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

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.