Epigenetics

Analysis of DNA Methylation Dynamics and Maternal Effects in Dairy Cattle Using the RUMIGEN Methylation Array

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Abstract

This work was supported by the European Union's Horizon 2020 Research and Innovation Programme, grant agreement No.101000226DNA methylation is a key epigenetic mechanism influencing gene expression, development, and phenotypic plasticity. However, it has a longitudinal nature and is determined by maternal and environmental effects which remain poorly characterised. This study aimed to investigate (1) the epigenetic effects of maternal lactation status on the methylome of newborn offspring, and (2) the longitudinal evolution of DNA methylation throughout the early life of dairy calves. Four hundred and seventy (470) blood samples were taken from newborn calves from lactating and non-lactating cows. Additionally, longitudinal blood samples from 22 of these calves were collected at five time points: at birth (T0), 6 months (T6), 1 year (T12), 18 months (T18), and after first parturition (PT). Genomic DNA was extracted using the Qiagen DNeasy Blood & Tissue Kit, subjected to bisulfite conversion, and hybridised to the RUMIGEN methylation array (Illumina Inc.), which contains more than 40,000 CpG sites across the bovine genome. Raw intensities were processed and normalised with Illumina GenomeStudio, and converted to β-values representing methylation proportion per CpG site. Missing values were imputed using the MICE algorithm. All animals were genotyped using the BovineSNP50 Illumina SNP array.Differential methylation between calves born to lactating and non-lactating dams was assessed using a Bayesian linear mixed model. The proportion of variance in DNA methylation levels at each CpG site explained by genomic factors-referred to as methylation "heritability" per CpG site-was estimated with BGLR using a genomic relationship matrix, a methylation matrix, and a matrix accounting for blood cell composition (B cells, γδ T cells, and granulocytes) to correct for tissue heterogeneity. For a subset of 3,099 CpGs that were significantly associated with maternal lactation status (pThese results demonstrate the potential of high-density methylation arrays to capture both intergenerational and developmental epigenetic variation in dairy cattle. They also show some progressive changes in DNA methylation levels in blood through the rearing period, which may have implications in breeding and management programs, as well as for precision breeding strategies.

Keywords: 2026

How to Cite:

López-Catalina, A., Teran, E., Gutiérrez-Rivas, M., Navarro, P. & González-Recio, O., (2026) “Analysis of DNA Methylation Dynamics and Maternal Effects in Dairy Cattle Using the RUMIGEN Methylation Array”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2285471. doi: https://doi.org/10.31274/wcgalp.23718

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