Three hundred years of Thoroughbred breeding: Could we have done better?

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How have our breeding decisions impacted on the Thoroughbred?
How have our breeding decisions impacted on the Thoroughbred?

Three centuries of selective breeding has largely failed to improve the genetic lot of the Australian Thoroughbred, research suggests.

Scientists who conducted a major pedigree analysis concluded that selective breeding had not efficiently alleviated the Australian Thoroughbred of its genetic load, the term used to describe the presence of unfavourable genetic material in the population.

The Thoroughbred horse population is one of the largest closed animal populations in the world.

All Thoroughbreds trace their ancestry back to three paternal lines in Britain, due to the narrow bottleneck at the foundation of the population.

More than 300 years of breeding practices have produced signatures of selection in the 21st century Thoroughbred population, contributing to the superior athleticism of the breed.

However, at the same time, these practices have increased levels of inbreeding and reduced the genetic diversity of Thoroughbreds compared with other domestic horse breeds.

University of Sydney researcher Evelyn Todd and her colleagues looked at the pedigrees of 135,572 individuals, representing all Thoroughbred horses that had one or more race starts in Australia between 2000 and 2011.

A genealogy of these individuals, dating back to the founders of the population, was also included in their work.

Although some lines of pedigree were incomplete, they had comprehensive pedigree information for all individuals in the racing performance data set, which they said made their inbreeding estimates, calculated as a coefficient, highly accurate.

The availability of extensive pedigree records not only allowed them to study broad population trends over time, but to determine whether the selection for optimal racing performance had eased mutational load.

“We found that selective breeding practices have not increased the overall performance levels of the population over time,” the study team reported in the journal, Scientific Reports.

“However, we found evidence for purging in the population that might have improved racing performance over time.”

They found that more than 80% of inbreeding in the current population was accounted for by a small number of ancestors from the foundation of the breed.

“Inbreeding to these ancestors has variable effects on fitness, demonstrating that an understanding of the distribution of genetic load is important in improving the phenotypic value of a population in the future.”

The researchers said population bottlenecks that occurred during the ancestry of the Thoroughbred, including the domestication of the horse and the foundation of the breed, might have increased the frequency of harmful gene variants through genetic drift.

“It is also possible that continued inbreeding of the Thoroughbred population over the past 300 years has inadvertently increased the frequency of deleterious variants in the population.”

Based on the racing performance of the 135,572 contemporary individuals in the study, the researchers were able to calculate the estimated breeding values (EBVs) of all individuals in their pedigrees (257,249 horses).

The large increase in EBVs at the foundation of the population indicated that early selection events resulted in an initial jump in the frequency of favourable genes.

“After this initial increase, the distribution of EBVs remains constant; demonstrating that selective breeding from the early 19th century was not effective in improving the racing performance of the population.”

The level of Wright’s inbreeding co-efficient had increased constantly during this time, which led the researchers to conclude that inbreeding had not effectively removed mutational load from the population.

“This explains why we observe strong inbreeding depression (that’s reduced biological fitness in a given population) as a result of inbreeding persisting in the contemporary population.

“We expect that this is due in part to a change in racing and training regimes over time that, in turn, has changed selection pressures on the population.

“In the 18th and early 19th century, Thoroughbred races were held over a distance of several miles, with each horse participating in multiple heats on the same day.

“In the 20th century, focus shifted to breeding sprinters and early developers for two-year-old racing.”

The researchers said their study had presented the effects of inbreeding and selection in a very large population with extensive phenotypic and pedigree records.

“Our analyses have shown that genetic load can still persist in a population even after many generations of inbreeding. However, we have also found evidence that multiple generations of inbreeding for selection can have positive effects on the overall genetic value of a population.

“We suggest that using EBVs whilst managing inbreeding levels will increase the efficiency of selection to reduce inbreeding depression in subsequent generations.”

They said the evidence also suggested that genetic load was unevenly distributed in the Thoroughbred population.

“Understanding the distribution of genetic load in the population will assist in breeding decisions to reduce disease alleles and improve the overall fitness of the population in future generations.”

Their findings, they said, opened the possibility of evaluating the effects of particular individuals on the fitness of the population in order to improve the observable qualities of the breed and reduce genetic load in the future.

The study team comprised Todd, Simon Ho, Peter Thomson, Rachel Ang and Natasha Hamilton, all from the University of Sydney; and Brandon Velie, from the Swedish University of Agricultural Sciences.

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
Scientific Reports, volume 8, Article number: 6167 (2018) https://doi.org/10.1038/s41598-018-24663-x

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

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