CRSB Panel Discussion: Using consumer research to understand sustainability drivers and motivations

At the Canadian Roundtable for Sustainable Beef’s semi-annual meeting, panelists Amie Peck (Canadian Cattlemen’s Association), Michael Young (Canada Beef), John Jamieson (Canadian Centre for Food Integrity), and Clay Holmes (InterCity Packers Meat and Seafood) provided some answers on what goes on in consumers’ heads when they think about beef.

As the food shortages in the early days of the COVID-19 pandemic showed, Canadians turned to their kitchen in droves for feel-good meals. Website clicks on recipes and food prep skyrocketed. While people certainly indulged their sweet tooth, they also cleaned the shelves of beef products. The beef trend, at least, looks like it’s here to stay. How can we capitalize on that?

Overall, Canadians trust the food system, and have a high positive impression of the beef industry. Beef is considered a high-quality product, and most Canadians are still eating at least “some”. Gen Z and millennials are more interested in how food is produced than previous generations, and willing to make purchasing changes based on how they perceive food items are produced. Millennials have a less positive view of the beef industry than previous generations, and feel more social pressure to avoid beef and/or choose what they believe are sustainable protein options. They tend to be skeptical but can be convinced by good information. This creates an opportunity to connect, dispel ideas around negative media content, and provide information to help them make nutritious choices.

Sustainability is a newer and growing point of discussion for the beef industry—but still not as important as cost, quality and safety. We are still in the early-adopter phase, with those consumers who want sustainable options willing to pay for it. After all, the cost of buying into sustainable certifications shouldn’t fall solely on the producers’ shoulders. Importantly, however, many consumers still don’t know that sustainable beef even is an option. And producers aren’t aware of the incentives to embark on this course. We need to communicate the beef message better to each group, and define what sustainability means instead of allowing the plant-based protein sector to drive the story. (As an aside, the Canadian Roundtable for Sustainable Beef won an award for its website on this very topic.) Consumers aren’t looking for perfection, but they do want to see effort and ongoing improvement. This is an opportunity to build more positive perceptions around feedlots, explain what they are and what their role is in the beef value chain.

Producers have the biggest role to play. These are the people consumers want to hear from. These are the people who can say they care about their animals and the environment, and that they are working to limit environmental impacts. We need to put a face on who ranchers are and what their values are.

These messages aren’t being heard well enough. Working on public trust needs to become part of the daily routine of producers to maintain that precious social licence. Some have hit social media incredibly successfully. Unfortunately, these are the pioneers not the norm.

CBIN: If you build it, they will come

“A hog barn is a hog barn, wherever it is located. The animals are kept indoors in very stable conditions. That makes it easier to produce offspring for very precise consumer markets,” says Dave Sibbald, Interim Chair of the Canadian Beef Improvement Network (CBIN). “We’re looking to develop that same predictability and scale it throughout the beef industry so we can better match consumer expectations and make the industry stronger at the same time.”

Unless they work in or around the beef industry, it may not be crystal clear to Canadian consumers that the beef sector doesn’t function like the pork or chicken industries. 80% of Canadian beef is raised on the range, using grasslands from coast to coast that aren’t suitable to produce any other food. This has led to a wide genetic diversity needed to derive the best animal for each environment and management approach, and to specialize in certain products (for example, grass-fed, commodity beef, hamburger).

“The point is,” continues Sibbald, “that different genetics maximize value from different landscapes. It’s not that we lag pork and chicken in applying genetics but that we need to apply genetics more specifically. I believe genetics are the most untapped component of the value chain. If consumers want superior T-bones, we can deliver that—but we have to apply those genetics at the beginning of the value chain.”

Selling the idea to traditional, independent-minded producers (many of whom are multi-generation ranchers, still on their original homesteads) that they should modernize their approach and talk to other parts of the value chain to help them understand what motivates consumers isn’t easy. Genetics is a complex science, not easy to communicate well, and not cheap to implement. Uptake has been slow. CBIN is expected to make the difference, as we describe here.

The result will be a better-tasting, higher-quality product in which the consumer plays a big role. Because, as Sibbald says so eloquently: why produce it if it doesn’t have a market? Indeed, demand evolves constantly. It’s up to producers to meet it. For example, during the early days of the COVID-19 pandemic, secondary cuts were ground into hamburger. Now, they are sought-after.

“Beef is an exciting, diverse product,” says Sibbald. “So, let’s do more of the good—that is, produce more of what we know today’s consumers want, and deliver a tasty, nutritional eating experience.”

The beef industry has fed Canada for generations. We produce 1.5 million tonnes of beef every year. In 2019, we exported 410,000 tonnes of it, or 41% of production valued at $3.1 billion. Those high numbers, which represent jobs and wealth for our country, are only possible because we have a reputation for high-quality beef.

“CBIN is not about maintaining market share,” explains Sibbald. “It’s about growing it. The global market is highly competitive, so we need new initiatives to confirm our leadership and support the great beef message we already have. No other country has anything like CBIN—even though their beef industries are just as fragmented as ours. We have an opportunity to establish our uniqueness in the domestic and global markets.”

The best that I can be

It was while studying Animal Science as an undergraduate that the concept of ‘how characteristics are inherited across generations’ struck Dan Hailemariam’s curiosity. He pursued that curiosity in a Master’s program in Applied Genetics at Addis Ababa University, Ethiopia. However, it was at the University of Bonn, Germany, where he completed his PhD on cattle molecular genetics that his ideas about his career and research coalesced.

“I see myself as always researching to understand more about animal science,” he says. “My goal is to help solve the challenges of modern dairy cattle production, specifically, improving feed efficiency and reducing greenhouse gas emissions.”

A post-doc position at UAlberta, screening biomarkers for dairy cow diseases under Dr. Burim Ametaj, brought Dan to Edmonton. When that project ended, he sought out Gentec as a centre with a good reputation in carrying out genetics research. In fact, he credits Gentec with helping him understand and define himself. He tells it this way:

“At one of my first group meetings, Graham [Plastow, Gentec CEO] talked about Gentec’s core values: trust, excellence, learning and leadership. He said, ‘if you’re not learning, come and see me.’ I thought, this is where I want to be. These are the values I share. I’m ambitious and I believe in hard work. Here, I can be the best of myself. His words changed my life, the way I think, and the way I do. I make sure I learn every day.”

Currently, Dan is a Research Associate working on a project out of UoGuelph with Gentec-associated researcher Christine Baes to develop genomic tools to enable implementation of selection to increase dairy cow resilience. The project is a 4-year international collaboration. As part of UAlberta’s dairy group, Dan is involved in expanding the reference population for feed efficiency and methane emissions, and developing methods to utilize milk spectra data.

Dan’s own research focuses on identifying biomarkers of feed efficiency, and understanding the metabolic adaptations of feed-efficient lactating dairy cows. He uses a systems biology approach that integrates multi-omics data (genomics, metabolomics and proteomics) to understand the physiology of feed efficiency. This approach also helps identify reliable, cost effective and easily-detectable biomarkers of feed efficiency, which could lead to tools that facilitate the selection for feed-efficient cows, and help dairy farmers save on feed costs and reduce the carbon footprint of dairy production.

One interesting result that has been published is “Comparative analyses of enteric methane emissions, dry matter intake and milk somatic cell count in different feed efficiency categories of dairy cows” in the Canadian Journal of Animal Science. In that research, the team showed that the most efficient cows consume 12.9% less feed and emit 15.5% less methane compared to the least efficient cows for the same level of milk production. The most efficient cows also had lower milk somatic cell count, indicating desirable correlation between subclinical mastitis and feed efficiency in dairy cows.

“At Gentec, every day is exciting,” concludes Dan. “I like my work because the more I engage, read, write, design and conduct experiments, analyze and interpret data, the better I am becoming, and the more I find myself. I feel good about it. I’m optimistic that I will be part of an accomplishment that develops tools to improve feed efficiency and reduce GHG emissions from dairy cattle.”

All Industry, All the Way

Jenny Patterson, a Gentec research associate, has built an enviable portfolio of industry support with pig companies in Alberta, Ontario and the US. As with all worthwhile things, this level of success didn’t come fast.

Jenny completed her MSc in Animal Science at UAlberta in 2001, specializing in Gilt Management and Reproduction. She then spent a couple of years at the Prairie Swine Centre in Saskatoon as a research assistant, where she was involved in running her first commercial trial in gilt management. She returned to the UAlberta as a research coordinator at the Swine Research and Technology Centre, for the Swine Reproduction and Development Program led by Drs George Foxcroft and Michael Dyck, where she became increasingly involved in large commercial research trials. Their research work focused on implementing management practices to better capture the true genetic potential of contemporary dam and sire lines by improving gilt management to maximize sow lifetime productivity, improving the impact of AI boars in the production system and improving efficiencies at the production level.

Her most recent work was as part of a coordinated National Pork Board research strategy at Holden Farms in 2014 to understand how birth-weight phenotype is a key factor in limiting sow lifetime productivity—and therefore important in the overall efficiency of replacement gilt management.

“As the project winds down, I was able to take some of the lessons learned and apply them to the industry,” she says. “Now, I’m partially supported by Sunterra Farms and Sunhaven Farms in Alberta, Hanor Company and PIC in the USA. Each group has slightly different goals: from gilt management to data collection and analysis to find areas for improvement.”

“I play a key leadership role in Gentec’s pork production efficiency initiative,” says Jenny. “The genetics are really good but translating them into industry is a challenge. We can do that by improving gilt management strategies—and resolving or reducing the gap between genetic potential and actual productivity.”

Among other tools, she uses data visualization to help make sense of the piles of data stored in production databases. What Jenny sends back to the industry client is a set of reports and recommendations to implement, and then manage and track the improvements.

“I enjoy the opportunity to use large production databases and going through that data to identify areas for improvement,” she says. “I firmly believe in making data-driven decisions.”

The industry partners provide excellent opportunities to foster important collaborative relationships—some of which started 15-20 years ago. Their international reach has seen projects land in Jenny’s lap from all over the Americas, and cover a wide range of farm types. Indeed, the next round of projects will see many of the same partners collaborating again.

It was as part of a National Pork Board study that Jenny got to know Gentec. Once the key birth weight phenotypes were determined, the team at Gentec completed association analyses between SNPs and the component phenotypic traits that determine litter size and litter quality (ovulation rate, early embryonic survival, placental development and uterine capacity) to identify genomic regions/genes and their potential biological functions and genetic improvement.

Jenny emphasizes that she is not a geneticist. Yet Gentec has opened plenty of doors to industry and academia.

“It was an honour to join the Gentec team in 2018,” she says. “As well as technology transfer directly to producers, another important part of my work is delivering research results at professional conferences, invited industry and technical meetings locally and internationally. Gentec has sown opportunities for me to help develop new projects; and I’m very excited to learn new skills and to use my expertise in new ways.”

Closing the information gap in the pig genome

The pig industry around the world has made huge improvements in desirable traits thanks to the knowledge afforded by the sequencing of the pig genome, the first draft of which was published in 2012. Yet, in spite of these improvements, which include facilitating genomics-enabled breeding that has increased the rate of genetic gain in some programs by up to 35%, about 10% of the pig genome was missing.

“The IGF2 gene, which has an impact on muscling that I and others reported 17 years ago, was missing,” says Alan Archibald, Personal Chair of Mammalian Molecular Genetics, The Roslin Institute. “So was the CD163 gene, which encodes a molecule essential for infection by PRRSV. In one of our projects, we edited that gene and rendered pigs completely resistant to the virus. So, a number of key genes of interest to people in the breeding sector were absent from the genome sequence or only partially represented.”

While 10% may not seem very much to the outside eye—and clearly some remarkable discoveries were made without it—some projects lacked information (annotations) to make the very best decisions, for example, for gene-editing. And although the long-range information available was good, unresolved redundancies, short-range order and orientation errors, and associated misassembled genes could lead to information loss.

The paper presents two annotated highly-contiguous chromosome-level genome assemblies created with new long-read technologies and a whole-genome shotgun strategy. Both assemblies are of substantially higher (>90-fold) continuity and accuracy than the previous genome sequence. Together with the annotation of another 11 short-read assemblies, the new sequence provides a much needed base for genomic research in pigs.

For example, Aniek C. Bouwman et al.at Wageningen University in the Netherlands reported at the World Congress on Genetics Applied to Livestock Production that the new genome improved the accuracy of inferring genomic sequence from marker genotypes and thus improving genomic predictions.

Is this now the complete pig genome?

“No,” says Archibald. “Small bits are still missing but this is a substantial improvement. It’s 400-700 times more continuous. In genomes made up of strings of bases (letters), the technology we used could only read 900-1,000 bases at a time: short bursts of information. Assembling the’ jigsaw puzzle’ was a challenge. For the new genome, we read 1,0000-20,000 bases/letters at a time, so the pieces of the puzzle just got much bigger.”

Nonetheless, 120 gaps still remain in the sequence. Archibald believes some of the missing parts may be important in terms of how the chromosomes function, but not in terms of information content. In other words, not interesting, unique or useful to the geneticist, and highly repetitive so difficult to sequence; like assembling an all-blue sky in the aforementioned puzzle.


Gentec CEO Graham Plastow is a member of the Stakeholder Advisory Group for a project related to BovReg(another Gentec collaboration) in Europe, called GENE-SWitCH. Archibald contributed to designing the GENE-SWitCH project proposal, and is a member of the project team.

“The pig genome sequence is not a GENE-SWitCH outcome,” says Plastow. “But it’s highly relevant as the primary aims of GENE-SWitCH include adding value to the pig and chicken genomes through enhanced functional annotation, i.e. noting/identifying which parts of the genome have key functions such as encoding proteins or regulating when and where each gene is expressed.”


“Pork is the most popular of all meats and, with a growing global population, we need to improve the sustainability of food production. The improved knowledge of pigs’ genetic make-up will help farmers breed healthier and more productive animals,” says Archibald. “The sequence has been available for two years, so consumers might unknowingly have seen a benefit already. Improvements in and of themselves are modest but if you apply them across thousands of animals, the benefits add up.”

ALES Graduate Research Symposium Report

By Jiyuan Li

The 4th Agricultural Life and Environmental Sciences (ALES) Graduate Research Symposium was held at the UAlberta on March 13, 2020. The event was sponsored by Gentec and others. This annual event is designed to provide students with the opportunity to showcase and share their research results, improve upon their public speaking skills, and enhance communication among the graduate students.

The symposium was divided into poster presentations and oral presentations. In the poster session, 21 students from the departments of Agricultural Food and Nutritional Science, Renewable Resources, Resource Economics and Environmental Sociology and Human Ecology shared their research progress. The posters covered a wide range of fields, such as food science, plant science, and human nutrition. During the session, presenters and listeners were engaged in high-quality communication and heated discussion.

The oral presentation session followed, at which 12 students showcased their research. Mohsen Hashemiranjbar Sharifabad, a Master’s student from Livestock Gentec, gave an excellent presentation on metabolomics and feed efficiency in dairy cows. He demonstrated the potential of metabolites as biomarkers for predicting feed efficiency, and introduced predictive models for dairy cows. He identified that his research benefited from the help of his supervisor, Gentec CEO Graham Plastow, and committee member Dr. Dagnachew Hailemariam. He also thanked his colleagues Anahid Hosseini, Janelle Jimenez, Xuechun Bai and me for attending the event and supporting him. After the presentation, Mohsen expressed how great it was to get feedback and comments from people with different scientific backgrounds. When asked what he learned from the event, he said that learning from the speech styles and content of others helped increase his knowledge.

Xuechun Bai and I attended the whole event, and engaged in interesting discussions with the presenters during the poster sessions. Attending the symposium is a great opportunity to learn and provides valuable networking opportunities for the students.

Culture Shock!

“The initial learning curve is pretty steep when you get to industry,” says Austin Putz, a newly-hired geneticist at Hypor (a Hendrix Genetics company). “And the difference in work cultures between academia and industry is pretty different, too.”

One of the differences he found is that, the pressure in academia is to focus knowledge on a deep dive of one issue, whereas in industry, a broader knowledge base is more useful. Austin did his PhD in Animal Breeding and Genetics under Jack Dekkers at Iowa State, where he contributed to Gentec-associated professor Mike Dyck’s Genome Canada project on resilience to disease in commercial pigs. The Gentec project gave him an opportunity to advance his learning in disease resilience and wean-to-finish data. Grants like these combine different strengths from different universities and allow interaction with industry benefit all parties. Austin’s interaction with other universities and industry partners led him to his current position with Hypor.

At Hypor, Austin manages many projects. His knowledge base has to cover mortality, heat stress, cross-breeding, genotyping, breed composition, bioinformatics and more, which he didn’t touch in his studies. The biggest difference, however, was databases; which Austin believes is the biggest gap between academia and industry.

“We’re well trained in many technical aspects but, in industry, we handle much larger datasets,” he says. “Some students still use Excel. That just won’t handle the high-level programming for data science and statistics, like R and Julia!”

One of the reasons for the larger datasets is that, unlike academia, where there’s a finite period of data collection before the student writes a thesis, in industry, you keep on going, making data management much harder to handle. This became an issue when Austin realized he had to adapt quickly to the structure of the databases to pull data from these complex systems. He also had to investigate SQL querying himself, on the job, and tackle Oracle Business Intelligence.

“As a student, I just wasn’t aware of the volume of data,” he says. “Some training through the Computer Sciences department would have been immensely helpful. Databases are by far the biggest challenge of on-the-job learning.”

The challenge goes as far as sharing documents and data with partners, where terminology such as EDI and APIare bandied about casually. It took Austin “many YouTube videos” to figure out the difference between the two, and what makes them night-and-day different to database people. (The answer is that older industry pipelines accept EDIs but haven’t moved to the newer, more sophisticated APIs.)

Austin is also an affiliate assistant professor at Iowa State. Through an industry partnership with Hypor, he dedicates 20% of his time to academic affairs in the Animal Breeding Group, where he spends most of his physical time. In this symbiotic relationship, he gains access to university resources, and the university has access to him, industry research and resources—giving Austin the rare ability to see both sides of the coin.

“The industry is slowly getting to the point that only a few large, very competitive companies remain,” he says. “Each company is gaining more resources to do their own research in-house. Hendrix for instance has 10-15 people in its central R&D department plus many PhDs and some engineers, as well as those within Hypor.”

This shows that the relationship with academia is evolving. The companies are turning more to academia for software development and licensing than anything else; for example with Iowa State, Wageningen in the Netherlands, Roslin Institute in the UK, and University of Georgia Athens.

One of the toughest parts about industry is the communication needed at all levels, especially as Hypor is an international company, active in ~35 countries. This can be anything from managing expectations on projects with your direct superior to explaining to producers at the farm level why we ask them to collect data we may not use in everyday genetic evaluations. Technology is a big help.

“There’s a balance between being brief and being long enough to be clear to others,” says Austin. “Learning that balance has taken a lot of time!”

Banff Pork Seminar; the experiences and insight from a student presenter

By Teresa Lantz

Every January for the last 14 years, Banff, Alberta plays host to the Banff Pork Seminar (BPS). The Fairmont Banff Springs Conference Centre currently accommodates this event, which brings together a wide array of university students, researchers, industry professionals and producers. This year, over 750 attendees from all over the world took in the sessions, including plenary talks about African Swine Fever, the plant-based alternative protein movement and wild boars in Canada.

The overall program aims to provide practical science with direct applications to the swine industry, ample networking opportunities, and lectures with relevant information for producers, students and researchers. In alignment with this, the BPS runs several competitions within the conference, one of which focuses on the creation and dissemination of new and relevant science by undergraduate and graduate students: the RO Ball Young Scientist award. Students must submit abstracts with their work to a poster competition for evaluation by the BPS awards committee. Four finalists then prepare a 20-minute presentation in addition to a poster to be a part of the ‘Innovators’ lecture series at BPS. This presentation is judged by a panel of industry professionals and researchers, who elect the top two student contenders to win a cash prize. This year, I was honoured to win second place. First place went to Julia Moroni, one of Gentec-associated researcher Mike Dyck’s students.

Caption: L-R: Teresa Lantz and Prof. Ben Willing

My poster focused on meat quality, while other topics discussed reproduction, nutrition and behaviour, which offered a well-rounded afternoon of learning. This is standard for BPS, with lectures for all interests, which are repeated (except for the ‘Innovators’) so participants are not limited on the topics they can learn about. Listeners were engaged in every presentation, confirmed by the significant number of questions fielded. To me, this meant each talk was appropriate for the audience. The scope of knowledge provided significant value and an invaluable experience for a young professional hoping to continue a career in this industry. The connections sparked from this opportunity will, I’m sure, prove vital in the coming years.

The BPS also provides excellent experience for young professionals and students in the generous opportunities to network without feeling the weight and awkwardness that traditional networking opportunities often pose. The BPS is friendly, open and personable—an environment sometimes not felt at conferences, particularly for students who may lack networking experience. By providing multiple, bite-sized time-chunks plus coffee and tea, talking to fellow attendees feels much more natural; particularly when you can reference your poster and presentation and take a quick sip before asking for a card. Finding a common connection or discussing the lecture you just listened to simply feels less intimidating!

One of the most interesting things I noted was the support and encouragement given by colleagues and network acquaintances upon learning of the competition—and from the other three finalists. We all were very happy to be sharing our research and this experience with one another. As finalists, we also volunteered during the event, so we spent significant time together. This camaraderie during competition was refreshing and showed a truth of young professionals; we support one another and are excited for our future and that of our peers as we pursue advancement in the Canadian swine industry.

The experiences and opportunities provided by the BPS for me as a graduate student, particularly with plans to defend my thesis shortly and move into industry, are extremely valuable. The connections made, and ability to show my name on this scale to such a variety of industry professionals, and adding this competition and an award to my CV will undoubtedly help in my eventual job search.

I recommend the BPS to all students in the swine industry and to those interested in the animal agriculture industry. The science is relevant and accessible, and the setting is unmatched! For researchers and industry professionals, this conference provides significant networking opportunities for the next generation of students graduating and an opportunity to gather with some of the prominent voices in the industry. Together, students can learn from the previous year and work on the emerging challenges while enjoying some wonderful mountain views. It is an excellent way to kick off the New Year. I hope to see you there in 2021!

For more information, check out the BPS website.

Wind, Rain, Cows and now… Fish

In April 2019, we spoke with Gentec PhD student Robert Mukiibi about his experience working with Ireland’s Teagasc on a joint project to find biomarkers for feed efficiency in cattle (read that article here). He concluded that, having already lived in four countries as part of his studies, he was pretty open to any geographical location for pursuing his postdoc.

That location turned out to be Scotland. As of November 2019, Robert is a postdoc at The Roslin Institute, a world-leading institute for animal science research that is part of the University of Edinburgh. While Gentec has many close contacts and collaborations with the institute from which Robert might have benefited, he did this old-school. He applied for the position prior to his graduation from University of Alberta, interviewed, and got the job.

Robert’s research to date has been in beef cattle. At Roslin, he’s working on fish! Specifically, it’s an Aqua FAANG project on improving functional annotation of farmed fish genomes. His part will involve molecular characterization of disease-resistance in farmed seabass using multiple functional genomic tools (genome-wide association studies, coding and non-coding RNAseq analyses, epigenomic analyses and genomic predictions). This functional information will be integrated into genomic prediction models to enhance the genomic prediction accuracy for disease resistance in farmed seabass. The work package is led by Ross Houston, who is also chair of aquaculture genomics at Roslin. The Aqua FAANG project is led by CIGENE in Norway, and includes 24 partners spread over the UK, France, Spain, Italy, Poland, The Netherlands, Greece and Germany.

“I was lucky,” Robert says. “Even though fish are new to me, I am able to carry over my experience and expertise in all the tools, techniques and technologies I learned at Gentec and Tegasc, in particular from the labs of my PhD supervisors Drs. Changxi Li and Sinead Waters. What will be new is working as one of several hundred employees, instead of the smaller groups at Gentec and Teagasc. I am excited to acquire new knowledge of the aquaculture world in Dr. Ross Houston’s lab.”

Another link is with the European FAANG project, BovReg, which includes Kinsella Composite cattle. Common activities, such as bioinformatics are being coordinated across FAANG projects, so Robert may well bump into some of his old friends at project events. (see PAG report).

Just before he arrived in Scotland, Robert’s publication (Liver transcriptome profiling of beef steers with divergent growth rate, feed intake, or metabolic body weight phenotypes), which features his Canadian and Irish supervisors as co-authors) won Editor’s Choice in the Journal of Animal Science. In this study, they employed transcriptomic analyses to identify genes and biological mechanisms associated to feed efficiency component traits in Angus, Charolais, and Kinsella Composite cattle. The study identified key processes related to liver nutrient metabolism (including amino-acid, carbohydrate and lipid metabolism) and immune-related processes related to feed-efficiency traits in beef cattle. In terms of the biological mechanisms, the results showed that underlying functions are largely the same across the three breed populations, however the genes within these functions or processes were majorly breed-specific.

Back in Ireland, Robert was mildly unimpressed by the daily wind and rain. He hasn’t exactly jumped from the frying pan into the fire but Edinburgh—facing the aptly-named North Sea—isn’t known for its palm trees and sunny beaches. We’ll have to wait for his verdict.

Plant and Animal Genome Conference XXVIII Highlights

by Xuechun Bai

The Plant and Animal Genome Conference (PAG), marketed as “the largest ag-genomics meeting in the world” takes place in the middle of January each year in San Diego, California. In the laid-back California atmosphere, San Diego is always a sunny, warm place to defrost from Alberta’s chilly winter. PAG XXVIII, held on January 11-15, 2020, brought together over 3,000 leading scientists, researchers, biologists, bioinformaticians, and industry representatives from around the world who presented their latest contributions and future research. Tianfu Yang (postdoctoral fellow) and I (PhD student) were so excited to represent UAlberta and Gentec at the meeting, and feel on the cutting-edge of genomics. A big Thank You to Gentec and Dr. Graham Plastow for sending us and helping me secure a Graduate Students’ Association Academic Travel Award.

L-R: Xuechun Bai and Tianfu Yang
The large crowds and packed schedule at PAG XXVIII covered a range of topics related to the genomes of plants and animals, so be sure to check out all the event materials through the Meeting App.

FAANG Workshop and Updates
FAANG is the Functional Annotation of ANimal Genomes project and works to understand the genotype to phenotype link in domesticated animals. PAG XXVIII provided a great opportunity to foster interactions and collaborations of the FAANG community and to communicate and exchange information regarding their recent FAANG contributions.
Dr. Christa Kühn, Director of Germany’s Leibniz-Institut für Nutztierbiologie (FBN), introduced the BovReg project, which is a part of the global FAANG initiative. BovReg aims to provide a comprehensive map of functionally active genomic features in cattle and help to understand associations between the epigenome and complex phenotypes related to robustness, health and biological efficiency. Gentec is excited and proud to participate and provide tissue samples from Kinsella crossbred animals characterized by feed efficiency ratios and methane production. “Team members and partners will have access to an internal database,” said Dr. Kühn. “BovReg will develop biology-driven genomic prediction tools by integrating biological knowledge of regulatory genomic variation and genomic selection methods for local and global cattle populations.” The results will advance our efforts in more environmentally sustainable cattle production and food security while respecting animal welfare.
Dr. Colin Kern, a postdoctoral fellow in Dr. Huaijun Zhou’s group at University of California Davis, presented their updates for the FAANG project. “We completed the first comprehensive identification of regulatory elements in farm animals across eight tissues in the chicken (White Leghorn), cattle (Holstein), and pig (Large White) genomes,” he said. The data and results from the FAANG pilot projects are available on the FAANG data portal and viewable on genome browsers via a UCSC track hub. These datasets will provide a resource for our Gentec swine studies to better annotate current GWAS results and improve the understanding of complex traits, including disease resilience and meat quality.

Swine Workshop
The swine workshop aimed to highlight updates on how the transcriptome, genome assembly and GWAS can be used to identify markers linked to important production traits in swine. It covered hot topics in complex production traits including meat quality, pig behaviour and aggression, feeding behaviour and feed efficiency, sperm quality, pig health and disease resilience.

Dr. Claire Rogel-Gaillard, a senior scientist at the French National Institute for Agricultural Research (INRA), presented her group’s work on updating the annotation of the swine leukocyte antigen (SLA) complex on chromosome 7 from the genome assembly Sscrofa 11.1. This work makes significant contributions to the study of disease responses because the SLA complex plays essential roles in the immune system, including peptide presentation and self/non-self-recognition. Dr. Rogel-Gaillard’s group reannotated the whole SLA genomic region, refined the annotation of 27 SLA genes, corrected the gene structures and names, and characterized the gene allele sequences and splicing variants. I was so excited to talk with Dr. Rogel-Gaillard afterwards during my poster session. As one of our collaborators on the pig project of disease resilience, Dr. Rogel-Gaillard was very interested in our studies and the results of exploring complete blood count as a phenotype for disease-resilience in pigs. She also offered to help me further annotate my GWAS results regarding the SLA complex. This help will make our GWAS results more meaningful and help us to better understand and explore the immune functions and responses related to disease resilience.
We also talked to and had lunch with Dr. Jack Dekkers and his group, who are also collaborators on the disease resilience pig project. His postdoctoral fellow Dr. Kyu-Sang Lim and PhD student Yulu Chen presented their results and indicated the potential of using the blood transcriptome and protein levels of young healthy pigs as biomarkers to improve pig disease resilience, respectively. Dr. Lim and I were excited that we found common results between his blood transcriptome analyses and my GWAS of complete blood count. This connection will strengthen our collaboration and enhance confidence to cross-validate and further develop our findings to improve pig disease resilience. The pig resilience project is led by Mike Dyck at UAlberta and is a partnership with PigGen Canada with funding from Genome Canada and other agencies, including USDA NIFA.
Dr. Joan Lunney is an international authority on pig immunology and genomics, a research scientist at the Beltsville Agricultural Research Center, and a collaborator on the PRRS Pregnant Gilt Model (PGM) that aims to assess maternal and fetal factors that could be predictive of PRRS severity and resilience in fetal pigs. “This study affirmed the diversity of fetal pig anti-PRRSV response within each litter. It has set the stage for more detailed analyses now underway to probe for key markers of fetal pig PRRS resilience,” said Dr. Lunney in the swine workshop. Talking with Dr. Lunney afterwards, I felt very lucky to participate in the sampling work for PGM during my time at University of Saskatchewan. And I will never forget how well and efficiently it was organized by our collaborator, Dr. John Harding, a professor there.
Genome editing and livestock farm animals’ health and welfare
Genome editing using CRISPR-Cas9 to improve farm animals’ health and welfare continues to be a hot topic. The simple disruption of the CD163 gene is a recent breakthrough in gene editing in pigs, and confers complete resistance to PRRSV infection. It is the only method that can fully protect pigs from infection with PRRSV and thus also from transmitting it. Gentec collaborator Dr. Andrea Doeschl-Wilson and her group at the Roslin Institute, University of Edinburgh, developed a genetic-epidemiological model to predict how gene editing may affect PRRS outbreaks and whether the dispersion of gene-edited pigs in a commercial pig herd could help to eradicate this devastating disease at a national level. Considering many different scenarios, Dr. Doeschl-Wilson suggests that PRRS eradication through gene editing alone is not feasible and would require large proportions of gene-edited pigs. Complementary methods, such as vaccination and introduction of genetically resilient pigs, are being explored in current Gentec projects with collaborators around the world. These findings would be significant to achieve the hitherto unprecedented opportunity to eradicate PRRS and improve pig health in the face of challenged commercial environments in the future.
It is always exciting to make new friends and meet Gentec people and old friends during the conference. PAG is such an informative meeting that offers a fantastic opportunity to catch up on the latest advances and technologies. I highly recommend this meeting as a great place to learn. Beyond this, PAG provides practical and informative workshops to train students and postdocs for academic and industry jobs with the latest tools and technologies, which can be applied to our studies and research work immediately. As representatives of UAlberta and Gentec, we will share our learning and experience with our friends, colleagues and collaborators.