Determination of the allele frequency of some genomic loci in a Holstein cattle population and its importance in individual identification

Abstract

Nowadays, the use of DNA sequences with genetic techniques and DNA polymorphism as genetic markers is increasing very rapidly. In this study, we examined the frequencies of seven different polymorphic loci in the cattle population of Istanbul University Veterinary Medicine Research and Application Farm. Thus, our aim was to examine and calculate the power of exclusion, match probability and power of discrimination of the seven loci, and examine the usefulness of the involved loci in identification tests. For DNA extraction, Chelex and Phenol-Chloroform-Isoamil alcohol methods were applied to the blood taken from animals. After measuring the amount and purity degree of DNA with a spectrophotometer, seven DNA loci were amplified by PCR. The amplification products were stained with EtBr and examined with 1.5% Agarose gel electrophoresis. Using clenaturated polyacrylamide gel electrophoresis and silver staining, PCR products were evaluated and phenotypes of the alleles were determined. At the end of the study, a mismatch to the Hardy-Weinberg equilibrium was observed in all loci but BMS1822. The highest heterozygosity ratio was 83.3% for BMS2270, and the lowest ratio was 31.4% for BMS2721 among the seven STR/microsatellite loci we studied. The highest exclusion probability was 0.662 for BMS 2270, and the lowest was 0.066 for BMS2721. The highest power of discrimination was 0.947 for BMS2270, and the lowest was 0.504 for BMS2721. The highest matching probability was for BMS3019 and BMS2721, and the lowest was for BMS2270 and BMS1822. It was observed that the loci in this study have very high power of discrimination and power of exclusion values when combined. Thus, these systems may be useful as markers in DNA profiling.