Associations of bovine beta-casein and kappa-casein genotypes with genomic merit in Holstein Friesian cattle

Abstract. The relationship between the index values used to evaluate the genomic value and essential markers such as casein genes provides important information at the herd level. Therefore, this study aimed to determine the association between casein gene genotypes and the indices of genetic merit in Holstein Friesian cattle. A total of 805 cows were genotyped using the Affymetrix® Axiom® array system. We used data composed of the total performance index (TPI) and net merit (NM) values as well as the predicted transmitting abilities (PTAs) indices, including milk, fat, fat percentage, protein, protein percentage, combined fat and protein (CFP), productive life (PL), somatic cell score (SCS), daughter pregnancy rate (DPR), livability (LV), udder composite (UDC), and feet–legs composite (FLC) of each animal. The statistical analysis consisted of a one-way analysis of variance (ANOVA) test followed by Tukey's test. The A2A2 and the AB genotypes were predominant in the CSN2 and CSN3 genes, respectively. The A2A2 animals were found to have higher TPI and NM values. Moreover, they exhibited higher PTA values for proteins, CFP, and PL. On the other hand, the A1A1 genotype was significantly associated with the highest UDC. Concerning the CSN3 haplotypes, the BB animals had higher protein percentage and PL than alternative haplotypes. The AA and AB haplotypes were found to be significantly associated with the highest SCS and DPR values, respectively. In addition, the BE haplotype had the highest NM. Selection procedures focusing on casein genes in dairy cattle are becoming increasingly common worldwide, especially for A2 milk. However, herd-based dynamics are also fundamental to providing a desired genetic merit for the animals. This study may be valuable for further analyses regarding selection decisions using the breeding values of candidate animals in commercial dairy herds.