Of cow cams, computing and genetics

Researchers will use imaging to determine cattle forage preferences to study how these relate to factors such as weight gain and methane production. | Western College of Veterinary Medicine photo

Project led by the Western College of Veterinary Medicine brings a suite of high-tech tools to beef improvement research

Spy cams, biometric data processing with machine learning, advanced genomics — the IntegrOmes initiative aims to push the latest tools to the edge in the service of improving beef cattle.

“It’s a perfect testing ground for these new tools, and they are new,” said Dr. Gregg Adams, the reproductive specialist at the Western College of Veterinary Medicine, which leads the project.

IntegrOmes (integrated omics for sustainable animal agriculture and environmental stewardship) will be based at the University of Saskatchewan’s Livestock and Forage Centre of Excellence (LFCE) just southeast of Saskatoon near Clavet.

The “omics” in the name refers to a suite of tools. Genomics looks at genes, proteomics at the proteins they produce under various conditions, phenomics at physical characteristics, and microbiomics at the complex microbial communities that live in, for example, the rumens of cattle.

IntegrOmes will look at some familiar performance questions such as feed conversion and disease prevalence, but also behavioural traits.

For example, can genes determine which heifers will grow up to be good mothers? To find out, the researchers plan to use digital photos and video to observe cattle over time on pasture and in enclosed spaces, such as corrals and barns. They will look for behaviours, such as how quickly a calf gets up after birth, and how well a cow accepts its calf in its attempts to nurse.

IntegrOmes partner AlphaPhenomics has provided the means to capture and analyze the data. The Alberta-based tech startup has developed imaging, hardware and software tools for “non-invasive biometric measurement of livestock.”

Adams said this behavioural data will be combined with measures such as udder size and calf weight at weaning. With this information, researchers will turn to another set of tools — genomics — to see if they can identify genes that are associated with good mothering. If they find such genes, they can be used to select for these traits in breeding programs, something called marker-assisted selection, and it would be applied to both cows and bulls.

“If we can identify a Simmental bull in a three-way or two-way cross that will sire calves that will be good mothers, that would be helpful,” Adams said.

Marker-assisted selection is new to the beef industry, but has long proven its worth for dairy cattle.

“The SNP technology in dairy cattle has been the single most important advance in genetic selection, I think, in the history of the dairy industry,” Adams said.

SNPs, or single nucleotide polymorphisms, are variations in genes that can be used as markers to guide breeding efforts. Adams said that for dairy, it has been a tremendous success story in terms of increased milk production. Steady improvements over the last 50 years mean today’s cows are producing three times as much milk.

It’s also a cautionary tale since chasing this single trait can come at the expense of others, such as fertility, something dairy breeders are now working to correct.

Fertility is Adams’ specialty, and he sees exciting potential for beef cattle.

“We know using conventional genetic selection, it’s not been considered very heritable, so progress is slow,” he said. “But if we use really targeted, SNP-based selection traits, we ought to be able to make real advances in fertility, so we can select at both the dam and the sire side.”

Is being a good mom genetic? IntegrOmes researchers are trying to find out. | Western College of Veterinary Medicine photo

One potential goal is timing ovulation in cows so whole herds of 100 animals or more could be served by artificial insemination in a single day. This would have immediate benefits for producers.

“It would be nice to have a calving season of three weeks rather than three months,” Adams said.

To support such efforts, IntegrOmes is also establishing a “biobank” at the LFCE for bull semen, cows’ eggs, and fertilized embryos. The facility will also be used in a parallel program to guide development and conservation of pure bison genetics.

The IntegrOmes research team includes a wide range of expertise, drawn from universities in Saskatchewan and Alberta, as well as Agriculture Canada and the Toronto Zoo. They are examining production indicators such as weight gain and feed efficiency, but also disease detection and control, and behavioural traits like forage preferences. Other projects will look at environmental aspects such as methane production from rumen micro-organisms under different feed and forage regimes.

As genetic testing technology becomes smaller and portable, Adams envisions tools that can be used directly by producers in their day-to-day management.

“You could pluck some hair, feed that into a hand-held device,” he said. “I think these tools are getting so we could actually take them with us to the herd, or the herd owner could have one of these devices that could rapidly screen certain specific bacteria or viruses.”

IntegrOmes is funded through $6.75 million over five years by the Canada Foundation for Innovation, matched with another $10.1 million anticipated from the Alberta and Saskatchewan governments, Saskatchewan Cattlemen’s Association, Agriculture Canada, the LFCE and its supporters.

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