Associations between casein haplotypes and milk yield traits of offspring from 5 Swiss Fleckvieh AI test bulls were investigated. The analysis was performed by using a daughter design, where each daughter inherited either paternal haplotype B-A¹-A-A or B-A²-A-A for alleles αₛ₁-, ß-, αₛ₂- and κ-casein genes. The substitution effects of paternal CSN2 A¹ versus A² on protein yield deviations (YDs) were significant (P < 0.05), whereas their effects on milk and fat YDs were not. The paternal substitution effects of the CSN2 A¹ versus the A² allele on protein YDs within the 5 sires did not reach the significance level. This is due to the contrary allele substitution effect of a sire compared to the other 4 sires. The effects of maternal haplotypes on milk, protein and fat YDs were not significant. However, it is noteworthy that the effects of haplotypes with a low frequency in the population deviate largely from the most frequent haplotype B-A²-A-A. The effects of ß-lactoglobulin (BLG) genotypes were significant for protein YDs but not for milk and fat YDs. The association between the paternal CSN2 A¹ and A² alleles and milk protein YDs within sires but not milk and fat YDs indicate an interaction, which might be a consequence of CSN2 heterogeneity or a closely linked gene that is contributing to the estimated effects.
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