The gene genie is out of the bottle, telling a powerful story about the horse

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The genetic diversity of the modern horse has dropped by 16% in the past 200 years, research reveals.

The worrying decline was noted by the authors of a recently published review marking 10 years since the first reference genome for the horse was published.

“It is not a coincidence that the last 200 years also cover the time of the development of horse breeds, the establishment of studbooks and the implementation of extensive selective breeding,” Terje Raudsepp and her colleagues reported in the journal Animal Genetics.

EquCab3.0 is the complete genome sequence of the Thoroughbred mare Twilight. 
EquCab3.0 is the complete genome sequence of the Thoroughbred mare Twilight. © Doug Antzak

The horse reference genome from sequenced from a Thoroughbred mare named Twilight.

Its availability, together with advances in genomics, had led to unparalleled developments in equine genomics, said the review team, comprising Raudseep, from Texas A&M University; Carrie Finno and Rebecca Bellone, from the University of California, Davis; and Jessica Petersen, from the University of Nebraska.

Recent achievements include the release of the next version of the reference genome (EquCab3.0) and the generation of a reference sequence for the Y chromosome.

Despite extremely low genetic diversity of the Y chromosome, it has been possible to trace the male lineages of breeds and pedigrees, and show that Y variation was lost in the last 2300 years or so due to selective breeding.

The modern-day collection of whole-genome sequences from hundreds of ancient horses is unique and not available for any other domestic species, they noted.

“These tools and resources have led to global population studies dissecting the natural history of the species and genetic makeup and ancestry of modern breeds.”

The authors note that humans have selectively bred horses for performance traits, appearance and temperament, resulting in 400–500 different breeds.

As next‐generation sequencing continues to become more affordable, whole-genome sequences of horses are being generated worldwide.

At the time of writing, 1936 were publicly available for the horse through the NCBI Sequence Read Archive.

This, they said, was a tremendous resource that provides investigators with a database of horse genomes to screen potential variants, and will aid future studies for many years to come.

Genomics‐based searches into the wild ancestry of the domestic horse and the origins of horse domestication have been ongoing for decades, they said.

“Yet the answers have only recently started to emerge, largely thanks to the contribution of whole-genome sequences from ancient equine samples.”

These studies reveal that, in addition to the two existing horses, the domestic (Equus caballus) and the Przewalski’s horse (E. przewalskii), there existed other, now extinct, horse lineages at the time of early domestication.

One lineage was initially identified from bones aged between 5000 and 43,000 years old, recovered from a broad sweep across the northern hemisphere. This lineage shared similarities with an extinct horse described as Equus lenensis.

Recent DNA work on a 24,000‐year‐old specimen from the Tuva Republic suggests that there may have been another genetically divergent lineage of horses in Siberia and the New Siberian Islands, although the genetic contact between E. lenensis and this “ghost” lineage remains unknown.

Evidence also points to an even more recent lineage, now extinct, that inhabited Iberia during the early phase of horse domestication.

Earlier, it was reported that that E. lenensis contributed 12.9% to the genetic makeup of domestic horses.

“However, the most recent study of 278 ancient equids and modern horses shows that none of the above extinct horse lineages contributed significantly to modern horse diversity.”

Przewalski’s horses released into the Mt Kalamaili Nature Reserve from the Xinjiang Wild Horse Breeding Centre. Photo: Z. Jiang,

DNA has also helped reshape our understanding of the genetic relationship between the two surviving horses — the domestic horse and the Przewalski’s horse.

“Until recently, the overall consensus, based on modern and ancient whole-genome sequencing, was that the two are separate species, diverged approximately 45,000 years ago, with extensive bi‐directional gene flow.”

All studies agreed that the domestic horse is not a direct descendant of the Przewalski’s horse.

“These views were recently shaken by a study of over 40 ancient horse genomes from Eurasia, providing striking evidence that the Przewalski’s horse is not truly wild, but rather a feral horse descended from the horses domesticated by the Botai culture some 5500 years ago.

“At the same time, all studied domestic horses dated from 4000 years ago to present show only 2.7% Botai ancestry, suggesting they descended from a different lineage of wild horses that subsequently went extinct.”

Ancient DNA studies have also attempted to decipher, but have not completely resolved, the timeline and geography of horse domestication.

Current archeological and DNA evidence suggests multiple sites of horse domestication, of which the earliest — around 5000 to 5500 years ago — was in the Western Eurasian steppes: Northern Kazakhstan (the Botai culture) and the Pontic-Caspian steppe, followed by additional candidate sites in Iberia, Eastern Anatolia, Western Iran, Levant and Eastern Europe.

“It is noteworthy that native breeds from the main domestication sites such as the Pontic-Caspian steppes still represent hotspots of genetic diversity for horses.

“However, even though the main candidate sites for domestication have been identified, the geographic origins of the modern domestic horse remain unknown.

“Given that the ancient Botai and Iberian lineages did not contribute substantially to modern domesticates … future studies of this timeline in other candidate regions of early domestication are needed.”

The authors traversed the acknowledged genetic cost of domestication for the horse.

These include extreme mitochondrial DNA diversity, an extreme lack of Y chromosome diversity, a high genetic load of harmful mutations, and some associated genetic changes arising from selection for traits considered desirable by breeders.

These include genes involved in the cardiac and circulatory system; bone, limb and face development; brain development and behavior; and coat color.

“The genomic cost of domestication and modern breeding is best illustrated by a striking discovery of a recent comparative study of ancient and modern horse genomes, showing that early breeders managed to maintain genetic diversity for millennia after domestication.”

It was this 2019 work that showed that the genetic diversity of the modern horse had dropped by 16% during just the past 200 years.

“Since domestication, the genetic diversity present in ancient horse populations has been exploited for selective breeding for a wide range of phenotypes.

“However, the creation of the about 500 specialized horse populations or breeds by intense artificial selection and the establishment of (closed) studbooks happened only during the past 100 to 200 years.”

These breeds can now be studied in detail for genetic makeup, signatures of selection and relatedness to other breeds.

Despite the large number of studies, the core findings are rather similar, they noted.

Collectively, modern horse breeds are characterized by high inter‐breed and low intra‐breed genetic diversity. The genomes of modern horses show multiple regions with signatures of selective pressures on performance traits and phenotypes. Clear signatures of selection are also found at known coat color locations.

The authors said the last 10 years have been unparalleled and decorated with outstanding achievements in horse genetics in almost all conceivable directions.

“The central pillar of support for this success is definitely the high‐quality horse reference genome combined with unprecedented advances in genomics technologies and global collaborations between researchers of diverse disciplines, clinicians, breeders and horse owners.

“It must be emphasized that the collection of genome‐level sequence data from hundreds of ancient horses from the past few thousand years is unparalleled and not available for any other domestic or non‐primate species.

“This unique resource allows researchers to track the evolutionary past of any genomic features, particularly the sequence variants that are associated with equine traits of importance, such as performance, coat color, disease and adaptations.

“This also demonstrates that the history of domestic animals cannot be fully understood without ancient genomic data.”

Ten years of the horse reference genome: insights into equine biology, domestication and population dynamics in the post‐genome era
T. Raudsepp C.J. Finno R.R. Bellone J.L. Petersen
First published: 30 September 2019

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

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