A Global Structural Variation Map Reveals Novel Variants for Body Conformation and Racing Ability in Horses

The selection of horses has been instrumental in shaping long-range mobility, advancing warfare strategies, and diversifying equine phenotypes. However, the structural variants (SVs) favored by this process remain largely unexplored. Utilizing high-fidelity Pacific Biosciences sequencing, we assembled three high-quality horse genomes, incorporating 237 Mb (9.48%) of novel sequences relative to the existing reference genome. These assemblies achieved an average Benchmarking Universal Single-Copy Orthologs completeness of 95.1%. By employing a graph-based approach, we genotyped 23,163 high-confidence, non-redundant SVs, which include 11,714 insertions and 11,449 deletions, across 390 horse genomes representing 61 breeds worldwide. Our findings provide evolutionary insights into the origins of diverse horse populations, through both SVs and single nucleotide polymorphisms. Notably, we identified a 273-bp deletion in the THSD7A gene and a 98-bp long terminal repeat insertion in the OPCML gene, both of which are significantly associated with racing ability and body index in horses (P = 3.87E−05 and 4.08E−05). These genes are linked to bone metabolism and racing ability, respectively. Luciferase assays demonstrated the regulatory potential of these sequences, showing they can significantly modulate the transcriptional activity of their associated genes. In summary, our findings highlight the potential of SVs as genetic markers and functional elements that shape equine phenotypes.