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).

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.

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 cattle. Microbiome. 7:6.
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.

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.”

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.”