Molecular Diversity of the Casein Gene Cluster in Bovidae: Insights from SNP Microarray Analysis

Abstract

The casein gene cluster spans 250 to 350 kb across mammalian species and is flanked by non-coding DNA with largely unknown functions. These regions likely harbor elements regulating the expression of the 4 casein genes. In Bovidae, this cluster is well studied in domestic cattle and to a lesser extent in zebu and water buffalo. This study used a cattle-specific SNP microarray to analyze 12 Bovidae taxa and estimate casein gene cluster variability across 5 bovid subfamilies. Genotyping identified 126 SNPs covering the entire casein gene cluster and 2 Mb of upstream and downstream regions. Dairy cattle, watusi, and zebu showed the highest polymorphism: 63.7–68.2% in the 5′-upstream region, 35.6–40.0% in the casein cluster, and 40.4–89.4% in the 3′-downstream region. Among wild bovids, only a ‘semi-aquatic’ lechwe revealed high polymorphism similar to cattle. Other species exhibited lower variability, ranging from 9.1–27.3% in the 5′-upstream, 8.9–20.0% in the casein, and 4.2–10.6% in the 3′-downstream regions. For the first time, genome variability data were obtained for impala, waterbuck, and lechwe. It appears that higher variability in cattle’s casein gene cluster may relate to its intense expression. This study confirms the effectiveness of cattle-derived microarrays for genotyping Bovidae.