Comparison of CSN2 A1 and A2 Allele and Genotype Frequencies in Simmental, Polish Red, and Polish Black-and-White Cattle

Background/Objectives: The A1/A2 polymorphism of the bovine CSN2 gene, encoding β-casein, is relevant to milk composition and breeding strategies for A2 milk production. This study aimed to compare the frequencies of A1 and A2 variants in three cattle breeds maintained in Poland: Simmental, Polish Red, and Polish Black-and-White. Methods: A total of 898 cows (568 Simmental, 273 Polish Red, and 57 Polish Black-and-White) were analyzed. DNA was isolated from hair follicles previously collected for routine parentage verification, independently of this study. The CSN2 polymorphism (rs43703011) was genotyped using a TaqMan allelic discrimination assay, with selected genotypes validated by Sanger sequencing. Results: Genotype and allele frequencies differed among the sampled populations. In Simmental cattle, A1A1, A1A2, and A2A2 genotype frequencies were 17.8%, 52.6%, and 29.6%, respectively, with an A2 allele frequency of 55.9%. Corresponding frequencies in Polish Red cattle were 30.4%, 49.5%, and 20.1%, with an A2 allele frequency of 44.9%. Polish Black-and-White cattle showed frequencies of 47.4%, 47.4%, and 5.2%, respectively, with an A2 allele frequency of 28.9%. Significant differences in genotype distributions were observed between the sampled populations (p < 0.001 and p = 0.007). Conclusions: The results demonstrate variation in CSN2 A1/A2 polymorphism frequencies among the studied cattle populations, with the highest A2 allele frequency observed in Simmental cattle. These findings suggest that CSN2 genotyping could support breeding strategies aimed at increasing the frequency of the A2 allele, particularly through the selection of A2A2 breeding animals.