The First Outbreak of Porcine Epidemic Diarrhea (PED) in Alberta

by Julia Keenliside DVM MSc
Veterinary Epidemiologist
Alberta Agriculture and Forestry

The Porcine Epidemic Diarrhea (PED) virus first made the jump from Asia to the USA in 2013. Since then, it has spread rapidly across the USA and parts of Canada. Until 2019, the Alberta pork industry had succeeded in keeping the virus out of the province. That changed on January 7 when the first case was confirmed in central Alberta. Three more cases followed in February and March in the Lethbridge area. As of August 2019, the outbreak is still limited to four farms.

PED is a viral disease that affects only swine and their relatives (including wild boar). Symptoms are often unmistakable, with large numbers of pigs affected by severe diarrhea, vomiting and refusal to eat. It is generally fatal in young piglets, but older pigs will recover completely within a week or so. An outbreak typically spreads rapidly, and producers may lose three to five weeks of piglet production, which takes an emotional toll. Despite its spectacular symptoms, people cannot become infected, and pork from affected animals is safe to eat.

The virus survives well in pig feces and on surfaces contaminated with feces from infected animals, especially when frozen. Transport trailers, equipment, boots and loading docks can all become contaminated and serve as sources of infection, allowing outbreaks to spread between farms. Biosecurity measures are the best prevention. However, it only takes a very small amount of virus to cause disease in nursing piglets, so it can occasionally sneak into even the most biosecure farms. Often, the source of the spread is never found.

PED likely entered Ontario in 2014 through feed containing contaminated porcine plasma from the USA. In contrast, evidence in Manitoba suggests the virus was brought in by contaminated American trucks loading pigs at Canadian assembly yards. Manitoba has reported 160 cases since then and Ontario 125. Manitoba experienced a large outbreak this spring with 60 cases since January.

Despite a detailed investigation, we still can’t be sure how the virus spread into Alberta. Swine traceability program data showed no transport links with PED-positive premises or contaminated vehicles coming from outside Alberta. Environmental surveillance samples did not show any contamination of assembly yards, abattoirs and truck washes in Alberta throughout 2019.

However, we did find some risk factors. For example, feed ingredient trucks from Manitoba and the USA did deliver ingredients directly to the first Alberta case. A piece of used and cleaned manure equipment from Manitoba was also brought onto the farm. Feed ingredients found on the affected farms originated from nine countries, four US states and five provinces, most of whom have PED cases.

Unlike Manitoba, Alberta farms are generally far apart, which slowed the spread of the virus. There were no direct transport links between any of the affected farms; and the industry did a good job in keeping biosecurity tight. The exact method of spread between the Alberta cases was not clear, as the usual risk factors of contaminated transport vehicles, assembly yards and abattoirs were ruled out. The three southern cases are within 20 km of each other. We know the virus spreads more easily through transport, people traffic or even the air when farms are closer together.

Risk factors that were identified during the investigation that producers should address include:

  • Changing boots and clothing every time before entering and leaving the barn, even when just going to the feed mill;
  • Washing, drying and disinfecting trailers every time they are used, even if going to abattoirs or assembly yards that have had negative environmental test results;
  • Working with suppliers to understand and reduce the risk from feed trucks and feed ingredients coming from PED-positive regions;
  • Being diligent in enforcing biosecurity when equipment and visitors come from PED-positive regions.

All four affected producers are working closely with their veterinarian, Alberta Pork and Alberta Agriculture and Forestry to eliminate the virus. One farm has depopulated, and is testing in preparation to refill. The other three are farrowing again, and moving hogs to market without any clinical signs. All four farms are working towards achieving presumptive negative status by the fall 2019.

PED is a reportable disease in Alberta. If you suspect PED, call a veterinarian and notify (mandatory) the office of the Chief Provincial Veterinarian  at 1-800-524-0051 (780-427-3448 after hours).

2019 ASAS-CSAS Annual Meeting Highlights

by Xuechun Bai

Austin, Texas, is a fantastic place for passionate ASAS and CASA members to feel the heat of summer and devote themselves to research and industry work of animal science. I feel so lucky to have been able to attend such a great conference, meet a great roster of speakers, take part in their research communication, and question a panel of experts. A big Thank You to Livestock Gentec and Dr. Graham Plastow for sending me and granting me a CSAS Graduate Student Travel Award.

There were too many amazing moments and symposia discussing hot topics and advanced research in animal science to share them all here, so be sure to check out all the event materials through the Meeting App.

Dr. Ignacy Misztal (University of Georgia) opened the Breeding and Genetics symposium with a keynote on the current status of genomic selection that has been dramatically simplified by the development of new methodologies, such as ssGBLUP—single-step genomic best linear unbiased prediction. Dr. Tom Lawlor (US Holstein Association), Dr. Egbert Knol (Topigs Norsvin Research Center) and Dr. Dan Moser (Angus Genetics Inc.) gave great talks about the tremendous impact of genomic selection on dairy, swine, and beef industries, respectively, including current achievements, challenges and future directions. Sessions about animal breeding and genetics broached the central question of how genomic selection has changed livestock breeding. Dr. Makram Geha (Corteva Agriscience) shared his research experience on genomic selection and gene editing in plant breeding, which allow us to broaden our horizons and learn advanced methodologies developed in plant science. Dr. Jack Dekkers (Iowa State University) provided an excellent summary of the meeting with an outlook of the future of increasing genetic gain and precision livestock breeding through machine learning, deep learning, and the development of breeding technologies.

The primary topic of the WAAP-CSAS symposium was improving the efficiency of livestock production. Dr. Graham Plastow gave a very inspiring talk about the role of genomics in enhancing efficiency in swine by addressing social and environmental aspects (such as disease and stress), to improve the sustainability of swine production.

Genome editing via CRISPR-Cas was another popular topic that sparked heated discussion. Dr. Kristin Whitworth (University of Missouri) presented exciting results of creating pigs that are fully resistant to PRRSV (porcine reproductive and respiratory syndrome virus) and TEGV (transmissible gastroenteritis virus) through genome editing. (However, they did not succeed with PEDV.**) Accordingly, talks focused on the global regulatory landscape for evaluation of products derived from gene editing and earning public trust in gene editing, which could help researchers, regulators, governments, and consumers to build better communications strategies on the development and application of this technique.

Other breeding and genetics sessions covered many different and exciting topics, such as the use of APY (Algorithm for Proven and Young) in many studies of genomic selection at the University of Georgia; the integration of microbiome information into the studies of meat quality, carcass composition traits, and host responses to PRRSV in swine.

As well, many sessions on animal nutrition, animal behaviour and welfare, animal health and companion animals were available. Taken together, they gave us new insights into animal science, current science and the next steps.

Last but not least, attending was an excellent opportunity to communicate with people from academia and industry, and to receive feedback and constructive criticism on my research during my poster presentation. It was also a great chance to network, share thoughts, and expand my knowledge with other academics and experts.

** See also the accompanying article (link above) by Julie Keenliside on PEDV in Alberta in 2019. Gentec also drew something of a blank in our initial work on genomics and PEDV suscpetibility.

 

 

 

Rumen microbiome affects feed efficiency and is associated with host genetics in beef cattle

With our global human population continuing to grow, there is increased competition for resources (e.g., land, water, and cereal grains) between people and livestock, especially beef cattle operations. Improving the feed efficiency of cattle would reduce the amount of feed consumed (especially cereals that could feed humans instead) with equal or higher production performance. Improving feed efficiency can also reduce the negative environmental effects (methane emissions and manure) caused by beef cattle operations.

By applying cutting-edge DNA and RNA sequencing technologies, we explored the rumen microbiome of beef cattle from three breeds on the same diet but divergent in feed efficiency [1]. We aimed to evaluate the breed effect on the rumen microbiome and generate a more conclusive understanding of the role of the rumen microbiome in feed efficiency. We observed differences between the rumen microbiomes of different breeds, as well as microbial features that differed between efficient and inefficient steers. These aspects were also specific to each breed, suggesting that interactions between the host breed and the rumen microbiome influence feed efficiency. We conducted a follow-up study [2], surveying a large cohort of beef cattle (n=709) raised under the same farm environment. Multiple factors, including breed, sex, and diet were identified to determine rumen microbiome profiles. We found that ~34% of rumen microorganisms are heritable elements affected by host genetics and genotypes, that are also associated with host feed efficiency traits and rumen metabolic measures. Therefore, cattle may control their rumen microbiome genetically and consequently influence their rumen fermentation and feed efficiency.

The cattle sampled for these papers were part of the Gentec “Kinsella Cattle Project” (Improvement of cow feed efficiency and the production of consistent quality beef using molecular breeding values for RFI and carcass traits). The Kinsella Project enabled the measurement of feed-efficiency and provided the genotypes and pedigree information for the genome-wide association analysis with rumen microbes.

Overall, our findings highlight a potential to manipulate and obtain a desirable and efficient rumen microbiome using genetic selection and breeding. It could be a useful strategy to further improve feed efficiency and optimize rumen fermentation through targeting both cattle and their rumen microbiome.

The work, funded by Alberta Livestock and Meat Agency, Alberta Agriculture and Forestry, NSERC, and an Alberta Innovates-Technology Futures Graduate Student Scholarship, brought together researchers in beef production, rumen microbiology, functional genomics, quantitative and statistical genomics. Notably, Agriculture and Agri-Food Canada scientists Changxi Li and Carolyn Fitzsimmons, both co-located at UAlberta, were essential in providing these elements for Fuyong’s analysis.

“Rumen microbe composition and abundance are novel quantitative traits in beef cattle. Characterizing variations of rumen microbes among animals and estimating their genetic parameters will also allow us to incorporate rumen microbe measurements into a multiple trait selection index to improve beef production efficiency” says Changxi Li.

The EC project on Ruminomics led by Prof. John Wallace in the UK subsequently reported similar results in dairy cattle.

The Gentec team is now investigating the genetic links of rumen microbes with other beef performance traits.

Fuyong’s papers are:

  1. Li, F., Hitch TCA, Chen Y, Creevey CJ, Guan LL. 2019. Comparative metagenomic and metatranscriptomic analyses reveal the breed effect on the rumen microbiome and its associations with feed efficiency in beef cattleMicrobiome7:6.
  2. Li, F., Li, C., Chen, Y., Liu, J., Zhang, C., Irving, B., Fitzsimmons, C., Plastow, G., Guan, L.L. (2019) Host genetics influence the rumen microbiota and heritable rumen microbial features associate with feed efficiency in cattle. Microbiome, 7:92.

A career well-remembered

Cambridge, UK 1988. Young post-doc Steve Moore stares out of the window at another rainy English day. In front of him, in the journal Nature, is an advert for a job at CSIRO, Australia’s national science agency, in Queensland. The accompanying image shows palm trees….

Steve got the job. Foregoing cancer research and the UK, Steve would remain with cattle for the rest of his career. He spent the next three years at the Rendle Research Laboratory and Belmont Research Station, the premierresearch stationfor the north Australianbeef industry and nicely situated on the aptly-named Tropic of Capricorn. He spent the following nine years in Brisbane, also for CSIRO, researching tropically-adapted animals.

Reorganizations started to feel like a fact of life at CSIRO. Steve no longer saw a future for himself there. Once again, he cracked open Nature, this time seeing an advert for a job in Alberta.

“Canada was spelled out in big letters down the side,” Steve remembers. “I thought I should jump before getting pushed.”

Steve got the job. In a 180-degree switch from the tropics, he found himself in Edmonton, where the temperature “soars” to -40C in winter. The job was Chair of Beef Genomics and the Alberta Bovine Genomics Program (ABGP), an organization he was to set up and run for 12 years at the University of Alberta.

“I remember going down to the Calgary-Airdrie area to look at yearling bulls with cross-breed producers,” says Steve. “We started to walk through the middle of them. I’m sure the guys were testing my mettle. They didn’t know that I’d been working with tropical bulls that are 6 ft at the hump. These bulls looked small in comparison. They parted like the Red Sea as we walked through.”

During that time, the ABGP enjoyed great support from the Government of Alberta, especially Cornelia Kreplin, and eventually morphed into Livestock Gentec, which broadened its mandate to other livestock industries in Alberta. Hence, Graham Plastow’s (a pig expert) appointment as incoming CEO after Steve. While the pig industry is completely integrated, with all sectors cooperating to achieve common goals, the beef industry is quite the opposite, making it very hard to work up and down the value chain. Canada has made significant efforts to change the information flow up and down the value chain, making all sectors better able to meet consumer preferences.

“Establishing Livestock Gentec remains one of the most satisfying parts of my career.,” says Steve. “Gentec is now a world-recognized centre for livestock genomics with links to other groups in Canada such as the University of Guelph, and beyond with groups in the USA and Europe. The best part was the students, who came from all over the world. They have since moved on and established their own careers in industry, government and academia in Canada, the USA, Europe, Asia and Africa.”

Initially, the position was for three years. Eventually, Steve and his family stayed for 12.By that time, he’d done what he set out to achieve, and he was happy to leave the ABGP/Gentec in Graham Plastow’s capable hands while he took on the role of Director, Centre for Animal Science for the Queensland Alliance for Agriculture & Food Innovation. This time, without the assistance of Nature.

Steve maintains his links to Alberta through research collaborations and as a Board member of Delta Genomics, a not-for-profit spin-off from Livestock Gentec serving the Canadian livestock industry. Steve and Fran’s children remain settled in Alberta, resulting in regular commutes across the Pacific.

Seven years later, Steve has once again achieved what he set out to do. This time, though, he decided to retire, although he will maintain his international engagements with the well-deserved new title of Professor Emeritus. And he has other plans.

“We just bought a property on the Gold Coast,” he says. “My next job is to tame it back to civilized state. That should keep me busy for a while.”

ISAG Meeting Highlights

by Elda Dervishi and Jiyuan Li

The 37th International Society for Animal Genetics (ISAG) conference was held in Lleida, Spain from July 7-12, 2019. Over 700 researchers from all over the world attended to present over 600 scientific contributions. Excellent oral presentations and posters demonstrated recent research advances in livestock and companion animal species. Canada was represented by 25 attendees. Among them, postdoctoral fellow Elda Dervishi and PhD student Jiyuan Li represented University of Alberta and Livestock Gentec with three posters.

ISAG had several plenary sessions, poster sessions and workshops. Dr. Yang Li (University of Chicago) proposed a formal model describing how genetic contributions to complex traits can be partitioned into direct effects from “core” genes and indirect effects from “peripheral” genes acting as trans-regulators. This model provides interesting new possibilities to help dissect complex traits in animal science.

A large number of the oral presentations reflected the wide interest in better understanding gene function in animal species and how this can improve different aspects of animal prediction and/or welfare. The Functional Annotation of Animal Genomes (FAANG) initiative investigates genomic functional analyses for cattle, sheep, fish and chicken, which were widely discussed. Dr. Christa Kuhn from the Leibniz Institute for Farm Animal Biology introduced the new EC Horizon 2020 project entitled “BovReg,” which is part of the FAANG initiative. Gentec is a member of BovReg; Elda and Jiyuan participated in the informal team get-together. The latter also participated in a post-conference FAANG workshop on metadata validation and data submission. The instructor emphasized the importance of standardizing and validating data to facilitate effective data sharing among the FAANG community.

Another topic was the potential role of the microbiome and epigenetics for gene editing. This is a “hot area” in animal genomics research. Dr. Luís Montoliu (Campus de Cantoblanco) gave a comprehensive talk on the current situation of genome editing including the tools used and their potential application in animal science.

Whole genome sequencing and RNA-seq are increasingly used in animal genomics research. New sequencing technologies such as ATAC-seq and single-cell RNA-seq have also become more popular together with ChIP-seq for chromatin analysis. These new technologies and analysis methods give us new insights into the function and network of genes and the genome. Again, they are an integral part of FAANG and BovReg.

An unforgettable gala dinner was served in the main building of the Old Cathedral built between 1300-1600, on top of the La Seu Vella mound. ISAG organizers really showed their hospitality. We tasted local cuisine and red wine produced by a local chateau. Everyone enjoyed the authentic Spanish food and the great view.

 

“Attending the conference was a great experience, giving us an opportunity to tell others about our work, to talk with so many excellent researchers from all over the world, to learn about new research going on in the world, to broaden our horizons and keep improving our academic ability,” reported Jiyuan and Elda. “We appreciate that our supervisor, Dr. Graham Plastow, supported our participation.”

Wind, rain and cows

Robert Mukiibi is finishing up his PhD in bovine quantitative and functional genomics related to feed efficiency. He’s been with Gentec for nearly four years. During that time, he has focused on improving feed efficiency in beef cattle through the genetic selection of more efficient animals using high throughput genomic tools. His research aims to identify genes and gene variants associated with feed efficiency through sequence transcriptomic data analyses of coding and non-coding species of RNA. The information obtained is then used to improve genomic merit estimation for breeding animals. Robert is also involved in imputation of genotypes from low density panels to high density and full sequence genotypes, and genomic prediction for feed efficiency traits in beef cattle.

This is where the Irish angle comes in. Canada and Ireland have common research interests in beef cattle genomics. In 2014, Robert’s supervisor Dr. Changxi Li at Gentec, UAlberta and Dr. Sinead Waters at Teagasc (the Agriculture and Food Development Authority, Ireland) were awarded a Teagasc-UAlberta Walsh Fellowship to work on the project: “DNA-based biomarkers for feed efficiency in beef cattle,” which helped support Robert’s own project: “Quantitative and molecular genetics of feed efficiency traits in Irish and Canadian beef cattle.”

“For my project, we are using the functional information of the bovine genome to improve accuracy,” says Robert. “I perform the gene expression, gene functional characterization analyses and genomic analyses in Canada. In Ireland, I perform the lab work to validate the gene expression results.”

Caption: Robert, Dr. Sinead Waters and Dr. Changxi Li at National University of Ireland, Galway

Robert has visited Ireland twice for his project, first in 2016 and again in 2018 with Dr. Li to enhance the joint research activities. During the 2018 visit, the pair presented at the National University of Ireland, Galway, and at Grange(see below). Robert’s Irish co-supervisor, Dr. Waters, is expected to visit Canada as part of the exchange.In 2017, Gentec hosted Teagasc’s Tara Carthy, who was working with Gentec’s Dr. Paul Stothard to identify structural variants in the bovine genome associated with important economic traits.

In Ireland, Robert worked at theAnimal Bioscience Research Centre Grange, one of the world’s leading beef production research facilities, outside a small heritage town called Trim in County Meath.

“Ireland really is as green as they say,” he winces. “It rains several times every day. It’s vital to carry an umbrella but it’s not always useful because of the strong winds.”

Similar to Gentec, the lab experience was all Robert could hope for. Cooperative and collaborative colleagues, unlimited access to lab tools and everything he might need to obtain reliable and reproducible results for the scientific community and industry. While there, Robert expanded on his social experience with visits to the pubs to see live bands, and watching Gaelic football. Such was the warm and welcoming working environment, that fellow students picked Robert up from his lodgings and brought him back—for which he was extremely grateful.

“The bus rarely runs on time and the frequency is very low,” he remembers. “So when it breaks down, I had to wait an hour for the next one.”

In terms of key points that might help other students decide where to study, Robert believes that Canada is a bit more student-friendly than Europe in terms of easily accessible healthcare, availability of student partner employment permits, availability of extra merit-based scholarships and affordable and efficient transportation through student passes. A major difference he highlights is the high cost of student accommodation in Canada compared to Europe.

Robert thanks Dr. Li and Dr. Waters, Teagasc, Alberta Innovates and the Department of Agricultural, Food & Nutritional Science at UAlberta for the wonderful opportunity of the Walsh Fellowship. He is already looking for a postdoc position for the fall.

“I’ve now lived out of my home country, Uganda, for more than 10 years in countries including Egypt for my undergrad, Sweden and the Netherlands for my MSc and now Canada for my PhD. So the next stop can be anywhere in the world. I’m open to suggestions.”

Taking the classroom into the barn

Hands-on practice helps student learning stick

The Ruminant Digestion, Metabolism and Nutrition course at UAlberta benefits from hands-on industry participation

ANSC461/AFNS561 is a “must-have” course for any student wanting to improve their knowledge and understand the principles of ruminant nutrition, digestive physiology and metabolism—and apply this knowledge in commercial dairy and beef operations.

“Industry contribution provides great opportunities for students to better understand the industry and put their skills in practice,” said course co-teacher and Gentec researcher, Dr Ghader Manafiazar.

One beef farm Blindman Beef and Bison Farm (check out the incredible photography) and one dairy farm Tuxedo Farm Ltd kindly volunteered to host the students and provide the required information for them to complete their project.

Blindman Beef and Bison Farm sits beside the Blindman River in the south-central region of Alberta, with about 300 Angus and Beefbooster cow-calf pairs. The farm backgrounds its own calves as a better marketing practice. Assar Grinde, the owner, is highly concerned about and focused on the animals’ welfare, practising antimicrobial stewardship and environmentally sustainability, and having third-party verification for the farm’s practices. Assar shared his pasture management, bale grazing, weaning, and grain processing practices in addition to feed and water analysis with the students.

Tuxedo farms Ltd. is a family owned and operated farm located northeast of Westlock, in North-Central Alberta. Diversification is a major goal. The farm feeds high-quality, home-grown corn, barley and hay to its dairy (337 cows, of which 285 milking cows) and beef herds. Management added 120 free-stalls in 2018, and will add more in coming years. The farm is equipped with advanced technologies, such as Herd Navigator and a body-condition scoring camera. Herd Navigator detects sick animals for treatment and those producing less than 10 L/day to go dry. Nelson Jespersen, the manager, asked his nutritionist, Jamie McAlister, and herd manager, Francis Kavanagh, to participate in our two visits, allowing the students to discuss many aspects of the dairy farm business and management in smaller groups with them.

At the end of the semester, teams of students presented their recommendations to Ghader and the farmers, with an opportunity for discussion and feedback.

“It’s one thing to learn theory in class,” says Ghader. “Learning by doing sticks better. Overall, the students appreciated the opportunity to act as a consultant and put their knowledge into practice.”

Ghader also invited Barry Robinson (a private consultant), Kris Wierenga (regional manager with Shur-Gain feed mills), Myrddin Jespersen (farm owner) and John Stephen (Senior Sales Professional with Elanco) to present on the opportunities and challenges in different segments of the industry. Barry talked about his experience as a nutritionist; Myrddin discussed the opportunities and challenges of owning and managing a dairy, beef and grain farm; John shared his insight about the pharmaceutical industry; and Kris talked about the commercial feed industry. This session encouraged students to look for the opportunities in these sectors and expand their networks.

“It’s important for industry to be part of this course,” says Ghader. “Their contribution allows students to see where they can fit their skills and what other skills they need before entering the workforce.”

Globetrotter

One woman’s search for a research home

From the Middle East to Europe and North America, Marzieh Heidaritabar talks to Gentec about the meaning behind international science.

Already, as a thirty-something, Marzieh Heidaritabar has lived in six countries as part of her studies and career. Such is the life of a scientist, these days.

“I always knew I wanted to go abroad for my advanced degrees,” she says. “The level of achievement at European and North American universities is higher than at home.”

Building on a Bachelor’s in her native country, Iran, Marzieh won a European Master of science in Animal Breeding and Genetics (EMABG) scholarship. She spent the first year at the renowned SLU (Swedish University of Agricultural Sciences in Uppsala) and the second at the Norwegian University of Life Science (NMBU) in Sá.

Wageningen University & Research (WUR) (in the Netherlands, where Marzieh completed her PhD in 2016 on genomic selection in egg-laying chickens) is my second home,” she says. “It’s a small—but highly social and connected—society of students. I was never bored.” Then, over to Aarhus University Foulum for a post-doc, where she already knew several researchers from collaborations with Wageningen.

“I was right about the European universities,” she says. “All of these are in small towns where students are the majority of the population. The facilities, computer labs and digital libraries are excellent, so are the teaching and technical support.

As a testament to the connectivity of the European science community, Marzieh didn’t have to learn any languages. With international reputations and a large international student body, almost all MSc courses are taught in English and the townsfolk are keen to practise their own language skills.”

During her PhD, she also spent several months at Iowa State University (ISU) in Ames, USA. “The ISU group is one of the best in quantitative genetics,” she says. “I learned a lot from my supervisors (Jack Dekkers is a long-time Gentec collaborator). People are hard workers and the group is so dynamic. I also met some faculty members and geneticists from other USA universities and companies.”

Then on to Canada. During Marzieh’s PhD, the Dutch company (Hendrix Genetics) that supplied her data also worked with Gentec CEO, Graham Plastow. Throw in some reminders about Gentec over the years through workshops, colleagues, some reading and fellow Iranians, and Marzieh decided to reach out.

Marzieh has been in Canada since late summer 2018. These days, she is working on swine data for the first time (data provided by Hendrix). She is exploring the potential benefits of whole-genome sequence (WGS) data to improve meat and carcass quality traits in genomic selection programs of purebred and crossbred pigs. Incorporating the biological information from WGS into genomic prediction models will lead to a better understanding of the genomic architecture underlying carcass and meat quality in swine.

Of course, there are pros and cons to moving around so much. Marzieh has learned about different research styles, communication styles, PhD content (North Americans expect PhD students to teach and take subject matter courses: not so in Europe), new cultures and lifestyles—an openness that hasn’t been available to her friends who chose to stay home.

“The disadvantage is that I always feel I’m not settled yet,” she says. “There’s a cost to physically moving your life from place to place. And there’s definitely an anxiety at the beginning about not being familiar with new towns, colleagues, culture and research. Special thanks to Dr. Plastow and other people from Gentec who welcomed me warmly so that I felt at home. I am very glad to be a member of Gentec.”

For someone who was raised to be quiet, it’s been a positive learning experience.

“I was shy,” she says. “Too shy to ask my supervisor for help. The student culture in Wageningen helped change that. You either get help or you don’t, but you have to ask! If I hadn’t left Iran, I wouldn’t be the person I am now.”

Canada: A role model for sustainable beef production

“Canada is ahead of the game when it comes to beef sustainability,” affirms Graeme Finn, a member of the Canadian delegation at the Global Conference on Sustainable Beef held in Ireland on October 9-12, 2018.

“What we’re doing here is right on track to keep the public informed. It’s good to see progress from the McDonalds’ pilot program to getting a cheque from BIX/Cargill for sustainable beef—and most of all, that other countries are looking to us for guidance. I’m pretty proud of where we are right now in the world.”

The Global Roundtable for Sustainable Beef (the conference host) is a global initiative that aims to improve the sustainability of the global beef value chain through leadership, science and stakeholder engagement/collaboration. It is the umbrella organization and governing body for initiatives in member countries, which includes Canada (hence our interest in this).


Caption: Canadian representatives at the conference

Of the 245 attendees, Canada had the biggest delegation: 15 people representing organizations as diverse as the Canadian Cattlemen’s Association, McDonald’s, A&W, BIX, Ducks Unlimited, World Wildlife Fund Canada, and three producers (including Graeme, who also represented the Canadian Roundtable).

On Day 1, Graeme took the Dawn Meats tour. Dawn Meats is one of the largest suppliers of beef into the McDonald’s system in Europe at the company’s fossil-fuel free (!!!) plant in Waterford. In 2017, the site became the first Irish food manufacturing company to be awarded BITC Ireland’s prestigious BWR (Business Working Responsibly) mark.

“Dawn buys all its meat from Verified Sustainable operations,” says Graeme. “No common market cattle. McDonalds does the same thing in Canada, so we’re aligned with Ireland on that. Cargill and McDonalds are the prime buyers of sustainable beef here. All our own beef goes into that chain, and we get the quarterly cheque.”

The tour also stopped at John and Catherine Powers’ farm in Waterford where calves are reared and finished as beef cattle for the McDonald’s Flagship Farm Program.

“It’s all bull meat,” says Graeme. “They don’t castrate any animals so, obviously, no synthetic hormones. It must be quite boisterous on that farm when the animals are young!”

Days 2 and 3 were in a more traditional conference format. Justin Sherrard, Global Strategist Animal Protein, Rabobank RaboResearch, Food & Agribusiness delivered the keynote address, focusing on leadership and the concept that the customer is always right.

“I didn’t totally agree with that,” points out Graeme. “How can customers be right if they don’t have the correct or the full information—or if they’ve watched Cowspiracy on Netflix? It makes sense that veggie burgers are trendy in a first-world urban setting but in developing countries, the cheaper option will always be meat. As their standard of living improves, they are moving towards more animal protein.”

Graeme presented on the impact of technology on producers and their operations. He believes the BSE crisis of 2003 drove producers to know their costs and to improve their winter management and grazing management—which turned out to be the best thing for the industry as it relates to sustainability.

“We already have traceability,” he says. “South Africa doesn’t even have RFID tags. The UK and Ireland have passports that follow every animal through the system throughout its life. It’s intense! They need to get with the Canadian model.”

Other presentations focused on the environmental side of sustainability, reducing emissions through innovative feeding strategies, sustainable beef production on the Canadian prairies and genetic improvement for animals on pasture.

Michael Lee, Chair of Sustainable Livestock Systems at Rothamsted Research, delivered the capstone address focusing on how livestock fit into the environment, not just as meat but also as wool fibre, cosmetics, leather, milk, fertilizer and beasts of burden. All biodegradable. Styrofoam… not so much.

“Attending a conference like this makes us more aware of where the trends are going,” says Graeme. “It’s important to know what’s going on in the world.”

Bioinformatics: Tomorrow’s career…

…where the jobs come looking for you, not the other way round.

In his lab in the Faculty of Agriculture, Life and Environmental Sciences at UAlberta, Paul Stothard and his students pore over their computers and monitors. Stothard is a bioinformatician; that is, he uses computers and software to analyze DNA and protein sequences and to connect them to traits of interest or mutations that could have beneficial effects.

Typically, bioinformatics “starts” after somebody has generated enormous amounts of ACGT letters (the sequence), recorded them in a giant text file, and handed the file over. Stothard then has to manage these huge datasets so that the data are stored safely yet accessible to others in an organized way.

To do this, Stothard relies on powerful computing resources. The innocuous-looking screens and computers in the lab are just the interface that connects to a remote hive of computer clusters that have tens of thousands of processors and thousands of terabytes of storage. Then there’s the software…. Stothard and his team do a lot of computer programming.

“A lab might get a new device for measuring gene expression that produces different data,” he explains. “We simply can’t rely on—or wait for—commercial software packages to follow so we create our own. We publish the code, and it becomes open source for others to build on.”

And that, as they say, is where it all began. Stothard’s background is in molecular genetics. It’s as he was working in the lab, studying how an embryo nematode decides to develop into a male or female, that he realized the tools were inadequate.

“I started writing my own software. I enjoyed it, and people started asking if they could use it, too. I decided to do a post-doc in David Wishart’s lab in Computing Science, where I could really focus on that.”

Bioinformatics is one of the fastest-evolving fields around. One exciting direction it is taking relates to how DNA is sequenced. Currently, when the sequences arrive from the lab, the data are in billions of small pieces of about 300 nucleotides (the letters) long. Stothard and his team have to stitch them back together into whole chromosomes. It’s not that much fun.

“Thank goodness ultra-long read technologies are on the horizon,” he says. “We may one day get entire chromosomes as single reads. We’ll be able to catch differences between individuals that we can’t see now because of the breaks.”

As well, the cost of sequencing will continue to fall so that, in a few years, hundreds of thousands of individual people, cattle, pigs, plants can be sequenced. That will provide more enormous datasets to work from.

In practical terms, any trait that can be improved through breeding can be addressed using bioinformatics. Essentially it leads to faster genetic improvement and can lead to new diagnostics. Stothard and his team are working on a variety of projects. One is a mutation in Dalmatians and Bedlington terriers that causes copper toxicosis. Finding the mutation could lead to a DNA test, and breeders would know which dogs to avoid breeding. A similar test would have been extremely useful in the last 20 years when hip dysplasia was accidentally bred into German shepherd dogs. Everybody is familiar with those consequences.

Gentec’s Chief Executive Dog (ie; belonging to CEO Graham Plastow) is a Bedlington.

In livestock, bioinformatics can help identify which animals are more feed-efficient than others, more disease-resistant or even the breed history. All lead to higher profit margins for producers. Disease-resistance also has implications for better animal welfare.

“If anybody is interested in a career in bioinformatics, now is the time,” says Stothard. “Research groups are drowning in data. They have a real need for people who can manage and analyze large DNA sequence datasets. And industry as well. My students have gone on to work in companies developing drugs, tools for animal breeding and even for software companies. There are openings from the Master’s to the post-doc level. As long as the candidate can demonstrate computer programming skills (not necessarily a degree).”

His own team is stretched to capacity. “I have way more projects than time to do them,” he says.

In the fairly near future Stothard will be looking to hire another bioinformatician for his team who can provide assistance to multiple researchers and isn’t tied to any given project. One of the first places he’ll look is: https://bioinformatics.ca/job-postings/. If this is a career that might interest you, it’s a good place to start.