The American Quarter Horse (AQH) is a breed that began to develop in the 17th century. The first AQH was brought to Slovenia in the autumn of 1995 and until November 2021 a total of 1.003 AQHs were registered in Slovenia. For genotyping, we selected horses from Slovenian Stud Book and their offspring. We genotyped 63 AQH at 17 microsatellite loci. We included 2.779 animals in the pedigree analysis, 705 currently living AQH in Slovenia represents the reference population. In the entire population, parents are known for 62,99% of animals, and in the reference population for 88,72%. The percentage of known ancestors in the entire population decreases after the first generation, and in the reference population after the third generation. The average inbreeding coefficient (F) in the Slovenian AQH population is 0,23% with 441 inbreed animals. In the entire population, we found 988 founders and 745 in the reference population. With 658 ancestors we can explain 100% genetic variability in the AQH population in Slovenia (in the reference population with 320 ancestors). The F-values based on pedigree information were predictably lower than those based on microsatellite data. The highest F based on pedigree information is 25% whereas the highest F based on microsatellites is 31,96%. There was no significant correlation between the inbreeding coefficients estimated using the pedigree data and microsatellites.
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