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

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

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.

• Jezik: Angleški jezik
• Ključne besede: Lipizzan horse, heritage breed, conservation genetics, inbreeding, genomic inbreeding, pedigree, small population
• Vrsta gradiva: Članek v reviji
• Tipologija: 1.01 - Izvirni znanstveni članek
• Organizacija: BF - Biotehniška fakulteta
• Status publikacije: Objavljeno
• Različica publikacije: Objavljena publikacija
• Datum objave: 23.09.2025
• Leto izida: 2025
• Št. strani: 18 str.
• Številčenje: Vol. 15, issue 19, [article no.] 2774
• PID: 20.500.12556/RUL-173857
• UDK: 636.1:575
• ISSN pri članku: 2076-2615
• DOI: 10.3390/ani15192774
• COBISS.SI-ID: 250133763
• Datum objave v RUL: 24.09.2025

Gradivo je del revije

• Naslov: Animals
• Skrajšan naslov: Animals
• Založnik: MDPI AG
• ISSN: 2076-2615
• COBISS.SI-ID: 519120409

Licence

• Licenca: CC BY 4.0, Creative Commons Priznanje avtorstva 4.0 Mednarodna
• Povezava: http://creativecommons.org/licenses/by/4.0/deed.sl
• Opis: To je standardna licenca Creative Commons, ki daje uporabnikom največ možnosti za nadaljnjo uporabo dela, pri čemer morajo navesti avtorja.

Sekundarni jezik

• Jezik: Slovenski jezik
• Ključne besede: konji, pasme, lipicanec, genetika, genomika, poreklo, koeficient inbridinga, majhne populacije

Projekti

• Financer: ARIS - Javna agencija za znanstvenoraziskovalno in inovacijsko dejavnost Republike Slovenije
• Številka projekta: P4-0092-2020
• Naslov: Zdravje živali, okolje in varna hrana