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

## TL;DR

This study compares pedigree and genomic methods to measure inbreeding in the Slovenian Lipizzan horse, showing that genomic tools provide a more accurate and detailed picture of inbreeding levels.

## Contribution

The study demonstrates how genomic measures complement pedigree records in small closed populations, offering insights into the temporal origin of inbreeding.

## Key findings

- Genomic estimators revealed higher inbreeding levels than pedigree-based estimates in the Lipizzan horse population.
- Most autozygosity in the population originated from distant ancestors, with limited recent close matings.
- Genomic measures can partition inbreeding into recent and distant components, improving conservation management.

## Abstract

The Lipizzan horse is an indigenous Slovenian breed maintained as a small, closed population with limited gene flow from other subpopulations. In such populations, safeguarding genetic diversity while controlling inbreeding is a key challenge, as excessive inbreeding may compromise fertility, health, and long-term sustainability. Traditionally, inbreeding is monitored using pedigree records, but pedigree-based estimates often underestimate the true level of relatedness. In this study, we compared pedigree-based inbreeding coefficients with genomic measures derived from SNP array data in 329 Slovenian Lipizzans. Genomic analyses can identify regions of the genome that are identical by descent (autozygosity) and distinguish whether they originate from recent or distant ancestors. Segment-based genomic methods, especially those relying on runs of homozygosity and homozygosity-by-descent, revealed higher inbreeding than pedigree estimates and indicated that most autozygosity originated from distant ancestors, with little evidence of recent close matings. Overall, our findings emphasise the value of combining pedigree and genomic information for monitoring genetic diversity. They show how genomic tools complement pedigree records, strengthen the sustainable management of the Lipizzan horse, and serve as a case study for other small, conservation-oriented populations.

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.