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Animal genetics2026; 57(4); e70182; doi: 10.1002/age.70182

Characterization of Lipizzan Horse Population From Lipica Stud Using Molecular and Pedigree Data.

Abstract: In this study, we analysed genetic diversity, population structure and inbreeding in the Lipica Stud Farm population by integrating pedigree records, microsatellite (STR) and genome-wide SNP data generated using the GGP Equine 70K BeadChip. The dataset comprised 233 horses from the Lipica Stud Farm, which served as the reference population for comparisons of diversity estimates based on pedigree-, STR- and SNP data. The STR data were originally generated for routine parentage verification and were included here to compare inbreeding estimates based on pedigree, STR and genome-wide SNP data. Pedigrees of the analysed horses were traced back to the 18th century, with the longest ancestral path spanning 35 generations. The mean pedigree inbreeding coefficient in the reference population was 11.55%, while ancestral inbreeding coefficients ranged from 5.93% to 15.42%. Microsatellite analyses revealed an average observed heterozygosity (Ho) of 0.68 and a mean of 5.9 alleles per locus, with STR-based inbreeding (F) ranging from 0.10 to 0.15. However, genomic inbreeding estimated from runs of homozygosity (F) varied between 0.09 and 0.28, with an average of 0.16. Selection signature analysis identified several putative candidate regions, whereas integrated haplotype score (iHS) analysis highlighted three candidate protein-coding genes (ZNF114, DENND5A, and TENM4). The ROH islands contained 24 genes previously associated with pigmentation, reproduction, muscle function, and other biologically relevant traits in horses. These results provide a comprehensive genomic characterisation of the Lipica Stud Farm population and offer important insights into genetic diversity and inbreeding patterns in the Lipizzan breed.
© 2026 The Author(s). Animal Genetics published by John Wiley & Sons Ltd on behalf of Stichting International Foundation for Animal Genetics.
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Publication Date: 2026-08-12 PubMed ID: 42586537DOI: 10.1002/age.70182Google Scholar: Lookup
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  • Journal Article

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

Overview

  • This research provides a detailed genetic analysis of the Lipizzan horse population at the Lipica Stud Farm, examining their genetic diversity, population structure, and degree of inbreeding through the use of pedigree information, microsatellite markers, and genome-wide SNP data.

Objectives of the Study

  • To analyze the genetic diversity of the Lipizzan horses using multiple data sources: pedigree records, microsatellites (STR), and genome-wide SNP data.
  • To assess the population structure and inbreeding levels within the Lipica Stud Farm population.
  • To identify genomic regions potentially under selection related to important traits.

Data and Methods

  • The study analyzed a total of 233 Lipizzan horses from the Lipica Stud Farm, serving as the reference population.
  • Three data types were integrated for analysis:
    • Pedigree data tracing back up to the 18th century, with ancestry going as far as 35 generations.
    • Microsatellite (STR) data originally collected for routine parentage verification.
    • Genome-wide SNP data obtained using the GGP Equine 70K BeadChip, covering around 70,000 genetic markers.

Key Findings – Inbreeding and Genetic Diversity

  • Pedigree analysis showed a mean inbreeding coefficient of 11.55%, indicating moderate inbreeding within this population.
  • Ancestral inbreeding coefficients ranged from 5.93% to 15.42%, reflecting the historical genetic background of these horses.
  • Microsatellite data revealed:
    • An average observed heterozygosity (Ho) of 0.68, indicating a relatively high level of genetic variability at these loci.
    • A mean of 5.9 alleles per locus, which is a measure of allele richness.
    • STR-based inbreeding (F) ranged between 0.10 and 0.15, slightly lower but comparable to pedigree estimates.
  • SNP-based genomic inbreeding, calculated from runs of homozygosity (ROH), varied more widely from 0.09 to 0.28 with an average of 0.16, indicating more nuanced inbreeding patterns detectable at the genomic scale.

Genomic Insights and Selection Signatures

  • Selection signature analyses helped identify candidate genomic regions that may be under selection pressures in this population.
  • Using integrated haplotype score (iHS) methods, three candidate protein-coding genes were highlighted: ZNF114, DENND5A, and TENM4, potentially related to breed-specific traits.
  • The runs of homozygosity (ROH) islands—regions with excessive homozygosity—contained 24 genes associated with:
    • Pigmentation patterns
    • Reproductive traits
    • Muscle function
    • Other biological traits relevant to horse physiology and performance

Significance and Implications

  • The study provides a comprehensive genomic characterization of the Lipizzan horses from the Lipica Stud Farm, integrating traditional pedigree data with modern genomic technologies.
  • The combination of pedigree, STR, and SNP data presents a robust picture of genetic diversity and inbreeding, which is valuable for breeding management and conservation efforts.
  • Identification of candidate genes and selection signatures lays groundwork for future studies on the genetic basis of important traits in the Lipizzan breed, including those affecting appearance and performance.
  • Such detailed genetic information aids breeders in making informed decisions to maintain genetic health and avoid excessive inbreeding, ultimately supporting the sustainability of this historic horse population.

Cite This Article

APA
Ferme T, Zorc M, Cotman M, Mesarič M, Dovč P. (2026). Characterization of Lipizzan Horse Population From Lipica Stud Using Molecular and Pedigree Data. Anim Genet, 57(4), e70182. https://doi.org/10.1002/age.70182

Publication

Animal genetics
ISSN: 1365-2052
NlmUniqueID: 8605704
Country: England
Language: English
Volume: 57
Issue: 4
Pages: e70182

Researcher Affiliations

Ferme, Tamara
  • University of Ljubljana, Biotechnical Faculty, Ljubljana, Slovenia.
Zorc, Minja
  • University of Ljubljana, Biotechnical Faculty, Ljubljana, Slovenia.
Cotman, Marko
  • University of Ljubljana, Veterinary Faculty, Ljubljana, Slovenia.
Mesarič, Matjaž
  • University of Ljubljana, Veterinary Faculty, Ljubljana, Slovenia.
Dovč, Peter
  • University of Ljubljana, Biotechnical Faculty, Ljubljana, Slovenia.

MeSH Terms

  • Animals
  • Horses / genetics
  • Pedigree
  • Microsatellite Repeats
  • Polymorphism, Single Nucleotide
  • Inbreeding
  • Female
  • Male
  • Genetics, Population
  • Genetic Variation

Grant Funding

  • J4-50133 / Javna Agencija za Raziskovalno Dejavnost RS
  • P4-0220 / Javna Agencija za Raziskovalno Dejavnost RS

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