A multi-institutional, international project called the Ruminant Telomere-to-Telomere Consortium (RT2T) is aiming to provide the complete genomes for over 300 ruminant species, or animals that chew cud, including cattle, sheep, and goats.

A genome is an organism’s entire set of DNA, the instructions necessary for an organism to develop and function. Access to an animal’s complete genome allows researchers to identify genes and genetic variations that contribute to various physiological traits, diseases, reproduction, and behavior, among many other things. In 2022, researchers generated the first complete sequence of the human genome. This accomplishment led to the discovery of genes contributing to diseases like cancer, allowing researchers to explore new treatment opportunities.

“We’ve had (genetic) sequencing for cows and sheep for years now, but there were chunks of their genomes that we were not able to sequence because the technology just didn’t allow it,” Stephanie McKay, associate professor in the College of Agriculture, Food, and Natural Resources at the University of Missouri, said. “Now, we’re able to sequence those bits and, like the Human Genome Project, we’ll be able to find new genes and look at different (genetic) mechanisms.”

Studying ruminant animal genetics has been challenging because the available reference genome sequences are incomplete, fragmented, or missing. McKay compares the study of the cattle genome to an incomplete encyclopedia set.

“The cattle genome has 29 autosomal chromosomes and one pair of sex chromosomes. Think of them as 31 books in an encyclopedia set. Imagine that one book is missing – but it’s not just one book. It’s the equivalent of one book of information spread out over all 31 books,” she said. “In some books, you might be able to make sense of the information even if something is missing based on the context. Sometimes, you can’t.”

When the genome is complete, or all 31 books have no missing information, researchers discover brand new information about ruminants and information that gives new meaning to things that are already known. McKay said that complete genomes for ruminant species will ultimately improve breeding and selection programs. Additionally, researchers are likely to learn about ruminant evolution, domestication, and genes that could help reduce the risk of infection, increase dairy and meat production, and help animals adapt to the changing environment.

Theodore Kalbfleisch, associate professor of veterinarian science at the University of Kentucky, said in a prepared statement that complete and accurate genomic information allows researchers to pinpoint specific traits and genetic variations beneficial for agricultural practices, such as improved milk production in dairy animals or enhanced wool quality in fiber-producing animals. He also said that he believes the completion of the project could revolutionize livestock management practices, giving farmers and breeders the tools to inform breeding decisions for healthier and more productive livestock.

McKay said that the research effort is altruistic, with researchers worldwide contributing to the completion of ruminant genomes. The project is currently underway, with a number of genomes in the process of being sequenced. Once the genomes are sequenced, scientists must correctly assemble the genetic information, a process that requires massive amounts of computer power. McKay added that the project has no definitive deadline and will likely take years to complete, considering that samples must be acquired, sequenced, assembled, and then analyzed before meaningful results are discovered.

Researchers have already been able to sequence the Y chromosomes of cattle and sheep completely. The Y chromosome is one of the two sex chromosomes involved in determining sex in organisms and has been difficult to sequence because it has highly repetitive DNA sequences. By studying the Y chromosome, researchers can answer questions about male-specific genes, breed-specific genetic diversity, sperm production and fertility, and the evolutionary history of cattle and sheep. Interestingly, the Y chromosome of cattle is more than double the length of the sheep Y chromosome.

The impact of the project will extend beyond agricultural implications. There are many endangered ruminants, including types of antelope, buffalo, and deer. Researchers can use genomic information in conservation efforts and develop strategies to improve the survival of certain populations by highlighting genetic vulnerabilities and strengths.

The consortium embraces an open science model, meaning that as the project’s data and results become available, they will be freely accessible to the global research community. McKay said that many of the researchers involved in the project regularly communicate with producers. She is hopeful that these conversations will continue as new information is uncovered that could benefit animal owners.

“We are learning new things every day from this project, and it will be interesting to take a look back in five years to see how far we’ve come,” she said.