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.

PANELIST DR. JASWINDER SINGH, MCGILL UNIVERSITY, CANADA

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.

PANELIST DR. ALISON VAN EENENNAAM, UNIVERSITY OF CALIFORNIA, DAVIS, USA

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.

 

 

 

 

 

 

Gentec goes to the “Olympics” of animal breeding

The scientific sessions at the 2022 World Congress on Genetics Applied to Livestock Production  (WCGALP ) in Rotterdam, the Netherlands, covered many aspects of livestock genetics including genomic predictions (with subtopics of methodologies and tools, challenges, use of complete DNA sequence for genomic predictions), statistical genetics, animal health and welfare, animal breeding in developing countries, novel phenotyping tools, and utilizing genetic diversity. Gentec Research Associates Marzieh Heidaritabar, Liuhong Chen and Dan Hailemariam provide some insights here.

A topic Marzieh is interested in is how to improve the accuracy of predicting genomic breeding values to improve animal selection to enhance genetic progress in commercial livestock breeding programs. She notes that University of California Davis scientists have developed a novel method called “NN-LMM”, which incorporates intermediate omics features (such as gene expression, metabolomics and DNA methylation) by adding middle layers between genotypes and phenotypes. NN-LMM has significantly better prediction accuracy than the commonly-used (standard) single-step genomic prediction approach. This shows the added value of omics data in genetic evaluations and, in Marzieh’s view, this novel approach could be a more useful way than the conventional method of estimating the genomic breeding values in companies’ routine genetic evaluations . Gentec is investigating these areas as part of the international BovReg project.

Liuhong is particularly interested in new methods for genomic selection since it has revolutionized livestock breeding. The methods have evolved from classic approaches to two-step approaches and to single-step approaches which have become the standard. As a result, single-step genomic selection was one of the hot topics at the conference. What will next-generation genomic selection look like? Listening to the talks from top researchers around the world, one could imagine next-gen genomic selection would integrate multiple innovative technologies, such as precision phenotyping, alternative genotyping, machine learning, functional genomics, and multi-omics approaches (as above) as well as gene editing. Gentec researchers have been working on many of these fascinating areas. See some of our 2022 articles on gene editing here and here.

Liuhong presented a new approach that enables the parallel implementation of Bayesian methods (a statistical workhorse for large datasets) for genomic prediction. He is continuing to improve the approach so that it can run efficiently with whole-genome sequence data. He is also working with Gentec CEO Graham Plastow, Gentec Director of Beef Operations John Basarab, and AAFC/Gentec researcher ChangXi Li to develop approaches that use breed-specific haplotypes to improve the estimation of genomic breed composition, retained heterosis and multi-breed genomic predictions in beef cattle. He comments “Attending conferences like this provided opportunities to learn from others and stay at the forefront of genetics and genomics research in livestock.”

Marzieh also attended presentations related to animal health and well-being. Novel welfare-related traits are increasingly receiving more attention in breeding programs in relation to maintaining social license and being included in breeding objectives (using multi-trait selection indices), particularly for group-housed species like chickens and pigs. These animals interact socially and can affect each other’s phenotype, meaning that, besides the direct genetic effects of the animal itself, the indirect genetic effects of its housemates can impact the phenotype of the animal. This seems to be particularly important for aggressive interactions/behaviours. For instance, in pigs, social interaction traits related to aggression were moderately heritable, and there were positive genetic correlations between the aggression traits and pig skin lesions. New findings showed that social interactions are also relevant for beef and dairy cattle for welfare and disease transmission. Researchers at Wageningen University developed a novel method, an extension of the classic social genetic model, for the breeding value estimation for social traits in large groups. This method, along with proper recordings of social interactions, could be very applicable in animal breeding  (see here).

Another interesting presentation from Wageningen was on the development and validation of an approach for pig breeders to better predict the purebred-crossbred genetic correlation from phenotype and genotype data of parental lines (based on approximated genetic variance components of parental lines). This approach could also be applied for other livestock animals in which crossbreeding is the main breeding scheme. (This is another area where Gentec and partners are active in pigs and beef cattle, where the majority of the commercial herd is crossbred. A recent publication on our pig work is here. ) On the cattle side, Ben Hayes (University of Queensland), leader of the 1000 Bull Genomes  project and an adjunct professor at UAlberta presented new work on improving genomic prediction in crossbred cattle in Northern Australia. He acknowledged some older Gentec work as one of two approaches that enabled their innovation (see here ).

The phrase “in the age of genomics, phenotype is king” is one Mike Coffey (SRUC) introduced to us at different Gentec events. Not surprisingly the use of novel phenotyping tools received a lot of attention at WCGALP. The tools include video, GPS, sensors and milk spectra. Recording or tracking behavioural traits and dry matter intake with camera systems and using machine learning to analyze the mass of data generated shows great promise for hard-to-measure traits. Among the different machine learning algorithms, the use of artificial neural networks was emphasized, as it takes into account the non-linear relationships between variables. It is possible to automate computer vision for monitoring important behaviors (tail biting and lameness) in the pig industry (see here).  One example is the Virtual Tag (VTag) software that substitutes hand-annotated data to accelerate pig behavioural studies. A 3D camera technology has been developed by Danish researchers to measure feed intake and body weight on individual cows in commercial farms. A high squared correlation (R2 = 0.9) between feed intake measured with scales and cameras was reported.

Under the theme of Functional Annotation of Genomes, papers related to the discovery of causal genetic variants and recessive defects for different traits in different species were presented. One example was detecting recessive loci responsible for increased mortality in cattle. The researchers screened for homozygous haplotype enrichment/depletion in groups of females in different life trajectories and identified 34 deleterious haplotypes with frequencies ranging from 1.5 to 7.6%. A Gentec collaboration with this group identified a missense variant within the host Synaptogryin-2 gene significantly associated with PCV2b viral load. In this follow-on study, the Nebraska team generated a porcine kidney 15 (PK15) clone homozygous for the “favourable” SYNGR2 p.63Cys allele using in vitro CRISPR-Cas9 gene editing. Infection of this edited PK15 clone demonstrated a significant reduction in total PCV2b replication starting 48 hours after infection compared to wild-type PK15 cells.  A nice example of using gene editing to confirm the effect of causative mutations to help increase our knowledge of the underlying biology of complex traits such as disease resilience.

In summary, WCGALP 2022 was a successful event that brought together livestock genetics and breeding researchers around the globe to share their ideas and results on the challenges facing the sector. Improving resilience of livestock species to the changing environment including disease is another area where Gentec is very active and that was identified as an important approach for the future.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

At the Grill with William Torres: To fart or not to fart. Meat is the answer!

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 cattle are NOT the villains of climate change, and how to argue that case.


Beef producers are under increasing attack by climate activists on the contribution to climate change cause by methane exhaled by cattle. Yet the world continues to lose common sense and deny the political weight this topic carries. Why is the obvious not so clear any more? If these politicians really cared about the environment like they say, they wouldn’t fly across the country for an impromptu photo op at the Calgary Stampede!

I’m not going to go into detail about how “bad” cattle are for the environment, instead let’s focus on the benefits of these ruminants.

First off, if ever you are defending the industry and/or are in an argument with an activist, NEVER—and I mean NEVER—just direct anyone to a scientific paper for proof of empirical evidence. When someone is arguing with emotion, they will never read a paper just for fun (Who does that, anyway?). Remember, this is like trying to convert someone to your religion, and telling them theirs is bad. If they’re not drinkers, why would you tell them to read John 2:1-11? That’s when Jesus converts water into wine. Just saying.

If you really want to present evidence, ask if they would watch a video? Let’s face it, most of us would rather watch something on YouTube than read a scientific paper. Here are some suggestions in my order of aggressiveness, lol

  • Cows and climate. Cows and climate by Frank Mithloehner. Yes, I know he’s a doctor but if you push the science you’ll lose the emotional battle. Mention that he’s European and doing work in California, one of the most active states fighting environmental changes.
  • How cattle impact climate change. How cattle impact climate change; a CBC report that summarizes all the great things Canadians are doing in under 3 minutes.
  • Protestor Diets by Quick Dick McDick. As much as it may seem that this video attacks a vegan diet, it puts a visual demonstration of all the equipment and resources needed to provide such diet. We can all use that reminder!

From an environmental standpoint, cattle play a unique role in maintaining topsoil; they till and fertilize the land naturally. They promote biodiversity and protect wildlife habitat by grazing on land that would otherwise remain unproductive for humans. They reduce the spread of wildfires, providing natural fertilizer… and so much more. Additionally, we don’t just do this improperly, we actually take into account head numbers to land-water ratio. We CARE about what we do—and that is our emotional defence.  We are stewards of the land!

Beef is actually healthier and more sustainable than ever before. Thanks to innovation, education and improved efficiencies, we can produce the same amount of beef with one-third less cattle than in the mid-1970s. Industry initiatives have created policing guidelines and global organizations, such as round tables of sustainability, so that we don’t just say we’re going to do things better, we can prove that we are doing it. Such improvements are responsible for making sure that beef cattle production in North America is only responsible for ~3.3% of greenhouse gas emissions. Compare that to Canada’s road transportation sector (18% in 2018) and the oil and gas sector (20% in 2019)!

transportation and electricity, which made up ~56% of totals in 2016.

My final advice is to not argue but understand where someone is coming from. There’s a good chance that they might not understand what we do. After all, it’s not just a job, it’s a way of life.

 

 

 

 

 

 

 

Roy Berg Kinsella Research Ranch Field Day showcases next-gen ranching tools

The Rangeland Research Institute  and Gentec partnered up on July 20, 2022 to host a field day at the UAlberta’s Roy Berg Research Ranch  in Kinsella, Alberta. The event focused on innovations in land and animal technologies to build climate resilience and showcasing pioneering tools and approaches, such as precision ranching, virtual fencing, drone use, GrowSafe feed bunks and genomics tools.

“You can tell this is very valuable to producers as they are engaged and asking questions,” said Mark Redmond, CEO of Results Driven Agriculture Research (RDAR). This is the first time researchers and producers have been face-to-face since COVID-19 began.

One of the Field Day’s main goals was to demonstrate to producers the work being done by UAlberta, researching precision ranching technologies, their benefits, drawbacks, and development, all for the benefit of the beef industry.

With access to the ranch, Gentec can take advantage of the massive cattle resources and trait-measuring technologies like an integrated scale in squeeze chutes and GrowSafe Bunks that allow for measuring feed intake. The cattle at Kinsella (Angus, Charolais, Hays Converters and the Kinsella Composite herds), their DNA along with measuring technologies allow Gentec to produce genomics tools to improve sustainability and productivity.

The Field Day had an unofficial goal as well: to demonstrate the collaboration of institutions that share the commitment to improve the productivity of the beef industry. Although the event was hosted by the Rangeland Research Institute and Gentec, people from different organizations had the opportunity to talk and present. Carolyn Fitzsimmons from Agriculture and Agri-Food Canada and Research Lead at the ranch welcomed attendees and talked about GrowSafe. Susan Markus from Lakeland College spoke about replacement heifer selection, and John Church from Thompson Rivers University spoke about using drones to manage rangeland. Master’s students from UAlberta also spoke about their projects at the ranch, along with Diego Martinez Mayorga, a student working at Gentec this summer, who spoke on genomics tools for terminal sire selection.

The event’s overarching theme was precision ranching, which is all about “putting the right animal in the right place at the right time,” says Edward Bork, professor at UAlberta and Director and Mattheis Chair in Rangeland Ecology and Management.

Attendees were taken on pasture walks where presenters from UAlberta spoke about their research projects and the benefits to the Alberta cattle industry. Visitors were treated to demonstrations of John Church’s “flying border collie”, AKA drones, and saw a grazing line in the middle of a pasture where a virtual fence stood, investigated the GrowSafe feed bunk system, and heard from experts in precision ranching tools. Ed Bork stated that “[UAlberta] is the industry test run, globally”, referring to its status as a global leader for rangeland ecology and rangeland management research.

The day concluded with thanks from UAlberta to producers for coming out and learning about the work being done.

“I’ve been coming for a long time” says David Andrews, Gentec’s Board Chair. “There’s always lots to learn every time, always something new. You get to actually interact with researchers, and this is a spectacular facility for research”.

One cow/calf and backgrounding producer expressed his appreciation, declaring that this was a “very useful day”. He was excited about the new technologies in development, and saw the applications for his own operations today. As a multi-generational farmer, he expressed his eagerness for his children and grandchildren to put to use the tools seen at this Field Day to real life:

“I wish I had 20 more years to see it all happen,” he said.

 

Jacqui Gironella and Diego Martinez Mayorga

Livestock Gentec

 

 

Ouch! My pen-mate bit my tail!

Farm animals who interact socially can affect each other’s phenotype, meaning that the indirect genetic effects of their pen-mates can impact the phenotype of the individual animal. This seems to be particularly important for aggressive interactions/behaviours. For instance, in pigs, social interaction traits related to aggression were moderately heritable, and there was positive genetic correlation between the aggression traits and pigs’ skin lesions. Tail- and ear-biting are the most common behavioural vices in growing-finishing pigs. Besides being an important welfare problem, they also have economic repercussions due to reduced weight gain, on-farm veterinary treatment, reduced carcass weights and condemnations.

Social interactions are also relevant for beef and dairy cattle for welfare and disease transmission. For example, if welfare-related traits like the foot structure of Angus cattle are added to profit-driven selection indexes, recording levels increased and the accuracy of the evaluation for these traits improved. Researchers at Wageningen University developed a novel method, an extension of the classic social genetic model, for breeding value estimation for social traits in large groups. This method, along with proper recordings of social interactions, could be very applicable in animal breeding.

 

Using genetic selection by including indirect genetic effects greatly improves the interaction among pigs by reducing damaging behaviour. However, environmental factors, such as the number of pigs/pen and diet, are crucial in achieving the desired goal. Building on work done in collaboration with researchers at Wageningen and Topigs Norsvin, Gentec (Graham Plastow, Clover Bench and Elda Dervishi) and the Swine Research and Technology Center are leading a project to develop management strategies to monitor and manage tail- and ear-biting in pigs. Live observations focus on counting skin lesions and determining the severity of biting. However, live observation can miss behaviours of interest because it only takes place for a short time during the day. Video recordings are monitoring feeding, drinking, and tail-biting behavior every Monday for 8 hours. In combination with saliva and blood analysis collection, we hope to provide a more complete picture of these behaviours. Welfare-related traits, like the number of skin lesions, can be added to selection indexes to improve the accuracy of the evaluation for these traits. We can also monitor the frequency and time the pigs spend interacting with the enrichment objects (for example a KONG).

Overall the results may lead to new recommendations for the swine industry on how to avoid and manage tail- and ear-biting. In addition, it might inform welfare-related codes of practices in Canada.

Gentec publications at WCGALP

BEEF

A machine learning approach for predicting the most and the least feed-effficient groups in beef cattle Shirzadifar, A.; Plastow, G.; Basarab, J.; Miar, Y.; Li, C.; Fitzsimmons, C.; Riazi, M.; Manafiazar, G.

From BovReg (and other projects eg GC Resilient Dairy etc)

Accuracy of genomic prediction of dry matter intake in Dutch Holsteins using sequence variants from meta-analyses Gredler-Grandl, B.; Raymond, B.; Chitneedi, P.K.; Cai, Z.; Panzanilla-Pech, C.I.V.; Fischer, D.; Bolormaa, S.; Chud, T.S.; Wang, Y.; Li, C.; Villanueva, B.; Fernandez, A.; Kuehn, C.; Lidauer, M.H.; Pryce, J.E.; Plastow, G.; Baes, C.F.; Charfeddine, N.; Veerkamp, R.F.; Bouwman, A.C.

Multi-dimensional functional annotation of bovine genome for the BovReg project Moreira, G.C.M.; Dupont, S.; Becker, D.; Salavati, M.; Clark, R.; Clark, E.L.; Plastow, G.; Kühn, C.; Charlier, C.

Comparative analysis of CAGE-Seq across tissues reveals transcription start sites unique to cattle Salavati, M.; Clark, R.; Becker, D.; Kühn, C.; Plastow, G.; Moreira, G.C.M.; Charlier, C.; Clark, E.L.

OTHER BOVINE

Functional SNPs and INDELs within regulatory elements associated with mastitis in Holstein cow using -OMICs technologies Asselstine, V.; Medrano, J.F.; Stothard, P.; Miglior, F.; Karrow, N.A.; Baes, C.F.; Schenkel, F.S.; Cánovas, A.

PIGS

Genome-wide association analyses and genomic prediction for pork meat quality traits using whole-genome sequence Heidaritabar, M.; Huisman, A.; Bink, M.C.A.M.; Charagu, P.; Plastow, G.

Prediction of breeding values for feed intake in pigs using individual versus group records along with correlated traits Zhang, C.; Kemp, R.A.; Dekkers, J.C.M.; Plastow, G.S.; Gao, H.

Multi-trait genomic estimation of genetic parameters for growth and carcass traits of Duroc pigs Akanno, E.C.; Thekkoot, D.M.; Zhang, C.; Bierman, C.; Plastow, G.; Kemp, R.A.

Large-scale cis-eQTL analysis of gene expression in blood of young healthy pigs using PigGTEx Kramer, L.M.; Teng, J.; Lim, K.S.; Gao, Y.; Yin, H.; Bai, L.; Liu, G.E.; Zhang, Z.; Fang, L.; Plastow, G.S.; Tuggle, C.K.; Dekkers, J.C.M.

Indicators of disease resilience from complete blood count and in vitro immunoassays data from young-healthy pigs Bai, X.; Cheng, J.; Fortin, F.; Harding, J.C.S.; Dyck, M.K.; Dekkers, J.C.M.; Field, C.J.; Rogel-Gailard, C.; Blanc, F.; Plastow, G.S.

GBP5 PRRSV resistance gene had no effect on pigs’ infectivity or susceptibility in a trial simulating natural infections Chase-Topping, M.E.; Plastow, G.; Dekkers, J.; Fang, Y.; Gerdts, V.; Van Kessel, J.; Harding, J.; Opriessnig, T.; Doeschl-Wilson, A.

Genetic relationships among immune response traits of young healthy pigs evaluated by immunoassays Bhatia, V.; Schmied, J.; Cheng, J.; Bai, X.; Mallard, B.; Fortin, F.; Harding, J.C.S.; Dyck, M.K.; Plastow, G.S.; Field, C.J.; Rogel-Gaillard, C.; Blanc, F.; Piggen Canada; Dekkers, J.C.M.

Methods and Tools: Software and Computing Strategies

Subsetted orthogonal data augmentation for fast parallel implementation of Bayesian models for whole-genome analyses Chen, L.; Plastow, G.

2022 4H Beef Carcass Competition: Genomics offers new tools for beef production

The stage was set on July 22, 2022, for over 100 kids from central Alberta to find out what their 6-month effort yielded. Members of 4H clubs had been feeding a steer through the winter, and were all keen to learn how their steer carcass placed in a regional and provincial competition. Oscar Lopez Campos from Agriculture and Agri-Food Canada graded the carcasses for both competitions. But before getting those all-exciting results, the 4Hers toured Olds College and attended a presentation on the beef market.

With this backdrop, enter Livestock Gentec. In the corner of the auditorium, on a foldable table sat reports with the name of each 4Her and the CCIA number of the steer they raised. Inside each report was an introduction to genomics, several individualized genomic values (genomically-enhanced gEPDs, a Feeder Profit Index value, genomic breed composition and genomic retained heterozygosity) and a description of each tool. This way, each 4Her could get a report on the expected performance of their steer/steer’s progeny, the steer’s breed makeup and the amount of hybrid vigour present in that animal—all from a small hair (DNA) sample. That might not seem significant to a 10-year-old 4Her but, in commercial operations, these data could be a deciding factor between a profit or loss when selling a given animal.

For Gentec, the benefits of attending 4H events and being involved with this organization are clear. We are reaching out to the future ranchers of Alberta and introducing them to a novel, easy and a relatively inexpensive way of gaining a large amount of information on their animals. Instead of having to backtrack through hundreds of records and pedigrees of sires and dams, they can get accurate gEPDs from a single hair strand.

While some of the 4Hers “get it”, plenty of them had no idea what we were here for. Parents, too. As one put it, “We thought you guys were here to make sure the carcasses weren’t swapped for the competition. We had no idea you could predict performance from DNA.”

Beef Industry Liaison Clinton Brons quickly changed that lack of knowledge with an introduction and appreciation for Gentec’s funders, as did Knowledge Translator Diego Martinez with a short presentation on the genomic reports. Soon after, parents and kids collected their reports and the Gentec’s team answered questions.

Questions ranged from what the Feeder Profit Index is, what the genomic breed composition of an animal tells them and how hybrid vigour impacts replacement heifers and cows.

Over 130 4Hers have been exposed to genomics through these reports since April 2022 so… does that mean that Gentec has 130 new producers willing to test their herds genomically? Not quite. Over the past few 4H events, we’ve seen that some parents are keener than others, ask for more information and even provide their contact for follow up. And some 4H leaders/executives have already introduced this tech to their farms, like Paul Franz who spoke to Gentec earlier this year. This showcases the importance for research organizations like Gentec to reach out to grassroots organizations like 4H to communicate and demonstrate the validity and importance of tools and resources that research yields for the industry.

The 4H experience in 2022 has been fantastic for Gentec as it has shown a new approach to share information. The approach is two-fold: 1. Educate young farmers about genomics so they might be willing to use these tools when they take the reins of an operation, and 2. Give young kids the information with the hope that Dad/Mom or Grandpa/Grandma read it, like it and use it on their farm (or at least reach out for more information).

It is Gentec’s mission to develop validated genomic solutions to improve the competitiveness of the beef industry. Collaborating with 4H has given us the opportunity to increase trust in our validated tools, which will overall increase the productivity and sustainability of the Canadian beef industry.

If you are a 4H member/parent/leader interested in collaborating with Gentec—or if you are a producer interested in talking to a Gentec representative about genomics or possible research projects you could be involved in, reach out to us at lsgentec@ualberta.ca.

 

By Diego Martinez Mayorga