Genetic research has shown that inbreeding is greatest in thoroughbred and standardbred horse breeds.
The study, published in the open-access journal PLoS Genetics, found thoroughbreds and standardbreds had the highest inbreeding co-efficients in an extensive genetic analysis of horse breeds.
The inbreeding coefficient is computed as a percentage of chances for two alleles - one of two or more versions of a gene - to be identical by descent.
Hanoverian, Quarter Horse and Mongolian horses had the lowest inbreeding co-efficients of the breeds studied, the researchers found.
Thoroughbreds rated at 0.15 in the co-efficient calculation, while standardbreds were at 0.12, indicating less inbreeding, despite most standardbred racing jurisdiction around the world allowing artificial insemination.
By comparison, the Hanoverian breed rated at 0.06, the Quarter Horse at 0.04 and the Mongolian horse at 0.02.
The researchers said that while their findings showed the genetic distance between individuals drawn from different breeds was relatively smooth, that was not the case within breeds, which it described as tri-modal.
To further investigate this distribution, the average genetic distance was calculated for each breed separately. It was lowest in the Norwegian Fjord and Icelandic horses and highest in the Hanoverian, Quarter Horse and Swiss Warmblood.
The team of researchers, across 18 academic institutions, evaluated more than 54,000 genetic samples from 14 domestic horse breeds and 18 evolutionarily related species.
The researchers said their analysis work showed the tight grouping of individuals within most breeds, the close proximity of related breeds, and less tight grouping in admixed breeds.
They said the results for the thoroughbred reflected the breed's low diversity, high inbreeding, and closure of the studbook to outside genetic influence for more than 300 years.
"Previous work has demonstrated that approximately 78 per cent of thoroughbred alleles are derived from 30 founders, and that a single founder stallion is responsible for approximately 95% of paternal lineages."
They said the impact of low diversity and high inbreeding could also be seen at a genetic level in standardbreds and the French Trotter.
The researchers found a close relationship between the Przewalski's Horse and the domestic horse.
As part of their work, they analysed genetic samples from zebras, asses, tapirs, and rhinoceros.
Their work, they said, would facilitate many genetics applications in equids, including identification of genes for health and performance traits, and compelling studies of the origins of the domestic horse, diversity within breeds, and evolutionary relationships among related species.
They noted that horses had held a valued place in human civilisation for over 5000 years through service in war, agriculture, sport, and as companions.
"Over the last several centuries, more than 400 distinct horse breeds have been established by genetic selection for a wide number of desirable phenotypic traits.
"In contrast to other large domestic animal species, including cattle, chickens, sheep, swine, goats and camelids, that are selectively bred mainly for production of food (meat, milk, eggs) or fibre, the domestic horse is primarily a utilitarian animal - bred for endurance, strength, speed, and metabolic efficiency.
"The horses' use as a work animal and means of transport required selection for individuals that were able to perform daily physical activity even when feedstuffs were scarce."
They said the natural athleticism of horses and their enforced intensive exercise regimes made them outstanding models for study of the musculoskeletal, cardiovascular and respiratory systems, while their natural susceptibility and resistance to infectious agents is useful in studies of the immune system.
"Understanding the genetic basis within and among breed variation in equine health, disease and performance traits will continue to provide important information on mammalian biology and genetic mechanisms of disease."