Genetic Variation At Distal Regulatory Elements In Casein Gene Cluster Is Associated With Milk Composition And Management Traits In Dairy Cattle

Genetic variation underlies differences in production traits in Cattle. One of the advances enabled by the recently completed bovine genome sequence is the ability to search for causative Single Nucleotide Polymorphisms (SNP) related to lactation traits. Historically the focus has been on SNP located in the coding regions of genes, likely causing miss‐functioning or impaired expression of the peptide. However, causative SNP in gene regulatory regions, both proximal promoters and distal regulatory elements, might have more lasting effects by causing changes in gene regulation. To identify potential distal regulatory elements in the casein gene cluster, encoding the major milk protein genes, we combined multi‐species comparative genome analysis and chromatin conformation studies. The bovine casein gene cluster is located on BTA6 and comprises four casein genes, CSN1S1‐ CSN2‐CSN1S2‐CSN3, as well as five physically linked genes. We identified a number of potential distal regulatory elements including the Beta‐Casein Enhancer (BCE) and Evolutionarily Conserved Region 3 (ECR3). We resequenced BCE and ECR3 genomic regions in a sample of 8 Brown Swiss, 8 Holstein and 8 Jersey cows that were unrelated in a three‐generation pedigree and a number of SNP were identified. These SNP were genotyped and tested for associations with milk production and management traits in 800 Holstein bulls and 300 Holstein cows. Significant results (p<0.01; FDR<0.05) were observed for one SNP in the bull population for productive life and somatic cell score PTA traits. The same SNP was also significantly associated with protein and casein percentages in the cow population. Two other SNP were associated with PTA protein percentage in bulls. By computational analysis we predicted the presence of potential binding sites for DNA‐binding proteins in the studied regions and found a number of sites for both inhibitory and activating factors. Several of these sites were conserved. Most of the SNP were in or close to conserved binding sites and can potentially interfere with binding of factors and the function of these regions. To provide support to these findings, we are examining if different genotypes for BCE and ECR3 have an association with gene expression differences in the casein locus and affect transcription factor binding. These results emphasize the importance of SNP variation in distal regulatory regions in relation to milk production and management traits in dairy cattle. These finding also indicate that epigenetic changes induced through external influences such as infection or nutrition could interact with genetic variation resulting in different susceptibility to these stimuli.