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