The value of genetics: selecting for resilience to disease

Bovine respiratory disease or BRD is usually caused by a variety of pathogens, both viral (bovine respiratory syncytial virus (BRSV), paraInfluenza 3 (PI3), adenovirus, bovine viral diarrhea virus (BVDV), and infectious bovine rhinotracheitis (IBR)) and bacterial (Pasteurella multocida, Mannheimia haemolytica, Histophilus somni, Mycoplasma bovis). This makes it a challenge for traditional biosecurity or vaccination. Unfortunately, the way that most beef cattle are finished compounds this problem in a number of ways. For example, the cattle are challenged with several types of stress in addition to the potential for infection by these pathogens. Stresses include weaning, transport, mixing with cattle from different sources, and change of diet. Our own experiences with COVID-19 may help you sympathize with these cattle in terms of them keeping healthy.

How important is BRD in Western Canada? Mike Jelinski (Veterinary Agri-Health Services in Airdrie) and Eugene Janzen (UCalgary) reported respiratory infections as the leading cause of antibiotic treatments in calves from birth to weaning. At least one calf was treated for respiratory disease on 77% of Western Canadian cow-calf operations (and BRD accounts for 65-80% of the sickness and 45-75% of the deaths in some feedlots).

Now, Gentec and its partners are taking a multidisciplinary approach to better understand the options available and the return on investment for different approaches. For example, Karin Orsel at UCalgary has been looking at how preconditioning (vaccination, different types of weaning, and handling) can reduce the incidence of BRD in the feedlot. This work is part of the Major Innovation Fund initiative on antimicrobial resistance (AMR) led by Prof Herman Barkema at UCalgary, as is a Gentec project looking at the potential to select for animals that are more resilient to polymicrobial diseases (BRD in cattle and PRRS in pigs). It made sense to combine our ideas, and look more closely at the problem. We have now been joined by Xiaoli Fan from REES at UAlberta who is also part of the AMR Consortium. She is modelling the cost effectiveness of the different potential interventions.

Although Gentec CEO Graham Plastow has long suggested the use of genetic selection for disease resilience, especially for polymicrobial diseases such as BRD (see here, here and here), the value of this approach is thought difficult to apply. Barriers include collecting the phenotypes required for progress and the low reported heritability of the trait. And until very recently, veterinarians and researchers have been skeptical about the value of using breeding to select for reduced disease susceptibility. The low heritability of the trait was one of the main reasons. However, recent work has reinvestigated the idea and provided strong support for its potential. Why? Well, it comes down to the R value – again perhaps you recall the importance of R in managing the spread of the COVID-19 pandemic. Researchers at Wageningen University combined the fields of genetics and epidemiology to show that selecting for animals that are less susceptible and less infectious has great potential for reducing the spread of animal diseases. Hulst and colleagues identified a major flaw in such criticism building on some of the work of Gentec collaborators, such as the late Steve Bishop and Andrea Doeschl-Wilson at the Roslin Institute. The Wageningen authors combined epidemiological models of transmission with quantitative genetic analysis of disease status to identify the potential response to selection for reducing the prevalence of endemic infectious diseases. Their results show that the typical heritability values seen support a very substantial genetic variation in disease susceptibility among individuals and, IMPORTANTLY, that eradicating infectious diseases by genetic selection IS possible. This is because previous genetic models ignored the positive feedback effects that occur when reducing the transmission of infectious diseases. These effects are related to concepts of herd immunity (again, see COVID-19) and contribute substantially to the response to selection. These authors conclude that the genetic variation in disease susceptibility that is available can translate into a large responses to selection in terms of disease prevalence and that this will “make it possible to eradicate infectious disease, at least in theory.”

With funding from RDAR (A Multidisciplinary initiative to apply genomics to reduce the incidence of BRD and antimicrobial use in western Canadian beef production: $363,000), the Alberta team is set to try to demonstrate this for BRD. The researche team including Fan, Orsel, Jelinski, and Brenda Ralston at Lakeland College will be working with two commercial feedlots to collect the evidence and find tools to enable selection to reduce BRD. We hope to build on this study in the future. Please contact us if you would like to know more and/or would like to be part of future studies.

Graham Plastow

CEO, Livestock Gentec







At the Grill with William Torres: A royal love for cattle

This month’s At The Grill feature by William Torres (former Research Manager at Cattleland Feedyards and popular presenter at Gentec conferences) reminds us of Queen Elizabeth II’s passion for agriculture.

It is world news that this 8th of September, 2022, Queen Elizabeth II passed away. She was the longest-reigning monarch in British history and she was also a lover of cattle and horses. While most of the world remembers her corgis, those in the agricultural realm know just how vast her involvement was. Let’s recap some of Her Majesty’s involvements.

In 2001, Prince Philip, the Duke of Edinburgh, had the idea of selling high-quality goods from the royal farms at Windsor and other small local suppliers to support smaller businesses in the area while providing customers with the best quality products Britain had to offer.

The royal farms at Windsor consist of 200 registered Jersey cows, a Sussex beef herd, 140 breeding sows, 1,500 Lohmann Brown hens, 1,000 acres of arable land and 2,000 acres of grassland, mainly used to feed the livestock.

According to the farm’s website , the late Queen’s Jersey herd is based at Prince Consort Farm in The Home Park. The original farm was designed by Prince Albert in the late 1850s. The original buildings were extended with new winter housing for the cows, and they now feature robotic technology. Additionally, the farm features automatic cow brushes as well as waterbeds for the royal herd to lie on.

YES! Real waterbeds. According to Mark Osman, the farm manager, “The water pushes underneath the pressure points, and the cows end up sort of floating.” Apparently, the entire royal family took part in choosing the water beds, which are also rather pricey.

While it is not known as to what will become of the royal farm, the milk is currently being sold to produce Windsor Castle ice cream.

In Scotland, the late Queen is fondly remembered for her long-standing enthusiasm and support for farming, rural life, and the countryside as well as her patronage and visits to the Highland Show. The late Queen raised Highland cattle since 1953 at her home in Balmoral.

She took part in, and visited many shows, like the Country Show at Saint John, Jersey herd in 1978. The breed was one of her favourites. The royal family’s Jersey herd is one of the oldest in the UK; some of the cattle can be traced back to 1871.

Personally, with my current involvement as President of a veterans’ support group, I have learned much about the devotion from our men and women to service and the Crown. One of our members with a farming background was presented to her during her coronation when he was only 10. He now stated, “Her Majesty has been the embodiment of duty and public service, seeing the country through seven decades where we have seen huge change in our nation and in our fields.”

From the agricultural point of view, Her Majesty, in an ever-changing and challenging world, has always been a constant and a great supporter, including here in Canada. Her examples of service, duty and loyalty are timeless, and ones that we can and will follow.


Gentec helps solve sex mystery

“How did they get THAT wrong?” mused Donagh Berry, Statistical geneticist at Teagasc in Ireland. “We asked producers for female DNA samples. These are bull samples!”

The physical differences between females and males are pretty clear. So, to paraphrase Donagh’s question, why this seemingly glaring error?

Let’s back up a bit…

The Irish Cattle Breeding Federation run a national program funded by the Irish government and the European Union to increase the productivity of the national beef herd by improving genetic merit. On average in Ireland, 83% of mated cows go into calf, which, in a herd of 1 million cows, means that 170,000 cows are walking around with no “output”. The benefit of simply increasing the pregnancy rate is putting more coin in producers’ pockets as well as improving environmental efficiency. The increase also means more meat on consumers’ plates.

Because using genomics tools can accelerate genetic gain, producers were asked to submit DNA samples of their cows and potential heifers in order to identify superior females to breed the next generation. Over 1 million samples were submitted.

Females have two X chromosomes; males have one X and one Y chromosome. That’s pretty simple. But as the DNA testing progressed, some anomalies were detected. A small number of samples were arriving with male DNA (i.e., one X and one Y chromosome) despite producers being instructed to submit samples from females. Hence Donagh’s question.

Producers had less faith in the technology, and more faith in the udders they saw in front of them. They sent in more samples from those animals. Wrong, wrong, wrong. The “heifers” still registered as male; and each side started digging in their heels. Donagh declared this mystery needed solving, and turned to his long-time collaborator, Gentec researcher Paul Stothard (UAlberta) for advice.

“I went to look at these heifers,” says Donagh. “They were definitely female. So I took yet more samples. It turns out that these animals are female on the outside but have the DNA of a male. In other words, they have the Y chromosome. Then I checked out the literature, and found that it was a known syndrome called Swyer, which exists in humans, too.”

Under necropsy, Donagh could see that the animals were female internally as well but infertile. Given the 680,000 genotypes generated at the time, and the eight anomalous results detected, Donagh and Paul deduced that the incidence of Swyer is 1 in 80,000 cows, about the same as in humans.

So what are the implications?

“Well, saving face is a big one,” says Donagh. “There’s always an undercurrent of skepticism about technology. An abnormal result like this puts the credibility of genomics into question. In Ireland, this could spread on social media, and the whole thing is in jeopardy.”

For producers, the implications are somewhat smaller—or 6-8 animals per million. A chromosome-counting technology is available for about $150 that detects karyotype abnormalities like Swyer, Edward syndrome, Turner syndrome and Down syndrome. Because these syndromes are so uncommon, Donagh doesn’t recommend this course of action.

But with current genomics technology that measures tens of thousands of pieces of DNA, Donagh and Paul discovered that seven of the eight cows were missing the SRY gene on the Y chromosome. (The eighth cow was an anomaly of an anomaly: she had the SRY gene. We don’t know why.)

“Detecting Swyer is as simple as adding DNA markers in the SRY gene on the genotyping platform already used at no additional cost. DNA markers on the rest of the Y chromosome already exist on these platforms” says Donagh. “A Swyer female will give you a signal for the Y chromosome but not the SRY gene on that chromosome because she doesn’t have it.”

Paul and Donagh have suggested DNA markers that companies can include on their platforms so that, when producers get their animals genotyped, they will get a result for Swyer as well. The group has already developed methodology to infer other chromosomal abnormalities, such as Turner Syndrome, again at no additional cost.

“We wanted to leverage the data to deliver more information,” says Donagh. “At the end of the day, producers are genotyping and getting information on parentage, abnormalities, congenital defects, etc. all from one sample. They get Swyer thrown in for free. You can argue that the incidence is low… but the cost is zero!”









Demonstrating Gentec’s Replacement Heifer Profit Index at the GWFA field day

A significant difference between the commercial and purebred cattle sectors is the lack of technology available to commercial producers to genetically evaluate their animals. The purebred industry has been using Expected Progeny Differences (EPDs) for decades but some of the traits assessed in full-blood cattle aren’t as economically applicable to crossbreds.

Gentec is working to increase the accessibility of genomics to commercial cow/calf producers in Western Canada so they can select more suitable breeding stock and increase their profitability. Gentec has developed the largest reference population for Western Canadian crossbred beef cattle, and created two DNA-based selection indexes for commercial cow/calf herds: a feeder profit index (FPI) and a replacement heifer profit index (RHPI). Each index aims to achieve objectives that are significant to feeder progeny and replacement heifer selection. Gentec has ongoing projects to measure these indexes’ validity, allowing producers to capitalize on the benefits of genomics for only $15/head—instead of the normal $45. Using a hair sample, the genome is assessed at the SNP level to detect the smallest differences in DNA. The results are called genomic-enhanced EPDs (gEPDs), which are about twice as accurate as regular EPDs.

The FPI aims to improve growth, feed efficiency, carcass value, and net return of feeder calves. The index was created by weighing relevant traits with their economic data, which can help producers detect changes in profits. The traits included in the FPI are post-wean average daily gain, feed intake, metabolic mid-weight, residual feed intake, and six carcass traits. The relationships between various traits were also accounted for, making it easier to improve multiple traits at once. Using the FPI can help produce progeny that perform more efficiently in a feedlot through the selection of better sires and dams.

The goals behind the RHPI are to improve the efficiency, fertility, and longevity of replacement heifers while maintaining or reducing production costs. One way to measure these three pillars is to quantify an animal’s genomic breed composition, which is referred to as the hybrid vigour score in the RHPI framework. By compiling the hybrid vigour score and gEPDs from up to nine traits, the RHPI is assigned to each female in the form of a numerical value, which can be compared with results from other females in a group. This is a great additional selection method as it offers a unique snapshot of their genome that can help producers make more informed decisions.

Our mission at the Grey Wooded Forage Association is to promote sustainable forage and livestock management practices. We are very committed to providing information to producers on new technologies to help them achieve their production goals and optimize efficiency. On June 22, GWFA hosted the ‘Livestock Roundup 2022’, a workshop and field event encompassing new products and solutions for cattle producers. Gentec was a significant contributor in both the workshop and field components. John Basarab and Diego Martinez Mayorga presented to the attendees about the indexes, and conducted a field exercise with the help of Clinton Brons to demonstrate the practical application of the RHPI, courtesy of Grant and Laura Smith. The opportunity to compare the phenotypes of live heifers with their gEPDs and hybrid vigour score was a great demonstration of how genomic assessments can influence decision making. All the heifers but one were black, and their RHPI results told us a lot more about their genetic makeup and potential value as a replacement female than what we could determine just by looking at them.

Although he is in the early stages of genomic testing, Grant Smith described the data as “well worth the $15/head to get a better idea of where your herd is at.” Getting a closer look at genotypes can help producers decide which animals they want to further invest in.

“I used the most expensive semen on the cows with the highest genomic score,” said Smith. “I plan on using it as a secondary selection tool to help increase uniformity. Gentec is committed to giving producers as much information as possible.”

The indexes can serve as an indispensable source of data when selecting breeding stock for commercial operations. With the agriculture industry striving for heightened sustainability and efficiency, there is plenty of room in the commercial beef sector for genetic progress. Having the ability to make important economic decisions earlier with the help of pertinent data will help producers save money and resources in a business with tight margins.

Annika Peckham

Grey Wooded Forage Association



Genome editing opportunities in agriculture: Perspectives on crop and livestock breeding

On August 11, 2022, Genome Canada hosted a webinar on the benefits genome editing can bring to agriculture, which Gentec researcher Niloofar Pejman summarizes for us here. The webinar is a nice add-on to our gene-editing series, which you can catch up on here, here, here, and here.


By 2050, the global population will reach nearly 10 billion people and in order to feed them, we need to double food production, but how?

Dr. Singh explained that before talking about technologies and ideas, we have to think about what crops or plants are needed to feed the world. Many kinds of cereal are very important for food security because the majority of calories come directly or indirectly from animals.

So if we want to double or triple the yield of cereals…is it possible? It would be a big challenge, especially in the face of significant yield declines (20-30%) in cereals due to climate changes via abiotic (heat, drought, salinity) and biotic stresses. Dr. Singh’s research focuses on the genetic dissection of important traits. Originally, he started with transposon mutagenesis and gene editing (GE) in small grain cereals for decoding and tuning genes.

He continued that GE is an amazing tool. It is revolutionizing agriculture, and will be very useful. He mainly uses CRISPR-Cas9, although many GE tools are available.

What is GE? Our crops were domesticated thousands of years ago. Since the last 100 years, our breeding techniques have not changed, so basically, it takes 20 years to have a new variety.

In the meantime, new tools are available such as speed breeding that allows us to cut maybe ten years. And we have a revolutionary technique, CRISPR-Cas9, with which we can develop new varieties in four or five years. Note that GE is a targeted alteration of DNA sequences, and does not bring new DNA from other species. He believes that the CRISPR-Cas9 system demonstrates great potential for developing generation cereal cultivars and regulating beta-glucan in oats.

Why oats? Oat is an important crop with multiple uses: grain, forage, fodder, silage and, most importantly, it has soluble dietary fibre (β glucan), which can reduce serum cholesterols and high blood glucose. So one potential application of CRISPR-Cas 9 is to enhance the nutritional value of oats to meet the growing food demand for β-glucan and improve abiotic stress tolerance in response to global warming, drought, salinity, etc.


Dr. van Eenennaam explained that many objectives visualized in plants are the same for animal breeders as well. She talked about livestock breeding, and conventional breeding acts on alterations of the genome brought through natural selection or artificial selection to give us obviously distinct breeds and behaviours and appearances. The huge discussion point is around sustainability. If we look at the alterations made between 1957 chickens and 2005 chickens using conventional breeding, we can see incredible changes in the rate of growth and food conversion. A similar change took place in the dairy industry since the introduction of artificial insemination in 1940 when we had a four-fold increase in overall production per cow.

The goal of animal breeding is to introduce useful genetic variation into the germline of selected parents such that genetic improvement is inherited by the next generation. There are a couple of ways of doing this. Dr. van Eenennaam explained about injecting the CRISPR-Cas9 into the one-cell bovine zygotes. The interesting thing is that both alleles (mom and dad) can be edited and produce non-mosaic homozygous animals that have alterations in both copies of the genome.

What might we knock out? Genes associated with disease susceptibility, allergens, unwanted development, thermo tolerance, etc.

She showed examples of different traits in different groups; for example, GE to produce porcine reproductive and respiratory syndrome virus-resistant pigs. These pigs are the first GE product taken through the regulatory pathway in the US for animals. Another example was GE to knock out a gene associated with sexual maturity in male pigs. In North America, male pigs are castrated to prevent boar taint, and that is an animal welfare concern. GE can control the sexual development hormones.

What might we knock-in? Genes associated with disease resistance, improved food quality/nutrition, unwanted development, etc.

We are still probably going to target improving food quality nutrition and disease, such as gene knocking of NRAMPusing CRISPR-Cas9 to create animals that are resistant to tuberculosis. Also, groups are working to produce pigs resistant to African swine fever.

Dr. van Eenennaam also talked about global GE regulations. The table shows that countries around the world have different kinds of regulations about GE in food and crops and gene editing in food and animals.

According to the table, for instance, Argentina, Australia, Japan and Brazil have already determined how they will regulate GE crops and livestock, allowing some GE products to pass regulation faster.

Canadian regulators have a unique stance toward products containing novel traits, such as GE animals, regardless of the process used to develop the product. So, new traits in foods require environmental and safety approval before being sold.

In summary, new breeding technologies, including CRISPR-Cas9, have enabled new opportunities to be explored in the breeding of plants and animals. In addition to enhancing our food supply, GE can improve animal welfare. Since GE does not involve introducing DNA from another species, many scientists believe it is less risky. However, in many countries, GE products are regulated differently, and the use of gene technologies remains controversial.

Niloofar Pejman

Visiting Scientist, Livestock Gentec









Reconnecting at CBIC 2022

The fifth annual Canadian Beef Industry Conference was supposed to take place in Penticton, BC in 2020 and again in 2021 but both years, organizers decided to take the event online. The theme for the 2022 conference was Reconnect Today, Invest in Tomorrow, and by all accounts, the program delivered.

Reconnection was evident before the conference began as people spotted each other in airports across Canada. There were handshakes, hugs, slaps on the back, and lots of groups gathered for drinks before boarding. The conference buzz definitely began in airports. As delegates arrived in Penticton, they continued to reconnect with colleagues, friends, and acquaintances from across the country whom they had not seen in years.

The first keynote speaker, Dr. Jody Carrington, hit attendees right in the gut with the reconnection theme. She’s a psychologist so some were skeptical about her ability to relate to a room full of cattlemen, but even the gruffest of cowboys admitted that her key messages resonated—and may have even moved them. The first of those messages is that we are wired to do hard things, but we were never meant to do them alone. Second, if you are not okay, the people you love and lead will not be okay. And third, when people are acknowledged, they rise. It was a very powerful moment when she asked everyone to take out their phone and text someone close to them the words “I don’t know if I tell you this often enough, but you matter to me.”

Thursday morning at CBIC always focuses on economic updates for the Canadian and North American cattle markets and the global economic outlook. This year, a new session on grain markets was added. The second keynote speaker, agri-food consultant and Canadian Agri-Food Policy Institute distinguished fellowTed Bilyea brought all the economic updates together, and gave attendees much to think about on the future of Canada’s agrifood industry. He spoke about the impact of the ongoing conflict between Ukraine and Russia, and about the role that food insecurity and China’s food needs and desires will have on agrifood policy. Key takeaways from Ted’s presentation are that power cannot be achieved without food security; reliance on food imports leads to food insecurity; diversifying trade to sub-optimal locations can create environmental damage as well as social unrest; and that China is facing some strategic choices. Success will entail geopolitical/geoeconomic collective action to encourage China trade along a more sustainable path.

CBIC also featured panel discussions and presentations about the Canadian Beef Advisors’ 2030 goals; diversification of cattle operations including retail, wine, cannabis and biogas investments; economic and environmental impacts of implantation; carbon credit programs; rangeland recovery; consumer attitudes towards beef and nutrition; and building a farm/ranch team.

After success offering courses as part of last year’s virtual conference, short afternoon courses were added to the program for the first time this year, including a hugely popular offering of Ranching for Profit; developing a direct-to-market business plan; range management; and farm financing options.

CBIC has been proud to have a strong youth component, with the Cattlemen’s Young Leaders program and Young Cattlemen’s Council holding their meetings and activities in parallel with the conference. There was a very strong and visible youth presence, but more impressive was the engagement and connections made between future leaders and leaders who have made a profound impact in long and illustrious careers.

The themes of reconnection and investing in tomorrow were evident in the programming, in the networking, and in the attendees who went home reinvigorated. For those who missed out, visit the CBIC social media platforms for updates. The volunteer social media team created a Twitter thread for every session that summarizes the highlights and key takeaways. Shorter highlights can be found on Instagram andFacebook.

Tina Zakowsky

Canadian Angus Association





At the Grill with William Torres: Look underneath the paint job on your heifers

This month’s At The Grill feature by William Torres (former Research Manager at Cattleland Feedyards and popular presenter at Gentec conferences) tells us why the Arm-Chair Rancher app will help producers make better decisions, and how they can contribute to the apps development

Ever wonder what else you can do to be a smarter producer? How can you make easier decisions from the comfort of your couch?

Well, that’s what the scientists at UAlberta are working on. Drum roll, please……Welcome to the “Arm-Chair Rancher” app: an analytic mobile app that helps beef producers better manage various aspects of their herds. The smart device app will help you make the most informed business decisions you can by leveraging the masses of data you already collect daily on features like herd genetics, feedlots and economics.

In my humble opinion, this is about to be an app that brings together all of the data we collect and don’t know what to do with. Think about it like an ancestry test–but for your cattle. Say you buy a black heifer and didn’t have all the information you would like to have but, even if you did, you wouldn’t know what to do with it. Now with a simple DNA sample, you can unlock the genetic makeup of your heifer, and obtain information that’s relevant like:

Actual breed composition

Profit index

Residual Feed Intake

Birth Weight

Body fat/intramuscular fat

The app is really being designed to assist ranchers. And it makes sense that Alberta’s data-rich cattle industry lends itself naturally to the development of an app. Part of the development is to build one that can use and identify live trends in everything from the weather, commodities, and beef prices. Taking the guesswork out of your equation can really save you some serious dollars.

“For artificial intelligence to work, a lot of data is needed, and while many areas in agriculture are not very digitized, there’s an enormous number and types of measurements for cattle, so there’s this huge potential for getting the data needed to make machine learning work.” Dr. Wishart (one of the developers) noted.

The app will help ranchers create scenarios to predict risk and potentially cut losses in their operations. It’s a function that would have been useful for the drought they experienced this summer, Wishart suggested.

So where can you get it? Well, the app is still being developed but you can definitely contribute to the data portion in the meantime. As everyone contributes their information, the data deepens. The more data contributed, the more valuable the overall app becomes. You’ll have the benefit of both visualizing your information and melding it with general information to come up with a solution that works for your scenario. The prototype app should launch in Fall 2022, and you could be part of it. All you have to do is contact Gentec.

The future is here. Imagine typing in your postal code, and based on historical weather data, the app can help predict future weather trends. For example, weather patterns from the past 40 years are accessible, which makes it possible to estimate what the weather could be like in your region, one month to several years from now. Take that, Star Trek!

The research is supported through Alberta Innovates under the agency’s Smart Agriculture and Food Digitization and Automation Challenge Program, and by Beefbooster.

For more information, contact Jennifer Stewart-Smith at Beefbooster.