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.

Livestock Gentec’s Jennifer Patterson will be presenting at Banff Pork Seminar (January 7-9th, 2025) in the breakout production session on “Sow Management.” She will be discussing “Gilt Development – Laying the Foundation for Future Performance,” alongside Courtney Werth, who will present on “Weight Watchers – Insights from Ontario Sow Herds,” and Chris Opschoor, who will talk about “Between Gestation & Lactation: A Transition is Made.” It promises to be a great session.

PhD graduate student Sonja Allen will present 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 our NSERC research collaboration with Hypor – Hendrix Genetics. Please come by and check out her poster.

BPS is always an excellent event for bringing the industry together. Our team will also be represented by Michael Dyck, Kayla Patey and Morgan Rioch, we look forward to seeing you there!

Jennifer will also be presenting at the Ontario Swine Conference in London, Ontario (March 25-26th, 2025). She will be part of a session on “Gilt Development for Longevity,” with TJ Klopp and Kendra Foran. This joint session will focus on “putting science into practice.”

On the beef side, several RDAR funded partners to Gentec will be presenting their research at the 2025 RDAR research showcase Jan 16 in Edmonton. Watch out for the presentations from Dr. Kajal Latimer, Dr. Brenda Ralston

From Livestock Gentec

Make it your resolution to bring genomic tools to your herd! We are accepting submission forms for our Livestock Gentec Adopting of Genomic Tools project. Learn more about it following the link below or scanning the QR code.

What do you have to do?

• Keep Cow based records – cow ID – entry date – cull date & reason – calf data each year
• Contact Livestock Gentec (780-248-1740; lsgentec@ualberta.ca) for a submission form and to arrange for Tissue Sampling Units (TSU)
• Collect TSU samples from the animals you would like to evaluate
• Send your TSUs and submission form to Livestock Gentec, 2-31 GSB, 9007-116 Street NW, University of Alberta, Edmonton T6G 2H1
• Pay only $20 per animal, with project funding paying for the other $22
• DNA pooling costs $5/animal + $20 for each group evaluated (20 animals/group)

What do you get?

• Genomic breed composition and hybrid vigour score for all animals
• Genomic Expected Progeny Difference values (gEPDs) for 12 traits including growth, feed efficiency, fertility and carcass traits
• Selection Index values for the Feeder Profit Index (FPI™) and Replacement Heifer Profit Index Score (RHPI™ Score)
• Visual rank for all animals based on FPI™ and RHPI™ Score
• For DNA pooling, only group level genomic breed composition and hybrid vigour score available

(left) submission form (right) learn more about livestock Gentec genomic tools for beef cattle

Learning opportunities from our partners

Records for Tracking Genetic Improvements email course free course from Beef Cattle Research Council (BCRC), in partnership with Alberta Beef Producers, Saskatchewan Ministry of Agriculture, Canadian Beef Breeds Council, University of Guelph and Maritime Beef Test Station

Link to online registration

Information on the new beef projects:

• Sire-based Feeder Profit Index for Beef on Dairy production and marketing systems, 2024-2027, PI Basarab (Sustainable CAP administered by RDAR)
• Using genomics to improve the profitability and sustainability of Alberta’s beef industry, 2024-2027, PI Basarab, co-PI Plastow (Sustainable CAP administered by RDAR)
• Evaluation of reduced enteric methane emissions in beef cattle using a novel vaccine at a research farm in Alberta, 2025-2028, PI ArkeaBio Inc., University of Alberta lead Basarab (Emission Reduction Alberta)
• Reducing Greenhouse Gas Emissions from the Canadian Beef Industry through the Development and Adoption of Genomic Tools, 2024-2029, PI Basarab (NSERC SSHRC)

For updates on the Gentec team, we are pleased to welcome Jordan Roberts as project manager. Jordan joined us in October. His role will support the coordination and execution of our beef genomics research and adoption projects. Jordan has an MSc in Biological Sciences specializing in animal physiology from the University of Calgary. He has spent his career in research and development in the agriculture and agri-food sector and held roles with industry, government and academia. Jordan looks forward to doing his part to supporting development and adoption of genomic tools in livestock!

We are also pleased to welcome back Everestus Akanno into a full-time role as senior research associate from January 2025. Everestus will be focusing on conducting research for our NSERC-SSHRC project: “Reducing Greenhouse Gas Emissions from the Canadian Beef Industry through the Development and Adoption of Genomic Tools”.

Congratulations to Gentec alumna Kristin Lee on obtaining her PhD from the University of Guelph in September. Her thesis, titled “Python Based Genetic Evaluation System for the Improvement of Multi-Breed and Crossbred Beef Cattle”, was co-supervised by Professor Angela Canovas and Professor Flavio Schenkel. The project was supported by AgSights, who contributed both funding and valuable industry knowledge. She is now working for Gentec’s partner Genesus Genetics Technologies Inc. in the role of geneticist, where she focuses on optimizing their genomic evaluation software and overseeing genetic improvement programs in nucleus farms.

One of the longest serving members of Gentec, Prof. Leluo Guan, continues from strength to strength following her move to University of British Columbia where she continues her world leading research program to study rumen microbiome and its roles in cattle production. Recent new grant funding includes “Novel and adaptive rumen microbiome targeted solutions for GHG mitigation in cattle”  as results of long -term collaborations among Gentec (University of Alberta), University of Guelph, University of Manitoba, and AAFC. This project is funded through NSERC Alliance through “NSERC-SSHRC Sustainable Agriculture Research Initiative (SARI)”.