-15%), somatic cell score and fertility (3%), and milk fat yield and content (1%). Incorporating DNA methylation data improved GEBV accuracy for eight traits, including six morphology traits, milk fat yield, and somatic cell score, with gains in accuracy ranging from 0.5% to 6.7%, as measured by the correlation between adjusted phenotypic performance and GEBVs. These findings pave the way for EpiChip data to improve predictive capacity beyond conventional genetic and environmental factors. The use of EpiChip data represents a promising step toward more accurate, efficient, and sustainable breeding and management strategies in the dairy industry. This project has received funding from the European Union's Horizon 2020 Programme for Research & Innovation under grant agreement n°101000226 (RUMIGEN) and from APIS-GENE (PolyPheme).

Keywords: 2026

How to Cite:

Sanchez, M., Besnard, F., Costes, V., Fouéré, C., Castro Dias Cuyabano, B., Patry, C., Le Danvic, C., Costa Monteiro Moreira, G., Asset, A., Boussaha, M., Jammes, H., Fritz, S., Kiefer, H. & Boichard, D., (2026) “The RUMIGEN EpiChip: a new tool for integrating epigenetics into dairy cow selection”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286554. doi: https://doi.org/10.31274/wcgalp.24048

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