Whole genome detection of sequence and structural polymorphism in six diverse horses.
Authors: Al Abri Mohammed Ali, Holl Heather Marie, Kalla Sara E, Sutter Nathan B, Brooks Samantha A
Journal: PloS one
Summary
# Editorial Summary Whilst the equine reference genome has been available since 2009, it represents primarily one genetic background, limiting our understanding of the substantial variation across the ~400 recognised horse breeds worldwide. Al Abri and colleagues sequenced whole genomes from six morphologically and geographically diverse horses—ranging from an American Miniature to a Percheron—generating comprehensive variant catalogues aligned to the updated EquCab3.0 reference, with coverage depths between 15–24× per animal. The analysis identified over 17.5 million single nucleotide polymorphisms, nearly 2 million insertions/deletions, and an average of 1,540 copy number variations and 3,321 structural variations per individual, with functional annotation revealing breed-specific genetic signatures including LCORL variants (present across all horses), ZFAT associations in smaller breeds, and a copy number variation in the Latherin gene potentially linked to thermoregulation through differential sweating capacity. Particularly relevant for practitioners managing athletic horses, the Latherin finding suggests genetic underpinning of heat tolerance and performance capacity, whilst size-related variants offer insight into the genomic architecture driving the extreme phenotypic diversity across equine populations. This newly curated variant database provides a substantially enriched resource for investigating the genetic basis of breed-specific traits—from performance characteristics to disease predisposition—with direct applications for selective breeding programmes and precision management strategies tailored to individual genetic profiles.
Read the full abstract on PubMed
Practical Takeaways
- •Genetic markers for body size and breed-specific traits are now catalogued and accessible, enabling targeted breeding decisions and selection for desired phenotypes
- •Latherin gene variations may explain differences in sweating ability and heat tolerance between breeds—relevant for selecting horses suited to specific climates and athletic demands
- •This reference database provides a foundation for future research linking genetic variants to performance, health, and adaptive traits of practical importance to breeders and trainers
Key Findings
- •Identified 17,514,723 SNPs and 1,923,693 INDELs across six diverse horse breeds with 15-24x genome coverage
- •LCORL gene associated with size variation found in all horses; ZFAT in Arabian/Miniature/Percheron; ANKRD1 in Mongolian Chakouyi horses
- •Copy number variation detected in Latherin gene suggesting evolutionary selection for thermoregulation and sweating capacity related to athleticism
- •Newly discovered variants created as user-friendly database for future studies of genetic basis of equine phenotypes