Global analysis of bovine milk protein variants using multi-breed DNA sequence data

Background To date, 63 variants of six major bovine milk proteins (αS1-CN, β-CN, αS2-CN, κ-CN, α-LA, and β-LG) have been described. These variants are caused by changes in the amino acid sequence of the mature protein, primarily resulting from missense variations in the exons of genes or splice sites. Several of these variants are known to be associated with milk production traits, cheese-processing properties, and the nutritional value of milk. In the past, milk protein variants have been identified in a limited number of breeds, especially in dairy cattle. The objective of this study was to investigate variation in milk proteins in a large number of cattle breeds based on whole genome sequencing data. Results We investigated variants of the six major milk proteins in 3,824 cattle representing 113 breeds with wide geographical distribution using whole genome sequencing data. 59 missense variants of milk protein genes that can alter the amino acid sequence of the mature protein were detected. Notably, 10 out of 11 missense variants in CSN3 were located within the region coding for the glyco-macropeptide, whereas the para-κ-casein region involved in micelle stabilization remained highly conserved with only one variant detected, suggesting functional constraint in this region. A total of 121 milk protein variants were identified based on different combinations of the 59 missense variants, of which 35 had been described previously. We detected 86 novel variants that had not been reported previously. These protein variants were likely missed in earlier studies due to technical limitations or the use of limited number of animals or breeds. Conclusion This study provides a comprehensive overview of milk protein diversity across global cattle breeds, offering valuable insights for improving milk quality and properties, guiding selective breeding and prioritizing variants for future functional investigation in the dairy sector.