We’re thrilled to welcome Dr. Chinyere Ekine-Dzivenu back to the University of Alberta and Livestock Gentec. Dr. Ekine-Dzivenu is a quantitative geneticist and livestock genomics scientist with extensive experience applying advanced genetic and genomic tools to improve livestock productivity, profitability, and environmental sustainability. She earned her PhD and completed a postdoctoral fellowship at the University of Alberta, where she applied genomic tools to enhance feed efficiency and carcass quality in beef cattle.

In her new role she is advancing genetic and genomic tools to improve the sustainability, profitability, and environmental performance of beef production in Canada while contributing to teaching and fostering international partnerships and collaborations that link and ensure research innovations translate into practical on-farm impact, reflecting her passion for climate-smart, farmer-focused livestock improvement.

She remains seconded to the International Livestock Research Institute (ILRI), where she contributes to designing genomic selection strategies and digital platforms, data systems, and farmer support services, to drive continuous improvements in smallholder dairy systems across sub-Saharan and Asia enhancing productivity profitability, and climate-resilience.

Her dual appointment strengthens collaboration between both institutions, aligning research with practical on-farm applications, expanding funding opportunities, and supporting capacity building, technology transfer, and climate-smart livestock improvement in both hemispheres.

Dr. Ekine-Dzivenu is passionate about mentoring students, training the next generation of scientists, and fostering multidisciplinary collaborations that bridge research and industry, ensuring tangible benefits for farmers.

The Canadian agriculture industry is striving to balance both sustainability and productivity, targeting net zero emissions by 2050 and a doubling in agriculture productivity by 2030 (Government of Canada 2024). Within beef cattle production in Canada, 53-54% of greenhouse gases (GHG) are from enteric methane emissions (Basarab et al. 2012). Therefore, measurement of beef cattle methane emissions is critical for the understanding of how feed additives, vaccines, diet quality, hybrid vigour, genetic selection for feed efficiency and other best management practices for mitigating methane interact with economically important traits. We can measure these enteric gas emissions from animals in several ways. For example, the GreenFeed Emissions Monitoring (GEM) System™, takes measures of methane, carbon dioxide and hydrogen from respired and  eructated (burps) gases of cattle during voluntary visitations to the system. While the GEM system provides automated and noninvasive collection of enteric gases, it is expensive specialized equipment that limits its use to primarily research sites. As such, low cost proxy measures can allow for large data collections at multiple sites. Expanding the collection of enteric methane measures will improve methodologies for reducing GHG from beef production. This could be useful when applied to development and validation of genomic breeding values and other mitigation strategies. This article will give some detail on how we are approaching this problem in our project.

The project “Reducing Greenhouse Gas Emissions from the Canadian Beef Industry through the Development and Adoption of Genomic Tools” with Livestock Gentec CEO Dr. John Basarab as PI, has been mentioned in previous articles [In the field Dec 2024; Livestock Gentec March 2025 Research Update; June 2025 NSERC pilot]. A  project goal is to develop a methane emission prediction equation using Near Infrared spectroscopy (NIRS) conducted on dried and ground fecal samples. 

NIRS measures the absorption of energy across the near infrared wavelengths (700-2500nm) of the electromagnetic spectrum. The absorption value from NIRS at certain wavelengths are associated with bend and stretch characteristics of various chemical bonds in a sample. We can use this variation to develop equations that predict useful attributes of the sample. For example: digestibility of of feed sample, moisture content in grain, protein content in milk, and fat content in ground meats have all shown good prediction and form the basis for industry quality testing.

In our case, we are analyzing NIRS of fecal samples to predict methane emissions. Enteric gas emissions in beef cattle are related to the fermentation of feed by rumen microbes. For example, archea microorganisms are a group of methanogens in the rumen associated with methane production. We believe we can utilize these spectra to predict GHG enteric emissions, based on the composition of metabolites in the feces. Project collaborator Dr. Amélie Vanlierde from Walloon Agricultural Research Centre in Belgium conducted similar research with fecal NIRS and observed a moderate prediction accuracy of fecal NIRS and beef and dairy cattle enteric emissions (Vanlierde et al. 2022).

NIRS data are rich in information about sample component composition. However, the data can be noisy with interference caused by factors unrelated to composition. These factors include attributes such as particle size and moisture content. Our mitigation for this is consistent methodology across sites and fecal processing. For fecal processing, samples are dried and ground to one mm to improve the consistency of the material for spectra collection. We also conduct a series of mathematical transformations to spectra to mitigate these noise factors. Both physical and statistical processing can be applied to improve the quality of NIR spectra data for analysis.

NIRS can collect absorption values every 0.5nm wavelength. This means there can be as many as 4200 absorption values for each sample. There is rich literature exploring the best statistical methods and evaluation techniques for NIRS data analysis. Researchers commonly use Partial Least Squares Regression (PLSR) to link an attribute to NIRS spectra. We can validate results with cross-validation or a training-test set split approaches. 

Figure 1: pre and post transformation spectra following SNV-D + first derivative transformation.

Finally, there are questions about the scalability of fecal NIRS as a proxy. Fecal drying and grinding, along with laboratory grade NIRS equipment which are expensive create barriers to data collection. These are good practices for the best quality data; however, there is value in exploring a more field-ready approach to expand the scope of potential data collection. To approach this goal, we are also collecting spectra using a portable NIRS on fresh fecal samples. In an ideal case, this would allow us to collect this data ‘chute-side’ at high volume.

Currently we have collected over 1350 spectra on 267 animals across four trials at three sites (Roy Berg Kinsella Research Station; Lakeland College and the Maritime Bull Test Station). Trials at Olds College Technology Access Centre for Livestock Production led by Sean Thompson are also underway. We will continue to run trials through 2028 and plan to add data from Dr. Gabriel Ribeiro at the University of Saskatchewan. These trials will include cows, heifers, bulls, native steers, and beef-on-dairy steers. Research sites will use a variety of feeds including high forage-based rations and high-grain finishing diets. This will help to produce a large dataset with high variability. The large and diverse dataset will help us to evaluate  these NIRS based enteric emission predictions.

Figure 2: Labelled fecal samples collected from Lakeland College by Dr. Obioha Duranna and team.

 Citations:

Basarab, J., V. Baron, O. López-Campos, J. Aalhus, K. Haugen-Kozyra, E. Okine. 2012.

Greenhouse gas emissions from calf- and yearling-fed beef production systems, with and without the use of growth promotants. Animals, 2:195–220.

Government of Canada 2024. Sustainable Development Goal 2: Zero hunger. https://www.canada.ca/en/employment-social-development/programs/agenda-2030/zero-hunger.html  [accessed August 27, 2025].

Vanlierde, A, F. Dehareng, A. Mertens, M. Mathot, A. Lefevre, et al 2022. Estimation of methane eructed by dairy and beef cattle using faecal near-infrared spectra. 73. Annual Meeting of the European Federation of Animal Science, EAAP, Sep 2022, Porto, Portugal. pp.333. ⟨hal-04792528⟩

Mark Johnson of OSU Extension recently published an article on the economics of herd expansion where he provides an excellent overview of the current value of replacement heifers and the economic drivers behind expansion decisions.

He highlights that while calf prices are at record highs, rebuilding the cow herd has been slow. Drought, high interest rates, and the capital required to purchase or raise breeding females continue to hold producers back. Yet, from a breakeven perspective, this may actually be the best time in years to add new females—today it takes about 2.75 calves to pay for a bred heifer, compared to 4.5 on average, and as many as 9 back in 2015.

 For those looking to expand their herd, we advocate using genomic tools to improve profitability and sustainability. Tools developed by Gentec, such as EnVigour HX™ (which measures retained heterozygosity to maximize hybrid vigor), and genomic indexes for heifer fertility and lifetime productivity  (Replacement Heifer Profit IndexTM and Feeder Profit IndexTM), allow producers to identify replacement females with the greatest potential for fertility, resilience, and long-term profitability.

By combining today’s favorable economic signals with genomics-driven selection, producers can reduce risk, improve herd productivity, and ensure that every replacement investment pays off well into the future.

Read Mark’s full article here:

https://www.angus.org/angus-media/angus-beef-bulletin/abb-extra/2025/08/fp_current-value-of-replacement-heifers

Contact Gentec today to learn how these tools can fit into your herd expansion strategy.

lgentec@ualberta.ca

Gentec’s producer pilot project for the NSERC-SSHRC funded project: Reducing Greenhouse Gas Emissions from the Canadian Beef Industry through the Development and Adoption of Genomic Tools is attracting interest across Canada. Most recently Dr. John Basarab (Livestock Gentec CEO) and Jordan Roberts (Project Manager), had a virtual meeting with CDPQ and Quebec beef industry stakeholders to discuss how genomic technologies can help the beef industry become more sustainable.

November 4-9, 2025 Livestock Gentec team members will be attending Farm Fair at the Edmonton Expo Centre. Farm Fair has many agriculture focused events and activities. If you want to learn more about our research or our projects, come by see the booth. Among the other events, will be Farm Forward a young producer ‘unconference’ with various sessions and activities. You can also catch Dr. Basarab at Farm Forward during at the Ask an Expert, event. This event uses a short individual interview style event to be more accessible. Attendees will be able to ask the experts about how they can apply their expertise to their operations.

We are also happy to share that Dr. Basarab’s research on genomics to reduce methane emissions in cattle is featured in the 2025 University of Alberta annual report on Research and Innovation. 

Jenny Patterson will be speaking at the upcoming  Swine Technology Workshop hosted by Alberta Pork in Red Deer Alberta on October 8th, 2025.This well-attended yearly event brings together producers and industry experts to discuss the latest developments in swine research and provides valuable networking opportunities for everyone who attends. This year, topics cover a wide range of industry relevant topics, including “Ventilation and What to Look For”, “Sow Mortality – Genetic and Management Opportunities”, “Sow Productivity and Grow Finish Optimization” and “A Day in the Life of a Slaughter Plant”. Jenny will be speaking on “The Quadrant” – highlighting the key components for gilts’ eligibility at breeding to improve sow lifetime productivity. We hope to see you there.

This pilot project will evaluate the adoption of genomic tools and genetic selection strategies on reducing GHG emissions and improving profit at the herd level as compared with the baseline of practice. These tools include genomic breed composition, hybrid vigour score, genomic Expected Progeny Difference values (gEPDs) for 12 traits balanced into a Feeder Profit Index™ and a Replacement Heifer Profit Index Score™.

In collaboration with Viresco Solutions and an industry based-advisory committee, the research teams will develop and test a carbon offset protocol for cow-calf producers. This protocol, if approved by Alberta Environment or Environment Canada, will allow cow-calf producers to aggregate and sell carbon offset credits to large final emitters. Genomic and genetic based Beneficial Management Practices (BMPs) over and above practice usual will be refined by the expert advisory committee. Producers enrolling in the project will be part of the validation and feedback process for the genomic & genetic selection BMPs, and will support economic and GHG emissions analyses.

Benefits to producers

• No cost for 100k SNP genotypes on pilot project enrolled animals
• Genomic values reports with genomic tools and their accuracies
• Workshops for implementation genomic/genetic selection BMPs to improve profit & reduce GHG
• Access to GHG emissions analysis results for your farm
• Input into Alberta Carbon Offset Cow Calf protocol development
• Future access to gEPDs for reduced methane emissions balanced into multi-trait indexes

Enrolment and Participation

1. Contact Livestock Gentec (403-660-4155); lsgentec@ualberta.ca)
2. Complete intake survey and intake forms
3. Collect tissue samples from pilot project animals
4. Collect production data for pilot baseline defined in supplied templates
5. Attend BMP workshop
6. Year 1 production cycle – genotyping and baseline operation data collection from cow-calf producers
7. Year 2 production cycle- implementation of pilot BMPs on farm
8. GHG emissions analysis and producer interviews
9. Producer summary session and Alberta Carbon Offset Cow Calf protocol review

Eligibility

• Cow-based records for reproduction and performance during baseline and BMP pilot implementation
• Tissue sample collection from breeding animals for genotyping and selection supplies provided
• Farm overview questionnaire for emissions, economic analysis and BMP implementation plan
• Willingness to participate in producer interviews
• Two on-site fecal collections for emissions proxy measures
• Permission for Livestock Gentec to use genotypes and farm data for analysis

One of Gentec’s Core Values is the transfer of science into practice by getting knowledge and tools directly into the hands of producers.

We focus on developing research projects that deliver clear value to the industry – often driven from the questions and needs from the industry itself. In doing so, we not only find answers to industry questions, but also help train the next generation of industry leaders.

We bring science into practice in many ways—through participation in industry conferences, local producer-focused meetings, podcasts, media interviews, farm visits, and on-farm team training, to name a few. We also focus on developing practical tools and resources that support informed, data-driven decision-making at the farm level.

Below are a few examples of how the Gentec Swine KKT team has been active in fulfilling our commitment.

Conference Spotlight: Science Meets Practice in Gilt Development

On March 25-26^th, Gentec’s Jenny Patterson was an invited speaker at the 2025 Ontario Swine Conference– marking the first year the London Swine Conference and Ontario Pork’s Annual General Meeting werecombined. The conference provided science-backed insights to help drive progress in Ontario’s swine sector with over 500 of the industy’s best in attendance.

Jenny joined TJ Klopp and Kendra Foran from Cedar Villa Farms in a session titled “Gilts: The Foundation of Your Herd – Science into Practice”. Together they delivered a combination of science based research findings with the practical on-farm side of raising and managing replacement gilts. TJ, a 7th-generation farmer from Zurich, ON, and Kendra, the Barn Manager at Cedar Villa’s Gilt Developer Barn, shared how their operation—marketing 100,000 hogs annually—puts science into practice.

Producer Meeting: Knowledge transfer to Alberta Producers

On April 30^th, 2025, Jenny Patterson was a special guest speaker at the Prairie Livestock Veterinarians Producer Meeting in Strathmore, Alberta. The event brought together a small group of Alberta producers for discussions on key industry topics.

PLV Veterinarian’s Dr. Jessica Law presented on “Industry and International Disease Updates” and Dr. Rienske Mortier spoke on “Practical Treatment and Euthanasia”. Jenny’s session, focused on “Gilt Development – Start with the End in Mind“.

PodCast Alert: Strengthening Gilt Development for Long-Term Productivity

In March, Jenny was invited to the Popular Pig Podcast with Matthew Rooda. The Popular Pig Podcast presents information on the latest trends, news, and research from various experts that guide the global pork industry.

As highlighted, Jenny and Matt discussed a variety topics including “Why a strong gilt development program is key to narrowing the gap between genetic potential and on-farm performance”, “How early culling and poor retention after parity one are major roadblocks to sow lifetime productivity—and what can be done about it”, and “What “fertility quadrant” targets you should hit for optimal breeding success—and why data and body condition tracking post-parity1 are just as vital”.

Strengthening Gilt Development for Long-Term Productivity | Jennifer Patterson

Research in Action: Gentec Back in the Barn with the NSERC Alliance Project

Our NSERC Alliance project with our research partner Hypor Genetics in Saskatchewan continues to move forward. This 4-year project will identify the underlying genetic and phenotypic relationships between different traits in order to achieve more balanced selection to improve sow lifetime productivity, production profitability and sustainability.

We are back in the barn this summer collecting more data and learning new things! We are delighted that Morgan Rioch joined us again, we highlighted her in the “Delicious Bits” article in August 2024.

New to the barn this summer, is of our MSc student, Kayla Patey. Kayla completed a Bachelor of Science in Agriculture, Animal Science at the University of Guelph in 2023 and joined the Gentec team in November 2023 as a Research Assistant, presenting her first poster at the Banff Pork Seminar in January 2024. Before that, Kayla left an exciting career in the gaming and film industry, first earning a diploma in Game Development before coming back to her agriculture roots.

Kayla’s focus will be related to “Litter of Origin Traits” and how pre-weaning growth performance is associated with pre-weaning mortality and subsequent selection and performance in the gilt pool.

Science into Practice: Supporting the farm team

A key part of Jenny’s role at Gentec is supporting Alberta’s producers by putting “Science into Practice”.

Jenny collaborates with industry groups with a focus on gilt management, with the goal of improving lifetime productivity and retention. She loves working with farm production data, through which powerful insights can be developed to make data-driven decisions that positively affect overall herd performance.

Through on-farm visits and virtual calls, Jenny connects with the people who make it all happen—the farm teams—looking at farm data and showing how it translates into day-to-day practices related to gilt development and sow lifetime productivity. In the December 2024 issue of Delicious Bits we shared positive feedback from an industry partner that our activities are helping get the information “to the people in the barn who can make the difference in performance”.

Livestock Gentec strives for research excellence. To be excellent in research we need to be productive and impactful. Just as important, we need to associate with excellent collaborators. We cannot directly quantify excellence, but there are useful metrics to show productivity and impact of research. For example, many sources look at number of published papers, citations, and H-index. H-index is a measure of how many well-cited papers a researcher has published (ie a higher H-index means a researcher has more articles with a high number of citations). Researchers may be familiar with these metrics from various online scholar profiles services such as Google Scholar, ResearchGate and ScholarGPS. These indexing tools are not perfect, but do a good job at consolidating publications online. Researcher profiles on ScholarGPS includes ranks and percentiles based on these productivity and impact measures. In this article, we explore these online tools, their limitations and collaboration as a qualitative aspect of research excellence.

For fun, we looked at our team and collaborators to see how well we stack up in some very active research fields. Livestock Gentec leaders Dr. Graham Plastow and Dr. John Basarab, are both ranked in the top 1% of over 1-million scholars ranked in Agriculture and Natural Resources. When we start looking at their specialties, their ranks jump further. With Dr. John Basarab ranked 58 for over 16,000 beef cattle researchers in publication and Dr. Graham Plastow ranked 176 in over 370,000 genomics researchers. Many of our collaborators also hold leading ranks on ScholarGPS. Dr. Changxi Li, Research Scientist with Agriculture and Agri-Food Canada is in the top 1-percentile for publications in genomics. Dr. Tim McAllister, Research Scientist with Agriculture and AgriFood Canada is a top 100 researcher in Agriculture and Natural Resources for publications. Dr. Michael Dyck, Professor University of Alberta is in the top 1-percentile for transcriptomic publications. Dr.  Carolyn Fitzsimmons, Research Scientist Agriculture Agri-Food Canada, is a top 1-percentile for Beef cattle publications as well. We have only highlighted a few, but going through this exercise, we appreciate how many of our partners contribute on a global-scale to their fields.

These metrics and ranks do not tell the full story of productivity. Seminal papers can drive the science forward, cementing their authors’ excellence, regardless of the metrics. Further, length of career will affect how these metrics as well. Adjusted H-index and alternative metrics exist to integrate those considerations. Another common limitation is indexing platforms can create multiple profiles for the same person, biasing against circumstances like changing institutions or names. Acknowledging these limitations, our high-ranking collaborators provide some validation.

We also want to raise the qualitative aspects of excellence in research. For example, sharing knowledge and experience are key to good science. In a healthy scholarly environment, diversity in thought improves ideas. Collaborations also facilitate added capacity through synergies and scale. Excellence in collaboration may be difficult to quantify, but the approach takes an effort worth recognizing. To ground this in an anecdote, Dr. Plastow and Dr. Basarab are involved in an application for Horizon 2025 with a European and Canadian livestock research consortium. This consortium includes researchers from Belgium, France, Netherlands, Denmark, and Canada. One aim in the proposed project is to develop and implement Near Infrared Spectroscopy (NIRS) fecal scans as a proxy measure for enteric methane emissions from beef cattle. Dr. Basarab is PI on collaborative project: “Reducing Greenhouse Gas Emissions from the Canadian Beef Industry through the Development and Adoption of Genomic Tools” awarded through a NSERC-SSHRC Alliance Grant for sustainable agriculture. This project is well aligned with the new European project as fecal NIRS is proceeding using samples collected from five research sites across Canada. If the application to Horizon 2025 is successful, we will greatly expand our capabilities in both projects to achieve the goal of developing a scalable enteric GHG proxy measure from faecal NIRS in beef cattle.

Metrics have their utility but are not comprehensive in defining excellence in research. Impactful research drives science forward and collaboration is one of our best tools. As such, Livestock Gentec focuses on impactful research and facilitating collaborations to achieve excellence in research. Livestock Gentec’s strategic-framework defines three focuses: excellence in local and applied research; excellence in global research collaboration; and excellence in recruitment, training and placement of highly qualified personnel. Our International Industry and Scientific Committee in its 2022 report summary highlighted the continued need to focus on participatory research and “develop a formalized strategy of integrating current students into industry” (see our strategic framework here). These perspectives challenge us to take a broad-view of research and collaboration success to achieve progress in industry and science.

Dr. John Basarab (RDAR Research Professor, Livestock Gentec CEO, University of Alberta) is PI on the Sustainable CAP funded RDAR administered project: “Sire-based Feeder Profit Index for Beef on Dairy production and marketing systems”. In this project we are developing genomic tools to support improved profitability of a beef on dairy production and marketing system. In Canada and globally, the mating of beef bulls to bottom end dairy cows to produce beef on dairy feeder steers for the beef industry is intensifying. In recent years, the dairy industry has required fewer replacement heifers. This means more dairy cows are available for producing beef on dairy calves. The reduction in replacement heifers is due to factors such as genetic progress in milk yield and cow longevity, adoption of reproductive technologies like sexed-semen and embryo implants, and social pressures limiting herd growth. Using beef breed genetics to produce these slaughter calves improves carcass quality and feed efficiency. We believe applying genomic tools values will produce more profitable beef on dairy feeder calves. Further, we expect a reduction in the greenhouse gas (GHG) intensity (kg CO₂/kg carcass beef) of beef on dairy production through improved feed efficiency, carcass attributes and the sharing of the dairy cow’s GHG emissions between milk and beef production.

In this project, we will conduct genetic evaluation on a historic and novel dataset from a beef on dairy production system to develop more accurate genomic tools. The dataset for this genetic analysis will be comprised of over 200,000 beef on dairy performance and carcass records, pedigree data and beef sire genotypes. We will supplement this dataset with feed efficiency and carcass phenotypes from about 1900 beef on dairy steers. These steers are being evaluated at Olds College with the Technology Access Centre for Beef Production and Thorlakson’s Feedyard from 2025-2027.

Despite production of beef on dairy calves increasing, the access to animals and historical data for research is a major challenge. That is where partners have been critical in bringing this project to life. Dr. Sandi Parr (Director of Cattle Analytics, GK Jim Group of Companies) and her team have coordinated the procurement, logistics and the compilation of the large historical dataset needed to conduct our analyses. These activities require planning well in advance of feed efficiency testing to align with facility availability and animal target sizes. To meet some of these challenges we are also utilizing the recently commissioned feed efficiency monitoring equipment (Growsafe Feed Intake System®, Vytelle®) atThorlakson Feedyard. We are excited to be among the first projects utilizing this new equipment. Thorlakson Feedyard is currently evaluating growth and feed efficiency on 380 steers for this project. The support of industry partners is critical for conducting this research. In turn, this research will support more profitable beef on dairy feeder production.

Dr. John Basarab and Jordan Roberts with Livestock Gentec were able to visit with project team members at Thorlakson Feedyard in March 2025. We saw the first Beef on Dairy steers feeding at the Vytelle® nodes to measure feed efficiency, see below. Top: Steers stick their heads through the bar to reach feed. The feed bunk is on a load bars and there is an RFID reader embedded in the rim of each feeding bunk. The animal has an RFID tag so changes to weight in the feed bunk (ie an animal eating) are attributed to their unique RFID tag. Bottom: Dr. John Basarab and Dr. Sandi Parr inspect the steers at Thorlakson Feedyards. Note the black coats on these Angus (AN) x Jersey (JE), AN x Holstein (HO) and AN x HOJE crosses!

Funding for the Sustainable Canadian Agricultural Partnership is provided by the governments of Canada and Alberta, cost-shared 60% federally and 49% provincially.

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