Characterization of Lipizzan horse population from Lipica Stud using molecular and pedigree data

Ferme, Tamara (author), Zorc, Minja (author), Cotman, Marko (author), Mesarič, Matjaž (author), Dovč, Peter (author)

In this study, we analysed genetic diversity, population structure and inbreeding in the Lipica Stud Farm population by integrating pedigree records, microsatellite (STR) and genome-wide SNP data generated using the GGP Equine 70K BeadChip. The dataset comprised 233 horses from the Lipica Stud Farm, which served as the reference population for comparisons of diversity estimates based on pedigree-, STR- and SNP data. The STR data were originally generated for routine parentage verification and were included here to compare inbreeding estimates based on pedigree, STR and genome-wide SNP data. Pedigrees of the analysed horses were traced back to the 18th century, with the longest ancestral path spanning 35 generations. The mean pedigree inbreeding coefficient in the reference population was 11.55%, while ancestral inbreeding coefficients ranged from 5.93% to 15.42%. Microsatellite analyses revealed an average observed heterozygosity (Ho) of 0.68 and a mean of 5.9 alleles per locus, with STR-based inbreeding (FSTR) ranging from 0.10 to 0.15. However, genomic inbreeding estimated from runs of homozygosity (FROH) varied between 0.09 and 0.28, with an average of 0.16. Selection signature analysis identified several putative candidate regions, whereas integrated haplotype score (iHS) analysis highlighted three candidate protein-coding genes (ZNF114, DENND5A, and TENM4). The ROH islands contained 24 genes previously associated with pigmentation, reproduction, muscle function, and other biologically relevant traits in horses. These results provide a comprehensive genomic characterisation of the Lipica Stud Farm population and offer important insights into genetic diversity and inbreeding patterns in the Lipizzan breed.

• Language: English
• Keywords: genomics, Lipizzan horse, microsatellites, pedigree, selection signature, SNP array
• Work type: Article
• Typology: 1.01 - Original Scientific Article
• Organization: BF - Biotechnical Faculty; VF - Veterinary Faculty
• Publication status: Published
• Publication version: Version of Record
• Year: 2026
• Number of pages: 16 str.
• Numbering: Vol. 57, issue 4, [article no.] e70182
• PID: 20.500.12556/RUL-185613
• UDC: 636.1:575
• ISSN on article: 1365-2052
• DOI: 10.1002/age.70182
• COBISS.SI-ID: 287665411
• Publication date in RUL: 13.08.2026

Record is a part of a journal

• Title: Animal genetics
• Shortened title: Anim. genet.
• Publisher: Blackwell Science.
• ISSN: 1365-2052
• COBISS.SI-ID: 2344072

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, lipicanski konj, genetika, genetska pestrost, inbriding, populacije, Kobilarna Lipica

Projects

• Funder: ARIS - Slovenian Research and Innovation Agency
• Project number: J4-50133
• Name: Genetska osnova baročnih in delovnih pasem konj

• Funder: ARIS - Slovenian Research and Innovation Agency
• Project number: P4-0220
• Name: Primerjalna genomika in genomska biodiverziteta