Research Shows Genetic Diversity Among Thoroughbreds

Multi-phased research study led by the UK Gluck Center shows genetic diversity among Thoroughbred horses. 

The Thoroughbred horse is a remarkable product of human selection over several centuries, and the breed's health and athleticism has resulted in its use in the development of many, if not most, modern breeds of horse. 

Thoroughbred breeders have long been interested in maintaining genetic diversity and have been astute in selecting against genetic determinants that negatively impact health and fertility. At the same time, some worry that Thoroughbreds have become deficient in diversity. 

To better shed light on this topic, a team led by the University of Kentucky's Gluck Equine Research Center recently completed the first phase of a research study that will result in the most comprehensive analysis of the genetics of the U.S. Thoroughbred to date. Previous studies of Thoroughbred diversity were based on sampling small subsets of the genome. This study, by Ernie Bailey, PhD, Ted Kalbfleisch, PhD, both from the Gluck Center, and Jessica Petersen, PhD, from the University of Nebraska-Lincoln, is based on sequencing the entire genome of Thoroughbred horses.

The goals of the study are to create a database that catalogs the variation across the genome of today's Thoroughbred horses and to generate anonymous (by horse) data that will create a foundation of knowledge for use in monitoring changes in genetic diversity over time.

According to Bailey, the completion of their first phase of research in 2021 documents that the diversity among Thoroughbred horses is consistent with that found for other domestic animals and that falls within the range for other breeds of horses. 

During this phase, 1,000 Thoroughbred samples were collected from horses in Kentucky, California, Florida, and New York. Pedigrees of the horses were examined and 120 were selected for whole-genome sequencing to capture as much of the genetic variation of the population as possible. As a result of sequencing these horses, a catalog of 15 million DNA variants among U.S. Thoroughbreds is being created. This catalog can be used to monitor future changes in the Thoroughbred population as well as to construct computer models to assess how changes in breeding practices may affect the genetic structure of the population.

The second phase of research that is set to get underway will be a sequencing project that aims to help protect the breed from deleterious recessive genes. The appearance of variants will be identified, and programs will be used to predict whether those variants might have a potentially negative effect on a gene. Additionally, the team is interested in using part of a survey of the whole breed to get at overall frequencies of genes.

"We can whole genome sequence every animal that is suspected of suffering from a deleterious recessive condition and look for possible causes; if none are proven we can archive the DNA in a database for comparison with future horses that appear with similar disease phenotypes," Bailey said. "If we wait until a recessive deleterious disease occurs in 1% of the population, then 18% of all Thoroughbreds will already be carriers. This approach allows us to detect such genes before they become so prevalent."

Importantly, these data will be publicly available so researchers at other institutions can perform studies of specific traits or genes. The genetic data, and the approach used in generating them, also represent a new tool available for breeders to use in maximizing the genetic potential of each foal and in ensuring the Thoroughbred's status as an elite population of equine athletes.  

If you are interested in learning more about this project, please contact Bailey (ebailey@uky.edu). If you are interested in supporting this project through financial contributions, please contact Danielle Jostes (danielle.jostes@uky.edu).