Inbreeding takes measureable toll on Thoroughbred performance, study finds

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A 10% increase in inbreeding, based on inbreeding coefficients, is associated with a 7% lower probability of ever racing.
A 10% increase in inbreeding, based on inbreeding coefficients, is associated with a 7% lower probability of ever racing. Photo by Keith Luke

Inbreeding in Thoroughbreds has a measurable impact on the prospects of horses ever racing, researchers have found.

The scientists also identified a single genetic marker which, if inherited from both parents, drops the prospects of a horse ever racing by nearly a third.

The study, published in the Proceedings of the Royal Society B, highlights how genomics-informed breeding has the potential to reduce inbreeding depression and avoid damaging carrier matings. This, in turn, would improve the health of the Thoroughbred population and boost racehorse welfare.

Professor Emmeline Hill, a horse geneticist with University College Dublin, and her fellow researchers said inbreeding in livestock populations is difficult to avoid because of the often closed nature of the gene pool. Nonetheless, limiting inbreeding is likely to reduce the impact of undesirable inherited features.

Until now, they said, the functional or clinical consequences of inbreeding in the Thoroughbred population, which has low levels of population genetic diversity, were not known.

“Given the current pedigree structure of Thoroughbreds, avoiding breeding close relatives is challenging and the increasing levels of inbreeding in the population indicates that existing strategies to mitigate inbreeding may be inadequate,” they said.

In their study, they quantified inbreeding in 6128 horses born in Europe and Australia, of which 13.2% were unraced.

They found that a 10% increase in inbreeding, based on inbreeding coefficients, is associated with a 7% lower probability of ever racing.

Further, they identified a single genetic marker that has a major negative effect on the chance of ever racing if inherited from both parents. The marker is linked to a gene involved in bone development and repair.

The authors calculated that horses who inherit it from both parents are 32.1% less likely to ever race, independent of the inbreeding coefficient.

The haplotype, dubbed THR14, overlaps a candidate gene, EFNA5, that is highly expressed in cartilage tissue, which when damaged is one of the most common causes of catastrophic musculoskeletal injury in racehorses.

Hill, commenting on Twitter, said more research is needed to test if the marker is associated with injury risk in racehorses. “Nonetheless, avoiding producing double copy foals and reducing the marker frequency in the breed will improve racing chances,” she said.

It will only affect animals if inherited from both sire and dam. Today, 1% of horses are double-copy for the harmful marker and thus have a three-times lower chance of racing. More than 10% of Thoroughbreds are carriers, capable of passing it on to offspring. One in six stallions is a carrier.

Hill said pedigrees illustrate broad breeding patterns. However, they do not show true levels of inbreeding in an animal, based on identically inherited genes from the sire and dam. Nor do pedigrees show if an animal carries a genetic marker, or is a double copy for a harmful marker.

Pedigrees, she said, can be augmented with genetic information.

Discussing their study, the researchers said some breeders consider that the duplication of influential ancestral horses in a pedigree may be advantageous. Indeed, the findings show that inbreeding in the distant pedigree is not disadvantageous to breeding goals.

“However, more recently shared common ancestors … have a considerable negative impact on the viability of a horse for racing and contribute to wastage in the population.” It is likely, they said, that such matings involve a higher proportion of rare, harmful alleles, which cumulatively cause the inbreeding depression observed.

They acknowledged that there are many reasons why a foal may not become a viable racehorse. However, musculoskeletal fractures are the most common cause of death at all stages of development, training and racing, and are a major welfare concern.

The known biological functions of EFNA5 and the haplotype association with the lower probability of racing identified in the study give rise to the hypothesis that it may play a role in musculoskeletal injury risk. This must be tested in a population of horses, they said.

In summary, the authors said genome-enabled breeding strategies would help to avoid inbreeding depression, and avoiding double-copy foals with the haplotype that reduces the chances of racing could improve economic returns for breeders and positively impact animal welfare.

“Industry-guided monitoring of genome-wide inbreeding over time will be important to maintain sustainable populations of horses, with particular attention focused on higher resolution information that can be obtained for deleterious haplotypes such as THR14.

Hill summarized the position on Twitter, saying that genomic tools can improve the industry goal of breeding viable horses to race. “Harnessing genomic tools will improve economics for breeders and individual animal health and welfare.”

The study team comprised Hill, with University College Dublin and Plusvital Ltd; Martin Stoffel and Josephine Pemberton, with the University of Edinburgh; Beatrice McGivney, with Plusvital Ltd; and David MacHugh, with University College Dublin.

Hill Emmeline W., Stoffel Martin A., McGivney Beatrice A., MacHugh David E. and Pemberton Josephine M. Inbreeding depression and the probability of racing in the Thoroughbred horseProc. R. Soc. B.2892022048720220487
http://doi.org/10.1098/rspb.2022.0487

The study, published under a Creative Commons License, can be read here.

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