Genetic Diversity and Population Structure in Seven Lipizzan Populations Based on Microsatellite Genotyping

Lipizzan horses, bred for over four centuries, represent a unique genetic, cultural and historic resource. This study assessed genetic diversity and population structure across seven European Lipizzan populations, with emphasis on the Bosnia and Herzegovina population. A total of 547 Lipizzan horses were genotyped using 12 microsatellite markers. The parameters of genetic variability, admixture level and migration rate were calculated. The mean number of alleles, effective number of alleles and Shannon's information index were 5.78, 3.24 and 1.31, respectively. The average fixation indices were estimated to be F_IT = 0.05 (SE = 0.02), F_IS = -0.02 (SE = 0.01), and F_ST = 0.07 (SE = 0.01). The level of genetic diversity observed within each Lipizzan horse subpopulation shows similar fluctuations, with the lowest values observed in Bosnia and Herzegovina and the highest in the Slovak Lipizzan population. The observed heterozygosity was lower than the expected heterozygosity. The Hardy-Weinberg equilibrium was maintained in Serbia, while minor deviations occurred in other populations, most notably in Slovakia. Nei's genetic distances were highest between Slovakia and other populations, particularly Bosnia and Herzegovina. The population structure analysis confirmed admixture involving Bosnia and Herzegovina, and the migration pattern corresponded to geographic proximity and breeding practices. These findings provide a valuable basis for developing breeding strategies to reduce inbreeding and preserve genetic diversity.