Spatial Structure of the Lipizzan Horse Gene Pool Based on Microsatellite Variations Analysis

The aim of this study was to determine the current state of genetic diversity and to assess the substructure and spatial structure at individual level based on analysis of microsatellite variations within Lipizzan horse population. The genomic DNA samples were obtained from totally 418 horses, originating from Slovenian (357) and Slovak (61) studs. A set of 13 microsatellite markers (AHT4, AHT5, ASB2, HMS1, HMS2, HMS3, HMS6, HMS7, HTG10, HTG4, HTG6, HTG7, and VHL20) have been used for analysis of genetic variability. Across all microsatellite loci the average number of alleles 6.65 and effective allele number at level 3.37 were found. The obtained Shannon's information index (I=1.37) indicated high degree within population genetic diversity. The prevalence of heterozygous genotype in sample confirmed also the average value of observed heterozygosity (Ho=0.67) and FIS index (-0.026). The most of the genetic variation in sample was conserved within individuals (95%) and the subdivision of horse populations explained only 4%. Similarly, the obtained pairwise values of FST index (0.02) and Nei's genetic identity (0.90) reflected mainly common ancestors used in breeding history of both population. But the principal coordinate analysis showed the division of individuals into the two separate clusters according to the studs where they come from. The membership probability resulted from spatial structure analysis suggested that the frequencies of alleles varied across the two regions that indicated the evidence of strong distinction in relation to the current breeding status of analysed populations and strategy of studs.