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Home / Equine Research Bank / Animals (Basel) / Comparing Genomic and Pedigree Inbreeding Coefficients in th...
Animals : an open access journal from MDPI2025; 15(19); 2774; doi: 10.3390/ani15192774

Comparing Genomic and Pedigree Inbreeding Coefficients in the Slovenian Lipizzan Horse as a Case Study for Small Closed Populations.

Abstract: In small, closed populations such as the Lipizzan horse, maintaining genetic diversity while limiting inbreeding is a key challenge in conservation breeding. The Lipizzan is an indigenous Slovenian breed with a small population and restricted gene flow from other subpopulations. Inbreeding is traditionally monitored with pedigree-based coefficients, but these often underestimate realised autozygosity, particularly when pedigree depth is limited. This study compared pedigree-based inbreeding (F_PED) with four genomic estimators (F_HOM, F_ROH, F_HBD, F_GRM) in 329 Slovenian Lipizzan horses genotyped with a 70K SNP array. Data were processed in PLINK and R. Segment-based estimators (F_ROH, F_HBD) revealed higher inbreeding than F_PED and partitioned autozygosity into recent and distant components. F_ROH identified long homozygous segments reflecting recent inbreeding, whereas HBD classification showed that most autozygosity came from distant ancestors. Correlations between pedigree- and genomic-based coefficients were moderate (ρ = -0.18-0.56), while genomic estimators showed strong agreement. These results demonstrate that genomic measures complement pedigree-based metrics by providing a fuller picture of inbreeding and its temporal origin. Incorporating genomic estimators into routine monitoring can improve mate selection, reduce inbreeding depression, and support sustainable management of genetic diversity in the Lipizzan horse, while offering a case study for other small populations with conservation goals.
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Publication Date: 2025-09-23 PubMed ID: 41096369PubMed Central: PMC12524321DOI: 10.3390/ani15192774Google 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 compares traditional pedigree-based and modern genomic methods for measuring inbreeding in a small, closed population of Slovenian Lipizzan horses.
  • The findings highlight how genomic tools can better capture the extent and history of inbreeding, supporting improved conservation management.

Background and Objectives

  • The Lipizzan horse is a native Slovenian breed characterized by a small population size and limited gene exchange with other subpopulations, which poses a risk of increased inbreeding.
  • Maintaining genetic diversity and controlling inbreeding in small closed populations are crucial for avoiding inbreeding depression and ensuring long-term breed viability.
  • Traditionally, inbreeding has been monitored using pedigree-based coefficients (F_PED), which estimate the probability that two alleles are identical by descent from a common ancestor.
  • However, pedigree-based estimates can underestimate actual inbreeding, especially if pedigree records are shallow or incomplete.
  • The study aims to compare pedigree-based inbreeding coefficients with multiple genomic estimators to evaluate how well these methods assess realized inbreeding and to understand their complementarity.

Methodology

  • Sample: 329 Slovenian Lipizzan horses genotyped using a 70K single nucleotide polymorphism (SNP) array.
  • Data Analysis Tools: PLINK and R software were used for genomic data processing and analysis.
  • Inbreeding Measures Compared:
    • F_PED – Pedigree-based inbreeding coefficient.
    • F_HOM – Inbreeding based on observed versus expected homozygosity.
    • F_ROH – Based on runs of homozygosity (long homozygous DNA segments), indicating recent inbreeding.
    • F_HBD – Based on homozygous-by-descent segments, allowing classification of autozygosity by different ancestor timeframes.
    • F_GRM – Based on genomic relationship matrix.

Key Findings

  • Genomic estimators that use segments (F_ROH, F_HBD) captured higher levels of inbreeding compared to pedigree-based coefficients, suggesting that traditional methods underestimate realized inbreeding.
  • F_ROH detected long homozygous segments, reflecting inbreeding from recent ancestors.
  • In contrast, F_HBD partitioned inbreeding into recent and distant sources, showing that much autozygosity originated from ancient common ancestors.
  • Correlation between pedigree-based and genomic-based inbreeding coefficients was moderate (correlation coefficients ranged from -0.18 to 0.56), indicating incomplete agreement.
  • Strong correlations were found among genomic estimators themselves, reflecting consistency across genomic-based methods.

Implications and Applications

  • Genomic measures provide a more detailed and accurate assessment of inbreeding levels and history than pedigree data alone in small, closed populations.
  • Incorporating genomic estimators into routine genetic monitoring can enhance mate selection strategies by identifying individuals with lower inbreeding and avoiding mating pairs that would increase autozygosity.
  • This approach helps reduce the risk of inbreeding depression—which can negatively affect health, fertility, and survival—and supports the sustainable genetic management of the breed.
  • The study provides a valuable case study applicable to other small endangered or closed populations with similar conservation challenges, suggesting a generalizable benefit of combining pedigree and genomic data.

Conclusion

  • The study demonstrates that genomic inbreeding estimators complement traditional pedigree-based methods by offering a fuller picture of inbreeding levels and their temporal origins.
  • Access to genomic data enables more informed genetic management decisions for conservation breeding programs, improving the maintenance of genetic diversity in the Slovenian Lipizzan horse and potentially other small, closed populations.

Cite This Article

APA
Luštrek B, Šimon M, Turk K, Bogičević S, Potočnik K. (2025). Comparing Genomic and Pedigree Inbreeding Coefficients in the Slovenian Lipizzan Horse as a Case Study for Small Closed Populations. Animals (Basel), 15(19), 2774. https://doi.org/10.3390/ani15192774

Publication

Animals : an open access journal from MDPI
ISSN: 2076-2615
NlmUniqueID: 101635614
Country: Switzerland
Language: English
Volume: 15
Issue: 19
PII: 2774

Researcher Affiliations

Luštrek, Barbara
  • Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia.
Šimon, Martin
  • Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia.
Turk, Klemen
  • Department for the Selective Breeding of Equidae, Clinic for Breeding and Health Care of Horses, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000 Ljubljana, Slovenia.
Bogičević, Sanja
  • Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia.
Potočnik, Klemen
  • Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia.

Conflict of Interest Statement

The authors declare no conflicts of interest.

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