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

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

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

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

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

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

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

by Xuechun Bai

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

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

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

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

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

As of September 2019, Germany’s Leibniz-Institut für Nutztierbiologie (FBN) is home to BovReg—a $9 million, EU-funded project dedicated to generating a comprehensive functional annotation map of the bovine genome and applying that knowledge to validate novel models for biology-driven genomic prediction. The knowledge will allow breeders and producers to improve traits, such as robustness, health (especially udder health) and biological efficiency. A parallel focus on animal welfare will consider the physical limits of cattle, ensure that efficiency in one trait does not harm others, and provide options for reducing antibiotic use safely.

“Functional genomics in the livestock sector is very much a ‘black box’,” says Dr. Christa Kühn, Director of the FBN. “It’s like driving a car without a map. You want to go to Munich but all you can do is go in that general direction. You might reach the city… you might not.”

Furthermore, phenotypic data collected from the big breeds cannot be applied directly to the smaller breeds. Former Gentec CEO Steve Moore remembers being aghast to find out that gEBVs do a great job on Holsteins but not on Jerseys.

“We have a causal variant and some markers ‘in the neighbourhood’ but, for the small breeds, we’re not reaching Munich,” says Kühn, staying with the metaphor. “Data that BovReg collects from, for example, Brown Swiss, Braunvieh, Montbeillarde, Normande and Nordic red cattle will be important for those regional breeds and for others, too. They will help maintain biological diversity in the national herds.”

To achieve its goals, BovReg brings together experts in bioinformatics, molecular genetics, quantitative genetics, animal breeding, reproductive physiology, ethics, social science and dissemination/ commercialization from 13 countries (11 European, plus Australia and Canada). Canada, in particular, plays a special role.

At the core of the project Gentec will provide 24 tissue samples from Kinsella crossbred animals characterized for feed efficiency and methane production. These samples are one of three sets that will undergo detailed next-generation genomic analysis in the European labs collaborating in BovReg. In addition, Gentec will provide data from 7,000 samples of composite, Angus and Charolais phenotypes for feed efficiency, methane production, carcass and quality traits and 500 samples of commercial crosses  for health traits. The samples have been comprehensively analyzed for genomic structures, and have produced genotypic, phenotypic and transcriptomic data, which are an important component of genetic analysis. BovReg reviewers rated this contribution so highly that they recommended funding for it.

“It is quite exceptional that the EU funded Canada’s contribution—even as a symbolic gesture,” says Kühn. “It happens in less than 5% of cases. The reviewers insisted, due to the substantial impact of the samples. The Kinsella animals bring diversity, which is an issue in livestock breeding, and an advantage of the Kinsella vs purebred beef cattle populations.”

BovReg will be a first official collaboration between Gentec and this European team, even though Gentec CEO Graham Plastow (seen hiding behind his sunglasses at the BovReg kick-off meeting here) and Christa Kühn have known each other for a number of years.

“This is a really exciting opportunity for the Gentec team, which includes Ellen Goddard, Carolyn Fitzsimmons, Leluo Guan, ChangXi Li, John Basarab and Paul Stothard,” says Plastow. “It allows us to build on our investments over the last 10 years in characterizing the populations at the Roy Berg Kinsella Research Ranch, the Lacombe Research and Development Centre and beyond, placing our animals at the centre of a major international initiative with many of the world’s leading bovine research teams. That work was funded by Alberta Agriculture and Forestry, Agriculture and Agri-Food Canada, Alberta Innovates, Genome Alberta, Genome Canada and the Beef Cattle Research Council, industry partners and other organizations.”

Within BovReg, team members and partners will have access to an internal database. Externally—and part of the data-sharing plan—eight partners are active in the global FAANG (Functional Annotation of ANimal Genomes) consortium, whose data are publicly available, free of charge, opening the possibility of citizen scientists becoming involved in the spirit of Open Science. Key partner, European Molecular Biology Laboratory, hosts the FAANG Data Coordination Centre (the official repository of all FAANG-related data produced globally) and will ensure that data deposited are convenient for input and retrieval, giving them extra value. In addition, four partners are Steering Committee members of the 1000 Bull Genomes Consortium. Integration into these global initiatives will facilitate dissemination to a wider academic community. Although BovReg is dedicated to basic research, it will reach out to the public and policy makers to ensure support for its objectives.

“The use of the Democs card game and the availability of free resources will improve the public’s motivation to engage in the discussion on the promises, values and consequences of science in livestock genomics in general—and of BovReg deliverables in particular,” says Kuhn. “I truly hope this will advance our efforts in sustainable agriculture and food security.”

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.