Estimation of genetic parameters and detection of chromosomal regions affecting the major milk proteins and their post translational modifications in Danish Holstein and Danish Jersey cattle

Background: In the Western world bovine milk products are an important protein source in human diet. The major proteins in bovine milk are the four caseins (CN), alpha(S1)-, alpha(S2)-, beta-, and k-CN and the two whey proteins, beta-LG and alpha-LA. It has been shown that both the amount of specific CN and their isoforms including post-translational modifications (PTM) influence technological properties of milk. Therefore, the aim of this study was to 1) estimate genetic parameters for individual proteins in Danish Holstein (DH) (n = 371) and Danish Jersey (DJ) (n = 321) milk, and 2) detect genomic regions associated with specific milk protein and their different PTM forms using a genome-wide association study (GWAS) approach. Results: For DH, high heritability estimates were found for protein percentage (0.47), casein percentage (0.43), k-CN (0.77), beta-LG (0.58), and alpha-LA (0.40). For DJ, high heritability estimates were found for protein percentage (0.70), casein percentage (0.52), and alpha-LA (0.44). The heritability for G-k-CN, U-k-CN and GD was higher in the DH compared to the DJ, whereas the heritability for the PD of alpha(S1)-CN was lower in DH compared to DJ, whereas the PD for alpha(S2)-CN was higher in DH compared to DJ. The GWAS results for the main milk proteins were in line what has been earlier published. However, we showed that there were SNPs specifically regulating G-k-CN in DH. Some of these SNPs were assigned to casein protein kinase genes (CSNK1G3, PRKCQ). Conclusion: The genetic analysis of the major milk proteins and their PTM forms revealed that these were heritable in both DH and DJ. In DH, genomic regions specific for glycosylation of k-CN were detected. Furthermore, genomic regions for the major milk proteins confirmed the regions on BTA6 (casein cluster), BTA11 (PEAP), and BTA14 (DGAT1) as important regions influencing protein composition in milk. The results from this study provide confidence that it is possible to breed for specific milk protein including the different PTM forms.