Study Connects Rise in Inbreeding to Larger Books

A 2011 study showing an increase in inbreeding in the Thoroughbred during a 45-year period from 1961-2006 also concluded the majority of the increase occurred during the last 10 years of the study period—a time coinciding with a sharp rise in the number of stallions being bred to books of 100 mares or more.

Dr. Matthew Binns was the lead author of the study "Inbreeding in the Thoroughbred horse" that appeared in a June 2011 edition of Animal Genetics. The genotyping of 467 Thoroughbreds born between 1961-2006 showed an increase in the average inbreeding coefficient. More significantly, the study notes, the majority of the increase occurred during 1996-06, when the number of North American stallions breeding 100 or more mares in a given season rose from 14 to 128.

In 1996, 14 North American stallions covered 100 mares or more. Only five years earlier only one stallion—Alydar—had bred a book of mares exceeding 100.

"My conclusion was that the data was showing the start of a trend that could become worrisome and needed monitoring," Binns told BloodHorse. "It was starting to show this increase as a result of the big books."

The first U.S. stallions to cover 100 mares in a season was Calumet Farm's Secreto in 1987 and Alydar in 1991. By 2006, the North American stallions covering books of 100 or more mares represented 3.8% of 3,992 active stallions. The number of active stallions began tumbling in 2008 on the heels of the Great Recession and by 2018 was down to 1,214. The percentage of stallions covering books of 100 mares or more rose, however, to 7.4%. The percentage of stallions covering books of 125 or more mares also increased to 5.1% in 2018, up from 4.5% from 2015-17.

"It is worrisome that the increase in inbreeding that we observe is there, not spread out over a 40-year period, but is concentrated in the period following the dramatic changes made to breeding practices in the mid-1990s," the study states. 

The study's conclusions also noted that the loss of genetic diversity observed is not excessive but still found the sharp rise over the 10-year period a concern.

"In a population, horses span the whole range (by inbreeding coefficients)," said Dr. Ernie Bailey, a geneticist at the University of Kentucky's Maxwell H. Gluck Equine Research Center and a co-author of the study. "There is not a profound change in the population and there is no one inbreeding coefficient, it depends on the individual and it could be 5%, it could be 20%. The average is going to be 11%. The news is that there is a trend, not the precise value."

Inbreeding in itself is not a problem, said both Bailey and Binns.

"When you have a closed population and you are selecting for some trait and trying to get rid of the genes that don't contribute to that trait, the result is a loss of diversity," Bailey said. "That involves inbreeding. You admire the performance of this ancestor so you try to increase the genes from that ancestor into your current generation.

"We fully expect, if we are doing a good job with selection, that we are going to decrease diversity and increase inbreeding. If you don't see that, then you are wasting your time," he continued.

The important caveat, according to Bailey and Binns, is that breeders must be vigilant in identifying any deleterious traits and work to eliminate them in their breeding programs.

"Animal breeding is a two-edged sword. You are increasing the genes you like but you can also inadvertently pick up genes that are deleterious, that could be reflected by some loss in fitness," Bailey said.

"In the real world, you have recessive mutations that are deleterious and harmful and that inbreeding increases the chances of them finding one another and giving you a problem—a disease or unsoundness," Binns added.

Increased inbreeding can produce a number of negative effects, of which a common one is low conception rates. Binns said reproductive depression is particularly hard to spot in Thoroughbreds because a period of substantial improvements in veterinary reproductive medicine has occurred parallel to the rise in book sizes.

"Those could cancel each other out," Binns said.

The study also suggests that the Thoroughbred gene pool may include genes related to unsoundness, as indicated by the decline in averages starts per foal, which was documented in an analysis done by BloodHorse in 2008. The BloodHorse study showed the average starts per foal dropped 35.6% from 20.42 for foals born in the 1970s to 13.15 for foals born in 2000-03.

"Unfortunately, we know in this business that unraced mares go to breed because they have good pedigrees," said Binns. "In some cases they are unraced because of accidents, but in others they are unraced because they had some soundness issues, yet they still go into the breeding pool."

Concerns about the trend toward increased inbreeding and the potential for increased exposure to genetic problems moved The Jockey Club board of stewards to propose Sept. 6 that stallion book sizes in North American be capped at 140 mares. The decrease in the number of mares bred along with the increase in mares bred to a select group of stallions is "signaling a worrisome concentration of the gene pool," the stewards stated in an announcement calling for comments on the proposed rule change.

By limiting book size, the stewards' hope is that the mare population will get bred to a more diverse group of sires.

Binns said The Jockey Club proposal seemed "like a reasonable place to land."

"You are cutting the big books back a little bit, which means other stallions get more of a chance and that makes the genetic diversity in the breed a bit better," he said. "It is complicated, and you can make convincing arguments on both sides. The sensible route forward would be for someone to update the study I'd done and see if the increase in inbreeding has continued on the same trajectory. If it has, then you can use that as part justification to say, 'We think we are going to run into a problem, so we should anticipate it.'"