Characterization of selection on immune regulatory elements and MHC gene diversity in Holstein cattle

The objective of this study was to develop a hybrid capture tool for targeted sequencing of immune regulatory elements and MHC BoLA (Bovine Leukocyte Antigen) genes in Holstein cattle, and to assess how 6 decades of breeding-associated evolutionary and demographic processes may have shaped these regions of the genome. Using published epigenetic data sets, we identified 70 regulatory regions of interest (ROIs) that become more accessible in response to infection. We then combined low-pass whole-genome sequencing (Skim-seq) with targeted hybrid capture of these ROIs and BoLA genes to characterize genetic variation across groups and to identify variants potentially associated with differences in immune function in Holsteins. Three groups of Holstein cattle were used in the study: unselected Holstein cows, contemporary Holstein cows and contemporary elite Holstein bulls. Runs of homozygosity (ROH) analyses revealed a genome-wide loss of diversity in contemporary Holsteins. Refining this analysis, we applied F_ST calculations to screen for variants that most distinguish unselected from contemporary Holsteins. We identified variants located within immune-related ROIs that are predicted to have allele-specific regulatory effects, as well as reduced diversity at the critical antigen-presenting gene BoLA-DRB3 in contemporary Holsteins. Although these findings do not establish direct effects on immune phenotypes, the loci identified are known or predicted to participate in immune function and therefore represent biologically plausible targets. This study defines a set of candidate coding and regulatory regions for future investigation. By highlighting genomic changes in both noncoding regulatory elements and MHC genes, these results offer a foundation for follow-up studies aimed at understanding how production-focused breeding may be balanced with maintenance of immune-related variation in cattle.