IntegrOmes

The beef cattle industry is an integral driver of Canada's economy, contributing $18 billion to its annual GDP, but it’s facing serious issues regarding productivity, sustainability and disease.

Guided by cutting-edge studies on the healthy microbiome, Integrated Omics for Sustainable Animal Agriculture and Environmental Stewardship (IntegrOmes) is a $17-million project that will work to conserve Indigenous Canadian species through the creation of a bison genome biobank. The project will also enhance the productivity and sustainability of commercial livestock for meat quality, animal health and food safety.

Development of omic tools that target livestock productivity, genetic diversity, disease investigation and surveillance will usher in a new era of animal agriculture and ecosystem health for Canada and the world. Based at the University of Saskatchewan (USask) Livestock Forage and Centre of Excellence (LFCE), the IntegrOmes team will combine controlled real-time livestock investigation with genomics tools to contribute to the sustainability and profitability of one of Canada's vital industries.

The team aims to develop new diagnostic tools for producers, inform policy-making around antimicrobial resistance, revitalize the bison populations and provide positive benefits to Indigenous cultural heritage.

Led by Dr. Gregg Adams, a professor and researcher at the Western College of Veterinary Medicine (WCVM), IntegrOmes brings together world-class research and multi-sector expertise in a variety of areas: animal reproduction, reproductive technologies, epidemiology, beef cattle health and disease, genetics, genomics, microbiomics, and bioinformatics. Members of the internationally recognized team are from the University of Saskatchewan, University of Alberta and University of Calgary as well as the Toronto Zoo and Agriculture and Agri-Food Canada (AAFC).

This team has an outstanding track record, with more than 1,000 scientific publications and 24 patents to its credit. Core team members are leading prestigious national research projects:

• Genomic ASSETS (Antimicrobial Stewardship Systems from Evidence-based Treatment Strategies) for Livestock, a Genome Canada-supported project that is developing new evidence-based livestock treatment strategies for antimicrobial stewardship
• Bison Research Group, which has already produced the world’s first in vitro fertilized (IVF) bison calves, born in 2016. Infrastructure proposed in the IntegrOmes project will build on this outstanding track record, cementing Canada’s leadership on the global stage.

USask has invested $38 million in the LFCE, a globally unique, state-of-the-art facility that was developed in partnership with leading industry organizations and end users to bring together every link of the livestock production chain.

With a land base of over 3,640 hectares (9,000 acres) and more than 3,500 head of cattle and 200 bison, the LFCE is the largest and most comprehensive centre of its kind in Canada. It enables Canadian and international scientists to focus on critical and timely issues related to livestock health, reproduction, nutrition, genetics, public safety and environmental issues facing the livestock industry. This unique livestock research facility is the foundation from which IntegrOmes will enhance Canada’s collective research capacity and form new synergies to find solutions to multi-dimensional challenges.

The IntegrOmes facilities will provide the LFCE with the critical pieces it needs to accelerate research in sustainable livestock production and species conservation. Using the LFCE’s Native Hoofstock Centre, IntegrOmes will develop the world’s first bison genome biobank. With a focus on conservation of threatened Canadian species, IntegrOmes will help to develop:

• germplasm collection
• fixed-time artificial insemination
• transvaginal ultrasound-guided oocyte collection
• embryo transfer to produce live healthy offspring

The LFCE maintains beef bulls and part of its cow-calf herd at the Goodale Teaching and Research Farm. New construction will add advanced genome biobank facilities that will be used to process germplasm for in vitro fertilization, embryo culture and cryopreservation. The project will enhance animal handling facilities to improve sample collection and to address challenges associated with handling bulls.

These sites will link to a proposed core multi-user genomics/phenomics and microbiomics research laboratory on the USask campus that will house a MALDI-TOF mass spectrometer, sequencing platforms (Next-gen and Nanopore), computational capacity, and other key instruments to enable genetic trait-selection, disease diagnostics and microbial metagenomics.

Another key aspect is a mobile laboratory that will allow team members to conduct field work at remote locations across North America. The mobile lab will be equipped to collect samples for DNA extraction and initial analysis, as well as for collection, processing and cryopreservation of germplasm.

Leveraging strong linkages with Parks Canada, Zoological Parks, and Indigenous organizations, IntegrOmes has embarked on an ambitious initiative to meet two critical challenges for Canada:

• conservation of the North American bison — an iconic species — using tools and strategies that can be extended to other endangered species
• maintaining competitiveness and sustainability in the livestock sector, an industry of critical importance to Canada

Though seemingly distinct, these two veterinary challenges are deeply intertwined, and IntegrOmes will integrate the use of genomic, microbiomic and phenomic tools to provide solutions for these pressing issues facing both wild and domestic ruminant livestock in Canada.

Goals of IntegrOmes

• Develop a bison genome biobank that will be used to revitalize North American bison and serve as a model for worldwide conservation efforts
• Enable adoption of genomic tools for the beef cattle industry that will address health and welfare issues and environmental sustainability as well as food quality, quantity and security.
• Develop on-farm, genomics-based, real-time diagnostic tools in partnership with industry producers and diagnostic laboratories — providing the Canadian beef cattle industry with effective methods for targeting antimicrobial resistance
• Conduct leading studies of the healthy microbiome — particularly of reproductive and respiratory systems — that have major impacts on livestock production
• Develop better screening and surveillance tools for domestic and wildlife species that will mitigate the spread of zoonotic and production-limiting diseases

Through these activities, IntegrOmes will inform conservation practices and efforts to combat antimicrobial resistance on a global scale, elevating Canada’s position as a global powerhouse in One Health research.

These facilities will also provide ties to a number of Canadian and international consortiums, including the following:   

• Functional Annotation of Animal Genomes (FAANG) project, a co-ordinated international effort on seven continents to accelerate the genome to phenome
• 1,000 Bulls Genome Project, a database in Australia containing the full genome sequence of nearly 4,000 cattle
• Genomic ASSETS for Livestock project (USask)
• NSERC/Beef Cattle Research Council Industrial Research Chair (USask)

USask ranks first in Veterinary Sciences and second only to the University of Alberta (U of A), in dairy and animal science agriculture among the U15 research-intensive universities. Through IntegrOmes, USask will consolidate key partnerships with the U of A and Saskatchewan Polytechnic (Sask Polytechnic):

• U of A provides increased opportunities for collaboration and knowledge translation through its ranches, Livestock Gentec and industry, government, and private sector partners
• Sask Polytechnic will provide unique training opportunities for real-world data handling through its Digital Integrated Centre of Excellence.

In concert with livestock associations, conservation leaders and Indigenous partners, IntegrOmes will foster an approach that will enhance competitiveness of Canada’s leading livestock industry and increase the capacity of species conservation and cultural restoration.

Home to Canada’s only dedicated zoo-based reproduction lab and full-time reproductive physiologist, IntegrOmes will continue to build on the Toronto Zoo’s collaboration with the USask Bison Research Group to establish the world’s first functional bison genome biobank. This biobank will model the way for biosecure transport of genetic resources for restoration of threatened species.

As one of Canada’s major conservation agencies currently working to revitalize bison, IntegrOmes has integrated two Parks Canada scientists into the project, enabling the increased ability to develop and translate new technologies across multi-sector boundaries. Bison have strong cultural significance for Indigenous communities. Poundmaker Cree Nation, Federation of Sovereign Indigenous Nations (FSIN) and Assembly of First Nations (AFN) have expressed support of IntegrOmes. Wanuskewin Heritage Park, a unique Indigenous-led park, is at the forefront of bison revitalization efforts — this partnership provides a mechanism for knowledge sharing.

IntegrOmes will continue to work closely with founding partners of the LFCE — the Beef Cattle Research Council and the Saskatchewan Cattlemen’s Association — to meet industry-identified priorities. Agriculture and Agri-Food Canada’s Canadian Animal Genetic Resources (CAGR) program is a longstanding partnership between AAFC and USask with a mandate to meet mutual aims of preserving Canadian livestock breeds and genetic diversity, as well as to develop new techniques to conserve germplasm. IntegrOmes will enhance the capacity of the CAGR program to preserve the genetic diversity of Canada’s wild and domestic livestock.

Prairie Diagnostic Services (PDS) is Western Canada’s regional veterinary diagnostic laboratory based at the WCVM. With PDS as part of our team, we increase our ability to develop diagnostic tools with primary end-users to promote uptake into the commercial stream.

The International Union for the Conservation of Nature estimates that more than 30,000 species (about 27 per cent of all assessed species across the globe) are threatened, including the North American bison. The iconic bison species holds great cultural significance to Indigenous peoples in Canada, and its conservation is a timely issue of widespread interest to Canadians.

Without immediate intervention, the North American bison as a pure species will become extinct. A genome biobank represents one of the best opportunities to revitalize the bison species and will serve as a leading model for other threatened Canadian species such as caribou.

The Canadian cattle industry is one of the largest exporters of red meat and livestock in the world and annually contributes $18 billion to Canada’s GDP. To retain its competitiveness in a global economy, the cattle industry must address changing consumer expectations, uncertain markets, new international frameworks around globally pressing issues such as antimicrobial resistance and the environmental impact of beef production.

Integrated omic tools will address issues of food quality and security, strengthen antimicrobial stewardship, and improve the industry’s production, competitiveness and environmental impact. Collectively, IntegrOmes will enable innovation that generates benefits for livestock producers, veterinarians and diagnostic end-users, federal, provincial and territorial governments and global policy makers as well as zoos and conservation agencies.