Genomes of six horse breeds sequenced

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© Lyn Marshall

Researchers who sequenced the genome of horses from six breeds have identified genetic variations that likely drive some of the many differences in body size and conformation seen in breeds around the globe.

The first domesticated horse reference genome assembly, EquCab 2.0, was completed in 2009, using a Thoroughbred mare named Twilight. The latest updated version of this publicly available reference genome, using DNA from the same mare, is known as EquCab3.0.

But, as Mohammed Ali Al Abri and his fellow researchers point out, there are about 400 geographically and physiologically diverse breeds of horse.

To enrich the current collection of genetic variants in the horse, the study team sequenced whole genomes from six horses of different breeds: an American Miniature, a Percheron, an Arabian, a Mangalarga Marchador, a Native Mongolian Chakouyi, and a Tennessee Walking Horse.

They then and mapped them against the EquCab3.0 genome.

In total, they identified and functionally annotated an average of 17,514,723 Single Nucleotide Polymorphisms (SNPs). These are the most common type of genetic variation, each representing a difference in a single DNA building block.

They identified 1,923,693 Insertions/Deletions (a type of genetic variation in which a specific sequence of DNA building blocks is either present or absent); as well as an average per horse of 1540 Copy Number Variations (when the number of copies of a particular gene varies from one individual to the next) and 3321 Structural Variations (SVs), which involve changes in the structure of an organism’s chromosome.

Insertions/Deletions can cause genetic disorders, with Lavender Foal Syndrome one such example in horses.

There were more insertions (66%) than deletions (34%) found, unlike what is seen in humans.

Insertions/Deletions are rarer than SNPs and are thus more likely to be unique to a breed of horses than to be shared between breeds, the researchers say.

The researchers, writing in the open-access journal PLOS ONE, said their results revealed presumed functional variants including genes associated with size variation such as the LCORL gene (found in all horses), ZFAT in the Arabian, American Miniature and Percheron horses, and ANKRD1 in the Native Mongolian Chakouyi horse.

They also detected a copy number variation in the Latherin gene that may be the result of evolutionary selection impacting thermoregulation by sweating, an important component of athleticism and heat tolerance.

The newly discovered variants were formatted into user-friendly browser tracks and will provide a foundational database for future studies of the genetic underpinnings of the diversity seen within the horse.

The study team comprised Ali Al Abri, from Sultan Qaboos University in Oman; Heather Marie Holl and Sara Kalla, from Cornell University in New York; Nathan Sutter, from La Sierra University in California; and Samantha Brooks, from the University of Florida.

Al Abri MA, Holl HM, Kalla SE, Sutter NB, Brooks SA (2020) Whole genome detection of sequence and structural polymorphism in six diverse horses. PLoS ONE 15(4): e0230899. https://doi.org/10.1371/journal.pone.0230899

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

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