Secrets of horse genetics for conservation, breeding

"Because of its complex structure, the Y chromosome is much harder to sequence, making our knowledge of it far from complete," said Dr. Gus Cothran, a professor emeritus in the VMBS' Department of Veterinary Integrative Biosciences (VIBS). "In fact, scientists used to believe that the Y chromosome lacked genetic variety, which we believed meant that it didn't contribute much to species diversity."

However, Cothran's new research collaboration, led by the University of Veterinary Medicine Vienna, has uncovered that the Y chromosome does have meaningful variation and is important for species diversity.

"As we recently published in the journal PNAS, we can actually trace the male lineage of horses using the Y chromosome, which was something we could not do before," Cothran said. "With this new information, we can better reconstruct the last 1,500 years of horse breeding history and evolution."

Decoding The Y Chromosome

For decades, the Y chromosome has been difficult for scientists to study. When the human genome was first published in 1990, it didn't even include the Y chromosome, which received its first complete sequence in 2023.

"The Y chromosome has many sections that repeat, and even some that are palindromes -- the same forwards and backwards. It makes it challenging to understand which genes are encoded there," Cothran explained. "Getting a basic Y chromosome sequence of any mammalian species is quite hard."

As technology has improved, computers have made it easier to process these sections of DNA, which has dramatically changed Y chromosome research.

"We were able to screen a worldwide collection of horse DNA samples and study where modern stallions trace their roots to," Cothran said. "Horse breeding has been linked to human history for nearly 4,000 years, and for most of that history, humans have used stallion-mediated breeding. This study allowed us to see major breeding influences and how historical expansion routes contributed to the spread of horses."

Studying Paternal Ancestry

Stallion-mediated breeding is the preferred method used in horses for several reasons, one being that it's much easier to analyze a stallion's fertility than a mare's.

"Stallions can have hundreds of offspring over the course of their lives, while mares can only carry one or two foals at a time, making it difficult to judge the performance of her offspring quickly," Cothran said.

Currently, pedigrees are how horse owners and breeders find out which stallions are in a horse's ancestry, which gives information on the traits a horse may have inherited. However, pedigrees are recorded manually, and they may go back only a few generations.

"Our recent research enables us to go back much farther, to see what evolutionary lineages a horse has in its DNA," Cothran said. "We can now see the bigger picture of an individual horse's paternal ancestry."

Maintaining Genetic Diversity

Studying the evolutionary history in a horse's ancestry may soon become a vital part of equine breeding to protect the health and well-being of rare breeds; therefore, the researchers' new findings about the Y chromosome will have lasting impacts on the equine industry.

"One of the main dangers within breeding programs for some horses is inbreeding, which happens when mating animals are too closely related; in horses, it can cause genetic defects like club foot and loss of fertility," Cothran explained. "Thus, both breeders and equine conservationists are interested in using scientific research to promote genetic diversity.

"If you have a horse from a rare breed and there is more than one male lineage to choose from, you could, perhaps, select for the rarer of those lineages in breeding, which would help maintain diversity within that breed," he said. "With the new analysis capabilities provided by our research, we may discover that there are reasons to avoid crossing certain male lineages to protect the health of offspring or the future of the breed."