The genetic diversity and structure of the Haflinger horse population in the Czech Republic

Abstract. The aim of the study was to describe the current state of genetic variability in the Haflinger breed in the Czech Republic using microsatellite markers, taking into consideration the numerous imports of breeding animals from abroad during the last 20 years and their impact on genetic diversity and population structure. A total of 443 horses from five countries of origin (Austria – AUT, Germany – GER, Czech Republic – CZE, Italy – ITA, and Slovakia – SVK) bred in the Czech Republic were included in the study. A set of 16 microsatellite markers for parentage control from the International Society for Animal Genetics (ISAG) was used for genotyping. The total number of alleles in individual subpopulations ranged from 53 (SVK) to 117 (CZE). The mean number of alleles per locus was 6.69. Observed heterozygosity (Ho) values ranged from 0.69 to 0.71 in all subpopulations. The most variable and informative locus (in terms of polymorphic information content – PIC) was VHL20, and the least variable was HTG6. The Fis index was mostly negative or close to 0 for all populations and was −0.033 for the whole population. The overall Fst was 0.010, indicating a low level of differentiation between subpopulations. Cavalli-Sforza and Edwards chord genetic distances were low between the CZE, AUT, and GER populations, while the ITA and SVK populations were more distinct. The results of the discriminant analysis of principal components (DAPC) and the STRUCTURE analysis indicated a high degree of admixture among subpopulations. However, three to four genetic groups were clustered. The most distant populations were ITA and SVK, which we attribute to the low number of representatives in these subpopulations. A higher level of admixture due to gene flow was observed between the populations of GER, CZE, and AUT. Higher admixtures and the discovery of more distinct genetic clusters suggest that there is more significant gene flow from the countries of origin in the population of the Haflinger breed in the Czech Republic and that there is sufficient genetic variability and diversity to suggest sufficient opportunities for more intensive breeding.