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

OBJECTIVE: To estimate allele frequencies for genetic diseases in the American Quarter Horse (QH), including hyperkalemic periodic paralysis (HYPP), type 1 polysaccharide storage myopathy (PSSM1), malignant hyperthermia (MH), myosin-heavy chain myopathy (MYHM), glycogen branching enzyme deficiency (GBED), hereditary equine regional dermal asthenia (HERDA), and equine juvenile spinocerebellar ataxia (EJSCA), and to compare these frequencies over time among elite performance subgroups and a random cohort of registered horses. METHODS: In this prospective genetic survey, DNA was extracted from 300 elite performance QHs in 7 popular disciplines and 300 randomly selected QHs born between 2020 and 2024. Genotyping was performed with commercially available assays. Allele, carrier, and affected frequencies were calculated as proportion ± SE, compared across disciplines, and compared to a 2009 study by Tryon et al. RESULTS: Genotyping the top-performing QHs identified high HYPP (0.318 ± 0.050) and PSSM1 (0.386 ± 0.052) frequencies in halter horses. Glycogen branching enzyme deficiency frequency was high in reining horses (0.109 ± 0.032), and HERDA was high in cutting horses (0.135 ± 0.035). Genotyping randomly selected QHs identified low PSSM1 (0.012 ± 0.004) and high myosin-heavy chain myopathy frequencies (0.066 ± 0.010). Many of these allele frequencies in the random population have not changed over time (HYPP, GBED, HERDA) but have changed within specific subgroups. Equine juvenile spinocerebellar ataxia allele frequencies were low but detectable in the random, reining, and cutting populations. CONCLUSIONS: Disease allele frequencies in QHs are highly variable between performance subgroups. CLINICAL RELEVANCE: The establishment of allele frequencies allows for longitudinal monitoring to determine how genetic testing results are being utilized.