The relationship between precision medicine and livestock genomics

Having worked on various genomics projects that included human, bovine and the SARS coronavirus, Steven Jones, Co-Director and Head of Bioinformatics of the Genome Sciences Centre at the BC Cancer Agency in Vancouver, is well versed in the potential, development and application of genomics. As he said in his presentation, “Cancer is a genetic disease. [And] livestock too is all about the genetics.”

In many ways, human cancer genomics and treatment can be considered the “pointy end of the stick” given the cost and complexity of pursuing these solutions. In spite of this, parallels are plentiful, and the tools developed in the human sphere often trickle down to our pets and livestock. For example, understanding how and why certain genomic variations differentiate between an aggressive and benign tumour allows us to manage the tumour appropriately. This ability provides value in the same manner as understanding the variants that result in Angus instead of Hereford cattle.

These days, the computational analysis (not the sequencing effort) consumes most of the resources in the process of teasing out the genomic variations, insertions, deletions, copy number variations, regions where zero heterozygosity remains (indicating the loss of a chromosome) and expression necessary to develop genetically specific treatment protocols.

In doing this, the processes flow from discovering knowledge, learning how best to understand and interpret it, and transferring it to the end user, be they clinician or producer. Communication is always the critical element: “Some buy into it [the technology], and some have yet to be convinced. It’s a huge endeavour.”

Either way, for Jones, it’s a team pursuit involving 24 individuals across multiple disciplines who sequence [about] one human genome a day, progressing the science and ultimately looking for a cure.

Banff Pork Seminar 2018: Highlights

The Banff Pork Seminar is a technology transfer meeting for the pork industry. The conference program is coordinated by the Department of Agricultural, Food & Nutritional Science, University of Alberta, Alberta Pork, Alberta Agriculture and Forestry and other industry representatives. Two Gentec students attended this year, and provided the following reports.

Xuechun Bai

As a first-year graduate student, it was a great opportunity and experience for me to attend the 2018 edition. It was a great honour to present our project, share the idea of our next steps and network with lots of people. The valuable suggestions and feedback they provided will help us improve and develop our project. I was also a volunteer at the event. Although sometimes tiring, it definitely worthwhile to support attendees in this way and see people enjoy the event.

I was most interested in the newest innovations in the pig industry, which introduced some automation technologies that can improve the biosecurity, efficiency and precision of farm management (see more below). The session on swine health and antibiotics, which indicated the trend of raising pigs without antibiotics, was also impressive. It highlighted the importance of improving herd health by making genetic improvements and inspired us to study and work harder as part of Gentec.

Greg Peterson, one of the Peterson Farm Brothers presented the closing plenary in an interesting and innovative way by singing to advocate agriculture and their farm (they also produce entertaining and educational videos on their YouTube channel, some videos are parodies of popular songs and some are vlogs of their farming practices). I think it is really impressive to encourage young people to be more creative and use new methods such as social media to advertise modern agriculture and educate the public on research and the future of agriculture.

I hope I can attend the Seminar next year again, when I will be able to share and present more results and progress of my study.

Ziqi Yang

The ultimate goal of our livestock research studies is to feed the world and improve the quality of animal protein products. In terms of feeding the world, the plenary session provided a good opportunity to understand more about the agricultural economy.

Dr. Larry Martin spoke about “Using Futures & Options to Manage Price Volatility.” He said, “We constantly have a ‘bull bag’ and a ‘bear bag’ of things to consider; that’s what makes a market.” (A bull thrusts its horns up, while a bear swipes its paws downward. These actions are metaphors for the movement of a market. If the trend is down, it’s a bear market.) He explained several chart formations (Stylized Resistance and Support at Contract Highs and Lows) that producers can use to help them know price trends to decide where prices are going and what actions they should take to reduce losses. Essentially, he asked the audience to reframe the question they ask themselves: not “What do I think these hog prices are going to do?” but “As prices change, where do I take action and what action should I take?”

In a similar vein, Ron Plain talked about the “Hog Market Outlook and Pricing Methods.” Although ethanol production led to very high grain prices, causing financial stress for livestock producers in 2006-2013 and PED virus pushed 2014 hog prices to record highs, hog numbers have increased and prices have decreased. The world trade in pork is fairly stable with slight increases in the last few years, which are expected to continue.

In the session on “Personality Typing and Profiling: Effectively Communicating and Working with Various Personalities,” Trish Hyshka helped the audience do the Myers-Briggs personality test, categorizing themselves according to the four main types: “Artisan”, “Rational”, “Idealist” and “Guardian.” She illustrated how the performance and preferences of these personality types differ. Knowing more about your stakeholders’ personality (group or individual) can help determine how to work with them and get optimal results even if you are not in a position of authority. The theory sounds good but, based on my results, the results may not be applicable to everyone. I would prefer to discuss the theory’s applicability with my peers before putting it into practice, or find a course that takes the headline farther.

The Swine Health and Antibiotics session had three speakers. Egan Brockhoff introduced the recent antibiotics guidelines changes to reduce antimicrobial resistance, which include:

  • – removing growth promotion claims from medically important antimicrobials (MIAs),
  • – increasing oversight on importing veterinary drugs,
  • – increasing oversight on the importation and quality of active pharmaceutical ingredients,
  • – mandatory reporting of sales volume from manufacturers and importers to support antimicrobial use surveillance,
  • – facilitating access to low-risk veterinary health products as additional tools for animal health and welfare, and
  • – increasing veterinary oversight over all MIAs.

Clayton Johnson mentioned that animals raised without antibiotics would reduce average daily gain, average daily feed intake, caloric conversion efficiency and increase morbidity and mortality, especially for nursery pigs. Greg Wideman had some good suggestions on reducing these negative impacts, including measurement and review of biological and economic performance, elimination and control of critical diseases, etc. My research on resilience would be another approach.

Steve Savage gave high marks to the performance of global feed production over the past several decades in “The Future of Agriculture: Challenges, Threats, Barriers and Opportunities.” however, if performance is going to increase even more in the future, different growers and producers in the agricultural sector will have to collaborate on creative strategies, such as setting up an independent certification system, to meet increasing demand and reduce the environmental challenges.

In the Newest Innovations session, Lee Whittington shared some technologies for improving pork farm management and production, such as satellite syndromic health surveillance and DrySist cleaning/baking process. Frédéric Fortin, from CDPQ (Quebec Pork Development Centre), introduced three new technologies (individual water intake recording system, infrared thermography and weight and conformation evaluation vision systems) used in the test station to provide faster more accurate data.

The water intake recording system is being used in our pig resilience project with Fred. Since water intake changes before symptoms of disease appear, it may be another health status index for producers to monitor. As well, pig body temperature usually increases after infection, for example from 39.3 °C to 40.2 °C in a single day after PRRSV infection. (Rossow, Kurt D., et al., 1994) Infrared thermography could monitor body temperature and pig movement in real time without handling but the current price (over $10,000) makes it expensive to apply in this way. Vision systems can also view pig movement with a tracking system and create 3D pictures from which to calculate a pig’s weight in the pen. However, since the pig needs to be alone in the pen for the 3D photo, it provides no advantage over traditional weighing methods. It is exciting to be involved in a project that introduces these new technologies as part of our research. This was one of the rewarding aspects of working at the test station for several weeks, as well as learning exactly how the project works at the action end.

Rossow, Kurt D., et al. “Experimental porcine reproductive and respiratory syndrome virus infection in one-, four-, and 10-week-old pigs.” Journal of Veterinary Diagnostic Investigation 6.1 (1994): 3-12.

To read the official proceedings, click here.

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Genotyping efforts in the Efficient Dairy Genome Project

The Efficient Dairy Genome Project (EDGP), led by Filippo Miglior at the University of Guelph and Paul Stothard at the University of Alberta, aims to reduce methane emissions (ME) and increase feed efficiency (FE) in dairy cattle by providing genomics-based tools to support selective breeding for these traits. Key to these efforts is collecting individual daily feed intake and methane emission data for cows and heifers in Canada as well in partner countries. With the addition of DNA information, genomic estimated breeding values (GEBVs) will be a much more impactful tool for producers in helping them reach their profitability and breeding goals.

At PAGXXVI, Stothard presented an update on the genotyping side of the project, focusing on work being done to add structural variants (SVs) to the picture. SVs contribute to a large proportion of the genetic variation in cattle but have been largely ignored because they are more difficult to detect than single nucleotide polymorphisms (SNPs). However, it is known from ongoing research, particularly in humans, that SVs have an important impact on phenotype. To begin to understand the influence of SVs on FE and ME, the team analyzed whole-genome sequences from over 500 dairy and beef cattle, the latter through a collaboration with the Sustainable Beef project led by John Basarab. Using high-performance computing and new software for detecting and visualizing SVs, the team has built one of the most complete and well-characterized SV collections to date. This resource will allow us to examine the influence of specific SVs on FE and ME, and could lead to the generation of more accurate GEBVs as well as a better understanding of which genes contribute to variation in these traits.

Amassing a large collection of phenotypic measurements is paramount to these efforts. An exciting recent development in this regard was the installation of 100 GrowSafe bins at Sunalta Farms in Ponoka, Alberta, which will provide the feed intake information on over 300 cows per year. Another important step towards delivering GEBVs was the creation of a centralized database for integrating the data from Sunalta Farms with similar information collected from research herds at the universities of Alberta and Guelph as well as by research partners in the US, UK, Denmark, Australia, and Switzerland. Over the next two years, the team expects to have FE and ME data on more than 8,000 and 3,500 cows, respectively. Although much work remains to be done, the project is well on track to deliver the tools needed to improve these challenging but important traits.

Early results from a new pig disease study could help industry reap profits

Early 2018 was an exciting time for the “natural disease model” established as part of our current Genome Canada project on pig disease resilience and sustainability. This is a very ambitious project that challenges naïve pigs with a cocktail of economically important swine pathogens. The project is two thirds of the way through, with samples and data collected on more than 2,000 pigs. We now have a critical mass of data, and some of the first analyses are beginning to show very interesting results, which we have just presented at PAG, the 2018 Banff Pork Seminar and the 2017 North American PRRS Symposium and NSIF Joint Conference (see YouTube video here).

Gentec CEO Graham Plastow presented the model and some of the latest results at PAGXXVI. The model was dreamt up by a team of researchers working closely with PigGen Canada, which represents the majority of pig breeding companies in Canada. Previous work shows that pigs could be selected for reduced susceptibility to the major diseases porcine reproductive and respiratory syndrome (PRRS) and porcine circovirus associated disease (PCVAD) but these diseases are multifactorial and involve numerous other pathogens so a single disease challenge may not provide the desired answer. Industry was asking: Would selecting for reduced susceptibility to these diseases pay off or should we also include the less destructive but endemic diseases at the commercial level that impact production?

One of the PRRS virus challenges at Kansas State University in our former Genome Canada-funded project intrigued the team and especially Plastow. Even though all the pigs in these challenges were infected and became sick, some recovered quickly and grew as well as the uninfected controls. This phenotype would undoubtedly be attractive to producers, especially if it occurred no matter what the underlying cause. Some challenge studies also suggested that the immune system was different in these pigs, even before challenge. What if these differences could be determined in healthy pigs at the top of the breeding pyramid? If these pigs and their progeny were more resilient to different diseases, it could revolutionize the selection of healthier pigs, potentially improving profits for producers, increasing animal welfare and reducing the use of antibiotics.

Austin Putz, a PhD student with Jack Dekkers at Iowa State University, has shown that new resilience traits being generated in the model are moderately heritable. A graduate student, Laura Tibbs, also working with Dekkers, is using data generated by John Harding’s team at USaskatchewan to show that natural antibodies may explain some of this variation. Other teams at UGuelph and UAlberta are working on their favourite assays and again generating predictors of resilience. The next stage is to validate these results and generate tools that can enable breeders to select for this valuable trait.

There is still a long way to go, but some of these first descriptions of resilience are very encouraging.

Calgary Stampede: UFA Cattle Trail

The UFA Cattle Trail at the Stampede features a live and interactive exhibition of the beef cattle industry in Canada. It focuses on the entire beef production chain from pasture to plate, and aims to give the public some insight on where our food comes from.

The live cattle exhibit showcased different breeds of cattle in a pen to demonstrate how GrowSafe technology allows researchers and producers to determine individual animal food intake vs. growth more accurately. Visitors enjoyed trying out the interactive auction mart and cattle-sized weigh-in chute. The miniature feedlot set-up demonstrated industry innovation and processes that ensure the safe and efficient production of beef. The feedlot exhibit also touched on the different types of feed and at what part of the growth cycle to yield the highest daily gain. Other parts of the Cattle Trail focused on animal welfare, medicine and transportation, and a large display showed the benefits of eating beef and how it can be prepared to provide a healthy and tasty protein option every day.

The goal of our Livestock Gentec booth was to highlight the importance of genomics in breeding better cattle—which raised a lot of interesting questions from visitors. People were curious about how to select which traits via genomics and how it might affect the cattle’s health and meat quality. A number of visitors expressed concern about humans eating meat from an animal with genetic abnormalities. There was also a lot of interest in how DNA testing works, and from what samples types we can obtain via DNA for testing. People were intrigued at how accurate high throughput DNA testing can be and how much information can be obtained from a relatively small DNA chip.

Due to our positioning next the feedlot setup, we received a lot of questions about the use of hormones and antibiotics on animals. Most people were initially leery about the use of hormones and antibiotics on cattle due to the negative ad campaigns and misinformation on the internet. However, when the use of antibiotics was explained to them from the angle of animal welfare, efficiency and sustainability, almost all of them left with a more positive view. We also stressed that Health Canada sets a very stringent limit of the level of these substances allowed in consumed beef, which are far below the amount that could pose a health concern. Most people were pleasantly surprised at how much producers care about their animals’ welfare and living conditions.

We also received a lot of questions about Angus beef and the Angus brand. It was very interesting to hear a good proportion of people assume that Canada only produces Angus beef or that Angus beef is the direct representation of Triple A meat. Some assumed that the only way to choose good quality beef is to look for the Angus brand. Many are unaware that Certified Angus beef is a brand, and that a lot of the good beef in grocery stores is not Angus. We had some very in-depth conversations about why each breed has different traits that producers might want: e.g. maternal traits and marbling in Angus, overall larger sized and more docile behaviour in Herefords. I brought up the use of cross-breeding cattle and how increased heterosis will yield a much healthier animal. We also included how Envigour HX ™ could help producers determine what breed composition they have in their herd and how they could use the tool to help determine if they have achieved their breeding goals. We spoke to a couple of aspiring producers from abroad who were interested in bringing some North American cattle seedstock and breeding into their population.

The overall theme of conversations at the Cattle Trail was one of education and interaction. Visitors were inspired by the showcase and willing to strike an open conversation on any question about the beef production and the beef industry. Most people were concerned about how the foods on their plate affect their health. The major topics of conversations circled around food safety, nutrition and animal welfare. I gathered that the general public find food production rather confusing. As industry representatives, we should create more awareness through public exhibitions like the UFA Cattle Trail or social media to engage people in open discussions about our food-processing pipelines and shedding a positive light on the use of science to improve food production, safety and sustainability

Olds FutureFarm Expo

By Janelle Jimenez

The objective of the Olds FutureFarm Expo was to help producers bring technological advancements to their farming operations. As such, it included many demonstrations, tours and agriculture-based seminars over a three-day period (July 6-8, 2017); and over 100 exhibitors were set up indoors and outdoors to market their products ranging from the business side of farming to the application of future-forward techniques and tools. Companies involved with bioremediation and sustainable farming technologies including the use of microbial inoculations and bacterial catalyst to open up previously unusable land for farming were strongly represented. There was also big focus on using drone technologies.

The winner of the Canada 150in150 competition (Delta placed second) gave a thrilling presentation on a project that used the waste grain from beer production to grow edible mushrooms. He demonstrated how he was able to grow a specific strain of mushrooms in a fraction of the time they take to grow in nature. In total, 23 seminars took place, with other themes on drone navigation to help manage farms and survey land accurately, the use of continuous-charging battery-power systems, and carbon tax credits. There was also discussion regarding pest control, farm energy management, indoor aeroponic farming, and the pros and cons of GE/GMP alfalfa.

A number of educational tours also took place. The brewery tour took participants through the Olds College teaching Brewery and the hops crop, and allowed participants to taste the locally-brewed beers. Participants also toured the botanical gardens and constructed wetlands, where over 20 acres of wetland used to demonstrate the treatment of water runoff from the college campus.

The second tour gave information on a research project using RFID-based (ID tags that transmit data using radio frequency) data acquisition software that tracked animals’ food intake to learn about feed conversion into muscle. Another project examined how thermography can help detect bovine respiratory disease, with the goal of commercializing the technology and increasing cattle value in the industry.

As at the Cattle Trail, Ying Yee and I did our best to interact with visitors, and generally the feedback on our presentations and messages was very positive. Many people were interested in the upcoming Cow Forage Gentec Tour at the Lacombe Research Centre.

Overall, the event offered a great variety of interesting and useful themes that of great interest to the agricultural community.