‘DNA doesn't lie’: New genetic study illuminates genetic diversity in North American Thoroughbreds

LEXINGTON, Ky. (Jan. 28, 2025) — Researchers from the University of Kentucky Martin-Gatton College of Agriculture, Food and Environment (CAFE) — in collaboration with the University of Nebraska-Lincoln, University of Minnesota and University of California-Davis — have unveiled the most comprehensive genetic study of North American Thoroughbred horses to date. Published in Scientific Reports, the findings provide an essential baseline for understanding how selection in this iconic breed impacted genetic diversity over the past five decades.

Using whole-genome sequencing (WGS), the research team analyzed the DNA of 185 Thoroughbreds born between 1965 and 2020. Their work aimed to generate data that could be used to address concerns about inbreeding and genetic diversity within the breed, offering breeders valuable insights to guide future decisions.

“The impetus for this study was to quantify the extent of genetic variation and inbreeding in Thoroughbreds,” said Ernest Bailey, professor in the Maxwell H. Gluck Equine Research Center at Martin-Gatton CAFE and the study’s lead author. “By identifying trends, we’re equipping breeders with the data needed to make informed choices that preserve the breed’s health and performance.”

The study compared two groups of Thoroughbreds: 82 horses born between 1965 and 1986, and 103 horses born between 2000 and 2020. Researchers identified more than 14 million genetic variations, revealing that horses from the older generations carried slightly more genetic diversity, while horses in the younger generations showed modest increases in inbreeding.

“Selective breeding focuses on enhancing desirable traits like speed and stamina, but it can also increase the risk of amplifying harmful genetic variants,” said Jessica Petersen, associate professor at the University of Nebraska-Lincoln Department of Animal Science. “Our data gives breeders a clearer roadmap and tools to navigate these challenges.”

One notable discovery was a 10% increase in the frequency of a genetic variant linked to the “speed gene,” which influences sprinting ability. This trend reflects a shift in breeding priorities toward shorter-distance races.

“DNA doesn't lie,” said Ted Kalbfleisch, professor in the Department of Veterinary Science and study co-author. “This change in the genome aligns with the growing popularity of shorter, faster races and demonstrates how breeding decisions leave measurable imprints on the genetic makeup of the breed.”

Despite concerns about declining health and durability in Thoroughbreds, the study found no evidence of genetic issues. By analyzing “runs of homozygosity” — stretches of identical DNA inherited from both parents — the researchers detected a slight rise in inbreeding in horses in the younger group but stressed that it isn’t inherently problematic.

“Inbreeding can help solidify positive traits, like speed or endurance,” Petersen said. “However, it’s also important to monitor and avoid harmful genetic combinations. With tools like WGS, scientists can proactively identify and manage risks before they impact the breed.”

The study’s practical applications are clear: by identifying genetic risks, it is possible that in the future breeders can test stallions and mares for harmful variants and adjust pairings to prevent inheritance. This approach protects the health of individual horses while preserving the breed’s athletic excellence.

“The data shows that breeders have done a good job,” Bailey said. “Genomic tools make this clear at the DNA level but are unlikely to replace a breeder’s insights and intuition in the quest to create a better racehorse. However, these are precisely the tools we need to monitor and respond to hereditary problems that may arise.”

The project was funded by the Koller Endowed Funds to the Veterinary Science Department at UK. The work was conducted in connection with Agricultural Experiment Station Projects at UK and University of Nebraska-Lincoln.