Allele frequencies of 7 inherited disorders in performance and random cohorts of American Quarter Horses (2020-2024).

Inherited disease allele frequencies in Quarter Horses vary substantially by performance discipline, necessitating targeted genetic screening.

This prospective genetic survey estimated allele frequencies for seven inherited disorders in American Quarter Horses (QHs) by genotyping 300 elite performance horses across seven disciplines and 300 randomly selected registered horses born between 2020 and 2024. The disorders assessed included HYPP, PSSM1, MH, MYHM, GBED, HERDA, and EJSCA. Results revealed marked variation in disease allele frequencies across performance subgroups. Halter horses exhibited notably high HYPP (0.318 ± 0.050) and PSSM1 (0.386 ± 0.052) allele frequencies, while GBED frequency was elevated in reining horses (0.109 ± 0.032) and HERDA was high in cutting horses (0.135 ± 0.035). In the randomly selected cohort, PSSM1 frequency was low (0.012 ± 0.004), whereas MYHM frequency was relatively high (0.066 ± 0.010). Comparison with a 2009 baseline study indicated that several allele frequencies in the general population have remained stable over time (HYPP, GBED, HERDA), though changes were detected within specific performance subgroups. EJSCA allele frequencies were low but detectable in random, reining, and cutting populations. These findings underscore the importance of discipline-specific genetic screening strategies and provide a longitudinal framework for monitoring whether genetic testing is meaningfully influencing breeding decisions in the QH breed.

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