TaqMan allelic discrimination assay for A1 and A2 alleles of the bovine CSN2 gene

Abstract

Alleles A1 and A2 of the Bos taurus CSN2 gene are the most frequent in a number of dairy cattle breeds. In this study, a new allelic discrimination assay using TaqMan fluorogenic probes was developed to detect single nucleotide substitution characterizing the A1/A2 alleles of the CSN2 gene. The method was validated using DNA samples of known genotypes with different concentrations and the results were compared with those for the commonly used problematic ACRS-PCR. We found the TaqMan method to be more effective, 100% reliable and hundred times more sensitive for testing the CSN2 genetic marker in cattle than the ACRS-PCR. As it enabled a rapid analysis of a large number of DNA samples in uniform format without previous DNA quality assessment and without the requirement for post-amplification manipulations, it presents an effective tool for the analysis of large-scale sample sets. The method was applied for testing on a sample of 120 Czech Holstein dairy cows. The observed relative genotype and allele frequencies were as follows: A1A1-0.20, A1A2-0.51, A2A2-0.29; A1-0.45, A2-0.55.