Associations between milk protein genetic variants and production traits in New Zealand dairy cattle

Records on 7574 first lactation cows were used to investigate the associations between milk protein genetic variants and 305-day milk, fat, and protein yields. Friesians, Jerseys and Ayrshires and their crosses were represented in the data. Milk samples were typed for three casein (Cn) proteins alpha(s1)-Cn (B,C), beta-Cn (A(1), A(2)), kappa-Cn (A,B), and one whey protein beta-lactoglobulin (Lg) (A,B). The model used to describe the data included the additive genetic effect of animal and the four protein phenotypes. Hypotheses testing involved a test of the breed by protein phenotype interaction for each of the four milk proteins and, where appropriate, a test to determine whether the difference between the homozygotes was significantly (P<0.05) different from 0, as well as a test to determine whether the heterozygote was significantly different from the midpoint of the two homozygotes. The interaction between breed and beta-cn phenotype was significant for milk, fat and protein yields, while the interaction between breed and kappa-Cn phenotype was significant only for protein yield. The interaction associated with kappa-Cn was a scale effect, while the interactions associated with beta-Cn resulted from reranking of breed across the protein phenotypes. Across breed, alpha(s1)-Cn BC cows produced 1.9% less milk and 0.6% more protein than BE cows, while the differences between the phenotypes for fat production were small. The beta-cn A(2) allele was associated with increased production in the Friesians, with A(2)A(2) COWS producing approximately 2% more milk, fat and protein than A(1)A(1) cows. The opposite effect was found in Jerseys, where A(2)A(2) COWS produced 3-4% less milk, fat, and protein than A(1)A(1) cows. The B allele of kappa-Cn was associated with a 0.6-3.5% increase in production. The beta-Lg BE phenotypes produced approximately 1.3% less milk and protein and 1.2% more fat than the AA phenotypes.