By: Genome Alberta

Alberta may be famous for its beef, but the province is also home to a thriving pork sector. Canada is the third largest global pork exporter, and approx. 20% of that pork is raised here in Alberta. Healthy pigs are foundational to this success, and genomic tools are helping pig breeders maximize pig health and reduce the impact of disease on animal welfare.

As demand for protein grows both here and around the world, maintaining healthy, productive herds is a high priority for the pork industry. Disease resilience, the ability to be minimally affected by disease or to rapidly return to normal after pathogenic infection, has become an area of particular interest for pork producers and breeders. Improving the disease resilience of our nation’s pork could have wide-ranging benefits:

• Better for pigs: Staying healthy means a better quality of life for animals too. No one enjoys being sick, and the same is true for livestock suffering from illness. Improved disease resilience means pigs get sick less often and infections are less severe, thereby improving animal welfare.
• Better for pork producers:Caring for sick animals takes money, time and resources, and infectious diseases impact pigs’ ability to grow and produce litters. The two most common diseases affecting commercial pigs – Porcine Circovirus Associated Disease (PCVAD) and Porcine Respiratory and Reproductive Syndrome (PRRS) – cost Canadian pork producers $100 million every year. With healthier pigs, high-quality pork can be produced at lower cost, which benefits producers and consumers.
• Better for Albertans:The health of people, animals and the environment depend on one another – this is core to the One Health approach. Infectious diseases that affect animals can sometimes mutate and spread to people and this risk increases when farm workers are exposed to infected livestock. On the other hand, the more antibiotics are used to control the spread of disease, the greater the risk that pathogens will develop antimicrobial resistance. Improving the disease resilience of livestock helps ensure a safer, more secure food supply and workforce, while also reducing reliance on antibiotics.

Just as breeders can select for bigger, faster-growing pigs, they can also select for pigs that are better at fighting off illness. However, doing so is often easier said than done. While previous research has identified genes that are important for disease resilience in pigs, selecting pigs on the basis of these genes alone could have underwhelming results. Genes interact with the environment and the rest of the genome in complex ways, and a gene associated with improved disease resilience might have a negative impact on other desirable traits, like body size and growth rate. A holistic approach that considers the whole genome is needed.

Swine Research & Technology Centre, University of Alberta – South Campus. Photo Credit: Hussain Al-Rikabi.

To tackle this challenge, a research team led from the University of Alberta partnered with PigGen Canada to accelerate the improvement of disease resilience in pigs. PigGen Canada is a not-for-profit representing Canada’s pig breeding companies, whose mandate is to maximize the potential of genomics for its member organizations and producers. Through the development of genomics-based selection tools, the project aimed to increase the rate of genetic improvement.

The project tested several biological and genomic markers that had already been identified as promising indicators of disease resilience. By presenting pathogens to pigs in a controlled environment, researchers were able to understand which genes contribute most to disease resilience and develop genomic tests to detect key indicators. The focus was to concentrate on the genomic markers that, if selected, would maximize the overall health of the animal. Such findings would help pig breeders develop superior animals from their breeding program.

Michael Dyck, Professor of Animal Biotechnology at the University of Alberta and Lead Researcher for the PigGen Project. Photo Credit: Hussain Al-Rikabi.

To mobilize this information, the project contributed to the development of PigDB, a vast database of pig genomic data. Large datasets enable researchers to compare traits and solve health challenges that are simply not possible with individual herd data. With the help of tools like bioinformatics, machine learning and AI, researchers can leverage these datasets to analyze thousands of variables at once.

Pig breeders understand this value, but sharing genomic data from their herds with other companies would normally risk exposing proprietary information. With robust data management and stewardship in place, PigDB allowed companies to pool their samples while keeping their proprietary data protected. All companies contributing data can now compare their samples against a large population dataset with the assurance that only they can see their own samples. This helps individual producers improve efficiencies in their business, and provides valuable insights to the industry as a whole.

“Since its inception, PigGen Canada members have understood the benefits of collaborative research. A great example is our project The application of genomics-based tools to select for pig disease resilience. This project leveraged past work to develop and apply genomic-based tools directly to breeding programs, many of which are already in use by our members. This would not have been possible in such a short time frame without the collaboration and resources of PGC members, the funding from Genome Alberta and excellent work from U of A.”

Tom Rathje, Board Chair, PigGen Canada

This model of collaboration has allowed improvement in pig health industry-wide, and has even drawn the interest of researchers beyond Alberta. Researchers in Europe have already requested permission to use the dataset, believing it will help them identify biomarkers for other disease factors. And as PigDB draws more interest, it grows more valuable. As a living database, users can continue to add samples, enabling researchers to do more powerful analysis and expanding what we can learn from it.

In addition to helping pig breeders boost their herds’ resilience to serious diseases, these datasets are an invaluable tool for addressing emerging threats to the pork industry. Through partnership between Genome Alberta and Results Driven Agriculture Research (RDAR), a new  initiative aims to provide solutions to One Health challenges including the emerging threat of African Swine Fever (ASF). ASF is a devastating virus that has a mortality rate of 100%. While ASF has not yet been detected in Canada, the virus has spread rapidly through Europe, Asia and Africa and poses a significant risk to the Canadian pork industry. There is currently no vaccine for ASF.

The new research initiative will provide up to $5,000,000 in funding for research projects that utilize genomic-enabled technologies for solutions to One Health challenges and benefit to Alberta producers. The initiative includes a number of areas including the challenge of understanding of the population genetics and disease resilience of invasive wild pigs – a likely disease vector if ASF were to enter North America.

As Albertan pork producers continue to raise the bar for the quality of their product and the welfare of their animals, genomics have become a critical tool in the fight against disease.

This article was originally published by Genome Alberta: genomealberta.ca

Originally published January 22, 2025 on BeefResearch.ca

Bull sale season will soon be in full swing, meaning now is the time to determine the bull selection criteria and budget for purchasing your next herd sires.

Considering that a bull’s contribution to the genetic makeup of a beef herd in a single breeding season is more than a cow may contribute in her lifetime–a bull may sire 25 or more calves per year while the average cow produces fewer than 10 calves–selecting genetically superior bulls is the quickest way to improve herd genetics. But how do you determine which bull is right for your operation?

Match Your Breeding Program to Your Operational Goals

The first step in identifying which bull or bulls are right for your farm is to clearly establish both the long- and short-term goals of your operation. These goals, along with the management practices and infrastructure that fit those goals, will determine the breeding programs and genetics required to achieve them.

There are a variety of breeding programs available, and effective sire selection requires an understanding of the characteristics of your own operation and the genetics available for purchase. Intentionally aligning a bull’s genetics to your operation’s goals will contribute to enhanced revenue and reduced costs.

As an example, let’s look at three scenarios with different operational goals and what breeding program might be suitable for each:

• George retains ownership of all his calves (steers and heifers) through slaughter. Because he doesn’t retain replacement heifers, a terminal crossbreeding systemis probably best suited to meet his goals. Both two-breed and three-breed terminal crossbreeding result in 100 percent of offspring heterosis, leading to calves with higher growth performance.
• For producers like Susan, who are selling their entire calf crop at weaning, increasing weaning weights is a primary focus. Choosing a crossbreeding program with high calving ease and the added benefit of hybrid vigour would likely be ideal for her operation.
• Jeff retains replacement females for his breeding herd. To support his goal, he could focus on crossbreeding to develop F1 crossesthat should result in higher reproductive efficiency and longevity. Alternatively, he could focus on outcrossing (breeding to non-relatives or distant relatives) within a single breed. This system can be used to maintain performance levels and restore lost performance due to inbreeding depression.

Focus on Traits That Matter to Your Operation

After your operational goals and breeding programs are determined, the next step is to evaluate the traits of importance.

Expected progeny differences (EPDs) have been available in the beef industry for decades and are a helpful tool when making selection decisions on desirable traits. Expected progeny differences can be used to estimate the difference between the predicted average performance of an animal’s future progeny and the average progeny performance of another bull. For example, a bull with a weaning weight EPD of +60 is expected to wean calves that are 20lbs heavier than a bull with a weaning weight EPD of +40.

Access a comprehensive beef cattle genetics glossary that explains key terms and concepts.

Many EPDs exist, from calving ease and weaning weight, to ribeye area and marbling, to cow weight and stayability. The EPDs you focus on will be dependent on your operational goals.

With the variety of EPDs available, it can become overwhelming to determine the contribution of a potential herd sire to improving the traits of interest. By focusing on economically relevant traits (ERTs) you can narrow your selection focus to the EPDs that matter most for your breeding goals.

Economically relevant traits are those that are directly associated with a source of revenue or a cost.  Not all EPDs represent ERTs – instead they use a related (or indicator) trait to estimate the ERT. For more information and examples of ERT versus Indicator traits, read the BCRC blog post Using Economically Relevant Traits.

Let’s revisit the farm scenarios from earlier:

• Since George retains ownership of all of his calves through to slaughter and does not retain replacement females, emphasis should be placed on sires with favourable carcass trait EPDs such as postweaning gain, carcass weight, marbling, fat depth and rib-eye area.
• With Susan’s goal of improving weaning weights to maximize profits when selling the calf crop at weaning, more emphasis should be placed on traits such as weaning weight and calving ease.
• Since Jeff is retaining replacement heifers for his breeding herd, traits such as direct and maternal calving ease or stayability should be a top priority for bull selection.

In addition to individual EPDs, many genetic evaluations offer selection indices which combine several traits into one overall economic value for the animal. These are calculated by placing an economic weighting on individual EPDs to create a multi-trait selection model for different types of broad production systems (generally maternal or terminal). Differences in two animal indices is the expected average value differences of their calves.

Know Your Bull Budget Prior to the Bull Sale

The purchase of a bull is an investment in the long-term profitability of your operation. With prices ranging from $2,000 to over $20,000 per head, it is important to ensure that your investment is adding value in the right places while still working within your budget. Different bull traits will have different impacts on your bottom line. Saving money on a low-priced bull may cost you in the long run if it moves you further away from your operational goals.

The BCRC’s Bull Valuation Calculator is designed to provide an estimate of how much a bull is worth using individual on-farm numbers. The bull value obtained in the calculator is only an estimate and may not reflect the true breakeven price. However, this interactive tool can be used as a general guideline and demonstrates how changing different variables can affect the cost or value of a herd sire.

Setting Your Herd Up for Success

Purchasing the best bull for your operation’s needs starts with good record-keeping to identify your operation’s strengths and weaknesses. Regularly collect and analyze data to track your herd’s performance. This will help you to make informed breeding decisions and track the progress of your herd over time.

Selection of a bull is one of the most important decisions you, the cow-calf operator, will make this year, and it is vital to your operation’s success. As breeding season approaches, this is a great opportunity to evaluate the goals of your operation and create a plan to accomplish them.

Originally published on BeefResearch.ca

Jordan Roberts, Tiago Valente, and John Basarab

Genomic tools can add value to your cow-calf breeding decisions, though genotyping has a cost. Your willingness to invest in genotyping will affect what information is available to you. However, there are ways you can apply genomic tools to add value to your herd over a range of investment levels. Livestock Gentec is a research centre of excellence at the University of Alberta with a goal of increasing adoption of genomic technologies by commercial livestock producers. As such, we think it is important for producers to understand more about genomic technologies, innovations in the field, and how to apply them. In this article, we discuss a few practical considerations for using genomic tools to improve the profitability of your herd and provide an update from the Livestock Gentec research group.

Using Hybrid Vigour to improve profitability

The genetic improvement of your herd can drive profitability. An important part of genetic progress is optimizing hybrid vigour. Put simply, hybrid vigour is the improvement in performance of hybrid offspring over the average performance of the parents. ‘Retained heterozygosity’ is a measure proportional to hybrid vigour, the formula considers the number and proportion of breeds contributing to the makeup of the individual to assign a value. This technical detail matters, as Basarab et al. (2018) found that each 10% increase in retained heterozygosity resulted in linear improvements to 200-d weaning weight (+3 lb), pregnancy rate (+2 percentage points), weaning rate (+3 percentage points), days in the herd (+51 days), and lifetime productivity (+79 lb over 5 parities). It is estimated that >40% of cows and calves in Canada would benefit from a 30% increase in hybrid vigour (Basarab et al. 2018). This means many commercial producers have a large opportunity to improve hybrid vigour and therefore profitability. To understand your opportunity for genetic improvement driven by the adoption of genomic tools, the ‘gold standard’ is to test each individual breeding bull and replacement heifer; however, a good low-cost alternative is testing a pooled DNA sample from a group of heifers.

Use of DNA pooling strategy can provide herd-level genomic breed composition and hybrid vigour. This is because there is a very strong relationship between measures from individual samples and DNA pooling for genomic breed composition (r=0.95 to 0.99) and hybrid vigour (r=0.99) (Valente et al., 2024, unpublished). This means a producer can benefit from accurate herd-level genomic breed information for a fraction of the cost. The pooling groups can be adjusted to optimize the cost benefit, as their “smart selection”, can turn this evaluation into actionable insight.

Caption: Report showing herd level genomic breed composition.

Individual Genotyping and Multi-Trait Selection Indexes

We can apply genomic tools with even more resolution by genotyping samples from all animals. When identifying individuals to genotype in your herd, we recommend the following prioritization: breeding bulls, replacement heifers and then cows/calves. This follows the potential for genetic improvement. With individual genotyping data, you can determine genomic expected progeny differences (gEPDs) in addition to genomic breed composition and hybrid vigour for all animals in the herd. These raw genomic values can be overwhelming as there can be many gEPDs.  This is clarified by using an economic model to quantify the relationship between the gEPDs and net return or profitability; some gEPDs are related to profitability while others are not and are excluded from the index. Thus, a multi-trait selection index is the sum of economically relevant traits based on economically weighted gEPDs based on the associated gross income and cost of each trait. The Replacement Heifer Profitability Index^TM scores developed by Livestock Gentec also includes retained heterozygosity to help identifying the best heifers that should be kept in the herd with a higher probability of staying longer in the herd and producing more calves over their lifetimes. Having these index values on an individual level gives a profitability-based ranking of animals for herd management decisions such as breeding and heifer retention.

Research Update from Livestock Gentec

In addition to educating producers on currently available genomic tools, we also think it is important to be aware of innovations in the field. Below are two projects the Livestock Gentec team are working on to further genomic technologies in beef.

Using genomics to improve the profitability and sustainability of Alberta’s beef industry. The aim of this project is to increase adoption of genomic tools in the industry and evaluate the effectiveness of these multi-trait selection indexes (e.g., Feeder Profitability Index^TM; Replacement Heifer Profit Index^TM ) with a large producer representation. Gentec is increasing the size of the reference data sets to enhance accuracy of gEPDs. To grow these data sets we are enrolling producers willing to share records from their herds, as well as to genotype their animals. Participants get access to steeply discounted genotyping and a detailed report including the genomic values discussed above. See more details below on how to participate. This project is cost-shared by the federal and provincial governments under the Sustainable Canadian Agricultural Partnership and is led by John Basarab as Principal Investigator.

How to participate:

• KEEP COW BASED RECORDS – cow ID – entry date – cull date & reason – calf data each year
• Have a DNA testing strategy
• Contact Livestock Gentec at 403-660-4155; lsgentec@ualberta.ca
• Request sample submission form and arrange for Tissue Sampling Units (TSUs) & applicator
• Pay $20/sample, with project funding paying for the other $32/sample
• Received all genomic breed composition, hybrid vigour score, MBVs, FPI^TM, RHPI^TM, easy to read reports and access to 100k SNP genotypes
• Work with Livestock Gentec to receive the most value from your data

Caption: (Left) learn more about Livestock Gentec’s genomic tools; (right) Sample submission form.

Reducing Greenhouse Gas Emissions from the Canadian Beef Industry through the Development and Adoption of Genomic Tools. One of the aims of this project is to evaluate fecal near-infrared spectroscopy as a low-cost proxy for measuring methane production in commercial cattle. The project will also measure methane emissions, feed intake and feed efficiency while taking many fecal samples from about 1900 beef cattle from various locations in Canada, though most will be in Alberta. In this project we will develop DNA based multi-trait selection index for cow-calf producers to reduce GHG emissions from their herd, while improving their profitability. As well, we will develop a carbon offset protocol so that cow-calf producers are incentivized to implement best management practices, like genomic selection for improved feed efficiency and reduced methane emissions, to reduce their herd-level GHG intensity of beef production. This project is funded by a NSERC-SSHRC Sustainable agriculture research initiative grant awarded to John Basarab as Principal Investigator.

Firstly, we would like to welcome Thi Lai To back to the Livestock Gentec team.      Lai is a research technician who will be helping with genotype inventorying and order proc     essing in the “Using genomics to improve the profitability and sustainability of Alberta’s beef industry” project and lab work and coordination for the NSERC project: “Reducing Greenhouse Gas Emissions from the Canadian Beef Industry through the Development and Adoption of Genomic Tools”. Lai is very passionate about innovations and applying new technology in livestock research. She likes to plan out/detail projects keeping herself busy in the labs and continuously explore new learning opportunities. Outside of work, she enjoys making no weekend plans, which allow her “to just do whatever I feel like: having a long walk, cooking or staying at the library.”

Pictured: Thi Lai To, Laboratory Technician setting a great example with PPE use in the lab.

While we are sad to see him go, we want to congratulate Dr. Tiago Valente on his new position with AbacusBio and wish him the best of luck in his future endeavours. Please reach out to lsgentec@ualberta.caif you require any assistance for matters Dr. Valente was supporting.

Livestock Gentec knowledge upcoming knowledge transfer activities Spring/Summer 2025

Dr. John Basarab Livestock Gentec CEO, will be giving several presentations over the next few months:

Researcher spotlight

Dr. John Basarab has been featured on the webinar series Researcher spotlight Thursday, March 13, 2025. Dr. Basarab discussed innovative genomic tools developed by Livestock Gentec and the University of Alberta to help commercial beef producers boost their profitability, reduce the carbon footprint of beef production and help cattle adapt to changing environments. It will be posted on this link shortly:

https://www.ualberta.ca/en/alumni/media-library/researcherspotlight.pdf

He will also be giving presentation at the following events:

• Gateway Research Organization (GRO) AGM March 28 at 11:00 am in Hazel Bluff Hall, 15 min west of Westlock
• Genetics and Breeding seminar for the for Peace Country Beef & Forage Association on June 4 in Valleyview, Alberta
• DNA Webinar Carcass Competition Windup for July 22 in Lacombe

Jennifer Paterson will also be sharing research results and knowledge from her projects at events and online:

Jennifer will be presenting at the Ontario Swine Conference on March 26th (https://ontarioswineconference.ca/day2/). This joint presentation, in collaboration with TJ Klopp and Kendra Foran from Cedarvilla Farms (https://www.cedarvilla.net/about), is titled ‘Gilts: The Foundation of Your Herd – Science into Practice.’ The presentation will take a team-based approach, with Jenny focusing on the “Science”, while TJ and Kendra will cover the “Practice”. The discussion will emphasize both the opportunities and challenges of translating science into the barn.

Jenny also had the opportunity to speak with Matthew Rooda on the Popular Pig Podcast about Gilt Development. The episode will be released soon. You can check it out at Popular Pig Podcast https://popularpig.com/podcasts/

One of Livestock Gentec’s key focuses is supporting producers in putting “Science into Practice”. Jenny is passionate about taking sow farm data and turning it into valuable reports on gilt development – enabling the barn team to track progress and to make data-driven decisions. She has had the pleasure of conducting several online and on-farm visits with barn teams to discuss her two favorite subjects – data and gilt management.

The 2025 Banff Pork Seminar, held from January 7-9, was a major success, with 803 attendees from across the industry. Key topics included, labor, markets, trade, sow, nursery and grow-finish management, survivability, swine health, feed and nutrition and welfare. Networking breaks before and after the sessions provided valuable opportunities to connect with both old and new colleagues and friends in the industry.

Sow Management breakout session

Livestock Gentec’s Jennifer Patterson presented in the breakout production session on Sow Management, which was well-received, with the three presentations complementing each other nicely.

Jennifer started off the session discussing “Gilt Development – Laying the Foundation for Future Performance” and highlighted that effective gilt management from birth through parity 1 is crucial for improving sow lifetime productivity (SLP). Focusing on key practices such as early selection, efficient Gilt Development Unit (GDU) management, and ensuring proper gilt eligibility at first mating represent an opportunity to improve and enhance overall production. Jennifer challenged the audience to rethink their approach to gilt development, highlighting that the ultimate goal is not just a successful first breeding and parity 1 litter size but ensuring the “right” gilt reaches the farrowing room, which will improve early parity retention and, ultimately, lifetime performance of the breeding herd.

Courtney Werth from South West Ontario Veterinary Services, followed with her presentation on “Weight Watchers – Insights from Ontario Sow Herds”. She highlighted the importance of gilt weight at first service for influencing optimal lifetime performance of sows.  She then discussed the opportunity (and challenges!) to use precision livestock technology, particularly use of electronic sow feeders (ESF) in combination with weigh scales to implement precision feed intake curves during gestation to maintain ideal body condition with the goal to maximize production, improve retention and maximize feed utilization.

Chris Opschoor from Topigs Norsvin Research Center rounded out the session with his talk on “Between Gestation and Lactation a Transition is Made” where he highlighted the importance of ensuring that sows arrive in the farrowing room prepared for the physiological challenges of lactation. He discussed in detail the transition from late gestation to farrowing and its impact on the farrowing process, colostrum and milk production. Chris provided practical recommendations for managing the transition period, emphasizing that proper management and nutrition during this time plays a key role is subsequent performance and productivity.

Please see https://www.banffpork.ca/program/2025-speakers/ for more detail and to download the presentations.

Sonja Allen is exploring new strategies to improve sow lifetime productivity

PhD graduate student Sonja Allen presented a poster at BPS on “Preliminary insights into improving sow lifetime productivity and pig quality through phenotypic and genomic analysis”. This work is part of Gentec’s NSERC research collaboration with Hypor – Hendrix Genetics. Sonja highlighted that achieving profitability and sustainability in the Canadian swine industry requires optimizing Sow Lifetime Productivity (SLP) and that the swine industry faces challenges due to the early culling and mortality of young parity females contributing to the low retention rates and overall productivity.

Although in the early stages of her research, Sonja outlined the main objectives of her study: 1) identifying key traits of superior gilts and analyzing growth and feed intake during gestation and lactation, 2) exploring strategies to enhance litter growth and weaning weights, and 3) identifying genetic and phenotypic relationships between traits to improve SLP and production profitability. These insights are critical for improving gilt selection, management practices, and breeding programs in commercial swine production. We are excited about what she will discover in the future.

Dalhousie University, Lakeland College and University of Alberta are conducting simultaneous feed efficiency and enteric emissions assessments on beef cattle. These trials are part of our NSERC-SSHRC funded project: “Using genomic tools to reduce GHG & Methane in beef cattle”. Feed efficiency is measured with GrowSafe^® and enteric emissions are being measured with GreenFeed^® emission monitoring systems. We have genotyped and we are collecting fecal samples from these animals during the trial. We aim to develop molecular breeding values and selection indexes for green house gas emissions and production efficiency with the project      data. We will collect Near Infrared Spectra on the fecal samples to develop a low cost      proxy phenotype for enteric emissions by using ML and AI tools for processing the data. We are also in the process of coordinating with collaborators on additional research sites to contribute to the project dataset.

Pictured: Obioha Durunna from Lakeland College collecting fecal samples by rectal palpation for later Near Infrared Spectroscopy.

The project: “Using genomics to improve the profitability and sustainability of Alberta’s beef industry” is funded by a grant awarded to Dr. John Basarab in 2024, funded by Sustainable CAP and administered by RDAR. In this project we are collecting key phenotypic data from producers and providing informative genomic value reports. These genomic value reports provide the following data: genomic breed composition, retained heterozygosity, molecular breeding values for 12 phenotypes, and Livestock Gentec’s Replacement Heifer Profit I     ndex^TM and the Feeder Profit Index^TM. Further, producers participating in the project can genotype their animals at a discount rate ($20/animal). The genotyping cost is shared between the project and Neogen our sequencing partner. In exchange for the discounted genotyping and genomic values report, participating producers are required to collect some basic phenotypic data from their herds to enhance our reference dataset. We have already collected over 9,000 genotypes in this project     . If you are interested in participating, please see the QR codes to learn more and information to sign up. Please reach out to lsgentec@ualberta.ca if you have any questions.

Publications

Hailemariam, D., Manafiazar, G., Baes, C., Schenkel, F., Miglior, F., Stothard, P., Plastow, G. (2025) Circulating serum metabolites as biomarkers and predictors of residual feed intake in lactating dairy cows. Sci. Reports 15, 1709. https://doi.org/10.1038/s41598-025-85610-1

Hailemariam, D., Manafiazar, G., Baes, C., Schenkel, F., Miglior, F., Stothard, P., Plastow, G. (2025) Circulating serum metabolites as biomarkers and predictors of residual feed intake in lactating dairy cows. Sci. Reports 15, 1709. https://doi.org/10.1038/s41598-025-85610-1

Virtuoso, M.C.S., Aalhus, J.L., Juárez, M., López-Campos, O., Bruce, H.L., Li, C., Basarab, J.A., Plastow, G. Valente, T.S. (2025) Genetic parameters and genomic insights for meat colour traits of Canadian crossbred beef cattle. Can J. Anim. Sci. 105:1-13. doi.org/10.1139/cjas-2024-0074

Virtuoso, M.C.S., Aalhus, J.L., Juárez, M., López-Campos, O., Bruce, H.L., Li, C., Basarab, J.A., Plastow, G. Valente, T.S. (2025) Genetic parameters and genomic insights for meat colour traits of Canadian crossbred beef cattle. Can J. Anim. Sci. 105:1-13. doi.org/10.1139/cjas-2024-0074

Awards

University of Alberta Awards for Teaching, Learning and Research, Edmonton, 23 Oct 2024. Dr. John Basarab and Dr. Graham Plastow were again recognized for the 2023 ASTech award for Best in Agriculture.

Press

NSERC SSHRC funded project: “Using genomic tools to reduce GHG & Methane in beef cattle” was recently awarded and people are taking notice. John Basarab, Gentec CEO has given numerous interviews in recent weeks on this project:

• Nov 7, 2024, interview, hosted by Joey Slattery, 880 CHED, Edmonton
• Nov 8, 2024, interview with Kevin Ma, St. Albert Gazette (see link for feature in The Albertan)
• Nov 11, 2024, interview with Bassirou Ba, CBC Radio Canada
• Nov 11, 2024, interview with Jessica Ng, Radio Active, Edmonton

Presentations

John Basarab Livestock Gentec CEO has also presented our research at several association meetings recently. These presentations are a great way to communicate to the producer community and build interest in genomic tools. The presentations focused on profit opportunity with genomic improvement in Canada’s commercial beef herd, the value of hybrid vigour and the genomic tools Livestock Gentec has developed to help seize these opportunities.

• Manitoba Beef and Forage Conference, Portage La Prairie, MB, October 30, 2024
• BC Cattlemen’s Association – BCCA Town Hall, Courtenay, BC, November 16, 2024

Highlights from the George Foxcroft Reproduction Workshop at Leman 2024

On September 21^st, 2024, Jennifer Patterson and Michael Dyck hosted the “George Foxcroft Reproduction Workshop” at the Leman Conference in St.Paul, Minneosta. The workshop had an exciting line-up of world class speakers that addressed the theme “Managing the breeding herd in a changing environment”. We were pleased to have one of our biggest attendances to date, drawing in over 100 people from 14 different countries and from a number of industries (production, academia, media, nutrition, genetic services, consulting, sales).

We always measure the impact of the workshop, not only by the number of people in the room, but by the number of sows represented. This year, over 1.4 million sows were touched by people working directly for production companies, not including the many others that will have an influence.

The goal of these sessions is always to bridge the gap between science and practice and to foster networking opportunities for attendees. We accomplished this and hope that every attendee was able to take home valuable insights that they can implement in their own systems.

Special thanks to the University of Minnesota for their 18 years of partnership in organizing this workshop, and to Merck for their continued sponsorship and collaboration in designing this well-received program.

The presentations will be posted, please check back in the future.

https://sites.google.com/a/umn.edu/leman-swine-conference/current-years-conference

“The management of an efficient breeding herd must take into consideration a variety of ‘environments’, including the animals’ physiological environment, the housing environment, the regulatory environment and the technological environment, just to name a few. These ever-changing environments that affect production are driving the need for more sophisticated and adaptable management practices. In this session we will bring together experts to discuss technical and practical considerations in dealing with these evolving environments and how to maintain an efficient breeding herd. This workshop is designed for swine producers, veterinarians, and industry professionals looking to enhance their knowledge and practices in swine breeding management. Don’t miss this opportunity to learn from the best and network with peers in the industry.”

The “last mile” – delivering research results to the people who can make the difference

Gentec works closely with industry partners in making a difference on farm. Jennifer Patterson is at the forefront of improving pork production efficiency. It was very pleasing to receive recent positive feedback from a partner that these efforts deliver key learning “to the people in the barn who can make the difference in performance”.

This aligns directly with RDAR’s commitment to delivering research outcomes that make a meaningful impact on Alberta’s economy and landscape, referring to this as the “last mile” in the delivery and uptake of research results. RDAR CEO, Dr. Mark Redmond emphasized this at a meeting RDAR hosted in Lacombe on November 18th. The aim was to bring producers, researchers, agri-businesses and municipal leaders together “to learn about funding opportunities, what practices are being adopted on-farm, and what research is underway to drive improvements in central Alberta’s agricultural practices”.

Putting tools in the hands of barn staff, as Jennifer does, is maybe an example of the “last quarter or even furlong”. Thank you once again to all Gentec’s partners who make these things happen.

Livestock Gentec at Farm Fair 2024

Livestock Gentec shared a booth with University of Alberta Faculty of Agriculture, Life and Environmental Science (ALES), November 8 and 9. The event hosted show-animal competitions, booths from agriculture providers, producer meetings and lots more. We had a great time connecting with producers and the public on how we are advancing adoption of genomic tools in livestock. A special thanks to Dr. Rene Dery for coordinating the ALES booth.

(left) University team Nov 9 at the ALES booth, joined by ALES Dean Dr. Yada. (right) Livestock Gentec team members (Dr. Tiago Valente and Jordan Roberts) with research posters and tissue sample units on display.

While at Farm Fair John Basarab (CEO) and Tiago Valente (Research Associate) attended Farm Forward roundtable discussions hosted by Graham Neil–pictured below, and the Canadian Beef Breeds Council (CBBC) annual general meeting. John and Tiago had the opportunity to introduce themselves to the CBBC delegates and listen to several presentations.

Farm Forward roundtable discussions at Farm Fair 2024 in Edmonton

Publications

Olson CA., Li C., Block HC, McKeown L., Fitzsimmons C., Plastow G., Basarab JA. 2024. Residual feed intake measured as replacement heifers is indicative of residual feed intake measured as mature cows. Can. J. Anim. Sci. 00: 1–9 (2024), dx.doi.org/10.1139/cjas-2024-0065

Khakbazan M., Olson CA., Block HC., Li C., Basarab JA. Effects of feed efficiency, longevity, cow’s hybrid vigour, and lifetime productivity on profitability of cow-calf operations in central Alberta. Can. J. Anim. Sci. 00: 1–9 (2024), dx.doi.org/10.1139/cjas-2024-0065

Li H., Wang Y., Vinsky M., Valente T., Basarab JA., Li C. Accuracy of genomic predictions using single and multiple-trait machine learning methods in Canadian beef cattle population. J Anim Sci., 102. Suppl., 3, 33–34, https://doi.org/10.1093/jas/skae234.037

Alipanah, M., Valente, T.S., Abo-Ismail, M.K., Plastow, G.S., Basarab, J.A., Crowley, J.J., Akanno, E.C. (2024) Accounting for non-additive genetic variation in carcass quality traits of Canadian beef cattle. Can. J. Animal Sci. 104 doi.org/10.1139/cjas-2024-0008

Virtuoso, M.C.S., Hosseini, A., Aalhus, J.L., Juárez, M., Bruce, H.L., Li, C., Basarab, J.A., Valente, T.S., Plastow, G. (2024) Genetic parameter estimates for sensory and meat quality traits measured at 3 and 29 days of aging of beef from Canadian crossbred cattle. Meat Sci. 207:109351 doi.org/10.1016/j.meatsci.2023.109351

Virtuoso, M.C.S., Aalhus, J.L., Juárez, M., López-Campos, O., Bruce, H.L., Li, C., Basarab, J.A., Plastow, G., Valente, T.S. (2024) Genetic parameters and genomic insights for meat colour traits of Canadian crossbred beef cattle. Can. J. Animal Sci.

Chitneedi, P.K., Hadlich, F., Moreira, G.C.M., Espinosa-Carrasco, J., Li, C., Plastow, G., Fischer, D., Charlier, C., Rocha, D., Chamberlain, A.J., Kuehn, C. (2024) eQTL-Detect: nextflow-based pipeline for eQTL detection in modular format with sharable and parallelizable scripts. NAR Genomics and Bioinformatics, lqae122 doi.org/10.1093/nargab/lqae122

Robic, A., Hadlich, F., Moreira, G.C.M., Clark, E.L., Plastow, G., Charlier, C., Kühn, C. (2024) Innovative construction of the first reliable catalogue of bovine circular RNAs. RNA Biology 21: 52–74. doi.org/10.1080/15476286.2024.2375090

Oliveira, H.R., Sweett, H., Narayana, S., Fleming, A., Shadpour, S., Malchiodi, F., Jamrozik, J., Kistemaker, G., Sullivan, P., Schenkel, F., Hailemariam, D., Stothard, P., Plastow, G., Van Doormaal, B., Lohuis, M., Shannon, J, Baes, C., Miglior, F. (2024) Symposium Review: Development of genomic evaluation for methane efficiency in Canadian Holsteins. JDS Communications published online January 2024 doi.org/10.3168/jdsc.2023-0431

van Staaveren, N., De Oliveira, H., Houlahan, K., Chud, T., Oliveira Junior, G., Hailemariam, D., Kistemaker, G., Miglior, F., Plastow, G., Schenkel, F., Cerri, R., Sirard, M.A., Stothard, P., Pryce, J., Butty, A., Stratz, P., Abdalla, E., Segelke, D., Stamer, E., Thaller, G., Lassen, J., Manzanilla-Pech, C., Stephansen, R., Charfeddine, N., García-Rodriguez, A., Gonzalez-Recio, O., López-Paredes, J., Baldwin, R., Buchard, J., Parker Gaddis, K., Koltes, J., Peñagaricano, F., Santos, J., Tempelman, R., VandeHaar, M., Weigel, K., White, H., Baes, C. (2024) The Resilient Dairy Genome Project – a general overview of methods and objectives related to feed efficiency and methane emissions. J. Dairy Sci. 107: 1510-1522.doi.org/10.3168/jds.2022-22951

Ko, H., Pasternak, J.A., Mulligan, M.K., Hamonic, G., Ramesh, N., MacPhee, D.J., Plastow, G.S., Harding, J.C.S. (2024) A DIO2 missense mutation and its impact on fetal response to PRRSV infection. BMC Veterinary Research 20:255 doi.org/10.1186/s12917-024-04099-4

Moroni, J.L., Tsoi, S., Wenger, I.I., Plastow, G.S., Dyck, M.K. (2024) Placental transcriptome analysis in connection with low litter birth weight phenotype (LBWP) sows. Genes 15(6):703 doi.org/10.3390/genes15060703

In the field

Our project: “Using genomic tools to reduce GHG & Methane in beef cattle” is ramping up, so the team–Gentec and collaborators– went out to Roy Berg Kinsella Research Ranch to learn how to operate the Greenfeed Emissions Monitoring equipment. This equipment measures the enteric greenhouse gas emissions from cattle. Animals put their head into the gas measurement shroud to receive feed pellets. The animal’s RFID is then read, and as they are feeding, the enteric gases (CH₄, CO₂, H₂) and air are drawn up a sampling tube by positive air flow to an infrared sensor that quantifies gases. This enteric gas data will also provide a baseline for developing models for predicting enteric methane from fecal NIRs spectra. Some of the team also took in a web-based training to see how the data is collected, analyzed and reported by the C-lock software and analytics team. This latter aspect is an international collaboration with Belgian scientist Dr. Amélie Vanlierde with Walloon Agriculture Research Centre (CRA-W, Gembloux, Belgium) and French scientist Donato Andueza from The French National Research Institute for Agriculture, Food and Environment (INRAE).

Greenfeed Emissions Monitoring (GEM) system training session conducted by C-lock technician, on 29 Oct 2024 (left); Green Feed archived gas sensor data (right).

As global and national pressures to enhance the sustainability and efficiency of beef cattle production continue to grow, the Canadian beef industry requires a multifaceted approach to address these challenges. One promising and enduring solution lies in leveraging genetic and genomic technologies to enhance breeding strategies. By selecting for beef cattle with improved feed efficiency, producers can reduce feed resource use, lower emissions, and maintain the same level of production.

The focus of this research was to investigate the functional genetics underlying feed efficiency in Canadian beef cattle and identify functional SNP markers associated with this trait. Selecting for feed efficient (FE) cattle, measured by Residual Feed Intake (RFI; kg/d), has the potential to increase lean meat yield without requiring additional feed. Using RNA-Sequencing technology, we uncovered genetic mechanisms driving feed efficiency by identifying key regulatory genes, functional SNP markers, and associated QTLs. This approach enables the detection of genetic mutations (SNPs) derived from DNA sequence data that may influence feed efficiency, providing valuable insights for improving sustainability in beef production.

A population of 48 Canadian beef cattle from the Roy Berg Kinsella Research Ranch (Alberta, Canada), including 16 Angus, 16 Charolais, and 16 Kinsella hybrid composite animals were selected from a larger cohort of 738 cattle based on their extreme FE phenotypes. At slaughter, rumen papillae tissue was collected from each animal for RNA extraction.

The study identified 11 key regulatory genes (EIF4B, USP43, RHOD, SERPINB2, MYH1, MYL2, TCEANC, CKM, MYLPF, TNNC2, and ENSBTAG00000040518) that were significantly differentially expressed between high and low FE groups. These genes were linked to muscle contraction and muscle cell biological processes.

Analysis of functional SNPs revealed 1,137 uniquely fixed SNPs in the high FE group and 1,190 in the low FE group across breeds. When examining the co-localized QTL classes overlapping with these functional SNPs, we found distinct patterns:

• High FE SNPs evenly overlapped with four major QTL classes: Meat and Carcass (18.19%), Milk (27.34%), Reproduction (23.95%), and Production (27.08%), with a smaller proportion overlapping with Health (1.87%) and Exterior (1.57%).
• Low FE SNPs predominantly overlapped with Milk QTLs (59.65%), followed by Meat and Carcass (7.91%), Reproduction (14.95%), and Production (11.61%), with a smaller proportion overlapping with Health (2.83%) and Exterior (3.05%).

These findings suggest that less feed-efficient cattle may allocate more energy toward milk-related traits, while more feed-efficient cattle direct energy toward performance traits, such as meat production and yield. Selecting for higher feed efficiency in beef cattle could thus optimize energy partitioning for production-related traits, benefiting the beef industry.

The results of this research were presented at two major conferences and at the Ontario Beef Field Day:

• The American Society of Animal Science – Canadian Society of Animal Science – Western Section ASAS (ASAS-CSAS-WSASAS) conference in Calgary, Alberta, in July 2024.
• The European Federation of Animal Science (EAAP) conference in Florence, Italy, in September 2024.
• The Ontario Beef Research Centre (OBRC) Beef Field Day in Elora, Ontario, Canada in October 2024.

Authors: Stephanie Lam¹, Leluo Guan², Graham Plastow³, Ángela Cánovas¹

¹ Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada; ² The University of British Columbia, Faculty of Land and Food Systems, Vancouver, Canada; ³ Livestock Gentec, University of Alberta, Department of Agriculture, Food and Nutritional Science, Edmonton, Canada

This research highlights the importance of collaboration between the University of Guelph’s Centre for Genetic Improvement of Livestock and the University of Alberta’s Livestock Gentec, and now UBC with Leluo Guan’s move there, to leverage Canadian herd databases and deliver actionable insights to benefit beef producers and the entire value chain.