The presented paper gives an overview about genetic diversity in Pinzgau populations in Austria and Slovakia. In total, 12 442 animals were included in the study representing the reference population. All living herdbook cows, dual purpose and beef, from both countries with a maximum foreign gene proportion of 12.5 % were considered. Thus, four subpopulations were analysed. Parameters of diversity based on probability of identity-by-descent and probability of gene origin were computed by the methods of pedigree analysis. The average inbreeding coefficient (five generations taken into account) was 0.0186 (ΔF=0.0041), 0.0242 (ΔF=0.0047), 0.0151 (ΔF=0.0026), and 0.0126 (ΔF=0.0006) in the Austrian dairy (AD), the Austrian beef (AB), the Slovak dairy (SD) and the Slovak beef (SB) subpopulation, respectively. Effective population size ranged from 122.5 (AD) to 809.4 (SB). Effective number of founders was 67.3 and 106.6 in AD and SD and 73 and 212.3 in the AB and SB subpopulations. Effective number of ancestors was 29.59; 34.42; 42.36 and 73.81 in AD, AB, SD and SB, respectively. Effective number of founder genomes was 15.32; 18.15; 23.41 and 41 in AD, AB, SD and SB subpopulations, respectively. Similarities between subpopulations were calculated based on a cosine approach. The highest similarity was found between AD and AB (cosine value 0.9954). SD and AD subpopulations were very similar (cosine value 0.9181).
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