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BeeCSI: ‘omic tools for assessing bee health (2018)

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Overview

Honey bees are crucial to Canada’s agriculture and contribute up to $5.5 billion a year to our economy by pollinating valuable Canadian crops. However, the health of honey bees has been declining over the past decade, with Canadian beekeepers losing more than a quarter of their colonies each winter since 2006-07. The causes of bee declines are complex, variable over space and time, and often difficult to identify. This project aims to use genomic tools to develop BeeCSI – a new health assessment and diagnosis platform powered by stressor-specific markers. Working with beekeepers, industry technology-transfer teams, and diagnostic labs, in consultation with federal and provincial regulatory entities to ensure that the tools are implemented and accessible to the beekeeping industry by the end of the project.

TRIA-FoR: Transformative Risk Assessment and Forest Resilience Using Genomic Tools for the Mountain Pine Beetle Outbreak (2020)

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Overview

The current mountain pine beetle (MPB) epidemic has killed approximately 20 million hectares of mainly lodgepole pine forests in British Columbia and Alberta. Climate change and forest management practices have contributed to unprecedented range expansion of MPB. From its historic range in central British Columbia, MPB has spread through novel habitats in Alberta, establishing in a new host, the jack pine. Jack pine is a boreal forest species with a range that extends to the Atlantic Ocean, raising the spectre of continued eastward spread of MPB. Given the importance of lodgepole and jack pine to the forest industry, their central role in providing ecosystem services and their cultural importance, there is an urgent need to enhance resiliency of forests replacing MPB-killed stands, and to quantify eastward spread risk potential of MPB.

In TRIA-FoR, we will adopt a state-of-the-art multidisciplinary and integrative approach to develop genomics-informed knowledge, tools and application frameworks that mitigate risk for the present MPB epidemic and improve resiliency in future epidemics. Risk and resiliency will be investigated in the context of MPB-pine-climate interactions that affect MPB population dynamics, human dimensions in forest resource management, and impacts on diverse communities connected to forests at risk.

TRIA-FoR research encompasses three overarching goals. (1) Enhance lodgepole pine genetic resiliency to MPB. We will identify gene-based markers that predict MPB resiliency in lodgepole pine and identify traits that contribute to MPB resiliency. To understand how genetic resiliency translates into forest resiliency, we will model the impact of planting MPB-resilient lodgepole pine on outbreaking MPB populations. (2) Improve risk assessment efficacy for MPB northern and eastern spread into the boreal forest by examining MPB – pine host – climate interactions. We will test whether jack pine forests east of Alberta can support MPB populations, or whether expanding populations require immigration from the lodgepole x jack pine hybrid zone. In tandem, we will determine how overwintering temperatures and pine host characteristics in these marginal habitats affect MPB success. (3) Develop a social sciences framework of risk management planning and resilience building that can facilitate adoption of genomics-informed practices or technologies. We will investigate geographic, sociological, economic and policy aspects of risk related to the MPB epidemic, identifying factors that influence stakeholder willingness to adopt genomics-informed applications. This collaborative cross-scale research will enable a genomics-informed total risk and resilience management approach that can enhance forest health in the face of present and future MPB epidemics.

Optimizing a Microbial Platform to Break Down and Valorize Waste Plastic (2020)

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Overview

In Canada, 29,000 tonnes of plastic leak into the environment and oceans every year, creating severe environmental problems. Waste plastic kills 100,000 marine mammals annually, including whales, dolphins, seals, and sea lions, either through ingestion of plastic debris or entanglement in fishing gear. Another 2.8 million tonnes of plastic are sent to Canadian landfills, which creates a latent problem for future generations. Only 9% of plastic is recycled.

Despite the waste and environmental impact, plastic production is increasing in Canada, with an additional 4.8 million tonnes produced per year. Demand for plastic continues to grow because it is cheap to produce and has many important benefits. However, with a growing awareness of the environmental impacts of plastic, governments and manufacturers are working towards a zero-plastic waste future. Under this paradigm, plastics will be made with recycled or biodegradable components. For this change in paradigm to succeed, government, the public, and industry will all need to play a role.
In this project a Canadian-led team consisting of multiple universities, municipal governments, and industries will drive a shift to a zero-plastic waste future by harnessing genomics technologies to create a circular economy for plastics. Our goal is to identify and engineer bacteria and enzymes that can break down plastics into recyclable components or into valuable fine chemicals more effectively than chemical conversion-based technologies. On a second front our team will conduct a holistic investigation into the impact of these new plastic biotechnologies on society, the economy, and the environment. Preliminary estimates indicate that if 90% of plastic is diverted to recycling instead of landfill, Canada could avoid $500 million per year in costs, and create 42,000 jobs in new industries. The market for recovered waste plastic in the textiles sector alone is up to $600 million per year. We could also save 1.8 million tonnes of CO2 equivalents per year in greenhouse gas emissions. Globally, stopping plastics from leaking into the environment would avoid up to $13 billion per year in damage to marine ecosystems. Ultimately, we envision a future where plastics continue to contribute to the economy in a positive way, but without the concomitant negative impact on the environment.

This project is affiliated with the Contaminants of Emerging Concern Research Excellence Network (CEC-REN) at Queen’s University, which is an interdisciplinary research and innovation initiative. CEC-REN is focused on the detection and treatment of emerging contaminants in the natural and built environment that pose environmental and human health risks.

BIOSCAN–Canada (2020)

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Overview

The Global Risks Report 2020 from the World Economic Forum ranked biodiversity loss as one of the top five threats confronting humanity. Stemming this loss requires understanding how species interact and respond to changes in their environment, but this is impossible to accomplish with traditional morphological methods. DNA barcoding first emerged 15 years ago as a rapid, accurate way to discriminate species based on the sequence characterization of short segments of DNA. The International Barcode of Life Consortium, led by the Centre for Biodiversity Genomics at Guelph, involves research organizations in 40 nations which share the goal of cataloging all species and establishing a global biosurveillance system before mid-century.

Its current research program, BIOSCAN, is harnessing new technologies to make DNA barcoding faster and less expensive, advances that will broaden its application. Importantly, the technologies normally used to sequence whole genomes can be employed to gather DNA barcodes from thousands of specimens at a time. BIOSCAN–Canada is a core component of this global effort; its work will increase the cost effectiveness of DNA-based identification systems while also providing new biodiversity data with direct relevance to Canadians. For example, new species will be revealed from under-explored regions such as the Arctic and the ocean floor off British Columbia. DNA barcoding will also be used to illuminate interactions among species, such as which flowers a bee visited, and to track the shifting distributions of species in response to environmental change at previously impossible scales. Through community engagement, BIOSCAN–Canada will incorporate Indigenous ways of knowing into an accounting method for “natural capital” that extends beyond conventional economic metrics like the GDP.
By combining genomics-based biodiversity data with this accounting system, it will enable effective, timely environmental impact assessments and policymaking for the forestry, mining, and agricultural sectors as well as for conservation planning. Through such action, BIOSCAN–Canada will slow biodiversity loss, improve Indigenous relations through consultation, increase the sustainability of our agricultural and forestry sectors, and strengthen Canada’s leadership in global conservation efforts.

Fast Track Diagnosis of Stress, Disease, Phenology and Growth (FastPheno)

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Overview

The field of forest genomics has seen unprecedented advances during the past decade. A suite of genomic resources is now available for enhanced genomic selection and can be used to accelerate breeding cycles and to select genotypes that are better adapted and more resilient to future climate change and diseases. The large-scale phenotyping needed to assess adaptive traits in breeding populations with thousands of trees is now the major bottleneck hindering the rapid identification of the traits that enable trees to cope with climate change. This project will develop a drone-based precision phenotyping tool for assessing conventional and novel adaptive traits to complement the genomic selection research and operational programs of Natural Resources Canada and Ministère des Forêts, de la Faune et des Parcs du Québec. The economic impact of climate change is expected to be significant for Canada’s forest sector. The proposed technology will help the Canadian forest sector take advantage of genomic selection tools that may mitigate the impacts of climate change.

Introducing cold tolerance in hazelnut

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Overview

The Hazelnut, Corylus spp., currently considered a minor crop in Ontario, has gained tremendous interest in the horticulture industry as a highly desirable crop due to a guaranteed market demand. Our industry partner, Ferrero Canada, the manufacturer of the hazelnut-containing products Nutella and Ferrero Rocher, is the third largest confectionary group in the world, requiring approx. 40% of the current global hazelnut supply. For many years, Ferrero Canada has attempted to source hazelnuts in North America. Unfortunately, the lack of suitable cold hardy cultivars for the Ontario climate has hindered the ability of Ferrero to expand domestic cultivation. For instance, catkins (male reproductive structures that are needed for nut-set) are short lived and sensitive to frost, making the Ontario climate exceptionally problematic. The fluctuations between warm and cold weather during early spring can be quite damaging for commercial hazelnut (Corylus avellana L.) cultivars preferred by Ferrero. This project will provide genomics driven indoleamine-based “stress-buster” solutions to mitigate the impacts of climate fluctuations on field grown trees enhancing the productivity, sustainability and profitability of Ontario’s agri-food sector. Our strategies to improve thermo-tolerance of desirable hazelnut cultivars will utilize the proven capacity of indoleamines to mitigate stress. Indoleamines are potent plant growth regulators which can enable stressed trees to survive and support energy expensive processes of flowering and nut set. Indoleamines are produced across all life forms, therefore it is also possible to employ the root microbial network to further enhance their effects via plant-microbe interactions. Thermo-tolerance of desirable hazelnut cultivars can be improved by modifying indoleamine metabolism through horticultural management strategies (e.g. mulching or fertilizers), as well as, a direct application of indoleamine solutions. Elucidation of the metabolic mechanisms of indoleamines will lead to the development of effective tools for improving the survival of trees exposed to temperature fluctuations commonly experienced in Southern Ontario. The Gosling Research Institute for Plant Preservation (GRIPP), established with a mission to preserve endangered and agriculturally important plant biodiversity through research, education, and service programs provides resources, expertise, and access to germplasm for commercialization. Ferrero preferred cultivars from GRIPP collection will be screened to validate our proof-of-concept that the deployment of indoleamine compounds across various plant organs counters abiotic and biotic stresses in vitro and in the field. This research will provide an immediate, low cost solution to growers for mass cultivation of diverse hazelnut genotypes. Ferrero’s commitment to acquire locally sourced nuts will provide direct economic benefits to the Ontario hazelnut industry.

Development of an omics-driven beer yeast performance database to support the Ontario craft brewing industry

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Overview

The beer sector contributes $13.6 billion to the Canadian GDP and has an economic impact of more than 3X that of wine and spirits combined. The contribution of craft beer to the beer sector is growing and is predicted to triple by 2027. Nonetheless, craft beer competes with many imported beers. This, along with the ever-increasing demand for product diversity from consumers drives the industry to increase production efficiency and be innovative in the production process to decrease production costs and increase product quality. With this application we propose to provide craft brewers in Ontario with information that will drive production efficiency and product consistency, thereby limiting losses and increasing profitability.

The yeasts used in craft beer production are at the heart of the beer. Yeast diversity is one of the main tools used by brewers to create product diversity. Brewers tend to use standard production parameters, such as fermentation temperature and yeast nutrient management strategies, to generate beers with specific flavour profiles. A lack of understanding the optimal production parameters often leads to inconsistencies in beer quality and thus financial losses. In the three years allocated to this project we will determine the genetic composition of 40 commonly used and novel beer yeast strains to gain insight into its capacity to completed fermentations efficiently and to produce certain flavour compounds. We will also determine the optimal fermentation temperature and yeast nutrient needs for each of these strains and correlate the production procedures with specific flavour compounds produced by each strain. Towards the end of the project and in the subsequent two years the generated information will be compiled and integrated into a novel, publicly accessible Beer Yeast Performance Database for brewers to consult when designing brewing strategies. Rather than relying on generic production parameters, this information will allow brewers to approach more consistent brewing with predictable outcomes for individual yeast strains. We anticipate this resource, which will be maintained and updated as new information becomes available, will provide valuable information that will drive both innovation and consistency in beer production, thereby increasing profitability. It will help build a robust Ontario craft brewing sector that can compete effectively in the beer market.

Application of genomic-based technologies to improve the rate of genetic gain in Ontario winter wheat breeding

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Overview

Wheat (Triticum aestivum L.) is a staple food crop with an excess of 650 million tons of annual global production on more than 215 M ha of total harvested area. In Canada, wheat, with an annual production of more than 23 million tons, supports a Canadian farm industry of >$4.5B annually. Winter wheat production in Canada is primarily concentrated in Ontario, and mainly in South-western Ontario. With over 400,000 ha of annual harvested area, winter wheat produced in Ontario, accounts for more than 77% of total winter wheat production in Canada. A number of biotic and abiotic factors threaten the high productivity and quality of the Ontario winter wheat crop. Among the biotic yield-limiting factors, Fusarium head blight (FHB; caused mainly by Fusarium graminearum) has over the years been the most damaging disease in Ontario. In recent years there has been great progress made toward understanding genes in wheat. A recent major advancement was the release of a robust, high-quality annotated draft reference sequence of wheat. These advancements provide great opportunities for wheat scientists, including geneticists and plant breeders, to be able to improve the efficiency of genetic improvements in wheat. The ability to predict the performance of a given breeding line of wheat based on its DNA, has been shown to be one of the potential applications of genomics in plant breeding. This proposed research is designed to use the current state of knowledge in wheat genomics and genetics, to integrate genomic prediction in an active breeding program. The research team will also attempt to use state-of-the-art technologies of remote sensing to establish a high throughput system of remotely scanning and then identifying superior breeding lines. These technologies together with an accelerated breeding approach developed by the University of Guelph Wheat Breeding Program is expected to result in significant improvements in efficiency and speed of genetic gains in wheat breeding. Within 3 years of this project, we will have successfully developed new, advanced remote sensing analysis and diagnostic methods with the use of genomic technologies that will allow us to identify successful genetic lines that after additional field testing can be brought to market within the subsequent 2 years.

 

*This wheat breeding project was conceived and submitted by the late Prof. Ali Navabi, a professor in the Department of Plant Agriculture, who passed away March, 2019. Navabi joined U of G in 2008; since 2014, he held the Grain Farmers of Ontario (GFO) Professorship in Wheat Breeding. There he led and managed the very successful University of Guelph wheat breeding program, and was well known for his exceptional teaching and thoughtful guidance.

A genomics-derived assay for rapid determination of Eimeria spp. oocyst viability: Improving coccidiosis management in the poultry industry

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Overview

Coccidiosis, a disease caused by parasites of the genus Eimeria, is the major pathogenic disease in the poultry industry with associated costs of over $3 billion USD annually.  Live vaccination can control coccidiosis but its successful implementation can be difficult. Vaccination uses live, infective parasites to establish self-limiting and subclinical infection that stimulates development of robust protective immunity. Accurate dosage is paramount to vaccine success; administration of too many infective parasites will negatively impact bird health while administration of too few will fail to stimulate protective immunity. Vaccine potency is not static and is subject to many variables. Each vaccine lot must be tested in live animals so infectivity and correct dosage can be confirmed. Infection trials are time consuming, expensive, and only semi-quantitative, at best. We have demonstrated a prototype assay that provides rapid assessment of parasite viability (i.e. vaccine potency) based on measurement of actual parasite molecular activity. We have developed a protocol to measure biomolecules produced by vaccine parasite constituents upon exposure to specific stimuli, and shown that the abundance of these specific assay targets reflects actual parasite viability. Ongoing work aims to improve assay accuracy by identifying optimized biomolecule targets and to streamline the assay for ease of use. Additional work supporting assay development will further improve the accessibility and feasibility of vaccination by developing standardized molecular tools for rapid parasite species and strain identification (useful in identifying points of vaccine failure), and by extending the shelf-life of stored vaccines.  Our optimized viability assay will measure the precise viability of the constituents of live coccidiosis vaccines in several hours (as opposed to the 10+ days required for standard infection trials). This, combined with the above-mentioned molecular tools we are developing in support of the assay, will greatly improve the efficacy and accessibility of coccidiosis vaccines. This will maximize production efficiencies, profit for farmers, and sustainability of this globally important food-production industry, while minimizing its environmental impact. Improving the efficacy of coccidiosis vaccines will reduce the application of antimicrobial drugs in farming: an important step towards preventing the development of antimicrobial resistance, protecting biodiversity and responding to the demand of Ontario consumers for antibiotic-free agricultural products.

Metabolomic-based strain selection of microbial bioinoculants which alleviate impacts of drought stress in crop production

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Overview

The main goal of this project is to design a new biofertilizer formulation composed of carefully selected, beneficial bacteria that can significantly improve growth and yield of plants exposed to drought. A novel type of plant growth promoting bacterium (PGPB) that lives in symbiosis with plants and can produce uniquely high levels of plant growth regulators (hormones) that are known as cytokinins (CKs). The application of a PGPB as a bio-fertilizer for crop improvement presents an outstanding opportunity for sustainable and eco-friendly plant agriculture. The success of this newly developed biostimulant depends on the bacteria’s ability to deliver potent, biologically active hormones to plants cultivated under limited water availability. To select the most efficient bacteria we use cutting-edge technology (high resolution mass spectrometry) to identify a new range of plant growth promoting substances secreted by the PGPB. We also monitor plant growth responses to the treatment with the bio-fertilizer under optimal and drought conditions. An advanced screening tool developed in this project will be used to monitor storage integrity of the new bio-fertilizer composition and will help in the further selection for new microbial fertilizer formulations. The bio-fertilizer formula will be optimized for soybean cultivation; however, its universal growth promoting characteristics can be applied to other plant species, especially those frequently subjected to dry growing seasons. The implementation of the results of our work will take place in the two years after the project completion and will include up-scaling of the manufacturing process, legal registration of the formulation and marketing of the new product. Our plant growth enhancing bio-fertilizer will create an economic advantage for local soybean farmers and will benefit the Ontario market of plant nutrition solutions. This can lead to new jobs in manufacturing, distribution and marketing agri-sector, which will help improve Ontario’s new economy. Finally, since this effective bio-fertilizer is of natural origin, it will present excellent potential to reduce the use of agri-chemical products and aid in protection of Ontario’s environment.