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

Population genetic diversity and structure were analyzed among Lipizzan mare families in Hungary using microsatellite markers, revealing significant genetic variation, moderate differentiation among families, and the presence of rare, family-specific alleles important for conservation.

Background and Purpose

• Traditional pedigree analyses in horse breeds often miss detailed genetic variation within populations.
• The study focused on a Lipizzan horse population, a breed with historical family structures used for conservation and breeding decisions.
• Goal: To assess genetic diversity, population structure, and differences among mare families using molecular markers (microsatellites).

Methods

• Sample: 172 Lipizzan mares representing 29 distinct mare families in Hungary.
• Genotyping: 16 microsatellite markers recommended by ISAG/FAO for equine genetic studies were used.
• Microsatellites are highly polymorphic DNA sequences useful for evaluating genetic variation.
• Analyses included calculation of allele numbers, heterozygosity, polymorphism information content (PIC), inbreeding coefficients, and population structure assessments using principal component analysis (PCA) and STRUCTURE software.

Key Findings – Genetic Diversity

• All 16 loci showed polymorphism indicating genetic variability.
• Mean number of alleles per locus was 6.69—showing multiple genetic variants at each marker.
• Effective number of alleles was 3.56, reflecting the number of equally frequent alleles contributing to diversity.
• PIC value averaged 0.66, indicating highly informative markers useful for population genetic studies.
• Observed heterozygosity was slightly lower than expected but negative overall inbreeding coefficient suggested a general excess of heterozygotes—indicating low inbreeding at the population level.

Key Findings – Population Structure and Mare Family Differentiation

• Moderate genetic differentiation was observed among mare families, meaning some families had distinct genetic profiles.
• PCA and STRUCTURE analyses revealed admixture, or genetic mixing, among mare families indicating gene flow or shared ancestry.
• Seven private alleles (unique genetic variants) were identified at six loci, present only in specific mare families, highlighting the existence of rare lineage-specific genetic variants.

Implications for Conservation and Breeding

• Analysis at the mare family level uncovers hidden genetic structures not evident in broader population averages.
• Presence of private alleles suggests the importance of preserving specific mare families to maintain rare genetic variants.
• Microsatellite data provides a robust framework to design sustainable breeding programs that balance maintaining overall genetic diversity with protecting rare family-specific lineages.
• Findings support integrating molecular genetic information with traditional pedigree data for effective conservation management of Lipizzan horses.

Summary

• This study demonstrated that Lipizzan mares in Hungary possess considerable genetic diversity and family-specific genetic features.
• Population structure analyses revealed moderate differentiation and gene flow among families.
• The detection of unique alleles in certain mare families emphasizes the need for targeted conservation approaches.
• The approach used serves as an effective model for evaluating and managing genetic resources in historically structured breeds.