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

Overview

• This study measured the frequencies of genetic disease alleles in American Quarter Horses (QHs), comparing elite performance horses in various disciplines to a randomly selected group born between 2020 and 2024.
• The research provides updated data on how common certain inherited disorders are within different horse subgroups and tracks changes over time since previous studies.

Introduction to the Study

• The purpose was to estimate allele frequencies of seven inherited diseases in QHs: 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).
• The study compared these frequencies between elite horses competing in seven popular performance disciplines and a random sample of registered QHs born from 2020-2024.
• This comparison also evaluated how allele frequencies have changed over time by referencing a previous 2009 study (Tryon et al.).

Methodology

• Samples were collected from 300 elite performance QHs across seven disciplines and 300 randomly selected QHs from recent birth cohorts (2020-2024).
• DNA extraction was performed on all samples.
• Genotyping utilized commercially available assays specifically designed to detect the alleles associated with the seven disorders.
• Allele frequency, carrier frequency, and affected frequency were calculated with standard error (SE) to statistically quantify prevalence.
• Data were analyzed to compare frequencies across performance disciplines and between the elite and random cohorts.
• Results were compared to previously published allele frequencies to assess temporal changes.

Key Findings

• High allele frequencies in specific performance groups:
  • Halter horses showed notably high HYPP allele frequency (0.318 ± 0.050) and PSSM1 frequency (0.386 ± 0.052).
  • Reining horses had relatively high GBED frequency (0.109 ± 0.032).
  • Cutting horses exhibited a high frequency of HERDA (0.135 ± 0.035).
• Randomly selected QHs had different allele frequency patterns:
  • Low frequency of PSSM1 alleles (0.012 ± 0.004).
  • Higher frequencies of MYHM alleles (0.066 ± 0.010) than in elite performance horses.
• Equine juvenile spinocerebellar ataxia (EJSCA) alleles:
  • Detected at low frequencies across random samples, as well as in reining and cutting horse groups.
• Changes over time:
  • Some allele frequencies such as HYPP, GBED, and HERDA remained relatively stable in the random population since the 2009 study.
  • However, frequencies varied within specific performance subgroups, indicating selective pressures or breeding practices influencing these genes in certain disciplines.

Interpretation and Implications

• This study reveals a significant variation in disease-associated allele frequencies between performance disciplines, reflecting possibly breed popularity, breeding goals, and selective breeding for performance traits.
• Elevated frequencies of detrimental alleles in certain subgroups indicate a potential ongoing risk for inherited disorders, which breeders and veterinarians should consider.
• The data support the utility of genetic testing programs to monitor and potentially reduce the prevalence of these inherited diseases.
• Establishing baseline allele frequencies facilitates longitudinal surveillance, enabling the equine industry to track the effectiveness of genetic counseling and testing practices over time.
• The findings highlight the importance of targeted genetic management strategies tailored to specific QH performance disciplines.

Conclusion

• Allele frequencies for important inherited disorders in American Quarter Horses vary widely by discipline and differ between elite performance and random populations.
• While some allele frequencies have remained stable over the past decade, changes within specific groups point to ongoing genetic selection.
• Reliable allele frequency data support ongoing efforts for genetic disease management and improved health outcomes in QHs.