Population Structure and Genetic Diversity Among Lipizzan Mare Families in Hungary Based on Microsatellite Genotyping

The conservation of genetic diversity in historically structured horse breeds requires fi-ne-scale population genetic evaluation beyond conventional pedigree-based approaches. The present study assessed genetic diversity, population structure, and mare family differentiation in a Lipizzan horse population using 16 ISAG/FAO-recommended microsatellite markers. A total of 172 mares representing 29 mare families were genotyped. All loci were polymorphic, with a mean number of alleles per locus of 6.69 and a mean effective number of alleles of 3.56. The average polymorphism information content (PIC = 0.66) indicated high marker informativeness. Mean observed heterozygosity was slightly lower than expected heterozygosity, although the overall negative inbreeding coefficient suggested general heterozygote excess and low population-level inbreeding, whilst the genetic differentiation among mare families was moderate. The principal components and the STRUCTURE analysis indicated admixture among mare families. Seven private alleles were detected across six loci, highlighting the presence of rare lineage-specific variants. These findings emphasize the importance of mare family-based analyses for identifying hidden genetic structures that may not be captured by population-level averages. The integration of microsatellite-based diversity evaluation provides a robust framework for de-signing sustainable breeding and conservation strategies aimed at preserving both overall variability and rare lineage-specific genetic components.