A research group, led by scientists from the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard, has announced the completed sequence of the horse genome. The sequencing project was initiated three years ago, in conjunction with the Horse Genome Project which first sought to map the horse genome a decade ago, to benefit equine health. The new project, however, mapped the genome of the domestic horse, Equus caballus, to help study an unknown branch of mammalian evolution and learn more about the similarities and differences in mutations and genetic diseases between horses and humans.

According to the Broad Institute, horses and humans share an evolutionary history because—like most mammals—the two species share some of the same DNA. Horses also suffer from 90 known genetic diseases, which could benefit scientists studying hereditary disease in humans. Animal Geneticist Claire Wade, who worked on the project for the Broad Institute, told BioTechniques that E. caballus was selected because the researchers expected the genome to be similar to humans. “The horse was chosen to represent the mammalian order Perissodactyla within the mammalian family tree in evolutionary genomics,” said Wade, “That order also includes the rhinoceros and tapir. Of that group, horses were regarded as the animals with most relevance to human medicine and human interests.”

According to Wade, who is now a professor at the University of Sydney in Australia, the sequencing project was completed using the traditional Sanger method. The researchers analyzed DNA from an adult female thoroughbred and discovered that the genome is roughly 2.7 billion nucleotides. This is larger than the genome of the domestic dog, but smaller than both the human and cow genomes.

Wade said that the horse genome sequence, while useful, embodies the maximum amount of information that the Sanger method can supply. “The horse was one of the last sequencing projects to be fully conducted using Sanger sequencing,” said Wade. “It represents the peak of our understanding of mammalian assembly on that platform.” According to Wade, third-generation sequencing methods could reveal more about mammalian genomes, but the technology still has problems to overcome. “There needs to be sufficient read length to span longer repetitive sequences, and this represented a challenge with shorter-read-length massively parallel methods,” said Wade.

According to Wade, the researchers also examined DNA from a variety of other horse breeds including the American quarter, Andalusian, Arabian, Belgian draft, Hanoverian, Hakkaido, Icelandic, Norwegian fjord, and Standardbred breeds. The researchers evaluated the genetic variation within—and across—the breeds to create a catalog of more than one million single nucleotide polymorphisms (SNPs).

Though the genome was sequenced using Sanger technology, the research team still made use of Illumina’s next-generation Genome Analyzer I sequencing system to examine a locus affecting coat color. “We made use of the next-generation system to enable mutation discovery within a locus affecting an equine coat color trait,” said Wade. The color trait, known as the Leopard Complex, creates white spots across a horse’s coat. Horses that carry this trait are known to suffer from a form of night blindness, which also affects humans.

The researchers narrowed the list of genetic causes for the spotting trait down to 42 associated SNPs, including two mutations near a gene involved in pigmentation. Though the results indicate the feasibility of using horses for disease gene mapping, Wade acknowledged that there is still much to be revealed about how genetic differences affect phenotype. “We are still some way from knowing all there is to understand about DNA and how it influences phenotype. Understanding the subtleties of genomic regulation and epigenetic inheritance is still elusive,” she said. “I think we will remain busy for many years yet.”

Mapping the horse genome also revealed that only a small number of chromosomal rearrangements have occurred in horses, compared to the human genome. As a species evolves, chromosomes move to different locations on the genome. These rearrangements result in differing phenotypic expression of the chromosomes. When the chromosomes remain in the same location on the genome, traits in the species stay the same. This lack of movement of chromosomes is called synteny. According to the Broad Institute, the horse sequence indicated that more than 50% of horse chromosomes show synteny with a single human chromosome. This shows a long-standing level of continuity in the horse genome.

Sequencing the horse genome is significant because it adds to the general knowledge of evolutionary traits, said Wade. “From an evolutionary and comparative perspective, once we have high-quality representation from all orders of all phyla, we will probably be sufficiently resourced to answer basic evolutionary questions,” said Wade.

Wade suggested that endangered species might also benefit from genomic studies. “There are many animals that have special problems that might be assisted by the availability of genome sequence,” said Wade. “For example, the Tasmanian Devil in Australia is threatened by extinction due to a transmissible tumor. It would be wonderful to better understand how we can help them survive.”

Wade is lead author on the paper “Genome sequence, comparative analysis, and population genetics of the domestic horse,” which was published on Nov. 5 in the journal Science. The research was funded by the National Human Genome Research Institute, the Dorothy Russell Havemeyer Foundation, the Volkswagen Foundation, the Morris Animal Foundation, and the Programmi di Ricerca Scientifica di Rilevante Interesse Nazionale.