Genetic diversity within Thoroughbreds akin to other horse breeds, research finds

"Results suggest that the amount of variation found among Thoroughbreds is not exceptionally depleted when compared to . . . other horse breeds."
Image by Peter W

The Thoroughbred horse, subject to intensive selective breeding for centuries, is not exceptionally depleted in terms of genetic variation when compared to other horse breeds, researchers have found.

Breeders have always used pedigrees to manage the genetics of Thoroughbreds. Pedigree analysis is firmly rooted in our understanding of classical, Mendelian genetics.

However, pedigrees only track relationships. The actual genetic variation present in any animal can only be assessed by reading the DNA itself.

In 2006, the whole genome sequence of the horse was first reported. It was an expensive undertaking, but since then the costs of doing this work have fallen dramatically. Now, sequencing the whole genome of a horse is routine in research laboratories.

The DNA sequence contains information about the extent of genetic variation, relationship to other horses, relationship to other breeds, levels of inbreeding, and can even provide raw material for the discovery of potentially deleterious genes that interfere with the success of the breeder.

Ernest Bailey, Ted Kalbfleisch and Jessica Petersen, writing in the latest issue of Equine Disease Quarterly, discussed the findings of what they describe as a landmark paper published last August by Teruaki Tozaki and his colleagues from the Laboratory of Racing Chemistry and Japan Racing Association.

Tozaki and his fellow researchers described the whole genome sequencing of 101 Thoroughbreds in Japan.

While scientists have been identifying DNA variation in short regions for the last three decades, this study was unique in that these scientists collected data on all 2.41 billion DNA nucleotides of the 101 horses.

The work provides a baseline for comparison of different populations of Thoroughbreds, as well as a benchmark to assess changes over time.

The findings allow researchers to compare the variation found in Tozaki’s study to the variation found in other breeds.

Vidhya Jagannathan and her fellow researchers, in a 2019 study, sequenced the whole genomes of 88 horses of diverse breeds, including Warmblood, Standardbred, Quarter Horse, Arabian, Morgan, Franches-Montagne, Paint, Icelandic, Shetland, Akhal-Teke, Noriker, Welsh ponies, and one Thoroughbred.

“The two studies were similar in design,” they said, “so we can directly compare their results.”

The total number of single nucleotide variants (SNVs) found in the Jagannathan study was almost twice as large as those found in the Tozaki study.

“This illustrates the great amount of diversity existing among horses of all breeds,” Bailey and his colleagues said.

“However, when we examine the number of SNVs found in each horse (Max-Min), Thoroughbred horses fall within the range for the diversity of breeds.

“Specifically, while the Jagannathan study reported a range of 4.4 million to 6.6 million SNVs per animal, the Thoroughbred counts fall within that range, 4.8 million to 5.3 million.”

Two technical caveats bear mentioning here, they said.

“SNVs are just one type of DNA variant. Other types of variants exist, including DNA insertions, deletions, and repeats. Therefore, the total number of variants including those in other categories is certainly greater than the number of SNVs reported.

“Another — and perhaps very consequential — caveat is that the number of SNVs were determined through comparisons with reference to the genome of a Thoroughbred mare (the equine reference genome).

“If we were to use a different breed as a reference, say a Shire horse, we will see a larger number of variants for Thoroughbred horses when compared to this new reference, but less for Shires.

“Regardless of how we count the variants, these results suggest that the amount of variation found among Thoroughbreds is not exceptionally depleted when compared to the range of variation among other horse breeds.”

Arguably, some of the most important outcomes of this study are yet-to-be-generated products of the available data. For instance:

  • The information serves as a baseline of diversity to assess and model/predict changes in the future population resulting from current and evolving breeding practices;
  • The 12.1 million genetic variants identified among these 101 Thoroughbreds can be assessed to determine which may cause fitness problems, and those desirable for health and racing performance;
  • It can be applied to assist in detecting inappropriate modifications of DNA, called gene doping, done in order to enhance racing performance.

Equine Disease Quarterly is supported by Equus/Standardbred Station, Incl and M&J Insurance.

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