Dangers of inbreeding and the necessity to preserve sire lines in the thoroughbred breed

Inbreeding is the proportion of the genome identically inherited from both parents.

Inbreeding coefficients can be estimated from pedigrees, but pedigree underestimates the true level of inbreeding. Genomics can measure the true level of inbreeding by examining the extent of homozygosity (identical state) in the DNA of a horse. A mechanism to examine genomic inbreeding for breeding purposes has yet to be developed to be used by all breeders but once available, it must be considered as a tool for breeders.

Breeding of potential champion racehorses is a global multi-billion sterling or dollar business, but there is no systematic industry-mediated genetic population management.

Inbreeding in the modern thoroughbred

The thoroughbred horse has low genetic diversity relative to most other horse breeds, with a small effective population size and a trend of increasing inbreeding.

A trend in increased inbreeding in the global thoroughbred population has been reported during the last five decades, which is unlikely to be halted due to current breeding practices.

Ninety-seven percent of pedigrees of the horses included in a recent study feature the ancestral sire, Northern Dancer (1961); and 35% and 55% of pedigrees in EUR and ANZ contain Sadler’s Wells (1981) and Danehill (1986), respectively.

Inbreeding can expose harmful recessive mutations that are otherwise masked by ‘normal’ versions of the gene. This results in mutational load in populations that may negatively impact on population viability.

Genomics measured inbreeding is negatively associated with racing in Europe and Australia. The science indicates that increasing inbreeding in the population could further reduce viability to race.

In North America, it has been demonstrated that higher inbreeding is associated with lower number of races. In the North American thoroughbred, horses with higher levels of inbreeding are less durable than animals with lower levels of inbreeding. Considering the rising trend of inbreeding in the population, these results indicate that there may also be a parallel trajectory towards breeding less robust animals.

Note that breeding practices that promote inbreeding have not resulted in a population of faster horses. The results of studies, generated for the first time using a large cohort of globally representative genotypes, corroborate this.1,3

Health and disease genes

It is both interesting and worrisome to consider also that many of the performance-limiting genetic diseases in the thoroughbred do not generally negatively impact on suitability for breeding; some diseases, with known heritable components, are successfully managed by surgery (osteochondrosis dessicans, recurrent laryngeal neuropathy, for example), nutritional and exercise management (recurrent exertional rhabdomyolysis), and medication (exercise induced pulmonary haemorrhage). This unfortunately facilitates retention of risk alleles in the population and enhances the potential for rapid proliferation of risk alleles if they are carried by successful stallions.

Types of inbreeding

Not all inbreeding is bad. Breeders have made selections for beneficial genes/traits over the generations, resulting in some inbreeding signals being favoured as they likely contain beneficial genes for racing. Importantly, examination of a pedigree cannot determine precisely the extent of ‘good’ and ‘bad’ inbreeding. This can only be determined from DNA analysis.

Historic inbreeding (arising from distant pedigree duplicates) results in short stretches of DNA identically inherited from sire and dam. 

• This may be considered ‘good’ inbreeding.

• It has no negative effect on racing.

• The horse may be carrying beneficial mutations that have been maintained from distant ancestors through breeders’ selection.

Recent inbreeding (arising from close pedigree duplicates) results in long stretches of DNA identically inherited from sire and dam. 

• This may be considered ‘bad’ inbreeding.

• It is negatively associated with racing.

• The horse may be carrying harmful mutations that have not yet been ‘purged’ from the population.

Obviously, in terms of breeding, it’s always possible to find examples and counterexamples of remarkable individuals; but the science of genetics is based on statistics and not on individual cases.

Sire lines

Analysis of the Y chromosome is the best-established way to reconstruct paternal family history in humans and animal species. The paternally inherited Y chromosome displays the population genetic history of males. While modern domestic horses (Equus caballus) exhibit abundant diversity within maternally inherited mitochondrial DNA, until recently, only limited Y-chromosomal sequence diversity has been detected.

Early studies in the horse indicated that the nucleotide variability of the modern horse Y chromosome is extremely low, resulting in six haplotypes (HT). However, this view has changed with the identification of new genetic markers, showing that there is considerably more genetic diversity on the horse Y chromosome than originally thought. Unfortunately, in thoroughbreds, the male gene pool is restricted, with only three paternal lines remaining.

The Institute of Animal breeding and genetics of the Veterinary Medicine School at Vienna applied fine-scaled Y-chromosomal haplotyping in horses and demonstrated the potential of this approach to address the ancestry of sire lines. They were able to show the microcosmos of the Tb-clade in the thoroughbred sire lines. 

It is interesting to note that more than half of the domestic horses in the dataset (76 of 130) have a Y chromosome with a thoroughbred ‘signature’. These includes thoroughbreds, standardbreds, many thoroughbred-influenced breeds (warmbloods, American quarter horses, Franches-Montagnes, a Lipizzan stallion and the Akhal-Tekes).

The General Stud Book shows that thoroughbred sire lines trace back to three founding stallions that were imported to England at the end of the 17th century. 5 Now, the heritage of the thoroughbred sire lines can be better understood using Y chromosome information. It is now possible to clearly distinguish sublines of Darley Arabian, born in 1700 (Tb-d) and Godolphin Arabian, born in 1724 (formerly Tb-g, now Tb-oB3b). The third founder, Byerley Turk, born in 1680, was characterised by the Tb-oB1 clade. According to pedigree information, only few of the tested males trace back paternally to Byerley Turk, which are nearly extinct.

There are now 10 different Y chromosome sub-types known in the thoroughbred. Two come from the Godolphin Arabian, five come from Byerley Turk, and three come from Darley Arabian.

Even if genetic analysis shows that there was an error in the stud book recording of St Simon’s parentage and that horses descending from St Simon should be attributed to the Byerley Turk lineage, probably 90% of the current stallions are from the Darley Arabian male line. So, there is a true risk that we could lose a major part of the Y chromosome diversity.
Conclusions and solutions

We should do everything we can to ensure that thoroughbreds are being sustainably bred and managed for future generations. With the breeding goal to produce viable racehorses, we need to ask ourselves, are we on track as breeders? 

If inbreeding is negatively affecting the chances of racing and resulting in less durable racehorses, will this continue to affect foal crops in the future? How can we avert the threat of breeding horses that are less able to race? If the ability to race is in jeopardy, then is the existence of the thoroughbred breed at risk? 

International breeding authorities are studying the situation and thinking about general measures allowing the sustainability of the breed.

Breeders

What can individual breeders do to produce attractive foals that are safe from genetic threats? How do you avoid the risk of breeding horses that are less fit to race? 

There is no miracle recipe, and each breeder legitimately has his preferences.

An increasingly important criteria for the choice of a stallion is his physical resistance and his vitality, as well as those of his family. It is often preferable to avoid using individuals who have shown constitutive weaknesses, or who seem to transmit them.

The use of stallions from different male lines can make it possible to sublimate a strain and better manage the following generations. The study of pedigrees must exceed the three generations of catalogue pages.

In the future, genomics—the science that studies all the genetic material of an individual or a species, encoded in its DNA—will certainly be able to provide predictive tools to breeders. This is a track to follow.

Trainers

Trainers should be aware of the danger of ‘diminishing returns,’ where excessive inbreeding occurs. Today, when animal welfare and the fight against doping are essential parameters, it is obvious that trainers must be aware of the genetic risks incurred by horses possibly carrying genetic defects.

Together with bloodstock agents, trainers are the advisers for the owners when buying a horse. Trainers already know some special traits of different families or stallions, but genomic tools might become essential for them too.

Sources

1. Genomic inbreeding trends, influential sire lines and selection in the global Thoroughbred horse population Beatrice A. McGivney 1, Haige Han1,2, Leanne R. Corduff1, Lisa M. Katz3, Teruaki Tozaki 4, David E. MacHugh2,5 & Emmeline W. Hill ; 2020. Scientific Reports | (2020) 10:466 | https://doi.org/10.1038/s41598-019-57389-5

2. Inbreeding depression and durability in the North American Thoroughbred horse Emmeline W. Hill, Beatrice A. McGivney, David E. MacHugh; 2022. Animal Genetics. 2023;00:1–4. _wileyonlinelibrary.com/journal/age

3. Founder-specific inbreeding depression affects racing performance in Thoroughbred Horses. Evelyn T. Todd, Simon Y. W. Ho, Peter C. Thomson, Rachel A. Ang, Brandon D. Velie & Natasha A. Hamilton; 2017. Scientific Reports | (2018) 8:6167 | DOI:10.1038/s41598-018-24663-x

4. The horse Y chromosome as an informative marker for tracing sire lines Sabine Felkel, Claus Vogl , Doris Rigler, Viktoria Dobretsberger, Bhanu P. Chowdhary, Ottmar Distl , Ruedi Fries , Vidhya Jagannathan, Jan E. Janečka, Tosso Leeb , Gabriella Lindgren, Molly McCue, Julia Metzger , Markus Neuditschko, Thomas Rattei , Terje Raudsepp, Stefan Rieder, Carl-Johan Rubin, Robert Schaefer, Christian Schlötterer, Georg Thaller, Jens Tetens, Brandon Velie, Gottfried Brem & Barbara Wallner; 2018. Scientific Reports | (2019) 9:6095 | https://doi.org/10.1038/s41598-019-42640-w

5. Identification of Genetic Variation on the Horse Y Chromosome and the Tracing of Male Founder Lineages in Modern Breeds Barbara Wallner, Claus Vogl, Priyank Shukla, Joerg P. Burgstaller, Thomas Druml, Gottfried Brem Institute of Animal Breeding and Genetics, Depart. 2012. PLOS ONE | www.plosone.org  April 2013, Volume 8, Issue 4, e60015

6. New genetic evidence proves that the recorded pedigrees of the influential leading sires Bend Or and St. Simon were incorrect. Alan Porter; ITB 2021

7. Eight Belle’s breakdown: a predictable tragedy William Nack; ESPN.com 2008

8. Suzi Prichard-Jones: Founder of "The Byerley Turk & Godolphin Arabian Conservation Project"

Special thanks to Emmeline Hill for her help in the completion of this article

Jérôme Reynier - The French horseman’s pathway to success

Article by Katherine Ford

Take a look at the French trainers’ standings in September, and hot on the heels of the Classic powerhouses of Rouget, Fabre and Graffard in fourth place was Jérôme Reynier. Based in his native Marseille, still a couple of years shy of his 40th birthday, the discreet yet determined professional has climbed step by step to racing’s top table, and his ascension is far from over. 

I met Reynier at Deauville during the August meeting and interrupted his breakfast with half a dozen staff. “We have a family atmosphere and a good relationship. I’m not a difficult boss, but if there are decisions to be made, that’s my job. I don’t want anyone else to take initiatives without consulting me first. That’s why I’m always available in case there’s a problem,” Reynier admits.

What is striking with Reynier is an attention to detail, whether that be in the organisation of his training regime, his assiduous desire to answer any queries from any quarters, or his true passion and almost encyclopaedic knowledge of bloodstock and racing. Going back to the origins of his love of racing, he explains, “I caught the virus from my father who was an architect but passionate about racing and breeding. I was born in 1985, and that was the year that he bred his first horse, called Shaindy.” 

Reynier goes on to recount in great detail the destiny of Shaindy, who was bought back as a yearling and ended up Group-placed as a juvenile and winner of the then Listed Prix Djebel. It is easy to forget from the vividness of the description that at the time he was still in nappies and has no direct memories of the time. “It was magical, for a first homebred, carrying my grandfather’s colours. That caused a snowball effect with my father who bought more mares. He was lucky, but then you make your own luck.” 

Learning the trade

Just a few years later Reynier’s father sold all his burgeoning thoroughbred interests when his son was still too small to remember, in order to devote more time to his wife and family. 

However, the marriage broke down and his son remembers, “My parents separated when I was 12, and I went to live with my father who took me to Deauville sales to see if I took to the bloodstock world. It was all new to me, but I loved it and thought of nothing else from then on. 

“At school, I put sales catalogues inside my textbooks; so during lessons I was engrossed in the pedigree pages. I had never touched a horse in my life—my experience all came from books as there wasn’t even [French racing channel] Equidia at the time.”

At 15 years old, Jérôme Reynier had his first hands-on experience during a summer at Alain Brandebourger’s Haras de Chartreux, and the following summer his father sent him to Newmarket to learn English. “I spent two months with David Shekells at Old Mill Stud. He had two yearlings for Deauville sales, but I was only tiny and not strong enough to hold a yearling weighing 400kg. They were both monsters—a Nashwan and an Unfuwain—so my job for two months was to walk behind them to keep them moving forward. 

“Then during the journey from Newmarket to Deauville, I had to travel in the back of the horsebox at their heads all the way to stop them from fighting. It was a real test of my enthusiasm!”

Full marks for effort

Jérôme passed the test with flying colours, and his enthusiasm remained intact, more so than his academic career, which suffered from his obsession with thoroughbreds. “I failed my Bac [baccalauréat], and things weren’t easy then as I had no qualifications, contacts or references. When I went to the races at Deauville, I didn’t have access to any of the reserved areas; I saw racing as a very closed environment. For me, it was unattainable. During that summer, I worked at the Forien’s Haras de Montaigu to prepare the yearlings. After that, I applied to do a season at Coolmore, and they took me on from January to June in 2005; so I went to Ireland and passed my Bac as an external candidate.”

A fascination for pedigrees

Jérôme Reynier has stars in his eyes as he remembers his stint at Coolmore. “I worked in one of the small yards with barren or maiden mares, so there were no foals but some amazing pedigrees, and we took them to stallions like Sadler’s Wells, Galileo and Montjeu. I got to see the stallions and how the system worked. I was always more interested in the pedigrees and breeding aspect than the racing in the afternoon.” 

The Irish National Stud course followed in 2006 and while there, the determined and precocious Jérôme applied for and was accepted onto the Darley Flying Start programme. “I didn’t waste a minute!” he remembers. “In 2008 I was 22 years old and found myself with qualifications from the Irish National Stud and Darley Flying Start. The problem was that I was overqualified for my age. I needed work, but everyone considered that I was too young to take on the jobs in the breeding industry that I was qualified for. At the same time, my father fell ill so I went back to Marseille and as nobody would employ me, I set up my own business as a bloodstock agent. But I soon realised it was very difficult to earn a living without a large volume of trade. I knew a few people, but I didn’t have a network of clients. I was young and based in Marseille, so I didn’t tick the boxes…” 

It was therefore by default that Reynier began his successful training career, initially as a private trainer for the Ecurie Camacho Courses. “I was employed to train around 15 horses for them at Marseille, and in two years we had 38 winners and €800,000 in earnings with modest horses. It was a great way to start off, but after two years, I wanted my independence.” 

Starting from scratch

From four horses at the outset in March 2013, the ambitious professional soon made himself noticed and his stable grew. “I was getting good results, including in the Parisian region where I could find favourable entries and make a name for myself, rather than focusing on local races at Marseille. I’ve always tried to look beyond my immediate horizon. I had horses of a limited quality, but my passion was to find winnable races. I was back to what I loved—really hands on, mucking out in the morning, going to the track, driving the horses to races myself. I wouldn’t hesitate to make a long journey for a made-to-measure entry. I think that was the best period in my career as a trainer.” 

Reynier was hit hard by the untimely death of his father in November 2014 and doubled down to bury his grief in work, “to make him proud from where he is now.”

He was satisfied with his 40-capacity stable but in 2018 received a career-changing offer from powerful local owner Jean-Claude Seroul, whose orange and grey colours were a familiar sight in Marseille. They are now known far beyond, thanks notably to the exploits of prolific top-level winners Skalleti and Marianafoot.

Reynier took on the job as private trainer to Seroul’s 50-55 strong string, based just across the road from his own yard at the Calas training centre, 30km north of Marseille, “Mr Seroul has his own stable, his own horses and his own staff; it didn’t affect my own structure. They are two separate operations, and the strings don’t go out at the same time; so instead of having four lots with 30 riders in each, I have eight lots with 15 riders each time. It’s much more manageable as I like to give each rider precise instructions for including the exact position of every horse in each lot. All the details are indicated on the list, which is sent out the previous evening, and that organisation now allows me to delegate more; and for instance to spend the month here in Deauville where we have an allocation of 14 boxes and a rotation of horses. If we win six races here and a few places, it will be a good result.”

That August target was achieved with the highlight being a Listed victory for the Seroul-owned filly, Rose Premium.

Calas ticks all the boxes

The conversation moves back to Calas, described by Reynier as a “perfect” facility with a main 3km round track, which gives the opportunity to work left- or right-handed depending upon the day. It also offers an incline for interval training, as well as turf, sand and jumps schooling tracks. “We have all that we need, and the results are proof of that. I will never abandon Calas because it is a good training centre with a wonderful climate, and it allows us to create a very progressive programme for the horses. We all—Christophe Escuder, Fabrice Vermeulen and myself—like to run our horses as much as possible rather than over-train them, so we provide a lot of runners for the PMU. Our owners want to see their horses at the races, so as soon as the horse is ready, whatever his level, I find a race for him. I find the French programme clear and simple, with opportunities for all categories.”

Marseille was rocked in late 2021 as dawn raids saw three members of the Rossi family among several professionals taken into police custody under suspicion of the use of forbidden substances and conspiracy to defraud and fix races. Frederic, Cédric and Charley, who were responsible for around 150 horses at Calas, are currently suspended from training and under police investigation. Reynier comments, “It saddened me because I know Cedric and Charley (Rossi) well, and I am sure that they are not cheats. It’s been a tough time for the region to be in the spotlight for negative reasons, and there is also the risk that if we don’t generate enough runners for turnover on the PMU, they will reduce the number of races at our tracks.” 

The city’s best racecourse, seaside Marseille-Borély, is already under threat of closure and Reynier adds, “The lease has been extended until 2024. It’s perfectly situated for development, but it will be a disaster if it is lost; so that’s why it is important to keep an open mind geographically. I wouldn’t exclude creating a small satellite yard in Chantilly to start with to avoid too much travelling for some of the horses. Then why not extend the Chantilly stable to have two bases… But it is certain that the future lies in Paris, or maybe abroad.”

Plotting a path to success

Jérôme Reynier has always had the opposite of a blinkered approach and loves to see a well-made plan come to fruition, as his first stable star Royal Julius, winner of the inaugural Bahrain International Trophy, demonstrates. “When Bahrain created the new international race, the prize money was very generous. And the conditions were optimal for Royal Julius, who was a true right-hander who loved a fast surface and ten furlongs, so I set out to prepare and qualify him for that race. He needed to keep a high rating, so I sent him to Italy where it was easy for him to do well in Stakes company; whereas if I’d run him in a Gp. 3 in France and he’d finished fifth, his rating would have dropped and I would never have been invited there or to Qatar. He was a great horse for the stable, as was Master Spirit who was a “second hand” horse we received; and from being a handicapper, we managed to take second place in the Grand Prix de Deauville with him. I’ve been lucky to train some good horses, but it’s important to take good care of them to age well.” 

More recently, flag bearers Skalleti and Marianafoot have rewarded the patience and skill of their handler, along with Thunder Drum who joined Reynier for owner Lady Bamford. “It was particularly satisfying for me to receive beautifully bred horses for Lady Bamford and exceptional to win the Prix du Royaumont (Gp. 3) last year on Jockey-Club day with Thunder Drum, who couldn’t win a maiden in England as a juvenile. We had intended to run her in the Italian Oaks that weekend but made a last-minute change of plan due to a modest field and rain in Chantilly; and it worked perfectly! As for Skalleti and Marianafoot, they both had their best seasons last year at six years old, which is amazing. In fact, I was the leading French trainer on Gp. 1 wins, with the three victories of that pair. Cédric Rossi and André Fabre had two each!”

Prize money for happy owners and trainers

“We don’t have a star this year, but a lot of horses are earning their keep and that keeps the stable going. Take the example of Happy Harry, a son of Zarak that we claimed in January; in six months, he has earned €70,000 (the gelding boosted his earnings by a further €14,000 in prize money and owners’ premiums for a handicap win days after our interview). If I have 50 Happy Harrys, I’m happy! The French system makes this possible if you have a healthy horse who can run regularly. In England, if you have a decent horse, you either try and win some good races or you try the commercial route, win on the debut and then sell it on. It’s impossible to earn money with prize money in England, and I couldn’t train there. It’s a different policy. The French way of constructing a career is with a horse that might be just 80 percent ready for his debut and he will progress as he races. So, we can think of the long term rather than the short term. As long as we can keep our system in France with the PMU and decent prize money, we are privileged. We are the best country for racing in Europe or maybe in the world, but a whole generation of punters is on the way out, and I don’t see many young people betting on racing, so I often feel pessimistic.”

Despite his concerns, Jérôme Reynier is, as always, aware of upcoming opportunities and a changing of the guard, which may enable him to move even further up racing’s top table. “There is a whole older generation of trainers in Chantilly who are on the way out, so there will be opportunities. The new trainers who are there now and setting up soon will create a new dynamism. Maybe I will be a part of it and maybe I won’t…” 

One thing is certain, whatever Jérôme Reynier does or doesn’t become a part of will depend upon a carefully constructed plan, leaving little to chance and attracting more good luck his way.