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

Area of Science:

• Genomics
• Evolutionary Biology
• Animal Genetics

Background:

• Horse domestication and selective breeding have significantly impacted equine phenotypes, mobility, and warfare capabilities.
• Structural variants (SVs), a major source of genetic variation, have been largely uncharacterized in horses despite their potential role in trait evolution.

Purpose of the Study:

• To comprehensively characterize structural variants (SVs) across diverse horse breeds.
• To investigate the evolutionary role of SVs in shaping equine populations and phenotypes.
• To identify specific SVs associated with important traits like racing ability.

Main Methods:

• High-fidelity Pacific Biosciences sequencing was used to assemble three high-quality horse genomes.
• A graph-based approach was employed to genotype 23,163 high-confidence SVs across 390 horse genomes from 61 breeds.
• Luciferase assays were conducted to assess the regulatory potential of identified SVs.

Main Results:

• Assembly of three high-quality horse genomes yielded 237 Mb of novel sequences, increasing Benchmarking Universal Single-Copy Orthologs completeness to 95.1%.
• Genotyping identified 23,163 non-redundant SVs, including 11,714 insertions and 11,449 deletions, across 61 breeds.
• A deletion in THSD7A and an insertion in OPCML were significantly associated with racing ability and body index, respectively, demonstrating SVs' functional impact.

Conclusions:

• Structural variants are crucial genetic elements that have contributed to the diversification of horse breeds and phenotypes.
• Specific SVs in genes like THSD7A and OPCML have a significant impact on economically important equine traits.
• This study underscores the potential of SVs as valuable genetic markers for understanding equine evolution and improving breeding strategies.