Epigenetics

Farm-specific DNA methylation patterns and associations to age in dairy cattle

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Abstract

Epigenetic mechanisms, including DNA methylation (DNAm), allow plasticity in gene expression in response to environmental stimuli. Because of this, epigenetic information is a promising target for quantifying environmental effects and gene x environment interactions in phenotypic predictions. In dairy cattle, differences in DNAm have been associated with heat stress, mastitis, and interindividual differences in milk production and fertility. This study hopes to identify farm-specific DNAm signatures in dairy cattle by comparing animals across two farms. Both farms are Cornell University research farms near Ithaca, NY that broadly have similar management practices exemplifying New York State commercial dairies. Both have cows averaging around 41 kg of milk per day though the farms do differ in size. Farm A has around 175 adult cows (milking and dry) and Farm B has around 700 adult cows. Blood samples were taken from Holstein calves within 24-48 hours after birth (n=12 per farm) and from Holstein primiparous cows at 30±7 days in milk (n=12 per farm, mean age at first calving = 23 months). Genomic DNA was isolated from whole blood samples and sequenced via whole genome bisulfite sequencing. Reads were processed and methylation was called with Bismark. Further analysis was limited to CpG sites. DMRichR was used to compare global DNAm patterns and identify differentially methylated regions (DMR) between farms at each timepoint separately. Using smoothed DNAm levels across 20kb windows globally, PCA was able to visually separate animals by farm on PC2 at each timepoint. Between farms, 2 and 49 DMR reached genome-wide significance (FDR adjusted q-value 20% difference in DNAm levels across farms) in calves and primiparous cows respectively. In previous analyses that compared groups of similarly aged animals within a farm using the same sequencing data and methodology, no genome-wide significant DMR were identified showing that while few farm-related DMR were identified here, they represent an important finding. The fact that more DMR were identified between farms in older animals could suggest that prolonged exposure to different environments leads to more distinct DNAm patterns between farms. Differences in genetic background, diet, disease management, heat abatement, and stress levels between farms could be responsible for these differences in DNAm though more research is needed to fully understand which of these are driving the difference. In primiparous cows, DMR between farms were significantly enriched in Quantitative Trait Loci (QTL) for 57 different traits (adjusted p-value < 0.05) the majority of which were health and meat/carcass traits. DMR in QTL could result in differences in QTL expression and performance between animals on different farms, exemplifying the possible utility of DNAm information in quantifying gene x environment effects.

Keywords: 2026

How to Cite:

Jewell, S., Srikanth, K. & Huson, H., (2026) “Farm-specific DNA methylation patterns and associations to age in dairy cattle”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2287132. doi: https://doi.org/10.31274/wcgalp.24218

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