The American Quarter Horse has long been recognized as one of the world’s most versatile and genetically diverse horse breeds. But new research from the University of California, Davis, suggests that diversity is shrinking — and modern breeding practices may be playing a role.
A newly published study from the UC Davis Veterinary Genetics Laboratory examined how genetic diversity changed in the American Quarter Horse over a single generation while also evaluating the potential influence of assisted reproductive technologies, such as artificial insemination, embryo transfer, frozen embryos, transported semen, and intracytoplasmic sperm injection. The research was funded by the American Quarter Horse Association.
Maintaining genetic diversity is important because it helps preserve long-term breed health, fertility, and adaptability. Reduced diversity has been linked to an increased risk of inherited disorders and reduced ability to respond to changing environmental conditions.
Originally developed to help animals with fertility challenges, assisted reproductive technologies have become common in many performance horse breeding programs. These tools allow a small number of highly sought-after stallions — and increasingly mares — to produce far more offspring than would be possible through traditional breeding.
Researchers analyzed DNA parentage records from tens of thousands of Quarter Horse foals born in 2012 and 2022. The study found a 1.38 percent decline in genetic diversity over that single generation, based on the effective number of alleles, an important measure of population diversity.
“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,” said Tammy Canida, AQHA registrar with more than 40 years of experience.
Lead author Dr. Felipe Avila said the decline itself is not entirely unexpected for a closed registry breed.
“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 study also found differences between horses produced through assisted reproductive technologies and those conceived through traditional live cover. Foals produced using ART methods were consistently less genetically diverse than those conceived through live cover. Researchers also reported that mares used in ART programs were themselves significantly less genetically diverse than mares used for live cover breeding.
According to UC Davis Veterinary Genetics Laboratory Director Dr. Rebecca Bellone, that finding differs from what researchers have observed in other horse breeds.
“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 researchers emphasized that the technologies themselves are not necessarily the problem. Instead, breeding decisions that repeatedly concentrate genetics from a relatively small group of elite animals appear to be driving much of the observed decline. Modern reproductive technologies allow multiple embryos or pregnancies from the same mare in a single year while enabling popular stallions to sire hundreds of foals, increasing the concentration of certain bloodlines.
The findings come as AQHA continues to examine the breed’s long-term genetic health. During its March 2026 convention, the association approved the creation of a Genetic Diversity Task Force, which will develop recommendations for preserving and enhancing genetic diversity within the breed.
Researchers say the new study provides an important baseline for future monitoring as breeding technologies continue to evolve and become more widely used.