Assessment of Genetic Diversity Within Holstein Population using Bovine SNP Chip Data

Historically, both significant decline of genetic diversity and simultaneously increasingly rate of inbreeding are two serious threaded factors in worldwide dairy industry. With this motivation, the aim of present report was to investigate the intra genetic diversity criteria (linkage disequribrium, observed and expected heterozygosity, Fis statistics, MAF distribution, autozygosity rate and population stratification using principal component analysis) in Holstein cattle population using dense markers. An Illumina Bovine 50k SNP Chip (V2) ready genotyped file for 25 Holstein cows obtained for further investigation. Here, we used Plink software for statistical analysis and measurement of molecular diversity indices. Observed outcomes results addressed average of MAF (0.28), mean frequency of observed and expected heterozygosity (0.38, 0.37), Fis statistic (– 0.032), Fhom statistic (-0.028-0328. In addition, PCA graph showed a significant indicating high population diversity, which was in accordance with all other calculated parameters. As a final conclusion, high-density SNP markers seems be as an accurate tool applicable for high-precision intra-diversity analyses.