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!”

Banff Pork Seminar; the experiences and insight from a student presenter

By Teresa Lantz

Every January for the last 14 years, Banff, Alberta plays host to the Banff Pork Seminar (BPS). The Fairmont Banff Springs Conference Centre currently accommodates this event, which brings together a wide array of university students, researchers, industry professionals and producers. This year, over 750 attendees from all over the world took in the sessions, including plenary talks about African Swine Fever, the plant-based alternative protein movement and wild boars in Canada.

The overall program aims to provide practical science with direct applications to the swine industry, ample networking opportunities, and lectures with relevant information for producers, students and researchers. In alignment with this, the BPS runs several competitions within the conference, one of which focuses on the creation and dissemination of new and relevant science by undergraduate and graduate students: the RO Ball Young Scientist award. Students must submit abstracts with their work to a poster competition for evaluation by the BPS awards committee. Four finalists then prepare a 20-minute presentation in addition to a poster to be a part of the ‘Innovators’ lecture series at BPS. This presentation is judged by a panel of industry professionals and researchers, who elect the top two student contenders to win a cash prize. This year, I was honoured to win second place. First place went to Julia Moroni, one of Gentec-associated researcher Mike Dyck’s students.

Caption: L-R: Teresa Lantz and Prof. Ben Willing

My poster focused on meat quality, while other topics discussed reproduction, nutrition and behaviour, which offered a well-rounded afternoon of learning. This is standard for BPS, with lectures for all interests, which are repeated (except for the ‘Innovators’) so participants are not limited on the topics they can learn about. Listeners were engaged in every presentation, confirmed by the significant number of questions fielded. To me, this meant each talk was appropriate for the audience. The scope of knowledge provided significant value and an invaluable experience for a young professional hoping to continue a career in this industry. The connections sparked from this opportunity will, I’m sure, prove vital in the coming years.

The BPS also provides excellent experience for young professionals and students in the generous opportunities to network without feeling the weight and awkwardness that traditional networking opportunities often pose. The BPS is friendly, open and personable—an environment sometimes not felt at conferences, particularly for students who may lack networking experience. By providing multiple, bite-sized time-chunks plus coffee and tea, talking to fellow attendees feels much more natural; particularly when you can reference your poster and presentation and take a quick sip before asking for a card. Finding a common connection or discussing the lecture you just listened to simply feels less intimidating!

One of the most interesting things I noted was the support and encouragement given by colleagues and network acquaintances upon learning of the competition—and from the other three finalists. We all were very happy to be sharing our research and this experience with one another. As finalists, we also volunteered during the event, so we spent significant time together. This camaraderie during competition was refreshing and showed a truth of young professionals; we support one another and are excited for our future and that of our peers as we pursue advancement in the Canadian swine industry.

The experiences and opportunities provided by the BPS for me as a graduate student, particularly with plans to defend my thesis shortly and move into industry, are extremely valuable. The connections made, and ability to show my name on this scale to such a variety of industry professionals, and adding this competition and an award to my CV will undoubtedly help in my eventual job search.

I recommend the BPS to all students in the swine industry and to those interested in the animal agriculture industry. The science is relevant and accessible, and the setting is unmatched! For researchers and industry professionals, this conference provides significant networking opportunities for the next generation of students graduating and an opportunity to gather with some of the prominent voices in the industry. Together, students can learn from the previous year and work on the emerging challenges while enjoying some wonderful mountain views. It is an excellent way to kick off the New Year. I hope to see you there in 2021!

For more information, check out the BPS website.

Wind, Rain, Cows and now… Fish

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

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

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

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

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

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

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

Plant and Animal Genome Conference XXVIII Highlights

by Xuechun Bai

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

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

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

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

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

Gentec provides valuable contribution to Europe-led BovReg project

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.”

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.”