All Industry, All the Way

Jenny Patterson, a Gentec research associate, has built an enviable portfolio of industry support with pig companies in Alberta, Ontario and the US. As with all worthwhile things, this level of success didn’t come fast.

Jenny completed her MSc in Animal Science at UAlberta in 2001, specializing in Gilt Management and Reproduction. She then spent a couple of years at the Prairie Swine Centre in Saskatoon as a research assistant, where she was involved in running her first commercial trial in gilt management. She returned to the UAlberta as a research coordinator at the Swine Research and Technology Centre, for the Swine Reproduction and Development Program led by Drs George Foxcroft and Michael Dyck, where she became increasingly involved in large commercial research trials. Their research work focused on implementing management practices to better capture the true genetic potential of contemporary dam and sire lines by improving gilt management to maximize sow lifetime productivity, improving the impact of AI boars in the production system and improving efficiencies at the production level.

Her most recent work was as part of a coordinated National Pork Board research strategy at Holden Farms in 2014 to understand how birth-weight phenotype is a key factor in limiting sow lifetime productivity—and therefore important in the overall efficiency of replacement gilt management.

“As the project winds down, I was able to take some of the lessons learned and apply them to the industry,” she says. “Now, I’m partially supported by Sunterra Farms and Sunhaven Farms in Alberta, Hanor Company and PIC in the USA. Each group has slightly different goals: from gilt management to data collection and analysis to find areas for improvement.”

“I play a key leadership role in Gentec’s pork production efficiency initiative,” says Jenny. “The genetics are really good but translating them into industry is a challenge. We can do that by improving gilt management strategies—and resolving or reducing the gap between genetic potential and actual productivity.”

Among other tools, she uses data visualization to help make sense of the piles of data stored in production databases. What Jenny sends back to the industry client is a set of reports and recommendations to implement, and then manage and track the improvements.

“I enjoy the opportunity to use large production databases and going through that data to identify areas for improvement,” she says. “I firmly believe in making data-driven decisions.”

The industry partners provide excellent opportunities to foster important collaborative relationships—some of which started 15-20 years ago. Their international reach has seen projects land in Jenny’s lap from all over the Americas, and cover a wide range of farm types. Indeed, the next round of projects will see many of the same partners collaborating again.

It was as part of a National Pork Board study that Jenny got to know Gentec. Once the key birth weight phenotypes were determined, the team at Gentec completed association analyses between SNPs and the component phenotypic traits that determine litter size and litter quality (ovulation rate, early embryonic survival, placental development and uterine capacity) to identify genomic regions/genes and their potential biological functions and genetic improvement.

Jenny emphasizes that she is not a geneticist. Yet Gentec has opened plenty of doors to industry and academia.

“It was an honour to join the Gentec team in 2018,” she says. “As well as technology transfer directly to producers, another important part of my work is delivering research results at professional conferences, invited industry and technical meetings locally and internationally. Gentec has sown opportunities for me to help develop new projects; and I’m very excited to learn new skills and to use my expertise in new ways.”

Looking for a career path? Think agriculture!

Any well-motivated student with a good attitude can have a career in agriculture if they want it. So why do so many positions go unfilled?

“Mostly because there’s a disconnect,” says Frank Robinson, Professor of Poultry Production and Physiology at UAlberta. “Most animal science and animal health students are urban. Most of them don’t have a way to start getting experience with large animals so they can go on to get more experience. We have to break this cycle!”

So that’s exactly what he’s doing.

3-Day Animal Science Mini Internship Program

As of spring 2020, 364 students have participated in a three-day mini internship on poultry, dairy, pork, beef, equine and other farms during the fall and spring reading weeks. (The unusual notion was that “reading” week should actually have an academic component, not just be about skiing or beaches.) The last cohort comprised 118 students. Pretty good for a program that started only four years ago with 16 students.

And it’s low input, too. Students in the faculty of ALES can apply for $50, a statement of interest and an intake interview. Robinson trawls his network of producers, companies and sector associations. The faculty provides a travel/lodging allowance, if appropriate, and boots and coveralls that the students return at the end of their internship. (Robinson says his office smells like Canadian Tire.) And the hosts set up hands-on training that can range from calving, vaccinating chickens and often, plenty of mucking out (poop!).

 

The feedback is pretty positive. An overwhelming majority of the students report that they clarified and tested their career interests and felt more confident about their job prospects thanks to their new connections, and they learned how to apply their training/education in the real world. In fact, two students have done five (!!) internships, and over half the applicants are on their second one or more. The hosts also report enjoying the experience, wishing they had had similar support early in their careers.

Hosts also reported feeling more connected to the students. This is important since Robinson says that the most noticeable skill industry wants in a new recruit is communications: someone who can hold a conversation, not zone out on their phone the moment they have a second of down-time; someone who can be sociable, take direction, be part of a team and have fun doing it. So not necessarily the person who can pull a calf most efficiently, but the one who sees something that needs doing—and does it without being asked.

“Some farmers have hired students for the summer based on their experience with the program,” says Robinson. “That means success.”

Understanding that its recruits are mostly urban, the Faculty of ALES offers other opportunities for students to get their feet wet (literally).

AN SC101 – Principles of Animal Agriculture

Robinson has been teaching or co-teaching this course for over 40 terms. It’s an introduction to the structure of the livestock, poultry, and game ranching industries that covers the principles of animal management, breeding, feeding and current issues in animal agriculture.

“It’s the first farm-animal class, so we try to get their hands and feet dirty,” he says.

The students tour beef, poultry and dairy operations. They also do a project that involves farmers/farming, which could be as creative as building their own virtual farm with a $10 million start-up budget. At the end of the course, they pitch their farm, 3D models and budgets at a big evening event in an auditorium in front of a panel of judges. In a previous event, a real auctioneer sold the farms at the end of the evening, one of which went for $40 million. A tidy profit.

Back in 2018, Gentec CEO Graham Plastow volunteered as a panel member. “The enthusiasm of the students is infectious, and the judges have been known to get quite competitive about bidding for their favourites. That spilled over to the real fundraising auction where I bid on one of the Heritage chickens, which turned out be be money well spent as my hen was a very good layer.” (Sponsors can pick up eggs on a regular basis but they’re not necessarily from the spondored hen.)

Canadian Council on Animal CARE (CCAC) modules

While the 101 course and the internship give students a pretty good view of the producers’ perspective, if they’re going to study farm animals in a research environment, they need a different approach. UAlberta follows CCAC guidelines to deliver a three-hour session covering dairy cattle, swine and poultry (one session per species), taught by Robinson and other faculty and staff. On completion, the students are certified in handling that species, and can work with it in research. In the last two years, 240 students have been certified.

“City kids who haven’t been on a farm aren’t ‘fluent’ in agriculture or its techniques,” says Robinson. “Unless you grew up with mud on your boots, you don’t know how to halter a calf, move a pig or pick up a chicken. Students need these practical skills to get hired.”

Genomics: On the farm and off it

Tom Lynch-Staunton has a great job. He’s Regional VP for Alberta for the Nature Conservancy of Canada. He just started in August 2020. He manages the Alberta region conservation efforts, liaises with government, donors and landowners—and makes a point of getting out into the field. In fact, while he spoke to Gentec, he was driving to Bunchberry Meadows to meet a Natural Area Manager to learn about how the property has become a great resource for Edmontonians to experience a beautiful natural habitat.

But a career is (usually) a series of incremental steps. Tom’s started as a rancher on the family-owned Antelope Butte Ranch, where he became acquainted with genetic improvement from the producer’s perspective.

Our family was already using genetic improvement and crossbreeding to exploit hybrid vigour because we knew we could improve productivity, fertility, production efficiency, hardiness, survivability and overall health of the cattle,” he explains. “When genomics came along, it became much easier to select the best animals we wanted, and the best suited to our environment on the ranch. As the accuracy increases, we’ll be able to fit the right animals to plants, climate, soil and the landscape to increase profitability while maintaining or improving the health of the natural ecosystem. We’re still at the tip of the iceberg.”

Once at Gentec as Director of Industry Relations, Tom discovered the science behind what he was applying on the ranch; notably, the research process and the collaborations needed to move innovation into the industry.

Gentec is working on the issues that will be valuable to producers in the future—like reducing greenhouse gas emissions per animal, understanding the genomics of what makes a soil healthy, or ways to improve soil using that technology, improving livestock health, and using genomics at a landscape level to determine the best forages for each ranch. These issues are where Tom sees the biggest gains. Not to be forgotten are the background IT-type issues on how, for example to capture and interpret data quickly and easily to make decisions. And the data-sharing issues at an industry scale, which require becoming more integrated (like pork and dairy) so all parts of the value chain can share in the benefits.

“My time with Gentec was pivotal in my career,” he says. “It gave me a new perspective on how fortunate we are an industry to have such good livestock and plant research taking place in Canadian universities.” (See the YouTube video of “Rancher Tom” made while he was at Gentec.)

One of the things he particularly appreciated was a very effective spirit of collaboration. Tom has carried this model of “team successes” to every other job.

After Gentec, Tom held a dual rule with Canadian Cattlemen’s Association as Public and Stakeholder Engagement Manager and Alberta Beef Producers as Government Relations and Policy Manager. One of his responsibilities was collaborating with NGOs like the World Wildlife Fund, Ducks Unlimited and the Nature Conservancy of Canada to help conserve Alberta’s endangered native grasslands through cattle ranching.

“When an NGO talks positively about how ranchers can benefit conservation and stewardship, this helps change some of the negative perceptions of the beef industry,” he says, noting that the family ranch business has shares in the Waldron Grazing Co-op that partnered with the Nature Conservancy in one of the largest grassland conservation agreements in Canada.

During that time, Tom was a member of the Canadian Roundtable for Sustainable Beef, which recognizes the symbiotic relationships required for taking care of the environment and the economic viability of ranching. Then the opportunity arose at the Nature Conservancy, which strongly aligned with his view of the future.

As he points out, “It all started on the ranch, helped by Graham Plastow (Gentec CEO) and Gentec. My career path really highlights that if you know agriculture, you can also work in conservation and plenty of other fields.”

Gene Editing: A glimpse into the future of agriculture

“It’s an absolute revolution!” insists Bruce Whitelaw, Professor of Animal Biotechnology at The Roslin Institute, Scotland, of gene editing. “Scientifically, the potential is huge. It allows us to increase the genetic variations from which producers can select animals with traits they want to promote.”

Whitelaw and his team recently announced the potential to insert a variant of the RELA gene from warthogs and bush pigs into domestic pigs, which could make the latter resistant to African swine fever, a nasty and often deadly disease. Genus/PIC (at the behest of Graham Plastow, now Gentec CEO) funded the preliminary work to find the genetic variation many years ago but the project stalled for lack of technology to develop it. It has only now borne fruit because gene editing came along as the enabler. Other recent gene edits in pigs include the generation of GDF8 (myostatin) mutants to increase muscle, and resilience to diseases such as PRRS and foot and mouth disease.

This is gene editing as Whitelaw intended—with major application in resilience to disease, which is a major burden in livestock. Other applications he foresees include reproductive efficiency (increasing the number of females who bear multiple offspring, for example, rather than increasing the number of offspring per gestation) and gender selection, which is particularly important in the dairy industry where male offspring have little value, and which has been difficult to achieve beyond the sexing of semen. Farther down the line, it may be possible to introduce heat or drought tolerance from indigenous animals into mainstream animals, therefore expanding the footprint of livestock around the world. Used in this way, gene editing will help satiate the growing human population’s desire for animal protein.

But will producers want to use it?

“Producers are chasing it!” says Whitelaw. “What industry partners have to do is demonstrate applicability. The University of Missouri showed that you could edit variation into gene CD163 and create PRRS resistance in pigs. (Ed: Gentec reported this in our December newsletter. See source article here). Now, the task is to take that project, make sure the trait has no deleterious effects on other traits and show its true utility.”

And the Number One question since, if consumers don’t buy the product, it’s all moot—will they understand the difference between gene editing and genetic modification? The latter has had a rough ride over the years. Introducing transgenics didn’t go down well. Special-interest groups focused on nebulous health and environmental effects.

Gene editing, on the other hand, produces simple base variations that can happen naturally. Using Whitelaw’s RELA project as an example, the variation of that gene in warthogs and bush pigs may well appear in domestic pigs naturally—but evolution moves at glacial speed. Given the increasing global population, humans can’t wait that long. One person in seven is malnourished today. By the time we reach 9 billion, that figure is expected be one in three if we don’t increase production of agricultural protein. Genome editing can slash the standard 20+ generations of breeding required to introgress a gene allele back to just one; and eliminate evolution’s lop-sided variety in favour of specific alleles that increase food value.

For consumers to buy in to gene editing, two things have to happen in parallel: a full discussion with regulatory authorities to put in place an appropriate regulatory pathway to take the technology to market; and another full discussion—this time with the public—to convey that this is a good, safe technology.

“Gene editing does exactly what it says on the can,” says Whitelaw. “Every offspring carries mutations that neither the dam nor the sire has. Some are good, others not. Evolution selects the good ones. We’re doing exactly the same thing, except that we know the change is beneficial. Individual animals will be more robust, less sick and therefore have a better quality of life. That has to be a good thing at every level.”

Beef production in the pandemic: From producer to plate

COVID-19 has been complicated in many ways by uncertainty. Unlike many disease outbreaks, it is not about food safety or consumer confidence with food products – but rather about the effects of social distancing strategies and their impact on food production, distribution and consumer lifestyle factors.

As the pandemic unfolded, meat-processing sectors in Canada and the USA experienced rolling plant closures and slowdowns as industry invested over $50 million to ensure the safety of plant workers and protect against COVID-19. However, measures to address distancing requirements reduced production efficiencies and added costs to every aspect of operations. The reliance on human proximity in meat-processing sectors proved to be the weakest link in the supply chain, coupled with employee interaction away from the processing facilities.

Reduced slaughter volume created supply challenges in the retail sector and an estimated backlog of 125,000 head as of the end of May causing North American cattle prices to plummet as the log-jam grew. The lack of processing capacity and competitive bidding due to temporary closures or reduced output caused livestock in all sectors to back up on both sides of the border in the face of unprecedented demand.

Cow calf producers and backgrounders are able to keep their animals on grass or silage longer, and feedlot operators are able to switch to holding diets based on higher roughage and lower energy rations to slow the growth rate of animals. The type of animal, the weights and age all factor into the quality, value and market destination of the beef in the box. All these measures represent a significant increase in costs and resources for producers to slow down a system designed to deliver market-ready cattle 52 weeks a year.

The shutdown of restaurants combined with consumer buying trends to stockpile food added to the problem resulting in out-of-stock situations in food stores. This added fuel to the perception of a pending food shortage in Canada. Demand increase for beef across the board soared 100% at the highest point, with a huge run on ground beef. Processors could not provide the trimmings needed to keep up to ground-beef demand, resulting in higher-value cuts being utilized, which pushed prices higher and further reduced inventory for other beef cuts also in high demand. Imports of beef increased 14%, YTD May 30 vs. same time last year while exports went down 13% YTD April 30 vs. same time last year.

The pandemic continues to have an enormous and worldwide impact on agriculture and agri-food industries, although it is too soon to know the long-term impact of COVID-19 and how the changes made will affect future meat-processing systems. Canada is better equipped to handle the next pandemic or a resurgence of COVID-19 this fall.

“I hope the meat-processing industry will consider innovation, automation and robotic technologies to reduce the dependency of human contact to reduce the risk and increase productivity,” says Michael Young, President of Canada Beef. “The Canadian beef industry has a very bright future, post COVID-19. We have a high-quality product that’s in high demand in Canada and around the world.”

Solving AMR through a One-Health lens

The newly-funded Antimicrobial Resistance – One Health Consortium managed out of UCalgary* is about to play an important role in how we safeguard the eroding ability of antibiotics to save lives and prevent illness. Its role will be to leverage the capacity and expertise across Alberta, nationally and internationally to find solutions to a looming antimicrobial resistance (AMR) crisis in humans and animals that spills over to the environment—hence the one health approach. Currently, several thousand Canadians die every year from infections with multiple drug-resistant bacteria, and the rate of increase is exponential. Worldwide, the economic impact of these infections is estimated at US$100 trillion/year.

“In the beef industry, there’s a lot we don’t know,” says Dr. Herman Barkema, Scientific Director of the Consortium and NSERC Industrial Research Chair in Infectious Diseases at UCalgary’s Faculty of Veterinary Medicine. “And we can’t even talk about cow/calf and feedlot operations in the same breath because antimicrobial use and resistance differs in each sector.”

For example, calves are treated with antimicrobials on arrival at the feedlot, then they get medicated feed for the duration of their stay. How much resistance that produces, and whether it causes problems in run-off? Who knows? Then, there’s the health of the animal to consider. The public is playing an enormous role in wanting meat products that are raised without antibiotics, which is reducing on-farm use—but perhaps at the cost of sick animals not getting the drugs they need to stay healthy and productive. And of course, there are people—the producers and their families, and the workers in the industry all of whom may be impacted by AMR.

“If we get resistance against frequently-used drugs in the feedlot, we have a problem—and emerging evidence shows that antimicrobials ARE becoming less effective,” says Barkema. “The only way to protect people will be with drugs of last resort, and we should really be careful not to overuse those because they are exactly that… last resort!”

The Consortium’s 27 projects focus on treatment optimization, AMR surveillance, and infection prevention and control under three thematic areas: innovation and commercialization, education and societal impact, and policy, economics and sustainability.

So why are pharmaceutical companies not investing in new antibiotics? Any new drug is likely to be safeguarded like gold, and used only to treat multi-drug resistant infections. So, minimizing drug use is one way to combat resistance—but it doesn’t result in the large sale volumes needed to recoup the $2-4 billion costs to develop and receive regulatory approval for use of an antimicrobial.

Instead, the Consortium is looking to alternatives like phage therapy, new targets, biomarkers, stewardship, the microbiome, as well as optimizing the use of current treatments. It is also developing protocols to change the prescribing habits of veterinarians, pharmacists and doctors, and the usage practices of farmers and people. Vaccine development, hygiene protocols for people and animals, and genetic selection for disease resistance can all lower antimicrobial use.

“We are excited to be involved in this initiative as we know that some animals are more resilient to infectious disease than others,” says Plastow. “Identifying them is the challenge; however, our work in pigs and cattle is helping develop tools to do this. The team. including others at UCalgary like Karin Orsel and Frank van der Meer. have generated phenotypes and samples to push this effort forward. And Gentec’s Janelle Jiminez will be working with these researchers from April to find new funding to exploit these resources.”

Use practices are already starting to change. As of December 1, 2018, the over-the-counter sale of medically-important antimicrobials is no longer allowed. Such products can only be purchased with a prescription issued by a veterinarian. Those are the (relatively) “easy” administrative changes. The Consortium’s innovative solutions will take years to develop, test and employ, although consumer and retailer push (A&W, McDonalds, Maple Leaf, Sobeys, etc.) may accelerate uptake.

“Then,” says Barkema, “we’d better be ready to follow. Our results in beef will apply to other livestock, and connect to people and the environment. If we use less antibiotics in agriculture, there’s less run-off and less soil contamination. That means better drinking water and environment. Everything is linked.”

* The Consortium is Alberta-wide, comprising the universities of Calgary, Alberta and Lethbridge as well as Lethbridge Research Centre, Olds College, Lakeland College, Southern Alberta Institute of Technology and Northern Alberta Institute of Technology.

1,600 chickens… and counting

Because the Leghorn chicken is so prolific (up to 320 eggs/year!), it is the darling of the egg industry, and produces the vast majority of eggs in Canada. They lay white eggs, so it’s easy to tell. For those who prefer a brown shell, you can thank the Rhode Island Red and a few other breeds. Between them, they’ve locked up the market.

So what happened to the breeds we used to see around farmhouses, back in the day? Some of them are in trouble, with few individuals left, certainly not enough for a healthy population. Ten of these breeds (1,600 chickens total) find a home within the Heritage Chicken program at UAlberta (with another population at UGuelph, in case of catastrophe at one location).

“Currently, in-breeding is high among four of the breeds because they’re randomly mated,” says Marzieh Heidaritabar, the Gentec post-doc trying to develop a funded project for the program off the side of her desk. “But this isn’t efficient. Ideally, we want a proper breeding program to select the best animals. Genomics is the best tool to help us select the most diverse sires and females as parents of the next generation.”

Eighty-five chickens have already been sequenced. “That’s how we knew inbreeding was high in the first place,” says Marzieh. Now, another $70K is needed to finish the job, and fund students and tests. She plans to apply to NSERC this year to, hopefully, get the project rolling in 2021.

The goal would be to keep the unique genes in the breeds and increase the number of individuals over 2-3 generations to assess the success of the breeding program—but it may make more sense to merge the breeds if they are genetically close. Secondary objectives would be to examine immunity and behaviour, both of which may increase the suitability of the breeds for certain environments. Two other ongoing projects are working on perching and gait traits.

While Marzieh will go through traditional Tri-Council channels and the higher-tech GoFundMe platform, the program has been creative about fundraising in a different way. $175/year will get you a dozen eggs every other week for 10 months. Or you can adopt-a-rooster instead (similar program minus the eggs).

“Every little bit helps,” says Marzieh, “and it’s a great way to get the public involved.”

The First Outbreak of Porcine Epidemic Diarrhea (PED) in Alberta

Julia Keenliside DVM MSc
Veterinary Epidemiologist
Alberta Agriculture and Forestry

The porcine epidemic diarrhea (PED) virus first made the jump from Asia to the USA in 2013. Since then, it has spread rapidly across the USA and parts of Canada. Until 2019, the Alberta pork industry had succeeded in keeping the virus out of the province. That changed on January 7th when the first case was confirmed near Drumheller. Three more cases followed in February and March in the Lethbridge area. As of July 2019, the outbreak is still limited to four farms.
PED is a viral disease that affects only swine and their relatives (including wild boar). Symptoms are often unmistakable, with large numbers of pigs affected by severe diarrhea, vomiting and refusal to eat. It is generally fatal in young piglets, but older pigs will recover completely within a week or so. An outbreak typically spreads rapidly, and 3-5 weeks of piglet production may be lost, taking an emotional toll on pig caretakers. Despite its spectacular appearance, people cannot become infected, and pork from affected animals is safe to eat.
The virus survives well in pig feces and on surfaces contaminated with feces from infected animals, especially when frozen. Transport trailers, equipment, boots and loading docks can all become contaminated and serve as sources of infection, allowing outbreaks to spread between farms. Biosecurity measures are the best prevention. However, it only takes a very small amount of virus to cause disease in nursing piglets, so it can occasionally sneak into even the most biosecure farms. Often, the source of the spread is never found.
PED likely entered Ontario in 2014 through feed containing contaminated porcine plasma from the USA. In contrast, evidence in Manitoba suggests the virus was brought in by contaminated American trucks loading pigs at Canadian assembly yards. Manitoba has reported 160 cases since then and Ontario 125 cases. Manitoba has confirmed 60 cases as of July 2019.
Despite a detailed investigation, we still can’t be sure how the virus spread into Alberta. Swine traceability program data showed no transport links with PED-positive premises or contaminated vehicles coming from outside Alberta. Environmental surveillance samples did not show any contamination of assembly yards, abattoirs and truck washes in Alberta throughout 2019.
However, we did find some risk factors. For example, feed ingredient trucks from Manitoba and the USA did deliver ingredients directly to the first Alberta case. A piece of used clean manure equipment from Manitoba was also brought onto the farm. Feed ingredients found on the affected farms originated from nine countries, four US states and five provinces, most of which are infected with PED.
Unlike Manitoba, Alberta farms are generally far apart, which slowed the spread of the virus. There were no direct transport links between any of the affected farms, and the industry did a good job in keeping biosecurity tight. The exact method of spread between the Alberta cases was not clear, as the usual risk factors of contaminated transport vehicles, assembly yards and abattoirs were ruled out. The three southern cases are within 20 km of each other. We know that the virus spreads more easily through transport, people traffic or even the air when farms are closer together.
Risk factors that were identified during the investigation that producers should address include:
a) Changing boots and clothing every time before entering and leaving the barn, even when just going to the feed mill;
b) Washing, drying and disinfecting trailers every time they are used, even if going to abattoirs or assembly yards that have had negative environmental test results;
c) Working with suppliers to understand and reduce the risk from feed trucks and feed ingredients coming from PED-positive regions
d) Being extra careful when equipment and visitors come from PED-positive regions.
All four affected producers are working closely with their veterinarian, Alberta Pork and Alberta Agriculture and Forestry (AF) to eliminate the virus. One farm has depopulated, and is testing in preparation to refill. The other three are farrowing again, and moving hogs to market without any clinical signs. All four farms are working towards achieving presumptive negative status by the fall 2019.
PED is a reportable disease in Alberta. If you suspect PED, call a veterinarian and notify (mandatory) the office of the Chief Provincial Veterinarian.

Happy Birthday, gEBVs!

It all started with an idea…. Former Gentec CEO, Steve Moore’s PhD student, Stephanie McKay, thought about developing a SNP chip for applications in cattle, a project that eventually became part of her thesis. With input from Gentec bioinformatician Paul Stothard, plus Tim Smith and Curt van Tassel at the USDA and Jerry Taylor at University of Missouri, that first commercial SNP for cattle on a 50K chip ushered in a new era.

It wasn’t long before 50K SNPs grew to 700K thanks to the advancement of technology. The objective was to develop a tool to predict genetic merit in an animal. The 50K and 700K became the first tools used for large-scale genotyping of cattle and then other livestock species.

Until then, it took 5-7 years to get an accurate reading on a dairy bull’s merit. (Until somebody figures out how to milk a bull, any measure of milk production has to come from daughters, hence the delay.)

To illustrate the old system,” remembers Moore, “I was telling researchers in Australia that we’d sequenced the top bull in Canada, called Braedale Goldwyn. They said they’d sequenced the top bull in Australia… also called Braedale Goldwyn. He’d been dead for four years but was still the top bull in both countries because of the amount of semen stored and how long producers had to wait for new data.”

The dairy industry’s widespread use of artificial insemination (AI) turned out to be a good thing. All those stored straws turned into an amazing reference population that other livestock didn’t have.

“We could go back to the Fifties!” says Filippo Miglior, former Gentec-associated researcher, now Chief Scientific Officer and Vice President, Sector Innovation and Programs at Ontario Genomics. “Having this reference population provides the biggest difference in terms of accuracy.”

For the first time, producers pushed instead of needed pushing. Dairy producers export a lot of high-end animals and embryos. They wanted quality assurance of their genetics, not just third-party evaluation. With genomic testing at $45/animal (now down to $33) they could test their heifer calves, which helps improve herd management decisions such as which ones to keep or sell, which ones to breed with sexed semen, which ones carry a genetic recessive characteristic, etc.

“The rate of increase in usage in Canada was fantastic,” remembers Miglior. “One of the fastest across all dairy countries—5%/year.”

Now, bulls could be assessed at one year old or even at the embryo stage. The accuracy of genetic information for newborn males and females doubled and a major shift happened towards the use of much younger animals as parents and a significant gain in the intensity of selection, especially for young bulls bought by AI companies. As a result, those genomic-tested young bulls now occupy 70% of the market share and the progeny proven sires only 30-35%, a 180-degree switch. Rates of genetic progress have now more than doubled—even tripled for some traits.

A sea change happened in the AI sector,” says Brian Van Doormaal, Chief Services Officer at Lactanet Canada. “Any AI company can easily have their bulls receive a Canadian genomic evaluation simply with a DNA genotype so the industry has become extremely competitive. Most multi-nationals now own females, with internal programs to produce the most elite young bulls possible. Before buying bulls, which is now based on a new step of pre-genomic selection, they assess each bull’s genomic evaluations and a long list of characteristics, including undesirable recessive traits and haplotypes that negatively affect fertility.”

Since data was only required from a subset of bulls, other traits, such as fat content, A1 vs A2 milk, protein, volume, conformation, hornless or polled, embryonic death, mastitis, lameness, metabolic diseases could be included as well.

Beef cattle were a different story. First, the data simply weren’t there. Second, bulls are come and gone by the time they’re three years old. Third, AI isn’t the norm. But the real holdup is phenotyping animals that you don’t see close up very often. All of which led to a lag compared to dairy. That gap is closing as the larger operations realize they don’t need to wrassle down every last bull to pull a tail hair. While all the Canadian breed associations offer testing, the clear leader is the American Angus Association, which tests a massive 300,000 head/year.

“We always assumed that progeny is 25% related to each grandparent,” says Doug Blair (former CEO, Alta Genetics Inc.). “Genomics found that it’s more variable than that. The contribution from any grandparent may vary from extremes of 15% to 35% rather than 25%. Thus two fullsibs may have very different contributions from the 4 grandparental genomes. My analogy is that we used to forecast weather with ships in the ocean. Now we have satellites. Genomics has done the same for estimated progeny differences.”

So what might the future bring? As genotyping becomes cheaper, it will become a mainstream tool for every producer. It may even be possible to genotype every animal in Canada. This will be useful for traceability, genetic defects, parentage—and for solving issues such as fertility.

“We obtained huge benefits from genomic selection, very fast” concludes Miglior. “It’s a huge success story for Canada that we’ve achieved that in such a short time.”

21st Century Solutions for Canada’s Dairy Industry

Where once genetic and herd management services to the dairy industry came from separate sources, Lactanet Canada now integrates these services under one organization.

As of June 3, 2019, founding partners of the new Lactanet (Canadian Dairy Network, CanWest DHI and Valacta—the leading dairy herd improvement organizations responsible for genetic evaluations, milk recording and knowledge transfer) can offer access to modern herd management through improved technologies and software and more meaningful data. Not only will these integrated services make life easier for farmers, Lactanet will also offer new services, using the same current resources. These services will be offered before the end of 2020, and include remote electronic collection of on-farm data, a national dairy cattle traceability system and genomic evaluations for feed efficiency,

While the objective in creating the partnership was not to save money (although operational efficiencies are predicted), Lactanet’s Chief Services Officer, Brian Van Doormaal, points out that fees for current services to farmers and the staff delivering them, are not projected to change nor are genetic evaluation services to the industry.

What Lactanet will do is: better position the dairy sector to manage business risk, take advantage of operational synergies and efficiencies, integrate genetics with management services, stimulate innovation of new products and services, and build on the strengths of each partner.

“The sector as a whole will benefit,” says Brian. “We’ll be able to help farmers tackle the challenges of the Canadian dairy industry, which include lower milk prices, increased farm debt load and rising interest rates.”

Lactanet’s governance structure is designed to reflect the three founding organizations, and focus on services to Canadian producers: every member of the Board is a dairy farmer. Three additional important industry partners have a producer appointment to Lactanet: Dairy Farmers of Canada, Semex Alliance and Holstein Canada.

“Holstein represents over 90% of all dairy cows in Canada,” explains Brian. “And Semex is the largest Canadian farmer-owned A.I. company with national reach. Dairy Farmers of Canada is the national body that represents all licensed producers from coast to coast. In this way, the Lactanet Board covers the vast majority of services to farmers. As well, working with a Board of nine producers, with the ability to name two additional external directors, allows us to be more nimble in these early stages and ensure success. The Lactanet governance model is scalable, if needed, as the industry decides how to best meet the needs of dairy farmers and remain globally competitive.”