20.500.12556/RUL-173857 Comparing genomic and pedigree inbreeding coefficients in the Slovenian Lipizzan horse as a case study for small closed 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 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. Lipizzan horse heritage breed conservation genetics inbreeding genomic inbreeding pedigree small population konji pasme lipicanec genetika genomika poreklo koeficient inbridinga majhne populacije true false true Angleški jezik Slovenski jezik Članek v reviji 2025-09-24 09:39:25 2025-09-24 09:39:27 2026-01-06 08:29:11 0000-00-00 00:00:00 2025 0 0 18 str. issue 19, [article no.] 2774 Vol. 15 23 Sep. 2025 0000-00-00 Zaloznikova Objavljeno NiDoloceno 0000-00-00 0000-00-00 2025-09-23 636.1:575 2076-2615 10.3390/ani15192774 250133763 RAZ_Lustrek_Barbara_2025.pdf RAZ_Lustrek_Barbara_2025.pdf 1 7D6B3891AB05A3BAE9683D3C895D1603 1d3f2f79a80d0471142acc28ea3d5b15ce9288ce79b34fc479c7e1e5c9ca88fa 2c3d4d39-d98f-11f0-9328-0050569b8976 https://repozitorij.uni-lj.si/Dokument.php?lang=slv&id=223690 https://www.mdpi.com/2076-2615/15/19/2774 1 69afa296-9919-11f0-9328-0050569b8976 https://repozitorij.uni-lj.si/Dokument.php?lang=slv&id=218536 Biotehniška fakulteta 0 0 0