Genomic insights into population structure, local ancestry and within-breed relationships in the Norik of Muran horse

The Norik of Muran is a local Slovak draught horse with historical connections to Central European heavy horses. This study aimed to characterise the genomic structure of the Norik of Muran breed in relation to related but separately recognised Noriker breeds and other reference horse breeds through analyses of local ancestry, haplotype sharing patterns and recent family structure within the breed. The comparative dataset included Norik of Muran, Austrian Noriker, Silesian Noriker, Belgian Draught, Haflinger, Hucul and Norwegian Fjord, while Shagya Arabian and Quarter Horse were included as outgroups. Across these breeds, genotype data from 664 individuals were used, with 37 875 autosomal markers retained after quality control. For the main population structure analyses, a balanced dataset of 180 individuals was selected, with 20 individuals per breed and reduced genomic relatedness within breeds. Genomic relationships between the Norik of Muran and the remaining breeds were evaluated using allele frequency, local ancestry and haplotype-based analyses. Pairwise Wright’s fixation index was lowest between Norik of Muran and Silesian Noriker (0.01), followed by Norik of Muran and Austrian Noriker (0.02). Local ancestry inference assigned the largest proportions of the Norik of Muran genome to Silesian Noriker (40.61%) and Austrian Noriker (39.61%) reference populations, with a smaller proportion assigned to Belgian Draught (9.23%). Haplotype sharing analysis showed the highest between-breed sharing with Silesian Noriker and Austrian Noriker, from which Norik of Muran copied, on average, 108.38 and 108.14 haplotype chunks, respectively. Genomic reconstruction of recent family structure using 125 Norik of Muran individuals identified 76 parent-offspring relationships, nine paternal half-sibling groups and 10 maternal half-sibling groups, with the largest paternal half-sibling group including eight offspring. Obtained results indicate that the Norik of Muran has a genomic profile characterised by close relationships with Silesian Noriker and Austrian Noriker, a heterogeneous local ancestry profile relative to the analysed reference populations, and clearly detectable recent family structure. This information may support mating decisions within conservation breeding programmes, particularly those aimed at limiting repeated use of closely related animals, balancing sire contributions and preserving diversity at family level.