Abstract
<title>Abstract</title> <p>Heat tolerance and fertility distinguish indicine (Bos taurus indicus) from taurine (Bos taurus taurus) cattle, yet the epigenetic component of this divergence is poorly resolved, and methylation and expression are rarely measured in the same animals. We reanalysed public reduced-representation bisulfite sequencing in three progressively stricter stages, against a 108-gene panel of thermotolerance, tick-resistance, production and fertility loci with uniform ±15 kb windows (upstream and downstream). Discovery compared Angus and Nelore, recovering 160 differentially methylated cytosines (DMCs; methylKit, q < 0.05, methylation difference above 15%; 90 hyper- and 70 hypomethylated in taurine) across 50 genes, densest at PRSS16 and HSP90AA1. Principal-component analysis separated the subspecies (53.9% of variance). A systematisation across thirteen subspecies, seasonal and cell-type-resolved contrasts (Nelore vs Holstein, n = 3) returned up to 840 DMCs per constitutive contrast, stronger in lymphoid than myeloid lineages, and marked 95 genes, whereas the within-breed seasonal contrasts were near-silent. Crossing these findings with a four-tissue heat-stress transcriptome (9313 differentially expressed genes; DESeq2, adjusted p < 0.05) recovered 47 genes marked at both layers, 19 concordantly repressive, and a feature-weighted score nominated ten candidates centred on a heat-shock and somatotropic core (GHSR, HSPA2, HSPB1, PRLR, ITGB3) with tick-resistance loci emerging (GRHL3, PADI4; and PRSS16 in discovery). Fetal-liver whole-genome bisulfite sequencing corroborated GHSR, HSPA2 and PRLR. As a prospect, this compact, cell-type-resolved marker set offers a basis for epigenetic-informed selection and genetic-score validation, marking where same-animal validation should begin in tropical Girolando (Gir × Holstein).</p>