Genome-wide SNP analysis of Japanese Thoroughbred racehorses.

Summary

# Genome-wide SNP analysis of Japanese Thoroughbred racehorses Intense selective breeding for racing performance and specific phenotypes has fundamentally shaped Thoroughbred genetics, yet the genomic signatures of this artificial selection remain incompletely understood. Using the 670k SNP array to genotype 370 Japanese Thoroughbreds alongside other equine breeds, researchers mapped genomic regions under directional selection and identified evidence of historical inbreeding events that continue to influence modern population structure. Notably, the MC1R locus associated with chestnut coat colour showed evidence of earlier selection pressure on different mutations long before recent colour-specific breeding decisions, suggesting complex layering of selection events over the breed's history. The analysis revealed breed-specific selection signatures in Thoroughbreds and demonstrated that intense inbreeding both early in breed formation and pre-domestication substantially altered the genomic architecture we observe today. For equine professionals involved in breeding decisions, performance prediction, and health management, these findings underscore how concentrated the Thoroughbred gene pool has become and highlight the utility of genomic tools for understanding inherited disease risk, phenotypic variation, and the long-term genetic consequences of selective breeding strategies.

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Key Findings

• •MC1R locus associated with chestnut coat color shows evidence of selection for different mutations earlier than recent chestnut color selection
• •Multiple regions identified with Thoroughbred-specific selection signatures
• •Intense inbreeding early in Thoroughbred history and before breed formation significantly impacts modern genomic architecture

Conditions Studied