Equine

Population structure and runs of homozygosity in Irish horse breeds

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Abstract

Ireland has a long tradition of horse breeding with four native breeds, the Irish Draught (ID), the Kerry Bog Pony (KBP), the Connemara Pony (CP), the Irish Cob (IC), and the performance bred Irish Sport Horse (ISH). The ISH was traditionally an ID or CP crossed with a Thoroughbred (TB); more recently ISH breeders have incorporated Irish and continental European warmblood bloodlines to meet evolving sporting demands. The original ISH cross is now denoted by a Traditional Irish Horse (TIH) suffix to distinguish it from the modern ISH. Selection pressures on each of these breeds, bred for different morphological and/or economic features, can lead to genomic regions with reduced genetic diversity and frequent runs of homozygosity (ROH). The extent and frequency of these ROH can inform on the ancestry of an individual and its population. Therefore, the objective of this present study was to use SNP genotypes to identify genomic regions in 26,290 horses of 11 different populations (ISH, TIH, ID, CP, IC, KBP, TB, Holsteiner, Dutch Warmblood, Belgian Warmblood, and Zangersheide) subjected to selection pressures and to quantify the genetic diversity within each population with particular focus on the breeds of Irish origin. All horses were genotyped using the Equine80select genotyping bead chip. Autosomal SNPs with an unknown location on EquCab 3.0, a call rate ≤95% and a MAF ROH) in the KBP (3.05%) and the highest in the TB (15.60%). There were ROH identified on all autosomes in all breeds however the exact locations of these ROH varied by individual and by breed. The PCA analysis showed distinct clusters for the ID, IC, KPB, CP, and TB populations. In contrast all 3 continental warmblood breeds clustered together and were indistinguishable from each other. Recent introduction of warmblood bloodlines is observed in the ISH with clear differences identified between the TIH population and the more general ISH population in the PCA analysis and admixture results. In conclusion, these results illustrate genomic variations in both breed origins and their recent management.

Keywords: 2026

How to Cite:

Doyle, J. & Egan, S., (2026) “Population structure and runs of homozygosity in Irish horse breeds”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2284549. doi: https://doi.org/10.31274/wcgalp.23587

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