Genetic diversity in domestic horses: Temporal patterns, the influence of assisted reproductive technologies, and implications for the American Quarter Horse

Genetic diversity is the heritable variation within and among populations and is essential for the long-term health and selection potential of domestic horses. Previous studies show diversity across breeds is shaped by effective population size, founder events, artificial selection, and levels of inbreeding. While some closed-studbook breeds retain moderate genetic diversity, others have experienced rapid losses due to popular-sire effects and recent and extensive inbreeding. Even so, mare lines continue to help maintain genetic diversity within these populations. Assisted Reproductive Technologies (ART) have expanded the use of popular stallions, and the increasing application of ovum pickup (OPU) followed by in vitro embryo production (IVEP) may also concentrate genetic contributions from a limited number of mares. Yet, the overall impact of ART on equine genetic diversity remains largely unknown. Registration-based genetic data from the American Quarter Horse, a breed previously considered relatively genetically diverse, showed a 1.38% decline in diversity (based on effective number of alleles) in the last generation (2012 vs. 2022). Genetic diversity metrics indicate that 2022 foals produced via ART were less diverse than those produced by live cover (p < 0.01). Mares utilized in ART cohorts were significantly less diverse than those utilized in live cover (p < 0.01), while stallions were largely not different between groups. These findings suggest that ART-associated breeding schemes, particularly reduced diversity among mares, are contributing to the observed decline. Taken together these data establish baselines to monitor the clinical relevance of differences in genetic diversity across generations and cohorts in this breed. Understanding how ART interacts with breeding decisions to shape genetic diversity is critical for developing strategies that preserve variation while supporting industry goals including genetic gains.