The daily light/dark cycle of plants: possible benefits for agriculture

Richard (known as Glen) Uhrig, currently Assistant Professor at UAlberta’s Department of Biological Sciences, became interested in the circadian clock and light signalling of plants during his post-doctoral fellowship in Switzerland. There, he worked with world renowned plant scientist Dr. Wilhelm Gruissem at the Swiss Federal Institute of Technology on a multi-national EU Seventh Framework-funded project call TiMet Metabolism, which sought to better understand how the circadian clock is connected to plant metab

Glen’s own EU Marie-Curie Plant Fellows Co-Fund and NSERC post-doctoral fellowship-funded work spun out of this, and aimed to understand how and when proteins and cellular processes are regulated post-translationally over a 24-hour diurnal cycle. He explains it this way. “Humans have a circadian clock to govern physiological processes. Similarly, plants have a circadian clock but, to them, it’s a matter of survival.”

Through this work, he acquired a number of large datasets that are the foundation of his research program at UAlberta as well as a number of exciting leads.

“It’s very fundamental work” he says. “But we are looking at new avenues that could be relevant to agriculture.”

The circadian clock controls numerous cell processes including aspects of plant metabolism. When you understand how these processes are regulated at a high level, you can start to engineer or breed plants for specific traits. The possibilities are mind-boggling.

Among the findings are a number of cellular processes that are fluctuating dynamically at the protein level over the course of a 24-hour photoperiod. One of these processes is how well plants take up nitrogen and how much nitrogen they need to grow well. In most crops, nitrogen is provided in the form of high-energy fertilizers but the plants need carbon (from sunlight) to assimilate it. Glen’s lab found that a number of the core and related proteins for assimilating nitrogen are regulated by multiple post-translational modifications. These then correlate with the presence or absence of available carbon for assimilating nitrogen.

In the meantime, Glen is relishing the idea of starting a research program, and exploring unique niches—of which beef genomics is one. Shortly after arriving at UAlberta (he’s only been here six months), he reached out to Gentec CEO Graham Plastow and attended Gentec’s annual conference in October. Discussions may lead to another cloak-and-dagger collaboration that would integrate Glen’s expertise in proteomics and genomics into a large scale project called 5-dimensional omics that aims to create a comprehensive understanding of Alberta agriculture at the molecular level; from ground to grocer genomics.

“I’m taking advantage of opportunities to meet people such as Graham and beef producers,” he says. “The conference was eye-opening. Here’s a group of people specifically interested in engaging with academics and in using cutting-edge science. Probably, most people think these two groups don’t talk—but a lot of interesting ideas come to light when those connections are made.”

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.

Mike Lohuis talks to Gentec

You haven’t been with Semex very long, but what is your role as Vice President, Research and Innovation likely to entail?

“It’s very exciting! This is the first time Semex has had an executive level position focused solely on research and innovation, so it brings new focus on the R&D aspects of our business. It’s important because the industry is changing very quickly, and we need to focus on the technology that’s likely to shape the industry’s future—as developed by in-house and academic partners.”

So what has genomics led to?

“Genomic selection and advanced reproductive technologies have substantially transformed the industry. When I left Canada in 1998, multiple ovulation transfer was already being used to increase the reproductive capacity of elite females. But there was no way to distinguish between full siblings in genetic potential which limited the value of this technology. Since then, it has been interesting to watch as the science around genomic selection evolved to solve that problem and become a reality in the dairy industry.

Simultaneously, ovum pick-up (OPU) and in-vitro fertilization (IVF) technologies became a more effective tool to rapidly produce large numbers of offspring from the most elite young females.

If you consider the rate of genetic gain, increasing selection accuracy, selection intensity and genetic variation help increase the genetic improvement per generation. By reducing the generation interval (the time required to replace parents with their progeny), one can increase the genetic improvement delivered per year. By combining OPU/IVF with genomic selection, we’ve been able to increase selection accuracy of females because of genomic information. With males, we’ve given up some accuracy for speed by decreasing the generational interval. The intensity of selection has also increased because, instead of buying young bulls, collecting semen and creating progeny, which is very expensive, you can simply collect a hair sample, extract the DNA and test it in the lab. This also means that yearling bulls can now be used confidently as mating sires, which has significantly reduced the generation interval. Genetic variation doesn’t change quickly, but we are carefully monitoring the impact of these technologies on levels of inbreeding and genetic variation in the breeding population. At this point, we’ve almost doubled the rate of genetic improvement with the combined use of genomic selection and advanced reproductive technologies.”

 

Genomics doesn’t happen in vacuum. What changes have taken place around it?

“Technological leaps can cause disruptions in the marketplace and often lead to consolidation. You always have early adopters and those that are more risk-averse. In this case, some groups caught on to genomic selection and advanced reproductive technologies early and have done well by it. The marketplace itself can be another disruptor. Retail powerhouse Wal-Mart has continually put pressure on food prices, and now Amazon wants to sell food as well. Large retailers have demanded lower production costs, and producers have had to accept less for their products because there are always farms learning how to do it more cheaply.”

 

And as a result?

“We have significantly commoditized farm products. In some ways, it’s good as it drives down food costs but the return to individual producers has shrunk. So farm size has to go up for producers to make a living. We now have fewer, larger farms that don’t need as many companies servicing them. They prefer one supplier to service more of their needs. In response, we see some companies diversifying and others just getting bigger.”

Can we blame globalization?

“Global trade and the internet makes it easy to sell globally and provide for farmers around the world. Frozen semen is already very transportable, and the larger producers do their own insemination instead of bringing in a technician. If they have their own semen tank on the farm, anybody can deliver semen to that tank. It provides great selection to choose from but there isn’t the same loyalty to the local semen provider.

What role do you think Gentec plays in the industry?

“I got to know Graham Plastow in about 2005 when he was responsible for research at PIC. I always respected his approach and how he worked with multiple academic partners. He would encourage academic partners to develop their research in a way that industry could use and, if they were successful, increase the investment in them. It’s a nice model for generating useful research because you never know where the best innovations will come from.

We take it for granted that academics know what we need. Gentec seems to bring all the parties together. It does a nice job of creating a flow of information both ways.”

A big Thank You to Mike Lohuis for this in-depth interview. Click here to enjoy Part 1 again.

The Path to New Zealand

At our 2017 Livestock Gentec conference William Torres of Cattleland Feedyards focused on Pursuing Evidence-based Outcomes in the Beef Industry. The obstacles can be many… and varied… and driven by producer and end-user perceptions. Often, adopting best evidence-based practices is slowed by not knowing what these best practices are and how to apply them, or by a lack of coordination as to how to share their implementation, costs, and benefits across the various links in the supply chain. Just as often, however, difficulties arise due to nostalgia on the part of the producer aiming to preserve tradition and operate the ranch like “Grandpa” did, and on the part of the consumer seeking “natural” food free of many of today’s productivity-improving technologies that are necessary for the producer to remain in business.

However, several forces are converging to spur change. Environmental pressures and an increasing desire to ensure sustainable production are opening the door slightly and allowing scientific advances to pass through, as is the need to farm in the most efficient manner to ensure that nutritious food is also affordable food.

Stepping back from the idea that industry integration is a requirement, William focused instead on coordination, outlining some of the conditions that facilitate the use of genomics technologies with respect to sorting and managing animals at the feedlot level, and on areas where there is consensus on the social and economic benefit of pursuing change. These areas include the use of pain management tools for castration and de-horning procedures and the appropriate use of antibiotics to ensure animal welfare while preventing the development of antimicrobial resistance. When used as part of a disciplined pre-conditioning protocol, these measures help industry address animal welfare concerns and help optimize producer efforts and profitability.

Although not completely reflected in the edited version, William also spoke of the need to engage with those who disagree with you or don’t necessarily think like you, if only because they are often your customer. At its very worst, evidence allows us as an industry to do what society expects of us (even when society is ill-informed or we don’t agree with the direction of change) in a manner that imposes the least burden on us as producers. On more moderate ground, evidence also allows us as an industry to defend practices that are poorly understood, such as making the case that the use of medications in treating sick animals is the humane thing to do. At their best, evidence-based practices allow producers to make informed decisions on how to collaborate within the system to deliver the best possible beef in the most efficient and sustainable manner.

That said (and as an editor’s aside), there are also instances when the public shines a light on an industry practice that, while historic in precedent, is hard to justify today. Two practices often mentioned in the lay press are dehorning and branding. Industry is responding through the use of pain control medication in dehorning procedures and the use of genomics to select for homozygous polled bulls. Genomics also has the potential to supplant branding through the combination of the existing animal ID practices with DNA-based traceability markers. To view a summary of William’s talk, please click here.

Pursuing Evidence-based Outcomes in the Beef Industry

At our 2017 Livestock Gentec conference William Torres of Cattleland Feedyards focused on Pursuing Evidence-based Outcomes in the Beef Industry. The obstacles can be many… and varied… and driven by producer and end-user perceptions. Often, adopting best evidence-based practices is slowed by not knowing what these best practices are and how to apply them, or by a lack of coordination as to how to share their implementation, costs, and benefits across the various links in the supply chain. Just as often, however, difficulties arise due to nostalgia on the part of the producer aiming to preserve tradition and operate the ranch like “Grandpa” did, and on the part of the consumer seeking “natural” food free of many of today’s productivity-improving technologies that are necessary for the producer to remain in business.

However, several forces are converging to spur change. Environmental pressures and an increasing desire to ensure sustainable production are opening the door slightly and allowing scientific advances to pass through, as is the need to farm in the most efficient manner to ensure that nutritious food is also affordable food.

Stepping back from the idea that industry integration is a requirement, William focused instead on coordination, outlining some of the conditions that facilitate the use of genomics technologies with respect to sorting and managing animals at the feedlot level, and on areas where there is consensus on the social and economic benefit of pursuing change. These areas include the use of pain management tools for castration and de-horning procedures and the appropriate use of antibiotics to ensure animal welfare while preventing the development of antimicrobial resistance. When used as part of a disciplined pre-conditioning protocol, these measures help industry address animal welfare concerns and help optimize producer efforts and profitability.

Although not completely reflected in the edited version, William also spoke of the need to engage with those who disagree with you or don’t necessarily think like you, if only because they are often your customer. At its very worst, evidence allows us as an industry to do what society expects of us (even when society is ill-informed or we don’t agree with the direction of change) in a manner that imposes the least burden on us as producers. On more moderate ground, evidence also allows us as an industry to defend practices that are poorly understood, such as making the case that the use of medications in treating sick animals is the humane thing to do. At their best, evidence-based practices allow producers to make informed decisions on how to collaborate within the system to deliver the best possible beef in the most efficient and sustainable manner.

That said (and as an editor’s aside), there are also instances when the public shines a light on an industry practice that, while historic in precedent, is hard to justify today. Two practices often mentioned in the lay press are dehorning and branding. Industry is responding through the use of pain control medication in dehorning procedures and the use of genomics to select for homozygous polled bulls. Genomics also has the potential to supplant branding through the combination of the existing animal ID practices with DNA-based traceability markers. To view a summary of William’s talk, please click here.