Researchers at the Texas A&M College of Veterinary Medicine and Biomedical Sciences (VMBS) are shedding light on the Y chromosome in horses, providing insights that could guide breeding practices and support efforts to preserve breed diversity.

“The Y chromosome is notoriously challenging to sequence due to its complex structure, and our understanding of it has been incomplete,” said Dr. Gus Cothran, professor emeritus in the VMBS’ Department of Veterinary Integrative Biosciences (VIBS). “For years, scientists believed the Y chromosome lacked genetic variety, suggesting it had little impact on species diversity.”

However, a new collaborative study led by the University of Veterinary Medicine Vienna, with contributions from Cothran, has revealed that the Y chromosome harbors significant variation and plays a vital role in genetic diversity.

“Our recent findings, published in PNAS, demonstrate that we can now trace male lineage in horses using the Y chromosome—something previously impossible,” Cothran explained. “This breakthrough allows us to reconstruct over 1,500 years of horse breeding history and evolution.”

Unlocking the Y Chromosome

For decades, the Y chromosome has posed a significant challenge for researchers. When the human genome was first sequenced in 1990, the Y chromosome wasn’t even included; its complete sequence wasn’t achieved until 2023.

“The Y chromosome contains many repeating sections and even palindromic regions—sequences that read the same forward and backward—making it difficult to decipher which genes are present,” Cothran said. “Even obtaining a basic sequence for the Y chromosome in any mammalian species is incredibly difficult.”

Advancements in technology have now made it possible to process these complex DNA sequences, opening new avenues for research.

“With the help of improved computational tools, we analyzed horse DNA samples from around the world,” Cothran said. “This enabled us to trace the origins of modern stallions and understand how horse breeding has been shaped by human history over the last 4,000 years, particularly through stallion-mediated breeding.”

Tracing Paternal Ancestry

Stallion-mediated breeding, the dominant method in horse reproduction, has historically been favored for practical reasons, including the ability to assess stallion fertility more easily than mare fertility.

“Stallions can sire hundreds of offspring in a lifetime, while mares produce only a few foals, making it harder to evaluate their progeny quickly,” Cothran explained.

Today, breeders rely on pedigrees to determine a horse’s lineage, but these records are often limited to a few generations and prone to human error. The team’s research offers a deeper look into a horse’s paternal ancestry.

“With our findings, we can trace evolutionary lineages much further back, uncovering a horse’s broader genetic history,” Cothran said. “This gives breeders a clearer picture of traits passed down through male lines.”

Protecting Genetic Diversity

Understanding a horse’s evolutionary history could soon play a crucial role in breeding programs aimed at preserving rare breeds. The new insights into the Y chromosome have significant implications for equine health and conservation.

“Inbreeding is a major concern in some breeding programs, as it can lead to genetic defects like clubfoot and reduced fertility,” Cothran noted. “Breeders and conservationists are increasingly turning to scientific research to maintain genetic diversity.”

For example, breeders might use this research to prioritize less common male lineages within rare breeds to enhance genetic diversity. Additionally, identifying specific lineages to avoid crossing could help prevent health issues in offspring and protect breed longevity.

“With these new tools, we’re providing breeders with the knowledge to make more informed decisions, ensuring the health and sustainability of equine populations for future generations,” Cothran concluded.