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Animals : an open access journal from MDPI2026; 16(10); 1516; doi: 10.3390/ani16101516

Genetic Diversity and Population Structure in Seven Lipizzan Populations Based on Microsatellite Genotyping.

Abstract: Lipizzan horses, bred for over four centuries, represent a unique genetic, cultural and historic resource. This study assessed genetic diversity and population structure across seven European Lipizzan populations, with emphasis on the Bosnia and Herzegovina population. A total of 547 Lipizzan horses were genotyped using 12 microsatellite markers. The parameters of genetic variability, admixture level and migration rate were calculated. The mean number of alleles, effective number of alleles and Shannon's information index were 5.78, 3.24 and 1.31, respectively. The average fixation indices were estimated to be F = 0.05 (SE = 0.02), F = -0.02 (SE = 0.01), and F = 0.07 (SE = 0.01). The level of genetic diversity observed within each Lipizzan horse subpopulation shows similar fluctuations, with the lowest values observed in Bosnia and Herzegovina and the highest in the Slovak Lipizzan population. The observed heterozygosity was lower than the expected heterozygosity. The Hardy-Weinberg equilibrium was maintained in Serbia, while minor deviations occurred in other populations, most notably in Slovakia. Nei's genetic distances were highest between Slovakia and other populations, particularly Bosnia and Herzegovina. The population structure analysis confirmed admixture involving Bosnia and Herzegovina, and the migration pattern corresponded to geographic proximity and breeding practices. These findings provide a valuable basis for developing breeding strategies to reduce inbreeding and preserve genetic diversity.
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Publication Date: 2026-05-15 PubMed ID: 42193807PubMed Central: PMC13203804DOI: 10.3390/ani16101516Google Scholar: Lookup
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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 study investigated the genetic diversity and population structure of seven European Lipizzan horse populations using microsatellite genotyping.
  • The research focused particularly on the Lipizzan population in Bosnia and Herzegovina, analyzing genetic variability, admixture levels, and migration rates to inform breeding and conservation strategies.

Background and Objectives

  • Lipizzan horses are an ancient breed with over 400 years of selective breeding, valued for their genetic, cultural, and historical significance.
  • The objective was to assess the genetic diversity within and among seven Lipizzan populations from different European countries, with special focus on Bosnia and Herzegovina.
  • The goal was to understand population structure, admixture patterns, and migration to guide breeding strategies aimed at preserving genetic diversity and minimizing inbreeding.

Methodology

  • Samples: 547 Lipizzan horses from seven European populations were genotyped.
  • Genotyping: 12 microsatellite markers were used, which are short repeating DNA sequences useful for genetic diversity studies due to their high variability.
  • Analyses conducted included:
    • Calculation of genetic variability parameters such as mean number of alleles per locus, effective number of alleles, and Shannon’s information index.
    • Assessment of fixation indices (F-statistics) indicating inbreeding and population differentiation.
    • Tests for Hardy-Weinberg equilibrium to evaluate if populations are mating randomly or if there are deviations.
    • Nei’s genetic distance to measure genetic differentiation between populations.
    • Population structure analysis to detect admixture and migration patterns, particularly involving Bosnia and Herzegovina.

Key Findings

  • Genetic Diversity Metrics:
    • Mean number of alleles per locus was 5.78, indicating a moderate level of genetic variability.
    • Effective number of alleles was 3.24, showing how many alleles contribute meaningfully to genetic diversity.
    • Shannon’s information index was 1.31, reflecting the overall diversity and allele frequency distribution.
  • Fixation Indices:
    • Average F (inbreeding coefficient) was 0.05, indicating low but present inbreeding.
    • F_IS (within subpopulations) was -0.02, suggesting very slight excess of heterozygotes or random mating.
    • F_ST (among populations) was 0.07, showing moderate genetic differentiation among populations.
  • Population Specific Observations:
    • The Bosnia and Herzegovina population showed the lowest genetic diversity values.
    • The Slovak Lipizzan population exhibited the highest genetic diversity.
    • Observed heterozygosity was generally lower than expected, hinting at some inbreeding or population structure effects.
    • Serbia was the only population that maintained strict Hardy-Weinberg equilibrium, whereas Slovakia showed the greatest deviations.
  • Genetic Distance and Population Structure:
    • Nei’s genetic distances were greatest between Slovakia and other populations, especially Bosnia and Herzegovina, indicating higher differentiation.
    • Population structure analyses showed clear evidence of admixture involving Bosnia and Herzegovina, meaning gene flow between populations.
    • Migration patterns aligned with geographic proximity and known breeding practices, suggesting geographically nearby populations interbreed more often.

Implications

  • The findings highlight the importance of monitoring genetic diversity in Lipizzan horses to prevent loss of variability that can arise from inbreeding and isolated breeding programs.
  • Populations such as Bosnia and Herzegovina with lower diversity might require targeted breeding interventions to introduce new genetic material and reduce inbreeding.
  • This genetic information serves as a foundation for developing sustainable breeding strategies that balance preserving unique breed characteristics with maintaining genetic health.
  • Understanding migration and admixture patterns allows breeders and conservationists to coordinate efforts across countries, respecting historic breeding routes and practices.

Conclusion

  • The study provides a comprehensive assessment of genetic diversity and population structure in European Lipizzan horses using microsatellite genotyping.
  • It reveals moderate genetic differentiation among populations, variable levels of genetic diversity, and meaningful gene flow related to geography and breeding history.
  • These insights are critical for guiding future breeding decisions to ensure the long-term preservation of the Lipizzan breed’s genetic and cultural legacy.

Cite This Article

APA
Rogić B, Moravčíková N, Margeta P, Štrbac L, Zorc M, Kovács M, Vostry L, Kasarda R, Posta J. (2026). Genetic Diversity and Population Structure in Seven Lipizzan Populations Based on Microsatellite Genotyping. Animals (Basel), 16(10), 1516. https://doi.org/10.3390/ani16101516

Publication

Animals : an open access journal from MDPI
ISSN: 2076-2615
NlmUniqueID: 101635614
Country: Switzerland
Language: English
Volume: 16
Issue: 10
PII: 1516

Researcher Affiliations

Rogić, Biljana
  • Faculty of Agriculture, University of Banja Luka, Bulevar Vojvode Petra Bojovica 1A, 78000 Banja Luka, Bosnia and Herzegovina.
Moravčíková, Nina
  • Faculty of Agrobiology and Food Resources, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia.
Margeta, Polonca
  • Croatian Agency for Agriculture and Food, Ulica Kardinala Alojzija Stepinca 17, 31000 Osijek, Croatia.
Štrbac, Ljuba
  • Faculty of Agriculture, University of Novi Sad, Trg Dositeja Obradovića 8, 21000 Novi Sad, Serbia.
Zorc, Minja
  • Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia.
Kovács, Máté
  • Doctoral School of Animal Science, University of Debrecen, 4032 Debrecen, Hungary.
  • Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Böszörményi út 138, 4032 Debrecen, Hungary.
Vostry, Lubos
  • Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Science Prague, Kamycka 129, 16500 Prague, Czech Republic.
Kasarda, Radovan
  • Faculty of Agrobiology and Food Resources, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia.
Posta, Janos
  • Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Böszörményi út 138, 4032 Debrecen, Hungary.

Grant Funding

  • 12/2.3-403/24 / Ministry of Agriculture, Forestry and Water Management Republic of Srpska
  • GACR 24-14325L / Czech Science Foundation
  • 1/0316/25 / Ministry of Education, Research, Development and Youth of the Slovak Republic
  • APVV-20-0161 / the Slovak Research and Development Agency
  • 451-03-34/2026-03/200117 / Ministry of Science, Technological Development and Innovation Serbia

Conflict of Interest Statement

The authors declare no conflicts of interest.

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