Associations between milk protein polymorphism and first lactation milk production traits in Finnish Ayrshire cows

Genotypic effects of beta-casein (CN), kappa-CN, and beta-lactoglobulin (LG) on milk, fat, and protein production and fat and protein percentages were estimated for 18,686 Finnish Ayrshire cows in first lactation using an animal model. Casein genotype effects were estimated including individual beta-CN and kappa-CN simultaneously in a model and then as composite beta-kappa-CN. The A2 allele of beta-CN and the A allele of kappa-CN, as well as the A1 allele of beta-CN and the B or E allele of kappa-CN, appeared together more frequently than was expected. Because of linkage disequilibrium in the casein loci and, consequently, unbalanced data, some contradictory effects of casein genotypes were obtained with the two models. A well-founded way to estimate the effects of casein genotypes was to use beta-kappa-CN genotypes. Composite casein genotypes including the A2 allele of beta-CN were associated with the highest milk and protein production and the lowest fat content, those including the B allele of kappa-CN with the highest protein content, and those including the E allele of kappa-CN with the lowest protein content. The effect of the beta-kappa-CN genotypes on protein content was moderately strong, and the effect was somewhat smaller for other traits. The AA genotype of beta-LG had a favorable effect on milk and protein production, and the BB genotype had a favorable effect on fat content.