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Comparative Genomics Offers Clues to Przewalski's Horse Conservation Efforts

Przewalski's horse, Mongolia.

NEW YORK (GenomeWeb) – A University of Copenhagen-led team has sequenced dozens of wild and domestic horse genomes to get a look at the genetic features specific to Przewalski's horse — a species first found in the Asian steppes that is believed to represent the last true wild horses.

Based on new genome sequences for 33 modern-day domestic or wild horse samples, together with five museum samples going back to the late 1870s, the researchers identified variants and signs of selection that seem to set Przewalski's horses apart from domestic horses.

But the analysis, published online today in Current Biology, also uncovered genomic patterns that seem to stem from inbreeding and mixing with domestic horses during the more than 100 years that Przewalski's horses were bred in captivity after their extinction in the wild in the 1960s.

"[W]e … show that very early in captivity — in the early 1900s — domestic horses contributed significantly to some lineages of the Przewalski's horse pedigree," senior author Ludovic Orlando, a researcher with the University of Copenhagen's Centre for GeoGenetics, said in a statement. "It implies that not all of the surviving Przewalski's lineages represent the gene pool of wild horses equally."

First found in the 1870s, the Przewalski's horse was extinct in the wild less than a century later, the team noted. Since then, it has been raised in captivity, starting from a founding population of around a dozen Przewalski's horses. The Przewalski's horse population has since grown to more than 2,100 individuals and several hundred have now been re-introduced to reserves in China and Mongolia.

The animals are known for their squat build, short legs, and a mane that stands straight up. Though they can mate with domestic horses, Przewalski's horses are behaviorally, physically, and genetically distinct, carrying their genes on 33 pairs of chromosomes rather than 32, as in the domestic horse.

In an effort to not only compare domestic and Przewalski's horses, but also Przewalski's horses from the present with those found prior to captivity, the researchers sequenced the genomes of 11 Przewalski's horses to average coverage depths ranging from 18-fold to more than 23-fold, using Illumina paired-end sequencing technology.

They also sequenced the genomes of 21 domestic horses, including representatives from five breeds and one living hybrid, along with five Przewalski's horse samples from museum collections, stretching back to the late 19th century.

The team's analysis uncovered more than 500 copy number variants that differed between Przewalski's and domestic horses, along with 101 ancestry-informative markers found in the protein-coding sequences of the Przewalski's horse.

Compared to the domestic horses, the Przewalski's horses tended to have variants affecting genes implicated in everything from muscle contractions and cardiac conditions to signaling pathway, metabolic functions, and reproductive behavior.

The researchers' demographic modeling, meanwhile, indicated that domestic horses diverged from the lineage leading to Przewalski's horses some 45,000 years ago. However, gene flow patterns in the equine genomes pointed to intermixing between the species since that split — including a jump in introgression from domestic horses since Przewalski's horses started being bred in captivity.

Over the course of captive breeding, the Przewalski's horse genome has shifted in other ways as well, taking on features that reflect a rise in inbreeding and diminished heterozygosity in the population.

Nevertheless, the study's author noted that genetic diversity remains relatively high in the Przewalski's horse, despite the steep population declines it experienced in the past. And with the advent of new ancestry-informative markers, they are optimistic about the prospect of maintaining the species' diversity in the future.