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Archives animal breeding2026; 69(2); 323-336; doi: 10.5194/aab-69-323-2026

Genetic variability and associations of Trakehner and other horse populations in Lithuania.

Abstract: To obtain genetic parameters relevant for the management of animal genetic resources, this study provides a comparative characterization of the Trakehner (TRAK) horse population in relation to four other horse populations maintained in Lithuania - Arabian (ARAB), Baltic Warmblood (BW), Lithuanian Warmblood (LW), and Zemaitukai (ZEM). These populations represent diverse histories, selection goals, and breeding practices. Pedigree data ( 22 666) and parentage verification genetic data based on blood group markers ( 1293) were used to evaluate genetic diversity, population structure, and inter-population relationships. Despite a 25 % population decline in recent years, the TRAK population maintained moderate inbreeding ( 0.037) and a balanced genetic structure. The effective population size ( ) was lower than in BW and LW but higher than in the endangered ZEM population. TRAK retained a high number of alleles ( 3.83), with observed heterozygosity ( 0.460) slightly lower than that observed in open sport horse populations. Comparison of all individuals and the Lithuanian reference populations revealed stable or increased heterozygosity in currently breeding individuals, particularly within TRAK. Genetic distances and assignment tests confirmed close relationships among TRAK, BW, and LW, reflecting shared ancestry. In contrast, ARAB and ZEM populations remained genetically distinct. PCA and heatmap analyses further supported the separation between closed and open populations in the current breeding context. These findings highlight that population structure, historical gene flow, and management practices jointly shape genetic variability. The results can be used to optimize mating plans by balancing sire and dam contributions, monitor inbreeding and effective population size trends, manage gene flow between related populations (TRAK, BW, LW), and develop targeted conservation strategies for genetically distinct breeds such as ZEM and ARAB.
Copyright: © 2026 Alma Račkauskaitė et al.
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Publication Date: 2026-06-02 PubMed ID: 42238714PubMed Central: PMC13228154DOI: 10.5194/aab-69-323-2026Google 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 analyzed genetic diversity and relationships among the Trakehner horse population and four other horse populations in Lithuania to inform breed management and conservation efforts.

Objectives and Populations Studied

  • Objective: To obtain genetic parameters relevant for managing animal genetic resources among five horse populations in Lithuania.
  • Populations studied:
    • Trakehner (TRAK)
    • Arabian (ARAB)
    • Baltic Warmblood (BW)
    • Lithuanian Warmblood (LW)
    • Zemaitukai (ZEM)
  • These populations have diverse histories, selection goals, and breeding practices reflecting different genetic characteristics.

Data Used

  • Pedigree data of 22,666 horses to analyze lineage and inbreeding trends.
  • Parentage verification data based on 1293 genetic blood group markers to assess genetic diversity and confirm relationships.

Findings on Genetic Diversity and Population Structure

  • Trakehner Population:
    • Despite a 25% population decline recently, the TRAK population maintained moderate inbreeding coefficient (approximately 0.037), indicating controlled genetic health.
    • Genetic structure remained balanced.
    • Effective population size was lower than Baltic Warmblood and Lithuanian Warmblood but higher than the endangered Zemaitukai breed.
    • High number of alleles per locus (~3.83) was retained, showing good genetic variability.
    • Observed heterozygosity (0.460) slightly lower than open sport horse populations, indicating moderate genetic diversity.
  • Heterozygosity Trends:
    • Comparison between all individuals and currently breeding populations showed stable or increasing heterozygosity, especially in TRAK, suggesting effective genetic management.

Genetic Relationships and Differentiation Among Populations

  • Genetic distance analyses and assignment tests showed:
    • Close genetic relationships among TRAK, Baltic Warmblood (BW), and Lithuanian Warmblood (LW), likely due to shared ancestry and gene flow.
    • Arabian (ARAB) and Zemaitukai (ZEM) populations remained genetically distinct, indicating limited gene flow and unique breed identities.
  • Principal Component Analysis (PCA) and heatmap:
    • Supported separation between “closed” (genetically isolated) and “open” (mixed or gene-flow influenced) populations under current breeding practices.

Implications for Breed Management and Conservation

  • Population structure, historical gene flow, and breeding management practices collectively shape observed genetic variability.
  • Results provide:
    • Guidance for optimizing mating plans that balance contributions from sires and dams, minimizing inbreeding risks.
    • Monitoring tools for trends in effective population size and inbreeding over time.
    • Strategies to manage gene flow between related populations like TRAK, BW, and LW, maintaining genetic health while preserving distinctiveness.
    • Foundations for targeted conservation of genetically unique breeds such as the endangered Zemaitukai (ZEM) and the distinct Arabian (ARAB) lines.

Cite This Article

APA
Račkauskaitė A, Šveistienė R, Razmaitė V, Jatkauskienė V, Marašinskienė Š. (2026). Genetic variability and associations of Trakehner and other horse populations in Lithuania. Arch Anim Breed, 69(2), 323-336. https://doi.org/10.5194/aab-69-323-2026

Publication

Archives animal breeding
ISSN: 2363-9822
NlmUniqueID: 101701238
Country: Germany
Language: English
Volume: 69
Issue: 2
Pages: 323-336

Researcher Affiliations

Račkauskaitė, Alma
  • Department of Animal Breeding and Reproduction, Animal Science Institute, Lithuanian University of Health Sciences, Baisogala, 82317, Lithuania.
Šveistienė, Rūta
  • Department of Animal Breeding and Reproduction, Animal Science Institute, Lithuanian University of Health Sciences, Baisogala, 82317, Lithuania.
Razmaitė, Violeta
  • Department of Animal Breeding and Reproduction, Animal Science Institute, Lithuanian University of Health Sciences, Baisogala, 82317, Lithuania.
Jatkauskienė, Virginija
  • Department of Animal Breeding and Reproduction, Animal Science Institute, Lithuanian University of Health Sciences, Baisogala, 82317, Lithuania.
Marašinskienė, Šarūnė
  • Department of Animal Breeding and Reproduction, Animal Science Institute, Lithuanian University of Health Sciences, Baisogala, 82317, Lithuania.

Conflict of Interest Statement

The contact author has declared that none of the authors has any competing interests.

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