From winning it in 1964 to being in the pedigree of all 20 runners in the Kentucky Derby fifty years later, Northern Dancer’s impact on the thoroughbred breed continues to grow.

And while this ‘sire of sires’ sprinting legacy has been long celebrated, the recent news that in thoroughbreds, inbreeding is getting higher and largely going on unchecked, has geneticists very concerned.

A recent study that analysed the genomes of 10,000 thoroughbreds from around the world (the largest set examined to date) showed that 97 per cent of them trace back to the Canadian Champion.

Explainer: Inbreeding, also known as line breeding, is the practice of breeding horses who are closely related. While inbreeding makes it easier to predict what characteristics will be passed on, it also makes it more likely the animals will inherit negative characteristics. When this practice happens within a closed stud book, it speeds up the loss of genetic diversity of the entire population.

Dr Emmeline Hill, at the helm of genetics research at University College Dublin in Ireland, compares the accumulation of inbreeding facing the thoroughbred industry to climate change, stating that the striking increase in inbreeding during the last fifty years is due to ‘the popular sire effect’, whereby a limited number of stallions have a disproportionate influence on the genetic composition of the breed.  

In an interview, Dr Hill said “Inbreeding has always been high in thoroughbreds, but it is getting higher. It is likely that unchecked inbreeding in the thoroughbred will continue to increase in a market where there is high demand for particular sire lines. The problem with inbreeding is that it can compromise overall population fertility and health. This is a highly significant issue akin to global warming, where inbreeding is accumulating in the population, that must be addressed at an industry-wide level.”

The thoroughbred influence

Few breeds deserve the exalted reputation of the thoroughbred and none have influenced modern equestrian sport as much as it has.

Thoroughbreds have been used to enhance the athleticism and refinement of countless breeds around the world, including many Warmbloods, the Standardbred and the Quarter Horse.

In the last three centuries, their high reactivity has been selectively bred by indulgent breeders to make them run faster, jump higher and last longer than other horses. And while they are best known for their prowess on the racetrack, they are also well represented in disciplines like show jumping, three-day eventing, and polo.

Thoroughbreds have been bred within a closed studbook, with all registered horses being traced back to three foundation sires and around thirty mares. Artificial insemination and cloning are not permitted, so breeding practices contribute significantly to the breed’s current genetic diversity.

And it is not a good situation at all.

Addressing the challenge of genetic diversity

Cunco’s family tree, showing how he was an inbred descendant of Northern Dancer. An example of inbreeding, Cunco’s family tree, shows he has Northern Dancer on both sides of his pedigree. Image credit: Genome Research Limited.

In 2011, the Toronto Star reported that nearly half the horses running in the 2011 Kentucky Derby had Northern Dancer bloodlines in both their dam and sire bloodlines and that 18 of the 19 horses in the race were his descendants.

Due to a narrowing population of broodmares and the fact that there is only a small selection of ‘popular’ stallions (almost all owned by just two stud operations and derived predominantly from Northern Dancer bloodlines), the global gene pool of thoroughbreds is smaller than ever before.

In past times, long before plane transportation of horses was possible, thoroughbred stallions were only able to breed with mares located in their vicinity. Nowadays, with stallion shuttling a common practice, instead of breeding with a maximum of forty broodmares a year, a popular stallion might father as many as 300 foals in one year. Today, stallion owners can monopolize breeding choices, not only in their local area but all over the world.

Dr Hill warns of how inbreeding increases the chances of offspring inheriting recessive traits, stating this “may weaken the biological fitness of the population and hinder its ability to survive and reproduce – a circumstance known as inbreeding depression.”

A portrait of Northern Dancer Out of Northern Dancer’s first 21 foals, 10 of them were stakes winners. When he finally retired from stud services years later, he was the most-bred stallion of modern times.

Northern Dancer: The runt who took over the racing world  

The thoroughbred’s lean body, strong hindquarters, and refined, intelligent head were once instantly recognizable traits. But today, a thoroughbred could easily be mistaken for a muscular Quarter horse, just like Northern Dancer could.

The short-coupled stallion was not an aristocratical thoroughbred. Described as “short and stocky” and “a feisty Canadian colt that was dismissed time and again because of his size”, Northern Dancer ran with a quick choppy gait very different to the long, smooth striding thoroughbreds of his time.

ProPublica described him as the horse that nobody wanted to buy, who had sore feet and a volatile temperament.

He was so short that his grooms had to dig a hole (and later build a ramp) so that he could mount his mares, yet just like their gutsy father, his offspring were excellent racehorses.

Out of his first 21 foals, 10 of them were stakes winners. When he finally retired from stud services years later, he was the most-bred stallion of modern times. His sons and grandsons are among the best-known sires of this century, and he was equally successful as a broodmare sire.

It would be impossible to calculate the economic value of Northern Dancer’s legacy; he made many people in racing very rich, as did his descendants – but this was done at the expense of the breed’s genetic diversity.

A paradigm shift in racing

Some forty years ago, investors worked out that thoroughbred racehorses bred from sprinting lines matured earlier and ran faster (at least over short distances) when compared to slow-maturing thoroughbreds from staying lines.

Economically, they discovered racing two-year-olds offered a better return on their investment.

A thoroughbred from sprinting lines could be raced around twelve months earlier than a horse bred for distance running (a stayer), which made it cheaper to train a yearling for its first race and more lucrative to breed one to sell.

Add to that significantly higher prize money for two-year-old races – and we can understand why breeders all over the world wanted foals with sprinting bloodlines.

The genetics of speed

In the 1980s, when researchers tested a selection of champion racehorses competing racing distances under one mile and a quarter, they found that those horses had significantly higher proportions of fast-twitch fibres when compared to horses racing distances of 2400 to 3000 m. 

We now know that speed and stamina traits in horses have a genetic component associated with variants on the Myostatin gene.

  • Sprinters have the C:C genotype, which causes horses to develop more fast-twitch muscle during training and up to 12% more muscle mass on the body.
  • Stayers have the T: T variant and are born with a higher proportion of lean, flat slow-twitch muscle fibres and endurance traits for racing over long distances.

Today in Australia and New Zealand, only 7% of racehorses have staying (T: T) bloodlines, while almost 50% have the (C:C) sprint genotype.

Inbreeding is linked to muscle disease

By selectively breeding a large proportion of racehorses for traits that are desirable (like short-term sprinting power), we have put thoroughbreds and breeds that utilize their bloodlines (like Quarter Horses and Warmbloods) at risk of a number of heritable diseases.

Quarter Horses share the same MTSN variations as sprinters (this explains why they often look very similar) and are affected by a number of heritable muscle diseases caused by selective breeding for preferable muscle phenotypes.

Horses related to the bulky stallion Impressive are often affected by the painful and often fatal disease hyperkalemic periodic paralysis (HYPP), a disease that has never been observed in horses which are not descendants of his line.

A recent study on tying-up syndrome in Thoroughbred racehorses found a correlation between increased inbreeding and the prevalence of PSSM.

Thoroughbreds are also prone to debilitating conditions such as bone fracture and tendon injury and exercise-induced pulmonary haemorrhage, many of which are thought to have a genetic basis.”

A recent study on tying-up syndrome in Thoroughbred racehorses found a correlation between increased inbreeding and the prevalence of PSSM

A 2008 paper showed that more racehorses made it to the starting gate in 1968 than they did in 2008. Even with all the advances in science made over the past half-century, fewer racehorses today make the grade, and those that do, retire prematurely more frequently than horses forty years ago. (Thiruvenkada, 2008).

The changing face of the thoroughbred racehorse

Just like human runners, there have always been thoroughbreds born with more pronounced muscles which make them better suited to sprinting, while others were better suited to mid or long-distance racing, born with flatter, leaner muscles that could produce a continuous effort for longer.

Speed, stamina and distance-aptitude have always varied considerably within racehorses. But during the last two decades, the focus has been concentrated on speed alone.

In the 1700s, thoroughbreds were bred for endurance. Many of the early races were longer than nine furlongs, often with obstacles, so stamina was essential.

When a team of British researchers tested the DNA of thoroughbred stallions from that period (including the great Eclipse, who raced between 1769 and 1770), they discovered that every single one of them was a stayer type with the T: T variant.

At the end of the 19th century when race distances were shortened, breeding trends started to shift.

Where did all the stayers go? 

Stayer-thoroughbreds are generally taller, leaner and have longer limbs than sprinters. Good examples of this type can be found in Phar Lap or Makybe Diva.

They need more time to mature and develop than other types of racehorses, which puts them at odds with today’s fast-paced racing industry and its emphasis on producing yearlings that can bring in as much money as quickly as possible.

Stayers are bred for longer-term soundness and stamina. After finishing a career in flat racing, they often move on to compete in jump races before getting snapped up as eventers or hunters when they retire. Top eventers like Clifton Promise, the horse who won Badminton with Jock Paget, and Andrew Hoy’s Moonfleet, were from stayer lines.

Genetically, this phenotype of thoroughbred has a longer, higher neck to counter their body’s downhill effect on the forelimbs. They make powerful gallopers because they can shorten the body’s recoil length and lighten the forequarters with each enormous stride they take. Due to a high ratio of slow-twitch muscle fibres, they can outlast shorter striding rivals with their extraordinary stamina and endurance.

Sadly, there are not many stayers around anymore. And this is a problem not only for the racehorse industry but also for riders competing in eventing, hunting and showjumping.

There have always been thoroughbreds born with more pronounced muscles which make them better suited to sprinting, while others were better suited to mid or long-distance racing. Image Shutterstock.

Mighty muscles with Cinderella’s ankles

Like racing Quarter Horses, sprinters possess impressive strength that allows them to gallop with a compact stride to counterforce the impact of the ground underneath. Good examples of this conformation include Black Caviar and Takeover Target.

This type of horse typically has a flatter profile while galloping, a lower head carriage and a shorter neck, which pushes significantly more weight onto the forelimbs to move the centre of gravity forward. These horses are designed for turf-running as their strong muscle fibres encourage a compact stride, which counterforces the impact of the ground underneath.

Unfortunately, a sprinter’s muscle fibres tire quickly. Unlike horses bred for distance, their energy levels cannot be replenished during a race; thus, the depletion of power occurs quickly, putting them at a high risk of muscle fatigue, bleeding of the lungs and injury.

Racing Quarter Horses have a similar conformation and muscle fibre composition to sprinters, yet they have a lower incidence of injuries such as bowed tendons (the injury that curtailed Northern Dancer’s career). This could be explained by training and racing regimes.

Quarter Horse trainers believe that too much training will slow a sprinter down, and this theory may have some scientific basis: Quarter Horses are trained and raced over distances that closely mimic the naturally evolved “flight” behaviour of wild horses, namely, short distances that would be covered when escaping a predator.

Avoidable injuries and premature retirement 

Trainers often prepare racehorses bred for sprinting for the wrong distance, either as long-distance runners, or even jump racing candidates. The result is often catastrophic injury.

Sprinters, due to their muscle composition, are quick to fatigue compared to thoroughbreds selectively bred for stamina. If a jockey ignores this and pushes him to keep galloping anyway, eventually, the horse’s limbs will simply stop functioning properly, causing him to stumble, lose balance or fall instead of successfully negotiating the hurdles in front of him. This is the reason many injuries in racing occur at the later stage when the horse succumbs to the effects of fatigue and lactic acid accumulating in his muscle fibres.

Thoroughbreds with a high proportion of slow-twitch muscle fibres (stayers) have a better chance in these races since they have been selectively bred to be able to retain a reasonable level of aerobic fitness over distances.

A study by Animal Aid of the 11 equine fatalities at the four-day 2006 Cheltenham Festival shows that every one of the victims came from flat racing bloodlines. The same was true of the two horses that died at the 2006 three-day Aintree meeting.

Sprinters suffer from a higher-than-normal incidence of stress fractures and soft tissue injuries due to their heavy muscling and galloping style (which often puts more weight on the forehand).

Minor injuries are often misdiagnosed, and complications develop when young horses with unrecognized microfractures are given drugs to allow them to race. When they cant feel the pain, they gallop on weakened, unhealed bones. A study of two- and three-year-old racehorses euthanized due to catastrophic fractures during racing found that 77% of the horses had evidence of pre-existing stress fractures at necropsy.

A thoroughbred stallion walking in hand. Nowadays, with stallion shuttling a common practice, instead of breeding with a maximum of forty broodmares a year, a popular stallion might father as many as 300 foals in one year.

Northern Dancer had his career cut short by injury and according to ProPublica’s investigation, was under the effect of the diuretic Lasix on the day he won the Kentucky Derby. Outside of America, the medication is banned on race days. The investigation found that Northern Dancer, like many sprinters, suffered from bleeding (Exercise Induced Pulmonary Hemorrage EIPH). Findings from an Australian research project suggest EIPH may have a genetic component.

Genomic science technologies can help return genetic variability

While paper pedigrees only track (often inaccurate) documented relationships, genetic coefficient testing of parentage and inbreeding is an accurate way to measure the proportion of inbreeding in a horse’s DNA.

The widespread use of genomic-based monitoring may be our best hope in preventing a worsening of inbreeding in the thoroughbred population, and further loss of genetic variability.

Testing mares and stallions can help breeders make informed decisions and avoid mating closely related horses, reducing the odds of genetic diseases being passed down the line while slowing and reversing the negative effects of inbreeding.

We all know that injuries and breakdowns occur when young horses are pressured to perform when they are not physically ready or suffering from fatigue, and while there have always been risks present in the racing industry, these risks are amplified when racehorses bred to excel at sprinting are forced to compete over distance and vice versa.

Every thoroughbred is born with a specific blend of strengths and weaknesses, which vary depending on conformational factors inherited from the parents, and ultimately determine their success on the track and afterwards; with genomic testing, we can prevent wastage by working out the genotype of a foal (stayer or sprinter) to begin training at the right time in alignment with their developmental and physical capabilities.

Scientific contributions from the last decade have provided us with the means to understand horses like never before. As public understanding and concern for horse welfare grows, so does the need for improved education in genetic science, sustainable breeding and ethics. With advances in technology occurring almost daily, we no longer have an excuse not to use science to improve our horses’ lives and the sustainability of the horse sector.