Sean McGrath: 5th generation rancher, believer in genomics

In our September 2021 newsletter, we profiled Cherie Copithorne-Barnes and CL Ranches. In this edition, we expand on our brief introduction to Sean McGrath and Round Rock Ranching to discover a few more of the fascinating details about the Round Rock. Spoiler alert: it’s about as “Ponderosa” as it gets.

Round Rock Ranches traces its lineage back to 1906 when David Ganton filed the homestead application on the Battleford Trail. Here, 6 km north of the northern tip of the Battleford River between the Grizzly Bear and Benner Coulee junctions, young David planted the family flag. Since then, the branding iron has been passed to David’s son Charles, Charles’ daughter Mary, and then to her son Fred (Sean’s father). Today, Fred (who just turned 84) and his wife Anne, still help on the ranch with Sean and his wife Tanya handling the management as they improve the land and cattle to transfer responsibility to their three children who are growing up fast!

Today, the ranch consists of an Angus-based cowherd of 250+ head raised on 3,200 acres of land of which 85% is still native rangeland. The operation of the ranch is based on a few simple principles. The first is that “Mother Nature can do amazing things if you let her”. In practical terms, it means management working with nature and protecting the land so it can continue to operate for the upcoming 6th generation as it has done for the first five. This strategy allows native grasses to thrive while promoting healthy wildlife habitats, carbon sequestration and biodiversity.

The second principle is to maintain an outward focus. This has meant always trying to see Round Rock through the eyes of others, primarily their customers, be it a feedlot purchasing feeder cattle, a neighbour purchasing F1 replacement heifers or the consumer eating grass-fed beef.

The third is to create the “Best Beef in a Better World”, which flows out of working with, not against, the nature of the land, and starting with the end in mind. Logically, this leads to selecting cattle that best integrate with the land’s natural attributes and has resulted in the development of the ranch’s own Ranchmaker Herd. The Angus-based herd is bred to improve and optimize the balance between the maternal traits that drive fertility and profitability while delivering balanced growth and carcass characteristics that cattle buyers and consumers demand.

The ranch philosophy places a high degree of importance on hybrid vigour. In Sean’s words, “The research has repeatedly shown the advantages of heterosis (hybrid vigour) in terms of improved producer profitability,” continuing that, “Compared to a straightbred cow, the F1 cow averages the equivalent of weaning 1 extra calf (on average) in her lifetime through enhanced fertility, improved disease resistance, stronger maternal ability, and greater calver resilience and growth.” These are principles that John Basarab developed into EnVigour HX™ and Gentec continues to apply to developing value for commercial producers. See above links.

Typical of the practicality exhibited by ranchers (and the above focus on the customer), Sean does qualify that his own herd is largely straight-bred Angus, admitting that they do lose some of the associated benefits of hybrid vigour. In his view, however, this loss is more than offset by the greater flexibility provided by producing F1 replacements desired by their customers.

The evolution of Round Rock Ranch and the principles outlined above have led the ranch to become involved with and recognized by many industry and environmental initiatives. Among these, the ranch participates in many research initiatives relating to environmental health as well as beef production (including Gentec initiatives); Alternative Land Use Services (ALUS); has achieved Landscape Health Verification through the Cows and Fish REAL Beef Program; complies with Verified Beef Production Protocols; has an Environmental Farm Plan associated with the ALUS program; and was awarded the 2014 Canadian Cattlemen’s Association Environmental Stewardship Award (TESA).

After E-Day: The challenges and opportunities of Canada’s federal government regarding agriculture

Canada must have a plan to protect and invest in our agri-food systems so that it can be economically beneficial and sustainable in the long term. For that to happen, the right policies must be put in place, backed by strategic thinking, a systems approach, and supported by strong public-private partnerships and aspirational leadership. The Canadian Agri-Food Policy Institute brought together its 4 Distinguished Fellows (of whom Gentec-associated researcher Ellen Goddard is one) in a webinar, which we summarize for you below.

The idea behind CAPI’s Distinguished Fellows program is for these key thought leaders to collaborate over the coming year on issues important to agriculture (trade, one health, water and climate change) that lead to innovative policy thinking.

SUBHEAD As you look to build the framework for One Health and what that means in Canada, how is COVID a One-Health issue, and how does it relate to anti-microbial resistance (AM) and African swine fever?

Ellen Goddard: The important thing that happened in the past 18 months is science. Not just vaccines but many topics that spill over so, globally, we’re ahead of where we were before COVID. The spillover will start to emerge after the extreme phases.

Overall, I’d like to see a higher profile for the potential of these diseases. Agri-Food and Agriculture Canada (AAFC) has a core role to play in facilitating the national response to these diseases and to zoonoses. We understand these pathways exist but their study is compartmentalized, and we’re not consistent in our approaches when they interact between people and animals. At that point, it isn’t even clear which ministry is in charge. Could be the Ministry of the Environment or Natural Resources for wildlife, or AAFC or the Canadian Food Inspection Agency for livestock. And the Public Health Agency of Canada often doesn’t participate.

Canada has been lucky with AMR compared to European countries that are dramatically reducing their use of antimicrobials in livestock production because the development of AMR bacteria is affecting human health. We need to knock that on the head soon. All these challenges need to be facilitated through a federal ministry that interacts with other ministries and leads the provinces in terms of these actions.

SUBHEAD Climate and health were well-featured in the campaign, as was the debate and impact of carbon tax, exemptions for farmers, etc. What do you think governments are getting right and wrong?

Susan Wood-Bohm. That this government is continuing not restructuring gives us the opportunity to evaluate past performance and see what’s in front of us. The key document I focus on is the Pan Canadian Framework on Clean Growth and Climate Change. It shows that this government intends to link the post-COVID economic recovery to climate change, and what we can do to serve climate change goals and economic goals. The document is sound. The difficulty is that it isn’t fleshed out. Some programs have rolled out but we only tend to hear about them if they pertain to climate change, not agriculture. Part of that problem is that government doesn’t speak the language of agriculture, which is very important to the economy, so I’d say learn that language and understand that agriculture is a viable and economic force in this country, and a natural force to deal with climate change.


The Framework document has an annex that shows the government’s intention to reduce emissions from agriculture and look at what agriculture can to do help us address climate change goals. But again, it’s a framework document. It hasn’t been fleshed out. There haven’t been real actions. So going forward, we’re looking for real action—with producer organizations and producers. We need to hear their voices.

SUBHEAD. We didn’t hear anything about water during the campaign. We can expect droughts on the Prairies and too much rain in Eastern Canada. Water plays a role in attracting food processing to Canada. How do you see the dialogue around water policy playing out over the next four years? Will issues on the horizon focus attention on water?

Nicolas Mesly. Water will be THE issue of the 21st century. Canada has 17% of the world’s fresh water. When we export agricultural products—and we’re the fifth largest exporter in the world—we’re also exporting water. One issue to analyze is how provincial rules complement each other or interfere, and how that affects producers. Another issue is how fracking affects the water table and producers. We’ll also be looking at whether water is a commodity and should be subject to tariffs when it is exported. If we are in a resilient agri-food system, we will need water policies and management, and to conserve water. I look forward to working with CAPI on these issues.

SUBHEAD. Commentators noted that no attention was paid to foreign affairs and trade on the campaign trail—while Afghanistan was on fire. Canada is also left out of a new security partnership. The changing international landscape will reshape our foreign affairs strategy. How does agri-food fit in?

Ted Bilyea. The other panelists outlined a strategic position for Canada. We have an abundance of raw materials, particularly food, energy and minerals. The world can be as brilliant as it wants but it can’t live without these basics. My concern is that we have a potentially winning hand but we don’t know how to play our cards very well. That’s what I’ll be focusing on this year.

Canada has a reputation for high animal health that allows us to enter any market. In some cases, it’s worth $1/kg. Similarly, our crops are low-residue so can also go to high premium markets. Now we are moving into a world where climate change, water play a role. Countries have to meet the commitments they are making. And we see already that will cut production, significantly. Look at the EU. The same is happening in China. Most people haven’t spotted that we’re shipping fewer soybeans than expected, partly because the swine industry has some issues but there’s also not enough electricity to run plants because of carbon commitments. We’re in a new world where we don’t recognize the hand we have. As Nicolas was saying, countries are forced to divert water from agriculture to cities and even to preserve biodiversity, some close to home. That and the fact that you can only have certain animal density before you’re guaranteed a disease and you’re going to have more coming. All of those suggest we should be thinking more strategically about how we play with trade policy. The possibilities are significant where we could gain leverage and use it for good—not just to make money — to have a more sustainable, peaceful world.

SUBHEAD. If you were Trudeau writing a mandate letter to the new Minister for AAFC, What would you say is Job #1?

Ellen Goddard. We can’t stop people, animals or food from moving around the planet. If we don’t address these issues seriously, we can’t guarantee the quality of Canadian products. A lot of disease issues are flowing under people’s agendas, so I’d say develop a one-health policy that will guarantee the quality of Canadian food exports.

Susan Wood-Bohm. In 2017, the government released the Barton Report on the potential for agriculture to lead an economic recovery for Canada. It’s interesting that we’re now in a position where we have a significant economic recovery to address. The report suggested we could lead the recovery by responding to the needs of the global market, and that includes COVID, by addressing increasing protein demands and developing partners. That seems awfully relevant today. So, I hope the letter says: we have this report, it’s a good one. Get on with delivering it and look after issues like access to capital for producers.

Nicolas Mesly. AAFC is asking producers to increase organic matter in soil as a strategy to mitigate climate change. It’s driven by corn and soya pumping out the organic matter. Another thing has been the $40 billion of Trump money to buy farmers’ votes that’s being invested in US farms. We don’t have the same envelope or programs to protect our revenue. American producers are doing well. Our system works when prices are low. The forest is hiding the trees. China is pulling prices up so we have to think competitively. We need to play our cards right. It’s an opportunity but we have to discuss all the issues with the public and farmers.

Ted Bilyea. We need to up our game from cards to chess, so less whackamole. It’s that important. I agree with the speakers. I’d like to see AAFC place more emphasis on the strategic importance of agriculture on our health, economy, climate and so many other important files. It will have to lead on some of those files as well as just doing. And we need a shift in shared responsibility between federal and provincial governments from firefighting to more action and foresight and joint strategic planning. We might start with reactivating the outlook conference where we share knowledge with industry. CAPI will be good for that. It might be an avenue to take the outlook conference out of government and bring it to neutral ground.

As for competitiveness and innovation, it was left out of the campaign but it’s critical. The developed world has seen significant decline in R&D in agriculture. Government R&D has declined in that sphere and, in Canada, business investment in R&D has declined as well. But in developing nations, Brazil, China, the business portion has increased. So, we are seeing others take on the more interesting R&D portfolios, partly because we’re not good at commercializing. Canada was built on firsts: William Davies built Canadian Packers, imported the first genetics and we became world leaders in genetics for pigs and cattle. We need R&D productivity to race ahead but we won’t get there until government and business collaborate on R&D research.


Watch/listen to the entire webinar here.

Gentec, Genomics and One Health

As the first veterinarian to become incoming president of the Canadian Academy of Health Sciences, Dr. Jay Cross has an uncommon opportunity to bridge the health sciences to create One Health benefits. As a former Chair of Gentec’s Board, he knows that Gentec is already on this path.

“Many of Gentec’s goals align with improving animal health, which will reduce the need for antimicrobials and help with antimicrobial resistance,” he says. “Gentec also focuses on improving production efficiency—especially feed efficiency in beef cattle. When cows develop more meat from less feed, they produce less methane and have less impact on climate change. That benefits everybody.”

Jay chaired Gentec’s Board from 2013 to 2017. During that time and building on previous efforts, Gentec developed into a significant international player, resulting from its involvement in the early days of genomic sequencing of food-producing animals. The data gathered then allowed Gentec to move into identifying genetic markers associated with desirable production traits, such as disease resistance and feed efficiency.

“Gentec was an integral player in terms of advancing the science,” remembers Jay. “But it also worked with partners to translate that new knowledge towards producers. That’s an absolutely critical piece because it’s not a typical mandate for a university-based research organization where success is measured in papers published, grants won and students trained. In my time on Gentec’s Board and as Chair, translation was a major focus. Gentec had industry players at the table and embedded in all the major research projects.”

Unfortunately, Gentec then suffered a period characterized by short-term and reduced funding that limited its ability to attract, retain and develop people playing the vital industry liaison role. The strong liaison team, among them Tom Lynch-Staunton, could not be maintained. However, the new Strategic Plan, co-developed by Gentec and the beef industry, sends a powerful message that Gentec is positioning itself back into the game in terms of translation. Already, momentum is picking up with new Gentecker, Kira Macmillan, the extension specialist. The second strong signal to industry and funders is that Gentec will be providing services that create a revenue stream. Succinctly put, valuable services cost money.

Jay is a cattle breeder by background and current board chair of a new beef genetics and value chain company called Sendero and so he understands why the adoption of genomics has been slow. It’s complicated technology and, at first blush, looks pricey.

“Genomics butts up against two things,” he says. “The Number One question producers ask is: ‘how can I bring the cost down’? They can’t see themselves testing every animal in the herd. The Number Two question is:’ I get genetic evaluations done. Why do I need genomics as well?’.”

The arguments in favour of genomics are convincing. If producers were to do the math, they’d see genomics really is affordable. And they need it because it improves the accuracy of the evaluation significantly—of selecting the right animals for their production systems, which will save them money. That allows us to circle back to feed-efficient animals (for example) having One Health benefits beyond the individual pocketbook.

More importantly, in this fragmented industry, beef producers must remember that they are not competing against each other—but against other protein sources. Swine, poultry and even dairy have seen measurable increases in production efficiency and profitability because they have been quicker to adopt technologies such as genomics.

“Of course, beef producers can continue to ignore genomics or other technologies but they will be left behind,” says Jay. “The consequences aren’t strong yet but, in my lifetime, there will be a clear separation of producers who prefer the status quo and those who choose production efficiencies, sustainability and One Health. We have the tools. The Canadian Beef Improvement Network (CBIN) will not be able to achieve its goals without Gentec’s scientific expertise and translation capabilities to accelerate the adoption of technologies.”

Jay gives Gentec significant credit in getting the industry to see the value of genetic selection to improve cattle. So much so that the Canadian beef industry strategic plan identifies production goals that can only be achieved through ongoing research. The 2021 official launch of CBIN is another example of industry recognizing the merits of genetic selection, good management practices and data collection/analytics. All of these will help producers prepare for the growing consumer engagement with sustainability, animal welfare and antimicrobial resistance as these pertain to food and One Health.

“Taking pretty pictures of cows on green grass isn’t going to move the needle,” declares Jay. “We need changes in production practices. Gentec is poised to play that liaison role, and it needs the budget to do it. Ironically, people in government and industry often pointed to that as a strength but when the budget got tighter, it was the first thing to disappear. And it continues to be Gentec’s biggest risk and biggest strength.”

Gentec tools bring value to producers

Most groups that produce breeding values, genomically-enhanced or not, assume they work in practice but this isn’t always true. Results depend on the reference population being used. For example, purebred associations use databases of mostly purebred animals—but those reference populations are used mostly to produce commercial crossbred replacement or feeder cattle. Those databases don’t contain many crossbred animals.

“Gentec is different in that we built our database from crossbred animals in Western Canada,” says John Basarab, Gentec’s Head of Beef Operations. “So, our MBVs are exactly for the animals that are going to be the end product.”

The MBVs are created from a training database; then independently evaluated from another database of 2,268 commercial cattle that is kept aside for that purpose. Now, Gentec has MBVs for multiple traits, such as post-weaning growth, body weight, feed intake and feed efficiency, and carcass weight, yield grade, grade fat thickness, ribeye area, marbling, and lean meat yield. In short, the MBVs validate very well.

“But you don’t just pick one trait when you’re selecting bulls and replacement heifers for breeding,” Basarab points out. “You put all the traits you want—hopefully, the most economically-important ones!—together in a multitrait selection index. Gentec has produced two of these indexes: a Feeder Profit Index and a Replacement Heifer Profit Index for selecting heifers that are fertile, live a long time in the herd, and produce a calf every year (hybrid vigour).”

But… from the producer’s point of view, if you’re using DNA technology, you also have to buy DNA testing. That’s a hair sample from each animal that gets genotyped. The cost, about $35/sample, is manageable on a small scale. If you have 1,000 head, $35,000 is a big investment.

“We’re looking at DNA pooling to bring down the cost by about 90%,” says Basarab. “That’s a low-cost way of improving the hybrid vigour of the herd. Hybrid vigour is highly related to fertility, longevity, health resilience, and a lower carbon footprint—all highly desirable.”

So how does that work? At the lab, 50 hair samples are pooled into one big sample, which gets tested. The one genotype reveals the breed composition of the pool and its average hybrid vigour. A low score shows that only a few breeds are being used, hybrid vigour is low, and the producer would do well to introduce a new breed. At this level, producers can dip their toe into genotyping at a low cost and find out some interesting characteristics of their herd. For example, if two sires were in the mating group, you can know if one has been busier than the other, and then start matching group-level characteristics with pregnancy rate, calving rate or age at first calving.

“We think all three tools are going to be extremely useful for producers,” concludes Basarab. “Already, we have large-scale producers interested in the DNA pooling, and we have a project approved by RDAR. In fact, it was those large-scale producers who pressured us to research this area because the investment was too much. So, instead of $35,000… how does a few thousand sound?”

John Basarab, Gentec’s Head of Beef Operations, will be presenting on these tools at AgSmart Olds on August 10-11. Register for the conference here.


CRSB Panel Discussion: Using consumer research to understand sustainability drivers and motivations

At the Canadian Roundtable for Sustainable Beef’s semi-annual meeting, panelists Amie Peck (Canadian Cattlemen’s Association), Michael Young (Canada Beef), John Jamieson (Canadian Centre for Food Integrity), and Clay Holmes (InterCity Packers Meat and Seafood) provided some answers on what goes on in consumers’ heads when they think about beef.

As the food shortages in the early days of the COVID-19 pandemic showed, Canadians turned to their kitchen in droves for feel-good meals. Website clicks on recipes and food prep skyrocketed. While people certainly indulged their sweet tooth, they also cleaned the shelves of beef products. The beef trend, at least, looks like it’s here to stay. How can we capitalize on that?

Overall, Canadians trust the food system, and have a high positive impression of the beef industry. Beef is considered a high-quality product, and most Canadians are still eating at least “some”. Gen Z and millennials are more interested in how food is produced than previous generations, and willing to make purchasing changes based on how they perceive food items are produced. Millennials have a less positive view of the beef industry than previous generations, and feel more social pressure to avoid beef and/or choose what they believe are sustainable protein options. They tend to be skeptical but can be convinced by good information. This creates an opportunity to connect, dispel ideas around negative media content, and provide information to help them make nutritious choices.

Sustainability is a newer and growing point of discussion for the beef industry—but still not as important as cost, quality and safety. We are still in the early-adopter phase, with those consumers who want sustainable options willing to pay for it. After all, the cost of buying into sustainable certifications shouldn’t fall solely on the producers’ shoulders. Importantly, however, many consumers still don’t know that sustainable beef even is an option. And producers aren’t aware of the incentives to embark on this course. We need to communicate the beef message better to each group, and define what sustainability means instead of allowing the plant-based protein sector to drive the story. (As an aside, the Canadian Roundtable for Sustainable Beef won an award for its website on this very topic.) Consumers aren’t looking for perfection, but they do want to see effort and ongoing improvement. This is an opportunity to build more positive perceptions around feedlots, explain what they are and what their role is in the beef value chain.

Producers have the biggest role to play. These are the people consumers want to hear from. These are the people who can say they care about their animals and the environment, and that they are working to limit environmental impacts. We need to put a face on who ranchers are and what their values are.

These messages aren’t being heard well enough. Working on public trust needs to become part of the daily routine of producers to maintain that precious social licence. Some have hit social media incredibly successfully. Unfortunately, these are the pioneers not the norm.

CBIN: If you build it, they will come

“A hog barn is a hog barn, wherever it is located. The animals are kept indoors in very stable conditions. That makes it easier to produce offspring for very precise consumer markets,” says Dave Sibbald, Interim Chair of the Canadian Beef Improvement Network (CBIN). “We’re looking to develop that same predictability and scale it throughout the beef industry so we can better match consumer expectations and make the industry stronger at the same time.”

Unless they work in or around the beef industry, it may not be crystal clear to Canadian consumers that the beef sector doesn’t function like the pork or chicken industries. 80% of Canadian beef is raised on the range, using grasslands from coast to coast that aren’t suitable to produce any other food. This has led to a wide genetic diversity needed to derive the best animal for each environment and management approach, and to specialize in certain products (for example, grass-fed, commodity beef, hamburger).

“The point is,” continues Sibbald, “that different genetics maximize value from different landscapes. It’s not that we lag pork and chicken in applying genetics but that we need to apply genetics more specifically. I believe genetics are the most untapped component of the value chain. If consumers want superior T-bones, we can deliver that—but we have to apply those genetics at the beginning of the value chain.”

Selling the idea to traditional, independent-minded producers (many of whom are multi-generation ranchers, still on their original homesteads) that they should modernize their approach and talk to other parts of the value chain to help them understand what motivates consumers isn’t easy. Genetics is a complex science, not easy to communicate well, and not cheap to implement. Uptake has been slow. CBIN is expected to make the difference, as we describe here.

The result will be a better-tasting, higher-quality product in which the consumer plays a big role. Because, as Sibbald says so eloquently: why produce it if it doesn’t have a market? Indeed, demand evolves constantly. It’s up to producers to meet it. For example, during the early days of the COVID-19 pandemic, secondary cuts were ground into hamburger. Now, they are sought-after.

“Beef is an exciting, diverse product,” says Sibbald. “So, let’s do more of the good—that is, produce more of what we know today’s consumers want, and deliver a tasty, nutritional eating experience.”

The beef industry has fed Canada for generations. We produce 1.5 million tonnes of beef every year. In 2019, we exported 410,000 tonnes of it, or 41% of production valued at $3.1 billion. Those high numbers, which represent jobs and wealth for our country, are only possible because we have a reputation for high-quality beef.

“CBIN is not about maintaining market share,” explains Sibbald. “It’s about growing it. The global market is highly competitive, so we need new initiatives to confirm our leadership and support the great beef message we already have. No other country has anything like CBIN—even though their beef industries are just as fragmented as ours. We have an opportunity to establish our uniqueness in the domestic and global markets.”

The best that I can be

It was while studying Animal Science as an undergraduate that the concept of ‘how characteristics are inherited across generations’ struck Dan Hailemariam’s curiosity. He pursued that curiosity in a Master’s program in Applied Genetics at Addis Ababa University, Ethiopia. However, it was at the University of Bonn, Germany, where he completed his PhD on cattle molecular genetics that his ideas about his career and research coalesced.

“I see myself as always researching to understand more about animal science,” he says. “My goal is to help solve the challenges of modern dairy cattle production, specifically, improving feed efficiency and reducing greenhouse gas emissions.”

A post-doc position at UAlberta, screening biomarkers for dairy cow diseases under Dr. Burim Ametaj, brought Dan to Edmonton. When that project ended, he sought out Gentec as a centre with a good reputation in carrying out genetics research. In fact, he credits Gentec with helping him understand and define himself. He tells it this way:

“At one of my first group meetings, Graham [Plastow, Gentec CEO] talked about Gentec’s core values: trust, excellence, learning and leadership. He said, ‘if you’re not learning, come and see me.’ I thought, this is where I want to be. These are the values I share. I’m ambitious and I believe in hard work. Here, I can be the best of myself. His words changed my life, the way I think, and the way I do. I make sure I learn every day.”

Currently, Dan is a Research Associate working on a project out of UoGuelph with Gentec-associated researcher Christine Baes to develop genomic tools to enable implementation of selection to increase dairy cow resilience. The project is a 4-year international collaboration. As part of UAlberta’s dairy group, Dan is involved in expanding the reference population for feed efficiency and methane emissions, and developing methods to utilize milk spectra data.

Dan’s own research focuses on identifying biomarkers of feed efficiency, and understanding the metabolic adaptations of feed-efficient lactating dairy cows. He uses a systems biology approach that integrates multi-omics data (genomics, metabolomics and proteomics) to understand the physiology of feed efficiency. This approach also helps identify reliable, cost effective and easily-detectable biomarkers of feed efficiency, which could lead to tools that facilitate the selection for feed-efficient cows, and help dairy farmers save on feed costs and reduce the carbon footprint of dairy production.

One interesting result that has been published is “Comparative analyses of enteric methane emissions, dry matter intake and milk somatic cell count in different feed efficiency categories of dairy cows” in the Canadian Journal of Animal Science. In that research, the team showed that the most efficient cows consume 12.9% less feed and emit 15.5% less methane compared to the least efficient cows for the same level of milk production. The most efficient cows also had lower milk somatic cell count, indicating desirable correlation between subclinical mastitis and feed efficiency in dairy cows.

“At Gentec, every day is exciting,” concludes Dan. “I like my work because the more I engage, read, write, design and conduct experiments, analyze and interpret data, the better I am becoming, and the more I find myself. I feel good about it. I’m optimistic that I will be part of an accomplishment that develops tools to improve feed efficiency and reduce GHG emissions from dairy cattle.”

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.”

Closing the information gap in the pig genome

The pig industry around the world has made huge improvements in desirable traits thanks to the knowledge afforded by the sequencing of the pig genome, the first draft of which was published in 2012. Yet, in spite of these improvements, which include facilitating genomics-enabled breeding that has increased the rate of genetic gain in some programs by up to 35%, about 10% of the pig genome was missing.

“The IGF2 gene, which has an impact on muscling that I and others reported 17 years ago, was missing,” says Alan Archibald, Personal Chair of Mammalian Molecular Genetics, The Roslin Institute. “So was the CD163 gene, which encodes a molecule essential for infection by PRRSV. In one of our projects, we edited that gene and rendered pigs completely resistant to the virus. So, a number of key genes of interest to people in the breeding sector were absent from the genome sequence or only partially represented.”

While 10% may not seem very much to the outside eye—and clearly some remarkable discoveries were made without it—some projects lacked information (annotations) to make the very best decisions, for example, for gene-editing. And although the long-range information available was good, unresolved redundancies, short-range order and orientation errors, and associated misassembled genes could lead to information loss.

The paper presents two annotated highly-contiguous chromosome-level genome assemblies created with new long-read technologies and a whole-genome shotgun strategy. Both assemblies are of substantially higher (>90-fold) continuity and accuracy than the previous genome sequence. Together with the annotation of another 11 short-read assemblies, the new sequence provides a much needed base for genomic research in pigs.

For example, Aniek C. Bouwman et Wageningen University in the Netherlands reported at the World Congress on Genetics Applied to Livestock Production that the new genome improved the accuracy of inferring genomic sequence from marker genotypes and thus improving genomic predictions.

Is this now the complete pig genome?

“No,” says Archibald. “Small bits are still missing but this is a substantial improvement. It’s 400-700 times more continuous. In genomes made up of strings of bases (letters), the technology we used could only read 900-1,000 bases at a time: short bursts of information. Assembling the’ jigsaw puzzle’ was a challenge. For the new genome, we read 1,0000-20,000 bases/letters at a time, so the pieces of the puzzle just got much bigger.”

Nonetheless, 120 gaps still remain in the sequence. Archibald believes some of the missing parts may be important in terms of how the chromosomes function, but not in terms of information content. In other words, not interesting, unique or useful to the geneticist, and highly repetitive so difficult to sequence; like assembling an all-blue sky in the aforementioned puzzle.

Gentec CEO Graham Plastow is a member of the Stakeholder Advisory Group for a project related to BovReg(another Gentec collaboration) in Europe, called GENE-SWitCH. Archibald contributed to designing the GENE-SWitCH project proposal, and is a member of the project team.

“The pig genome sequence is not a GENE-SWitCH outcome,” says Plastow. “But it’s highly relevant as the primary aims of GENE-SWitCH include adding value to the pig and chicken genomes through enhanced functional annotation, i.e. noting/identifying which parts of the genome have key functions such as encoding proteins or regulating when and where each gene is expressed.”

“Pork is the most popular of all meats and, with a growing global population, we need to improve the sustainability of food production. The improved knowledge of pigs’ genetic make-up will help farmers breed healthier and more productive animals,” says Archibald. “The sequence has been available for two years, so consumers might unknowingly have seen a benefit already. Improvements in and of themselves are modest but if you apply them across thousands of animals, the benefits add up.”

ALES Graduate Research Symposium Report

By Jiyuan Li

The 4th Agricultural Life and Environmental Sciences (ALES) Graduate Research Symposium was held at the UAlberta on March 13, 2020. The event was sponsored by Gentec and others. This annual event is designed to provide students with the opportunity to showcase and share their research results, improve upon their public speaking skills, and enhance communication among the graduate students.

The symposium was divided into poster presentations and oral presentations. In the poster session, 21 students from the departments of Agricultural Food and Nutritional Science, Renewable Resources, Resource Economics and Environmental Sociology and Human Ecology shared their research progress. The posters covered a wide range of fields, such as food science, plant science, and human nutrition. During the session, presenters and listeners were engaged in high-quality communication and heated discussion.

The oral presentation session followed, at which 12 students showcased their research. Mohsen Hashemiranjbar Sharifabad, a Master’s student from Livestock Gentec, gave an excellent presentation on metabolomics and feed efficiency in dairy cows. He demonstrated the potential of metabolites as biomarkers for predicting feed efficiency, and introduced predictive models for dairy cows. He identified that his research benefited from the help of his supervisor, Gentec CEO Graham Plastow, and committee member Dr. Dagnachew Hailemariam. He also thanked his colleagues Anahid Hosseini, Janelle Jimenez, Xuechun Bai and me for attending the event and supporting him. After the presentation, Mohsen expressed how great it was to get feedback and comments from people with different scientific backgrounds. When asked what he learned from the event, he said that learning from the speech styles and content of others helped increase his knowledge.

Xuechun Bai and I attended the whole event, and engaged in interesting discussions with the presenters during the poster sessions. Attending the symposium is a great opportunity to learn and provides valuable networking opportunities for the students.