VGL Researchers Explore Genetic Diversity in the American Quarter Horse
A newly published study from the UC Davis Veterinary Genetics Laboratory (VGL), led by Director Dr. Rebecca Bellone, provides important new insights into how assisted reproductive technologies (ARTs) may be influencing genetic diversity in the American Quarter Horse. The publication reviews current knowledge regarding equine genetic diversity and presents a large-scale analysis of genetic data from the American Quarter Horse population. A primary objective of the study was to assess how genetic diversity changed over a single generation and to begin evaluating the potential impact of ARTs on these trends.
Maintaining genetic diversity is critical to the long-term health and sustainability of any breed. Reduced genetic diversity has been associated with an increased risk of recessive genetic disorders, decreased fertility, and a diminished ability to adapt to changing environmental conditions.
Assisted reproductive technologies, including artificial insemination, embryo transfer, frozen embryos, transported semen, and intracytoplasmic sperm injection (ICSI), were originally developed to improve reproductive success in animals with fertility challenges. However, their use has expanded significantly in breeds where these technologies are permitted, including among animals that have already produced numerous offspring. Modern reproductive techniques can achieve high reproductive efficiency using very small quantities of semen, enabling a limited number of individuals to contribute disproportionately to the gene pool.
The American Quarter Horse provides an important model for studying these trends due to its large global population and widespread use across diverse disciplines, including racing, ranch work, and performance events. Understanding changes in genetic diversity is therefore vital to the breed’s future. Recognizing this need, the American Quarter Horse Association (AQHA), which maintains the breed’s official registry and pedigree records, provided funding for the research.
Tammy Canida, AQHA Registrar with more than 40 years of experience, emphasized the significance of the study:
Our members care deeply about the future of the American Quarter Horse. By investing in research that expands our understanding of genetic diversity, we're providing knowledge that will benefit breeders, owners, and the breed itself for generations. We are grateful to the team at the UC Davis Veterinary Genetics Laboratory for their expertise and collaboration in conducting this important research, helping advance the scientific understanding needed to support the long-term health and integrity of the American Quarter Horse.”
This study represents the first large-scale temporal investigation of genetic diversity in the breed. Using DNA markers from the AQHA parentage testing program, researchers, including Dr. Felipe Avila, analyzed genetic data from tens of thousands of foals born in 2012 and 2022. The results revealed a 1.38% decline in genetic diversity over a single generation, as measured by the effective number of alleles, a key indicator of population diversity. Dr. Avila notes:
A decrease in genetic diversity is to be expected in closed book populations but it is important to identify the major contributing factors and ensure the rate of decline isn’t increasing over time”
The research also examined the specific effects of assisted reproductive technologies on genetic diversity. Foals produced through ART methods were consistently found to be less genetically diverse than foals conceived through traditional live cover. Furthermore, the study reported that “mares utilized in ART cohorts were significantly less diverse than those utilized in live cover (p < 0.01).”
Dr. Bellone notes:
The finding that reduced diversity among mares used in ART programs may be contributing to the observed decline differs from trends we have identified in other breeds, such as the Standardbred, where mares have been shown to play a role in maintaining overall genetic diversity.”
The study highlights the importance of integrating genetic monitoring into breeding and pedigree programs to balance selection goals with the long-term sustainability of the population.
At the March 2026 convention, the AQHA approved the formation of a Genetic Diversity Task Force. The task force will identify priorities and develop recommendations aimed at safeguarding the future genetic health of the American Quarter Horse. The findings from this study will establish a valuable baseline for the AQHA as it develops strategies to preserve and enhance genetic diversity in the breed.
To read the full publication, visit https://doi.org/10.1016/j.jevs.2026.106072