Building a Bovine Blood DNA Methylation EpiMap Related to disease Phenotypes

Background Epigenetic variations, particularly in response to environmental factors, play a crucial role in shaping immune identity and function in hematopoietic cells. This study investigates interindividual differences in DNA methylation among dairy cows, with the aim of enhancing our understanding of the adaptive capacity essential for sustainable animal production. We conducted whole-genome sequencing and DNA methylation analysis using enzymatic methyl-seq on whole blood from 60 Holstein cows. The study included five phenotype groups: mastitis, lameness, infertility, metabolic disorders and healthy controls. Results Among the 50 million CpG sites, 5.1% were identified as variable methylated cytosines (VMCs) and 94.9% as conserved methylated cytosines (CMCs). VMCs displayed variability in distal promoter regions, suggesting potential plasticity in the associated genes, while CMCs exhibited a bimodal methylation pattern near the transcription start site, indicative of tissue-specific functions. Notably, we identified motif enrichments related to genes potentially expressed in blood. An age-related analysis revealed a 1.4% faster decline in CMCs methylation compared to VMCs. Additionally, disease risk assessment may be achievable using as few as 586 methylation biomarkers, which could be used to select which cows to keep in the herd for additional lactation. Conclusion Our results suggest a dual role for VMCs and CMCs: while the stability of conserved sites is potentially associated with essential functions in cell development and homeostasis, variable sites may be involved in dynamically regulating gene transcription in response to internal or external stimuli. These insights underscore the epigenome’s role in immune regulation and adaptive resilience in cattle. Blood samples were collected from cows at a Vancouver farm between November 2020 and January 2021. A year later, we selected 30 cows that had been culled during the year due to complications related to infertility (BFR, n=6), mastitis (BMS, n=6), lameness (BFL, n=12), or metabolic disorders (BMT, n=6), which were not identified at the time of sampling. This culling reason was recorded in farm management logs and represented the primary cause for culling. These cows formed the “diseased group.” For comparison, we selected a second group of 30 cows that remained in the herd without any health issues. This second group represented the “control group.” The ages of the cows in both groups ranged from 1 to 9 years. The pairing of each subgroup with controls (6 vs. 6, 12 vs. 12, or 30 vs. 30) for the comparison analyses was performed by selecting individuals as close in age as possible, even though age was excluded as a covariate in the differential analyses. This allowed us to minimize age-related effects while focusing the analysis on disease-associated methylation differences.