They also examined a register, known as the Stud Book, which dates back to 1792 and identifies the parentage of purebred horses.
It emerged that most of the genes of the original founder population of 80 have been lost over time.
"About 28 horses contributed pretty well all the genes in today's population, that's despite the fact that there were about 80 horses recorded in the first stud book," Cunningham told the conference.
Mitochondrial DNA, which is inherited only through females, showed that a mare called Tregonwell's Natural Barb contributed the most genes — about 14 percent — of all the female lines.
On the male side, three stallions contributed most of the genes to today's stallions: the Darley Arabian, the Godolphin Barb and the Byerley Turk.
"Eventually the Darley Arabian raced to supremacy," Cunningham said.
Indeed, the Darley Arabian passed on its Y chromosomes (which is found only in males) to 95 percent of today's half million thoroughbreds.
Born in Syria in 1700, originally the property of Sheikh Mirza II, the bay colt was brought to England in 1704 by the British consul Thomas Darley.
Soon the horse became a champion stud, covering mares between the years 1706 and 1719 and siring many good runners. He died at the advanced age of 30 in 1730.
The research confirms that today's thoroughbreds have become more and more inbred. In the 1700s, they shared about a third of their genes. Today, that proportion has risen to nearly half.
DNA "fingerprints" of pedigree horses at 13 places (known as microsatellite DNA loci) on the horses' chromosomes showed that Shetland ponies shared 28 percent of their genes with the other horses, while Turkish, Egyptian and other thoroughbred horses shared about 35 percent to 40 percent of their genes.
According to Matthew Binns of London's Royal Veterinary College, the tight inbreeding has "some detrimental consequences."
The majority of thoroughbreds suffer from bleeding in the lungs, while orthopaedic problems, low fertility and abnormally small hearts are also common.
Developing a horse genome scanning panel would improve the general health of the horse population and even racing performances.
Binns told the conference that he planned to study the genetic material from bones of many ancient thoroughbreds in the attempt to uncover genes that explain why one animal runs faster than another.
Among the stallions who descend from the Darley Arabian, the researcher will investigate the code of life of Eclipse, the legendary 18th century racehorse.
A great-great grandson of the Darley Arabian, Eclipse ran in eighteen races and was never beaten.
He died in 1789, and his whole skeleton is still preserved.
"He was the greatest in history and to get a look at his genetic material will be pretty amazing," said Binns.
