Comparing genomic and pedigree inbreeding coefficients in the Slovenian Lipizzan horse as a case study for small closed populations

Luštrek, Barbara (author), Šimon, Martin (author), Turk, Klemen (author), Bogićević, Sanja (author), Potočnik, Klemen (author)

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 emonstrate that genomic measures complement pedigree-based metrics by providing a fuller picture of inbreeding and its temporal origin. Incorporating genomic estimators into routine onitoring can improve mate selection, reduce inbreeding depression, and support ustainable management of genetic diversity in the Lipizzan horse, while offering a case study for other small populations with conservation goals.

• Language: English
• Keywords: Lipizzan horse, heritage breed, conservation genetics, inbreeding, genomic inbreeding, pedigree, small population
• Work type: Article
• Typology: 1.01 - Original Scientific Article
• Organization: BF - Biotechnical Faculty
• Publication status: Published
• Publication version: Version of Record
• Publication date: 23.09.2025
• Year: 2025
• Number of pages: 18 str.
• Numbering: Vol. 15, issue 19, [article no.] 2774
• PID: 20.500.12556/RUL-173857
• UDC: 636.1:575
• ISSN on article: 2076-2615
• DOI: 10.3390/ani15192774
• COBISS.SI-ID: 250133763
• Publication date in RUL: 24.09.2025

Record is a part of a journal

• Title: Animals
• Shortened title: Animals
• Publisher: MDPI AG
• ISSN: 2076-2615
• COBISS.SI-ID: 519120409

Licences

• License: CC BY 4.0, Creative Commons Attribution 4.0 International
• Link: http://creativecommons.org/licenses/by/4.0/
• Description: This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.

Secondary language

• Language: Slovenian
• Keywords: konji, pasme, lipicanec, genetika, genomika, poreklo, koeficient inbridinga, majhne populacije

Projects

• Funder: ARIS - Slovenian Research and Innovation Agency
• Project number: P4-0092
• Name: Zdravje živali, okolje in varna hrana