135 Enhancing livestock resilience: epigenetic diversity in bovine

The sustainable livestock sector faces numerous challenges, including intrinsic and extrinsic factors that affect animals’ adaptive capacities. The concept of a “robust animal” has emerged, referring to animals capable of adapting to environmental changes while preserving their health and productivity. Specifically, methylation of CpG sites in haematopoietic cells confers specific identity and functions associated with adaptive and innate immunity throughout an individual’s lifespan. In this context, it is crucial to characterise and map the epigenetic mechanisms underlying animals’ adaptive capacities and their potential implications for sustainable animal production. To study the impact of reproduction technologies on the phenotypes of the next generation, we need a single tissue where DNA methylation can inform on the programming of the animal. The blood represents such tissue, and the interindividual variation must first be assessed to do epidemiological studies. The aim of this study was to identify inter-individual differences in DNA methylation across the bovine genome, specifically in identity of immune cells. Characterising the methylome of haematopoietic cells will enable precise phenotyping of immune competence, offering a new approach to identify resilient animals and a promising pathway toward more sustainable and responsible animal production. Using whole-genome sequencing, DNA methylation was analysed by enzymatic methyl-seq (EM-seq), utilising genomic DNA from total blood, for 48 Prim’Holstein cows raised on the same farm, exhibiting four different phenotypes based on culling reasons (6 mastitis, 6 lameness, 6 low fertility, and 6 low lactation) + 24 control. Among the 36 million CpG sites (covered with a minimum of 5 reads), variability analyses using twice the mean standard deviation allowed the establishment of a list of variable methylated cytosines (VMCs). Accordingly, 5.3% VMCs were identified, of which 2.52% showed no genetic variation and 2.79% were associated with SNPs or potentially epimutations. Additionally, a list of conserved methylated cytosines (CMCs) representing 94.7% of CpGs was generated. The VMCs specifically targeted three genes (UL16-binding protein 17, CD99 molecule, olfactory receptor family 52 subfamily S member 22), while the CMCs targeted 1604 specific genes and 25 526 in common, respectively, between 39% and 49% of these CpGs targeted a gene or its putative regulatory regions. Identification of promoter regions targeted by VMCs and enrichment analyses of networks and signaling pathways suggested different functions, with a global hypomethylation pattern for VMCs (<40%), suggesting activation of associated genes consistent with individual patterns. In contrast, CMCs exhibited a bimodal distribution with hypo- and hypermethylation, suggesting respectively activation and repression of genes, consistent with blood tissue functioning. Differential analysis of CpGs associated with the olfactory receptor family (2188 CpGs) revealed a differentially methylated region of 294 bp and 16 CpGs associated in chemoreceptor (OR5C1 201). This gene is potentially involved in immune system activation. These findings allow us to hypothesise about the epigenetic control of the immune response in bovine species.