Assessment and Distribution of Runs of Homozygosity in Horse Breeds Representing Different Utility Types.
Authors: Szmatoła Tomasz, Gurgul Artur, Jasielczuk Igor, Oclon Ewa, Ropka-Molik Katarzyna, Stefaniuk-Szmukier Monika, Polak Grazyna, Tomczyk-Wrona Iwona, Bugno-Poniewierska Monika
Journal: Animals : an open access journal from MDPI
Summary
# Assessment and Distribution of Runs of Homozygosity in Horse Breeds Representing Different Utility Types Genomic inbreeding varies substantially across horse breeds, with significant implications for breeding decisions and health management. Researchers analysed runs of homozygosity (ROH)—stretches of identical DNA inherited from both parents—across 571 horses from six breeds using the 65k Equine BeadChip, stratifying findings by horse type (primitive, light, and draft). Notable differences emerged in ROH number, length, and distribution between breeds, alongside variations in genomic inbreeding coefficients; crucially, the team identified "ROH islands" (regions of high homozygosity frequency) harbouring genes associated with breed-defining traits such as coat colour, muscle function, and skeletal development (including LCORL, CACNA1G, and zinc finger proteins), suggesting these are targets of recent directional selection. Conversely, certain genomic regions showed zero ROH occurrence across breeds, with 27 genes common to five breeds in these areas—notably genes regulating muscle contractility (CACNA1A) and myogenic processes (miR-23, miR-24, miR-27). These findings provide a genetic roadmap for identifying breed-specific markers and understanding the genomic architecture underlying functional traits, offering professionals a framework for more informed breeding strategies and early detection of potential inbreeding depression within their chosen breed populations.
Read the full abstract on PubMed
Practical Takeaways
- •Understanding breed-specific genomic signatures through ROH analysis can assist in breeding decisions and identification of breed-defining characteristics at the molecular level
- •ROH islands represent targets for future research into selection pressure and breed genetic distinctiveness, which may inform breeding programs focused on preserving breed traits
- •Identification of conserved no-ROH regions and genes across breeds suggests fundamental genetic requirements for equine muscle function that transcend breed boundaries
Key Findings
- •Significant variation in ROH distribution observed across six horse breeds with differences in genomic inbreeding coefficients between primitive, light, and draft horse types
- •Identification of 8-14 ROH islands per breed spanning genes involved in breed characteristics including LCORL, NOG, CACNA1G, and zinc finger proteins
- •Detection of 2-57 no-ROH regions per breed with 27 genes common across five breeds involved in muscle contractility (CACNA1A) and muscle development (miR-23, miR-24, miR-27)
- •ROH islands identified as potential signals of recent selection events with genomic regions showing high coverage across breeds