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!”

Solving AMR through a One-Health lens

The newly-funded Antimicrobial Resistance – One Health Consortium managed out of UCalgary* is about to play an important role in how we safeguard the eroding ability of antibiotics to save lives and prevent illness. Its role will be to leverage the capacity and expertise across Alberta, nationally and internationally to find solutions to a looming antimicrobial resistance (AMR) crisis in humans and animals that spills over to the environment—hence the one health approach. Currently, several thousand Canadians die every year from infections with multiple drug-resistant bacteria, and the rate of increase is exponential. Worldwide, the economic impact of these infections is estimated at US$100 trillion/year.

“In the beef industry, there’s a lot we don’t know,” says Dr. Herman Barkema, Scientific Director of the Consortium and NSERC Industrial Research Chair in Infectious Diseases at UCalgary’s Faculty of Veterinary Medicine. “And we can’t even talk about cow/calf and feedlot operations in the same breath because antimicrobial use and resistance differs in each sector.”

For example, calves are treated with antimicrobials on arrival at the feedlot, then they get medicated feed for the duration of their stay. How much resistance that produces, and whether it causes problems in run-off? Who knows? Then, there’s the health of the animal to consider. The public is playing an enormous role in wanting meat products that are raised without antibiotics, which is reducing on-farm use—but perhaps at the cost of sick animals not getting the drugs they need to stay healthy and productive. And of course, there are people—the producers and their families, and the workers in the industry all of whom may be impacted by AMR.

“If we get resistance against frequently-used drugs in the feedlot, we have a problem—and emerging evidence shows that antimicrobials ARE becoming less effective,” says Barkema. “The only way to protect people will be with drugs of last resort, and we should really be careful not to overuse those because they are exactly that… last resort!”

The Consortium’s 27 projects focus on treatment optimization, AMR surveillance, and infection prevention and control under three thematic areas: innovation and commercialization, education and societal impact, and policy, economics and sustainability.

So why are pharmaceutical companies not investing in new antibiotics? Any new drug is likely to be safeguarded like gold, and used only to treat multi-drug resistant infections. So, minimizing drug use is one way to combat resistance—but it doesn’t result in the large sale volumes needed to recoup the $2-4 billion costs to develop and receive regulatory approval for use of an antimicrobial.

Instead, the Consortium is looking to alternatives like phage therapy, new targets, biomarkers, stewardship, the microbiome, as well as optimizing the use of current treatments. It is also developing protocols to change the prescribing habits of veterinarians, pharmacists and doctors, and the usage practices of farmers and people. Vaccine development, hygiene protocols for people and animals, and genetic selection for disease resistance can all lower antimicrobial use.

“We are excited to be involved in this initiative as we know that some animals are more resilient to infectious disease than others,” says Plastow. “Identifying them is the challenge; however, our work in pigs and cattle is helping develop tools to do this. The team. including others at UCalgary like Karin Orsel and Frank van der Meer. have generated phenotypes and samples to push this effort forward. And Gentec’s Janelle Jiminez will be working with these researchers from April to find new funding to exploit these resources.”

Use practices are already starting to change. As of December 1, 2018, the over-the-counter sale of medically-important antimicrobials is no longer allowed. Such products can only be purchased with a prescription issued by a veterinarian. Those are the (relatively) “easy” administrative changes. The Consortium’s innovative solutions will take years to develop, test and employ, although consumer and retailer push (A&W, McDonalds, Maple Leaf, Sobeys, etc.) may accelerate uptake.

“Then,” says Barkema, “we’d better be ready to follow. Our results in beef will apply to other livestock, and connect to people and the environment. If we use less antibiotics in agriculture, there’s less run-off and less soil contamination. That means better drinking water and environment. Everything is linked.”

* The Consortium is Alberta-wide, comprising the universities of Calgary, Alberta and Lethbridge as well as Lethbridge Research Centre, Olds College, Lakeland College, Southern Alberta Institute of Technology and Northern Alberta Institute of Technology.

1,600 chickens… and counting

Because the Leghorn chicken is so prolific (up to 320 eggs/year!), it is the darling of the egg industry, and produces the vast majority of eggs in Canada. They lay white eggs, so it’s easy to tell. For those who prefer a brown shell, you can thank the Rhode Island Red and a few other breeds. Between them, they’ve locked up the market.

So what happened to the breeds we used to see around farmhouses, back in the day? Some of them are in trouble, with few individuals left, certainly not enough for a healthy population. Ten of these breeds (1,600 chickens total) find a home within the Heritage Chicken program at UAlberta (with another population at UGuelph, in case of catastrophe at one location).

“Currently, in-breeding is high among four of the breeds because they’re randomly mated,” says Marzieh Heidaritabar, the Gentec post-doc trying to develop a funded project for the program off the side of her desk. “But this isn’t efficient. Ideally, we want a proper breeding program to select the best animals. Genomics is the best tool to help us select the most diverse sires and females as parents of the next generation.”

Eighty-five chickens have already been sequenced. “That’s how we knew inbreeding was high in the first place,” says Marzieh. Now, another $70K is needed to finish the job, and fund students and tests. She plans to apply to NSERC this year to, hopefully, get the project rolling in 2021.

The goal would be to keep the unique genes in the breeds and increase the number of individuals over 2-3 generations to assess the success of the breeding program—but it may make more sense to merge the breeds if they are genetically close. Secondary objectives would be to examine immunity and behaviour, both of which may increase the suitability of the breeds for certain environments. Two other ongoing projects are working on perching and gait traits.

While Marzieh will go through traditional Tri-Council channels and the higher-tech GoFundMe platform, the program has been creative about fundraising in a different way. $175/year will get you a dozen eggs every other week for 10 months. Or you can adopt-a-rooster instead (similar program minus the eggs).

“Every little bit helps,” says Marzieh, “and it’s a great way to get the public involved.”

Coronavirus: the latest zoonose

Coronaviruses are a family of zoonotic viruses; zoonotic meaning that they can pass from animals to people. SARS is one example, ebola, MERS and H1N1 are others. The sources have been animals as varied as pigs, monkeys, poultry, civet cats and camels. The strain of coronavirus (named COVID-19) currently in the news has been declared a “public health emergency of international concern.” The race to find a vaccine or prevent deaths is intense. To help us understand more about coronaviruses and zoonoses in pigs and people, Gentec spoke to Dr. Egan Brockhoff, Veterinary Counsellor for the Canadian Pork Council.

Gentec: How do we know that the source of a human disease might be animals? How do we know to do a “reverse diagnosis?”

Dr. Egan Brockhoff: Scientists do a whole-genome sequence of the bacteria or the virus, then they look for similarities with other known bacteria or viruses. That indicates where it’s most likely to have originated. It might sound simple but it involves significant scientific exploration. For COVID-19, the pangolin seems to be the animal source. The fact that these animals are eaten makes them a likely source of the jump, but that still needs to be confirmed.

Gentec: Porcine epidemic diarrhea (PED) virus, which is a pretty nasty pig disease, is also a coronavirus that could spread to humans. Why hasn’t it?

Dr. Egan Brockhoff: PED is a delta coronavirus. COVID-19 is a beta coronavirus. Even though they’re part of the same family, they’re only very distantly related. PED is an enteric virus that causes intestinal illness whereas the beta COVID-19 infecting humans is a respiratory virus. Because they’re so different, PED isn’t likely to jump over to humans.

Also, COVID-19 is a new virus. Once it has adapted to its host, it’s not likely to jump back to animals. To give you an example, MERS came from camels and can still be found in camels. But when viruses adapt to a new host, they don’t re-adapt to their original host as easily. Now that COVID-19 has become a zoonose and infected humans, we’re not very concerned that it will jump back. If it does, it would probably go to its most recent host.

Gentec: We’ve seen how fast and how wide zoonoses can spread. Which organizations are involved in containing an outbreak?

Dr. Egan Brockhoff: On a global level, the World Health Organization is responsible for human health, and the OIE (World Organisation for Animal Health) is responsible for animal health. At the federal level in Canada, Public Health Agency of Canada and Health Canada are the competent authorities for human health, and the Office of the Chief Veterinary Officer for Canada and the Canadian Food Inspection Agency are the competent authorities for animal health. Then each province has a chief medical and veterinary officer as well. In other words, many organizations must work together to find the best methods of control.

Gentec: So how do they talk to each other? What do they monitor? How do they decide on the best actions to take?

Dr. Egan Brockhoff: Both the WHO and the OIE are in constant back-and-forth communication with their member states. In terms of COVID-19, both were consulted, and the WHO has now landed a body of experts into China to work on this disease. In fact, renowned Canadian epidemiologist Dr. Bruce Aylward will be leading that team.

Canada and other developed nations have a very robust infrastructure for communicating with the WHO and OIE but in other countries, that may vary more. In this situation, China is working very hard with its public health authorities to understand and contain the disease, and the WHO is assisting and communicating back to the OIE. But let’s be clear, COVID-19 is not an animal health outbreak, it’s a public health outbreak. The OIE doesn’t have to be highly engaged beyond helping the authorities understand the coronavirus in its most recent species.

Gentec: What actions are being or have been taken to mitigate spread of PED in animals?

Dr. Egan Brockhoff: Again, let’s be clear. PED is not a zoonose, it’s a highly infectious enteric virus—for pigs. So bioexclusion, that is, the external biosecurity efforts to take to keep disease out of the farm are key. For PED, critical steps including washing all incoming transports to ensure they are virus-free, making sure you limit access to the controlled access zone around the farm, ensuring that people who must enter the farm wear boot covers, remove their footwear and clothing when they step over the line and go through a shower on the way back. And of course, wearing farm-specific clothing.

African swine fever kills nearly all infected pigs. The same measures of bioexclusion will keep it out of the farm. Because it’s not an aerosol virus (transmission through droplets or particles in the air), it moves by allowing infected animals or products to move on or off a farm. For example, feeding contaminated food items to healthy pigs will expose them to this disease. Because people can’t get it, good basic bioexclusion will keep the virus from affecting the population.

Gentec: The founding head of Ontario Public Health has spoken publicly that travel bans for zoonoses are ineffective, xenophobic and not evidence-based. Do you agree? 

Dr. Egan Brockhoff: Every disease has unique features in terms of infectivity rates and routes by which it infects, so the story changes a bit but in general, that’s accurate. The WHO echoed those sentiments as well. Travel bans are not necessarily effective. Typically, with infectious diseases, people are infectious before they have clinical signs. The flu is a good example. All the early work done on COVID-19 echoes that. So, people can move all over the world before they know they’re infected. At best, travel bans can slow the spread but not contain it.

Gentec: Do you find that the public are informed and correctly informed about zoonoses, particularly those coming from pigs?

Dr. Egan Brockhoff: The public has every opportunity to access good information from the competent public health authorities. But there’s absolutely no question that social media has made it challenging for the public because there’s so much non-professional information out there as well.

Gentec: What’s your message to the public about zoonoses?

Dr. Egan Brockhoff: Washing your hands is one of the most effective things you can do to protect yourself from all infectious diseases, whether they come from other humans or from animals. Use good sanitation in the kitchen. And cook meat to a temperature that kills bacteria and viruses. You can use a food thermometer for that. Meat doesn’t have to be burnt to a crisp to be safe. And you don’t have to become a vegetarian either. Plenty of foodborne illnesses come through plants.

Gentec: Thank you, Dr. Brockhoff, for taking the time to do this interview.

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.

Beef cattle work in harmony with the grasslands

The importance of biodiversity is widely recognized. High profile reports include the UN IPBES 2019 report (United Nations Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services) and the OECD report entitled Biodiversity: Finance and the Economic and Business Case for Action (OECD, 2019). A coalition of 19 agriculture-centric companies called One Planet Business for Biodiversity has formed, aimed at scaling up regenerative agriculture to protect soil health, boosting cultivated biodiversity, and restoring and protecting high-value natural ecosystems, among other things. In a related initiative, General Mills has initiated a new focus on soil health in Canada and the US. Agriculture is both a major force for biodiversity protection and an impediment to protecting biodiversity. Public agencies and global supply chains are recognizing the risks to their future if biodiversity is not protected.

Canada’s grasslands are a vital and endangered resource. This ecosystem is home to significant biodiversity, and is often used as grazing land for beef production. The tricky balancing act is our ability to protect ecosystem biodiversity and optimize beef production. Carlyle (2019) identified the pros and cons of beef production together with  the production of ecosystem goods and services Clearly, beef cattle can be a positive influence on biodiversity protection in grasslands, and well-managed cattle grazing can contribute to grasslands’ sustainability.

The question of whether we are doing the best we can remains open. Genomics can help achieve the optimal balance between animals (bovine and wild) and plants on native and tame pastures. By understanding animal genetics linked to their grazing behaviour and the genetics of plant material in the pastures, science can identify the best animals for particular properties, which could be public or private lands.

The time is opportune, with many applications of new forms of precision agriculture (drones, wearable sensors) and the availability of analytical methods using big data and artificial intelligence or machine learning. This provides the opportunity to enhance beef production and the production of ecosystem goods and services. Investor pressures provide the economic need for more research and for adoption of precision management of our sensitive grasslands. Understanding how to manage cattle and grasslands optimally is an opportunity to get in front of consumer pressure to have a verified ‘sustainable’ beef product as part of their food choices.

Sustainability starts in the microbiome Part 2: Cows and food-waste streams

Cattle don’t just eat grasses.  They can also digest 99% of fruit and vegetables—even bread. Producers have been feeding cull potatoes and peels to cows for years, so the idea of feeding food waste to beef cows is nothing new.

“Ideally, humans should consume the food,” says Tim McAllister, Principal Research Scientist for Agriculture and Agri-Food Canada in Lethbridge, Alberta, “but for now, food waste represents a continuous stream of potential feed.”

Spoilage isn’t an issue if food waste is preserved as silage. If properly ensiled, the quality of the food could be conserved for years. The real issue is the excessive packaging that gets discarded along with the waste. McAllister envisions a system in which food waste from grocery stores or restaurants is separated from packaging and delivered to farms. Sounds simple? Not so fast…. Some regulatory and transportation issues have to be fixed, first.

Let’s take a box of blueberries as an example. They’re shipped from Nova Scotia to wherever they are going in plastic. If they don’t get sold at the retailer, they go to a landfill or composting facility. At that point, they are designated as hazardous waste, making it illegal to remove them from the disposal site. To complicate things even more, you can’t legally feed anything to cows that isn’t listed in the Feeds Act without a special certificate. You guessed it…Blueberries aren’t in the Act.

“Sadly, that’s a true story about the blueberries,” says McAllister. “I found them when I was visiting a commercial composting facility. Perfect condition. Couldn’t take them home.”

The issue here is consumer expectations. If grocery stores didn’t restock their shelves, those shelves would be bare within 2-3 days. That’s how fast the turnover is. Any remaining produce will look less appealing by then, especially if it has to compete with newly-stocked produce. What do consumers pick? The new produce. Two misconceptions are happening. Visually, we don’t like “wilted lettuce,” even though it’s perfectly safe to eat and poses no health risk. And we think poorly of stores that keep it on the shelves so they remove it to protect their image.

Then there are liability issues. Once the Canadian Food Inspection Agency has approved a feedstuff, the federal government could be liable if people or animals get sick from it. For example, the CFIA ensures that some waste products from the processing of cattle do not enter the feed or food chain. Ensuring the integrity of this system is important for food safety and for complying with export regulations.

“So you can see why the system evolved to how it is now, and why it is not easy to change,” says McAllister. “But we have to start somewhere to reduce and derive more value from these food waste streams. There’s not much point beating up on beef production over methane emissions while so much food ends up in the garbage. We need to use the leakage as feed if we’re going to take full advantage of the role beef cattle can play in a circular economy.”

NOTE FROM GENTEC CEO, GRAHAM PLASTOW: “The Brits are a bit ahead of Canada on this issue. One of the companies I worked with, SugaRich, has been taking wrongly-packaged food, like chocolate bars, etc., and turning it into ingredients for animal feed for many years. SugaRich is adamant that Food for Animal Feed should not be classified as waste.”