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

Northern Dancer - small in stature but a giant among thoroughbreds

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THIS ARTICLE FIRST APPEARED IN EUROPEAN TRAINER - ISSUE 46

Maryland - can slots solve the problem?

By Sean Clancy

It's come to this. The Maryland racing industry starts and ends at the same place, the same date, the same issue – the voters' booth come November. The slots referendum – the denouement – will decide once and for all whether Maryland will attain slots to help staunch the losses of horses, horsemen and handle to neighboring states.

The once storied tradition of Maryland racing has come to this. The slots uncertainty has replaced all that was Maryland racing – the spectacle of the Preakness, the buzz of the Maryland Million, the hype of the renovated dirt and turf courses at Laurel Park, the history of Sagamore and Windfields Farm and the legacies of Northern Dancer and Native Dancer. Today, ask anybody about Maryland racing and it goes no further than the slots referendum in November.

Destined to put 15,000 slot machines in five sites across five counties, the bill could generate up to $700 million in state tax revenue and pump nearly $100 million into the racing industry. Presently, the annual purse structure at Pimlico and Laurel taps out around $33 million. The numbers are complicated – a percentage goes to Standardbreds, another part goes to the Maryland breeders, some goes to facility improvements –  but any direction it's doled, the passage of the slots bill remains paramount to Maryland racing.

If there's a one-word answer to why Maryland remains in the throes of the slots woes, it's politics. The slots bill has been locked in dispute in Annapolis for over a decade. First there was Governor Paris Glendening's "No Slots" manifesto. Then Governor Bob Ehrlich's tepid endorsement of the slots bill was basically declared a non-starter. Gridlock on the Beltway has had more wiggle room. Finally, Governor Martin O'Malley decided, it's up to the voters. Yes or no. What's it going to be, yes or no?

That's when the 12-year odyssey to land slots in the state will come to a head. Vote yes, and Maryland racing receives a life rope. Vote no, and it slips further into oblivion behind states with slots-induced purses. Worst of all, the waiting game will finally be up and owners, trainers, breeders who have been hanging on will wait no longer. Pack your bags, this bus is leaving.

"I'm in the same spot as a lot of people are, hoping that come November something good happens for us," said trainer Mike Trombetta, who led all trainers last year in percentage at the major Maryland meets of Pimlico and Laurel. "We can start aiming in the right direction again. My worst fear is what would happen if November doesn't go well."

Richard Hoffberger, the president of the Maryland Thoroughbred Horsemen's Association, knows what will happen. He's represented horsemen throughout this maze of inefficiency.

"If it doesn't pass now, the people in Delaware Park, Philadelphia Park, Charles Town, they're going to break out the champagne," Hoffberger said. "We'd still have some semblance of a race meet but you've got no horses around here, I mean it's bad here. The racehorse business in Maryland sucks."
 
There was a time when Maryland's product towered above Delaware, Charles Town or anything offered in Pennsylvania. Those days are over.

At Laurel Park on a recent Thursday, the first race, a $25,000 claimer for 3-year-old fillies running for a $24,000 purse attracted three horses. The second for $10,000 claimers collected five runners. It didn't get much better through the rest of the card – 59 horses competed in nine races. It's not a titillating product. Turf racing on Laurel's state-of-the-art turf course will jump start the product in the spring and the Preakness build-up will invigorate the scene at least for a week in May. But there are fundamental flaws which damage the vibrancy of racing. Pimlico, the second oldest track in the country, remains decrepit and Laurel Park's facility is only marginally better. Laurel closes for much of the summer when the Colonial Downs meet in Virginia begins, leaving the turf course dormant for some of the most viable days of the year. The Maryland Jockey Club operates Bowie as a training center, adding to the accounts payable side of the ledger.

But still it's Maryland – the best racing state in the Mid-Atlantic area. They don't run the Preakness in Pennsylvania. The Washington D.C. International wasn't run in West Virginia. It's not the New Jersey Million, it's the Maryland Million. Bernie Bond didn't call Delaware home.

But here it lies in limbo – like a transplant patient, waiting for the call. The slots bill has tantalized horsemen in Maryland for over a decade. The jackpot has always been a house bill or a vote or a referendum away. Like teasing a Labrador Retriever with a tennis ball. Pumping up your racing product with slot money doesn't necessarily offer a palatable solution, but a necessary one when neighboring states Delaware, Pennsylvania and West Virginia employ slots to raise money for their racing product. They have forced the issue. Bigger purses across state lines create an exodus for horsemen and horses. It hasn't been a mad dash but more of a Chinese water torture as horsemen have moved in search of the almighty dollar. And that's a credit to Maryland horsemen, most have hung in there like they're defending the Alamo.

High-profile trainers such as Graham Motion, Tony Dutrow and Tim Ritchey have already taken that bus route off the Maryland racing circuit. Trainers who used to stick around Laurel Park for the winter now venture to other circuits like Oaklawn Park or Tampa Bay Downs. It's one thing to go to Gulfstream Park, but now they flee for tracks that used to operate well below Laurel's par.

"Aww, it's horrible," Trombetta said when asked what it was like to watch his state falter. "We went through this exercise every year for I don't know how many years now, and the best the legislators could come up with is to basically tell the voters, ‘Ah heck, you guys decide on this.' It's definitely frustrating."

Maryland's purse structure has slipped behind neighboring states. The slots-induced purses in West Virginia, Delaware and Pennsylvania have sapped Maryland's pool of horses. In a state that was renowned for its horsemen – the year-round lifers who trained a string, utilized a farm and bled Maryland are waning. Some stick around because they like the lifestyle, they own that farm and they keep thinking "one of these days..." Horsemen like Dickie Small, Larry Murray, Ann Merryman, Jimmy Murphy; they represent the old-school Maryland mystique. Then there are prolific number runners like Dale Capuano, Scott Lake, Ben Feliciano Jr. and Trombetta who win consistently wherever they go but stay despite the purses. How long any of them will last is the question and threat. If the bill in November fails, start crossing off the calendar blocks.

Hoffberger has lived the slots debate, from the time he and former Maryland Jockey Club president Joe DeFrancis stood up in front of the media at Pimlico Racecourse and tried to choreograph the impact slots could have on racing. That was three governors, one DeFrancis and countless horses and horsemen ago. Still no slots.

"The referendum is the big story," Hoffberger said. "If it passes, we should be in halfway decent shape. If it doesn't pass...we're a small-time market."

But will it pass?

Right now the proponents of slots are on the lead while the opponents lag about 20 points behind. But read the form.

"The anti-slot people are come-from-behind runners, and you've got to be at least 20 points ahead, because they'll come get you at the end," Hoffberger said. "We're about 20 points ahead now. What's that mean? It's almost a photo."

Most horsemen who were originally against slots have long since hugged the monster. Have a better plan to balance Maryland's budget shortfall? Another way to inject some life into to Maryland's racing and breeding industry? Think the lesser of all evils.

"We're competing with the state – the state's running a lottery system. We're competing with casinos in New Jersey that are funding purses to the tune of $25 million a year. We're competing with Delaware Park, with Pennsylvania, with West Virginia," Hoffberger said. "Is it the answer? No. But if you want to run a track meet, having a good pair of shoes is not the only answer, but if you don't get dressed up, you don't have a chance."

Breeders in the state continue to dress up, surviving on tradition and striving for change. Northview Stallion Station, near Northeast, continues to churn out winners with a stallion brigade led by Not For Love and Two Punch. The Pons family's Country Life Farm survives, despite being nearly engulfed in urban sprawl, ducking and jiving in search of the next Malibu Moon who will reach across state lines. Don Litz has led a small group of investors in the development of Maryland Stallion Station which houses eight regional stallions. Allen and Audrey Murray guide their family-oriented operation, Murmur Farm; the couple hit the jackpot buying and quickly selling Our Emblem, in middle of the firestorm created by War Emblem's victories in the Kentucky Derby and Preakness.

Dr. Tom Bowman of Northview sees a much bigger picture than just slots at racetracks.

"The whole thing is highly disappointing, but not surprising," Bowman said. "It runs much deeper than just the demise of the racetracks, it symbolizes a radical change in our state and the philosophy on our state's well being. We're no longer a state that sees agriculture as important. Most of the states that approved slots recognized the value of keeping their state an agricultural state and saw horse racing as a way to protect rural land and agriculture."

There's the rub, it's hard to convince politicians and citizens that open spaces actually keep taxes lower and slows the expense account. The more houses that grow in the fields, the more tax money needed to supply police, roads, education and everything required to keep a society moving.

"Several of my children work with me and the future isn't too bright for them in this state," said Bowman, who served as the president of the Maryland Horse Breeders. "With a magic wand, they can affect racing. Look at Penn National, they're up and running again and you're seeing some big-name trainers run there. But when you try to sell the slots legislation in this state, the open spaces, the agriculture, the horse racing, it means nothing to the politicians and their constituents. They can't comprehend how it's going to affect them."

All the Maryland breeders operate under the encroaching shadow of neighboring states' breeders incentive programs. Breeding

a Maryland-bred doesn't hold the same appeal as it once did. Pennsylvania, West Virginia, even a Delaware-certified program has leached some of Maryland's prominence.

Northview made the first tangible step to develop in other states, breaking ground on a division in Pennsylvania. Right now, yes, they're still tried-and-true Maryland but it's not unfathomable to think of them as one day being pure Pennsylvania.    "Northview is a little bit of an enigma because we have a couple of stallions that reach across state lines," Bowman said. "For two years we set a record of mares bred in Maryland but we noticed where the mares were coming from and where they were going. You have to be where the business is, we moved 30 miles up the road and the economic picture is grossly different. I don't like it but you can't be an ostrich."

Trombetta makes up another high-profile trainer moving into Fair Hill Training Center, one of the few thriving Thoroughbred entities in the state. The sprawling spread in the northeast corner of the state struggled to hold its own for years. Now it's booming. Prominent owner Earle Mack recently purchased two barns. Rick Porter of Fox Hill Farm purchased a barn site, flattened the existing barn and will place Larry Jones (of Hard Spun fame) there this spring. Tickets to Fair Hill Steeplechase Meeting are sold out.

Trombetta owns a small farm in Maryland, will train at a training center in Maryland, and will have horses at Laurel in Maryland. That's how committed he is to the state, but he also had horses at Gulfstream this winter, will have horses stabled at Delaware and will race his nearly 100 horses all over the East Coast.

"For me Maryland is home. It's where I grew up, where I came around the racetrack. It's got a long-standing history

and tradition. The Preakness is very nice and all, but it's more than just the Preakness," Trombetta said. "It's everybody in the industry in Maryland. But it's struggling. First the breeders, now the racehorses stables are the next ones to go. This thing is very much changing and evolving, and you've kind of got to roll with the punches as you go."

Trombetta has accepted that sometimes you have to dance with the devil.

"I'm not a big fan of the slots, but unfortunately it's the money that keeps everything rolling," Trombetta said. "When your competitors have that asset and you don't, you don't stand to stay at it very long."

See you in November.