Unlocking the ‘genetic magic’ of beef cattle

The new facility will allow USask to offer a new high-throughput genome sequencing service for western Canadian beef cattle producers and researchers.

“Picture being able to go into a sales ring and having not only the visual impression of what those animals look like, but being able to know for certain that within their genetics is the capacity to optimize for the specific traits you want,” says Dr. Scott Wright (PhD), director of the Livestock and Forage Centre of Excellence (LFCE).

IntegrOmes (short for Integrated Omics for Sustainable Animal Agriculture and Environmental Stewardship) is a large-scale project that’s focused on advancing genomics research on campus and enhancing capacity at the LFCE, the university’s world-class livestock research facility southeast of Saskatoon, Sask.

The wide-ranging research program, which includes development of the world’s first bison genome biobank at the LFCE, is supported by various organizations including the Canada Foundation for Innovation (CFI), Innovation Saskatchewan, Government of Alberta, Saskatchewan Cattlemen’s Association and USask.

The first phase of the IntegrOmes project focused on renovations for a new research and diagnostic genomics lab at the Western College of Veterinary Medicine (WCVM) with data storage capacity, set to open in early 2025. The second phase, which was completed in spring 2024, included renovations to the LFCE’s Native Hoofstock Research and Teaching Unit.

The third phase is construction of a new Beef Reprotech Facility at the LFCE’s Goodale Farm, with construction targeted to begin by summer 2025. While work on the new centre is yet to begin, it’s designed to complement the LFCE in collecting genetic samples. With this new resource, researchers can collect phenotypic (observable traits) data and genetic samples and sequence the entire genome of a beef cow, unlocking a wealth of genetic data not currently available to the cattle industry.

With expertise from across USask — including the WCVM, the LFCE, College of Agriculture and Bioresources (AgBio) and the Global Institute of Food Security — researchers aim to establish a national resource for genomic testing in beef cattle and support producers through enhanced genetic insights and phenotypic pairing. The team also includes national partners, such as the Toronto Zoo and Agriculture and Agri-Food Canada (AAFC).

Dr. Lynn Weber (PhD), the WCVM’s associate dean of research and graduate studies, says that current genetic testing of beef cattle in Canada is limited. It’s reliant on chip-based technology that analyzes specific single nucleotide polymorphisms (SNPs, pronounced “snips”) that serve as genetic markers for various traits in beef cattle. While useful, this testing provides only a limited view of the animals' full genetic makeup.

“The SNPs only look at 250,000 genes, which sounds like a lot, but it really isn't,” says Weber. “We want to replace the chip [technology] and sequence the whole genome so we can test a much larger number of genes.”

Weber adds that the data is collected and then sent to the United States for analysis and storage. As a result, researchers’ access to complete results is restricted since the genetic sequencing and associated genetic trait information known to the American company is proprietary.

“We actually can't access the data that was on those chips in the U.S. testing facility. So we can’t re-probe when new diseases pop up, or [if] we detect problems or just want more information,” says Weber, adding that sharing data openly helps to advance research much more quickly.

“Not only would this database be in Canada, but then it's also not a proprietary thing. It’s open data for researchers and for industry.”

While genome sequencing is a major factor in putting together the database, it’s only one piece of the entire puzzle. Once the genome is sequenced, researchers will need to match those genes to the genetic traits for which they’re responsible.

“In order to establish the database, we need to match the traits that we want — or don't want — with specific gene sequences,” explains Weber. “That's where the [Beef] Reprotech facility comes in.”

Wright says the LFCE’s well-documented cattle population together with industry data through the Canadian Beef Breeds Council provides an ideal foundation for this work, offering researchers access to over 3,500 cattle with detailed records. The LFCE herds will undergo sequencing, helping to establish the database at the Beef Reprotech Facility before expanding to commercial applications.

Integrating genomic research with the LFCE’s facilities offers an invaluable opportunity for Canada’s beef industry. While dairy, pork and poultry sectors have leveraged genetic testing to improve productivity, the beef industry has been slower to adopt these tools.

“There is a deep lag in the beef industry in terms of utilizing these genetic and genomic tools,” says Wright, noting that the costs associated with genetic technologies and complexity of the analytical tools were prohibitive.

“We are only now getting to the point where we can analyze these very, very large data sets,” says Wright. “The technology has advanced to the point where we’re within reach of a very practical utilization and application.”

For the beef industry, this means an opportunity to make better choices based on a deeper understanding of the entire genetic environment surrounding each animal, which Wright believes could become reality as early as three years after the building’s completion.

This increased testing would also play a key role in reducing the environmental footprint of Canada’s beef production. Wright says improved genetic testing could lead to cattle that are more feed-efficient, requiring less forage and producing fewer greenhouse gases.

“Currently the strongest thinking suggests that the easiest way to reduce greenhouse gas emissions in feedlot is to reduce the number of days to finish,” says Wright. “With this research, we can access the tools locked in the animal’s genome to really be able to drive out those efficiencies.”

The Beef Reprotech Facility — and the IntegrOmes project as a whole — represents a turning point for the beef industry, blending cutting-edge science with practical applications to improve sustainability and productivity.

“It’s about really making sense out of this genetic magic,” says Wright.

Article re-posted from WCVM Today. View original article.