Gene Editing: A glimpse into the future of agriculture

“It’s an absolute revolution!” insists Bruce Whitelaw, Professor of Animal Biotechnology at The Roslin Institute, Scotland, of gene editing. “Scientifically, the potential is huge. It allows us to increase the genetic variations from which producers can select animals with traits they want to promote.”

Whitelaw and his team recently announced the potential to insert a variant of the RELA gene from warthogs and bush pigs into domestic pigs, which could make the latter resistant to African swine fever, a nasty and often deadly disease. Genus/PIC (at the behest of Graham Plastow, now Gentec CEO) funded the preliminary work to find the genetic variation many years ago but the project stalled for lack of technology to develop it. It has only now borne fruit because gene editing came along as the enabler. Other recent gene edits in pigs include the generation of GDF8 (myostatin) mutants to increase muscle, and resilience to diseases such as PRRS and foot and mouth disease.

This is gene editing as Whitelaw intended—with major application in resilience to disease, which is a major burden in livestock. Other applications he foresees include reproductive efficiency (increasing the number of females who bear multiple offspring, for example, rather than increasing the number of offspring per gestation) and gender selection, which is particularly important in the dairy industry where male offspring have little value, and which has been difficult to achieve beyond the sexing of semen. Farther down the line, it may be possible to introduce heat or drought tolerance from indigenous animals into mainstream animals, therefore expanding the footprint of livestock around the world. Used in this way, gene editing will help satiate the growing human population’s desire for animal protein.

But will producers want to use it?

“Producers are chasing it!” says Whitelaw. “What industry partners have to do is demonstrate applicability. The University of Missouri showed that you could edit variation into gene CD163 and create PRRS resistance in pigs. (Ed: Gentec reported this in our December newsletter. See source article here). Now, the task is to take that project, make sure the trait has no deleterious effects on other traits and show its true utility.”

And the Number One question since, if consumers don’t buy the product, it’s all moot—will they understand the difference between gene editing and genetic modification? The latter has had a rough ride over the years. Introducing transgenics didn’t go down well. Special-interest groups focused on nebulous health and environmental effects.

Gene editing, on the other hand, produces simple base variations that can happen naturally. Using Whitelaw’s RELA project as an example, the variation of that gene in warthogs and bush pigs may well appear in domestic pigs naturally—but evolution moves at glacial speed. Given the increasing global population, humans can’t wait that long. One person in seven is malnourished today. By the time we reach 9 billion, that figure is expected be one in three if we don’t increase production of agricultural protein. Genome editing can slash the standard 20+ generations of breeding required to introgress a gene allele back to just one; and eliminate evolution’s lop-sided variety in favour of specific alleles that increase food value.

For consumers to buy in to gene editing, two things have to happen in parallel: a full discussion with regulatory authorities to put in place an appropriate regulatory pathway to take the technology to market; and another full discussion—this time with the public—to convey that this is a good, safe technology.

“Gene editing does exactly what it says on the can,” says Whitelaw. “Every offspring carries mutations that neither the dam nor the sire has. Some are good, others not. Evolution selects the good ones. We’re doing exactly the same thing, except that we know the change is beneficial. Individual animals will be more robust, less sick and therefore have a better quality of life. That has to be a good thing at every level.”

One challenge, many answers, three approaches

On August 19, an article titled, “Is the way cattle are grazed the key to saving America’s prairies?” made headlines in The Guardian. It describes how cattle are being turned out onto the Zumwalt prairie, the largest surviving native bunchgrass prairie in North America, to find out how grazing can be managed to benefit this ecosystem.

The very next day, folio released an article called, “Animal grazing reducing biodiversity around the world: study.” It summarizes a study showing that livestock grazing reduces the number and diversity of animals that depend on plants.

At first blush, it seems these studies are heading in opposite directions.

“Not necessarily,” says Cameron Carlyle, Associate Professor at UAlberta’s Faculty of Agricultural, Life and Environmental Sciences. “It depends partly on the research question and the approach. Both articles are examining native grassland but the first article focuses on conservation through easements and a particular grazing management system, while the second has a narrower question, only taking into account grazed vs. non-grazed land. If grazing prevents conversion to cultivation, for example, then habitat and biodiversity are likely being conserved even if grazing does reduce biodiversity compared to an ungrazed state.”

Instead, Carlyle is proposing a systems approach to enhancing grassland biodiversity and ecosystem services.

“Our idea,” he continues, “is to align cattle genetics and behaviour with desired landscape outcomes. Cattle behaviour affects landscapes as they decide where to search for food and which plants to eat. There’s some evidence of genetic controls on these decisions, for example, whether individual cows like to feed at top or bottom of a hill. If we can identify the genetic markers for those choices, we can have a better distribution of animals on the landscape or modify their effects on the landscape through the of types of plants they like to eat.”

Carlyle and multidisciplinary team including Livestock Gentec researchers propose to examine the genetic factors determining why cattle select particular habitats and plants, the vegetation traits that drive those choices (such as chemical content and nutrition) and the subsequent effects on microbial processes and ecosystem services. Their theory is that, as well as affecting the cows’ choices in what they eat, secondary plant compounds may also have a profound influence on their microbial symbioses with microbes, and hence digestion outcomes, which can affect production (nutrient uptake and weight gain) and environmental metrics (feed waste and methane emissions, etc.).

“If the condition of the grasslands improves in a way that also improves the producers’ bottom line, he says, “they stand a better chance of being protected than of being converted into cropland or subdivisions.”

VBP+: The beef you want is the beef you get

In 2018, McDonald’s became the first company in Canada to offer beef from certified sustainable sources. Harvey’s and others followed suit. But what does “sustainable” mean in this context? And who does the certifying?

“Well, McDonald’s has committed to source beef from operations certified to the Canadian Roundtable for Sustainable Beef’s (CRSB) standard through the Canadian Beef Sustainability Framework,” says Shannon Argent, Business Manager at Verified Beef Production Plus (VBP+). “So its suppliers need to demonstrate best practices on indicators such as soil health, water conservation, biodiversity, animal welfare and workers’ rights. As for the certification… VBP+ takes care of that.”

VBP+ provides training and resources for producers to use to add value to their operations, and the certification, after an audit, to prove they have met the required standards. Certification must be renewed annually. There are 60 indicators, all assessed against 36 of the CRSB’s indicators and other equivalencies, such as the Canadian Food Inspection Agency’s on-farm Food Safety Recognition Program and the National Farmed Animal Care Assessment Framework (VBP+ is pursuing accreditation for the latter).

“We are the link between the producers’ education to deliver what consumers want and the proof that it is being done,” says Argent. “In getting accredited by multiple organizations, we can achieve multiple outcomes (certifications) for producers with one visit.”

Certification is voluntary. If a processor wants to make certified-sustainable beef available to its customers, it may encourage producers through financial incentives. And while an extra dollar in their pockets is great, many producers are keen to be part of the solution to greenhouse gas emissions, food safety, antimicrobial resistance and animal care issues anyway. Education ups their game, and certification provides the proof of what they’re doing.

Each provincial commodity organization has a designated coordinator to provide webinars and workshops, and the national program provides an online training platform that is being updated to ensure content keeps up with the changing times. The coordinators educate hundreds of producers every year on what’s new in the field, how to implement best practices on their operation and how to document an audit. As such, education is the necessary first step to certification. A steady proportion of them advance to the full certification stage. Today, more than 60% of Canada’s beef production comes from VBP+-trained operations, and 20% of production comes from audited operations.

Proving sustainability through certification is one thing; demonstrating it to the public is another. As part of the education, producers are encouraged to contribute to debunking disinformation by opening their operations through social media to show the positive results of best practices.

Like every other sector, COVID-19 has slowed down the rate of certifications. To that end, VBP+ is considering remote audit technologies that can perform audits in locations where it’s not financially feasible to send an auditor. These technologies would be evaluated against an on-farm audit to make sure the outcomes are the same. If successful, they may provide a great opportunity to keep costs down in a low-margin market.

Genetics is another technology that plays a role in certification, as producers must demonstrate their innovations to improve quality and produce more beef using less resources. Testing using a tool like Delta Genomics’s EnVigour HX™ can be used to prove innovative practices. EnVigour HX™ is the first made-in-Canada genomics tool for crossbred beef cattle, combining parentage verification, genomic breed composition, and a simple Vigour Score (assessment of hybrid vigour) to assist in replacement selection.

“We often hear that beef production and its advantages and, conversely, how beef reaches customers are poorly understood,” says Argent. “We hope that, by providing these services and contributing to the broader message, VBP+ can help to bridge the gap.”

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.”

Beef production in the pandemic: From producer to plate

COVID-19 has been complicated in many ways by uncertainty. Unlike many disease outbreaks, it is not about food safety or consumer confidence with food products – but rather about the effects of social distancing strategies and their impact on food production, distribution and consumer lifestyle factors.

As the pandemic unfolded, meat-processing sectors in Canada and the USA experienced rolling plant closures and slowdowns as industry invested over $50 million to ensure the safety of plant workers and protect against COVID-19. However, measures to address distancing requirements reduced production efficiencies and added costs to every aspect of operations. The reliance on human proximity in meat-processing sectors proved to be the weakest link in the supply chain, coupled with employee interaction away from the processing facilities.

Reduced slaughter volume created supply challenges in the retail sector and an estimated backlog of 125,000 head as of the end of May causing North American cattle prices to plummet as the log-jam grew. The lack of processing capacity and competitive bidding due to temporary closures or reduced output caused livestock in all sectors to back up on both sides of the border in the face of unprecedented demand.

Cow calf producers and backgrounders are able to keep their animals on grass or silage longer, and feedlot operators are able to switch to holding diets based on higher roughage and lower energy rations to slow the growth rate of animals. The type of animal, the weights and age all factor into the quality, value and market destination of the beef in the box. All these measures represent a significant increase in costs and resources for producers to slow down a system designed to deliver market-ready cattle 52 weeks a year.

The shutdown of restaurants combined with consumer buying trends to stockpile food added to the problem resulting in out-of-stock situations in food stores. This added fuel to the perception of a pending food shortage in Canada. Demand increase for beef across the board soared 100% at the highest point, with a huge run on ground beef. Processors could not provide the trimmings needed to keep up to ground-beef demand, resulting in higher-value cuts being utilized, which pushed prices higher and further reduced inventory for other beef cuts also in high demand. Imports of beef increased 14%, YTD May 30 vs. same time last year while exports went down 13% YTD April 30 vs. same time last year.

The pandemic continues to have an enormous and worldwide impact on agriculture and agri-food industries, although it is too soon to know the long-term impact of COVID-19 and how the changes made will affect future meat-processing systems. Canada is better equipped to handle the next pandemic or a resurgence of COVID-19 this fall.

“I hope the meat-processing industry will consider innovation, automation and robotic technologies to reduce the dependency of human contact to reduce the risk and increase productivity,” says Michael Young, President of Canada Beef. “The Canadian beef industry has a very bright future, post COVID-19. We have a high-quality product that’s in high demand in Canada and around the world.”

From cattle to COVID-19: An unlikely journey

By Mikolaj Raszek, PhD

The lead-up

After finishing my PhD in Biochemistry, I took a break from science to think about what I wanted to do with my life and my degree. Eventually, I figured out that I wanted to start a business that provided access to DNA testing to those in need or who were curious to learn about their potential predispositions. Having made that decision, I needed an opportunity to surround myself in the study of DNA and genomics, to firm up my background and get some hands-on experience. This is exactly what happened at Livestock Gentec, one of my very favourite career opportunities. I still have fond memories of my colleagues there and the quality of the research.

By the time I arrived, I knew a bit about human genomics and the technologies used to delve into genetic data—but nothing about cattle. Lab work was no problem. I was surrounded by so many talented people that learning was easy. We studied gene expression differences of healthy cattle versus those impacted by bovine respiratory diseases. As a process of validation, we worked with RT-qPCR using cattle RNA with one of the best in-line instruments at the time: this type of assay that is now used to identify SARS-CoV-2 coronavirus in human samples. Calibrating the instruments is no easy feat so, now that these assays are run in millions around the world to test for SARS-CoV-2, I can tell you that some highly sophisticated efforts are being made to identify infected people.

But getting up to speed on the general background on cattle genetic research…? That took many hours and many journal articles. I pitched to Graham Plastow, Gentec CEO, that I should write a review of my information blitz, which led to an interesting niche topic for Leluo Guan and me: use of genomic technologies to study infectious agents in cattle. I loved that project precisely because it gave me the opportunity to learn from my bosses how to think outside the box when researching information. This was also my first foray into the serious study of viruses and their genetics, which quite fascinated me. I even proposed a project to study the cattle virome, but this was not even an emerging field at the time.

Eventually, Merogenomics was born, a company dedicated to building a catalogue of medically-relevant DNA sequencing services for clinics interested in setting up in this niche territory, and end-users who need such services. It has been a labour of love, fired by passion.

The redirect

The outbreak of the COVID-19 pandemic brought the company to a standstill. From the start, I suspected that we were witnessing an event not to be dismissed. My interest in viral genetics, born at Livestock Gentec, was reignited, and I have been deep in SARS-CoV-2 scientific literature.

To continue Merogenomics’s mission to help those in need, I’ve published blog posts on SARS-CoV-2. The first was on the origins of the virus itself and what science had to say about it, as this was hot topic from the start, only grabbing more media attention as the pandemic ballooned and people sought answers. In the second article, I switched from the genome of the virus to our own genetic predisposition. The third article was dedicated to current research into drugs, and the fourth on building immunity and vaccination. (This pattern matched that of the Gentec review. Apparently, those lessons stuck hard!)

The way forward

All this seemingly unconnected knowledge came together in February 2020 when I became a member of a multi disciplinary and multi-organization team dedicated to developing a new detection system for SARS-CoV-2 for rapid population screening. The team comprises many PhDs but most of them don’t have a molecular sciences background, opening the door for me be a valuable source of knowledge. Once again, I am in totally over my head—and I love it. Once again, I’ve had to learn at a blistering pace. I meet many business people, researchers and even physicians working directly with hospitalized patients in some of the most afflicted areas of the world.

Never did I imagine that learning about cattle viruses would one day lend itself to trying to fight a human pandemic.

 

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.”