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Abstract

Sustainable breeding of native breeds is essential to preserve genetic diversity and cultural heritage. Several native Nordic horse breeds are at risk of extinction and lack genetic characterization. This study aimed to analyze genetic variation and kinship within and among native Nordic horse breeds using whole-genome sequence data, and to compare results from using a Finnhorse genome assembly to that of the EquCab3.0 (Thoroughbred) reference genome. The breeds Dola Horse, North Swedish Horse and Coldblooded Trotter showed close genetic relationship for fixation index (0.03–0.08), and in principal component analysis. The other breeds showed stronger genetic differentiation, especially the Faroese Horse, with fixation index above 0.16 to all other breeds. This breed had the highest genomic inbreeding of 33% and the lowest heterozygosity of 12%. The Swedish Ardennes showed the lowest inbreeding at 14% and the highest heterozygosity of 16%. The mean identity by descent varied from 17% for Swedish Ardennes to 40% for Faroese Horses. The choice of reference genomes gave minor to moderate differences, suggesting that a closer related reference improves precision for fine mapping and understanding of the genetic landscapes of Nordic breeds. Together, the different analyses showed low genetic diversity in all breeds, and the general pattern of relatedness largely agreed with the known breed history. The results underline the importance of maintaining genetic diversity for the survival of the breeds.

Keywords

Whole genome sequence data; population genetics; genomic inbreeding; breed conservation; local breeds

Published in

Genetic resources
2026, volume: 7, number: 13, pages: 103–117

SLU Authors

UKÄ Subject classification

Genetics and Breeding in Agricultural Sciences

Publication identifier

  • DOI: https://doi.org/10.46265/genresj.TXWX7641

Permanent link to this page (URI)

https://res.slu.se/id/publ/146530