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Genetic History of the Thoroughbred

Genetic analysis clarifies the roots of the breed, and provides guidance for its future management

 Thoroughbred horses were not on the work agenda for An Foras Taluntais. This sport of kings rightly took second place to the economic concerns of ordinary farmers. However, one Minister of Agriculture in the l960’s had a notable interest in thoroughbreds, and he asked Dr. Tom Walsh whether the Institute could usefully add some scientific insights to the traditional lore on which thoroughbred breeding seem to be based. I was dispatched to see the Minister.
Thoroughbreds were not added to the Institute’s programme, but the encounter did lead to the formulation of some research plans which eventually bore fruit (13). At that stage, I was already doing part-time work in Trinity College. George Dawson took up the cause with enthusiasm, and together we persuaded Joe McGrath of Brownstown Stud, over a long and profitable lunch, to provide funds for a study of inbreeding in the thoroughbred. Gary Mahon joined the group, and the work began (14).
We started with the major problem in thoroughbreds: low fertility. On average, only two foals are produced for every three mares in the population each year. This is very poor fertility by the standards of wild horse populations or indeed any other annual breeding uniparous mammalian species. Our objective was to calculate inbreeding coefficients for a large number of mares and to see if this was in any way related to their reproductive performance.
We took all 10,569 mares in Volume 35 of the Stud Book, which covered the period 1961- 1964. The breeding history of each mare was traced through earlier and later volumes to cover her entire reproductive life (an average of twelve years). These lifetime reproductive histories were then, in each case, reduced to a single index of success for that mare. In parallel with this, we set out to calculate the inbreeding coefficient of each mare. This entailed creating a computer file of over 80,000 ancestors, from which we were able to calculate full inbreeding coefficients for each mare arising from the last five generations.

The results were somewhat surprising, with average inbreeding less than 1%, and no detectable relationship between it and fertility index. The first conclusion therefore was that there is negligible recent or current inbreeding in the population, and that it is not the cause of low fertility.
Carrying through of these calculations was an immense computing task, we believe the largest inbreeding calculation carried out up to then. With the computing power available at that time, it was not feasible to calculate full inbreeding coefficients back to the foundation of the population. We therefore calculated this second group of inbreeding coefficients on a sampling basis, by tracing sample lines from each fifth-generation ancestor back to the ultimate foundation animals.
This time, we found more inbreeding, as might be expected. The average level was 13%. There was still no detectable relationship to infertility. However, the structure of the data enabled us to make an estimate of the extent to which mare fertility is inherited (the Figure was 7.7%). When we put this together with the generation interval, we were able to calculate how much selection would need to be exercised in each generation to offset the kind of decline in fertility that might be expected with 13% accumulated inbreeding.
This calculation said that if as much of 8% of mares were culled for infertility in each generation, the resulting positive selection would be sufficient to offset the expected inbreeding depression. We thus concluded that neither long term nor recent inbreeding is a measurable source of present infertility. This turned our attention to other possible causes, and in a separate study we have been able to show that the unnaturally early start and to the thoroughbred breeding season may be a major cause of poor fertility.
These studies shed some new light on the genetic origins of racehorses. The modern thoroughbred population descends from a handful of stallions imported from North Africa and the Middle East into England in the l600’s. The foundation mares are less well documented, but many are believed to have come from the same sources.
For about a century, the population remained small, and thoroughbred racing was the sport of the very limited royal coterie. The Tudor and early Stuart kings maintained studs, although these were dispersed by Cromwell in 1649. After the Stuart restoration, the patronage of Charles II gave renewed impetus to thoroughbred breeding and racing. The sport developed strongly throughout the eighteenth century, and it was then that the three oldest classic races were established: the St. Leger in 1776, the Oaks in 1779 and the Derby in 1780.

In 1791, James Weatherby established his famous Stud Book, the foundation list of which comprised some eighty animals. From this narrow base, the thoroughbred population has expanded to the point where it now numbers over half a million world wide.
Our inbreeding calculations enabled us to quantify the contribution of these foundation ancestors to today's breed. The three "Pillars of the Stud Book" have always been recognised as the Godolphin Arabian (born about 1725) The Darley Arabian (1688) and the Byerley Turk (1960). Our analyses turned up a fourth sire, the Curwen Bay Barb which should rank with this group. He contributed an estimated 5.6% of the genes in the Current thoroughbred population, making him the third ranking contributor.

When we add all other foundation ancestors who contribute 2.5% or more to today’s population, we have a list of eleven animals in total, which between them are responsible for over half of the gene pool. The top thirty animals contribute over 80% of the genes. These figures simply confirm what has long been known: that today’s thoroughbred population had a very narrow genetic base. As part of these studies in thoroughbred horses, we had also attempted to measure the degree to which track performance is inherited. This can be expressed on a percentage scale, and our results showed, consistently, that about one third of the differences between horses in track performance could be attributed to genetic causes.
When this result is combined with the known selection intensity and rate of generation turnover, it becomes possible to calculate a measure of the rate of genetic change in the population. The results of these calculations suggested that the thoroughbreds should be improving, on average, at about 1% per year. However, when we looked for evidence of this in the winning times of classic races, we found that these have not been improving for the last forty years, despite evidence of steady improvement in the preceding century.

Barry Gaffney and I set Out to resolve this paradox (15). To do so, we analysed the performances of some 30,000 three years-olds over a twenty five year period, as reflected in their Timeform ratings. The resulting estimate of genetic trend confirmed the view that genetic change is taking place at about 1% per year. This leaves the paradox in place. Our best explanation of the plateau in winning times is that, for the best horses in the best races, there is a physiological ceiling to performance, probably attributable to lactic acid accumulation. This view is supported by evidence that performance plateaux are more pronounced in long than in short races.