The Ontario Regional Priorities Partnership Program (ON-RP3) is supporting Ontario-focused, industry-academic partnership projects that will positively impact Ontario’s agriculture and agri-food sector.
The funding is supporting proof-of-concept stage projects that will deliver genomics/genomics-derived technologies, tools and processes to provide solutions to industry-identified challenges or opportunities within the sector. ON-RP3 will help industry take applied research to the implementation and commercialization stages. These solutions will be implemented by 2024
Funded Ontario RP3 Projects
On December 5, 2019 Bettina Hamelin, President and CEO of Ontario Genomics, announced the eight successful ON-RP3 project teams. In total, eight projects are being funded across Ontario through a $2M investment by the Agricultural Adaptation Council and Ontario Genomics (through Genome Canada). This investment is leveraging $975,000 in industry contributions, for a total of over $2.95 M to drive genomics-derived technologies, tools and processes to create more jobs and grow the Ontario economy.
- Precision fertility and resiliency phenotyping in dairy cattle
- Using new emerging genomic tools to improve soybean yield and seed compositions in Ontario
- Genomics tools to reduce sow stress and improve piglet survival and overall performance
- Metabolomic-based strain selection of microbial bioinoculants which alleviate impacts of drought stress in crop production
- A genomics-derived assay for rapid determination of Eimeria spp. oocyst viability: Improving coccidiosis management in the poultry industry
- Application of genomic-based technologies to improve the rate of genetic gain in Ontario winter wheat breeding
- Development of an omics-driven beer yeast performance database to support the Ontario craft brewing industry
- Introducing cold tolerance in hazelnut
ON-RP3 Project Descriptions:
Academic Lead: Christine Baes, Associate Professor, University of Guelph
Industry Lead: Michael Lohuis, VP, Research and Innovation, Semex Alliance
As the world’s 5th largest exporter of agricultural products, Canadian farmers are poised to play a decisive role in meeting the 70% increase in world food demand expected by 2050. In 2017, $14.3 billion worth of manufactured shipments of milk and dairy products were made, with approximately 33% of those coming from Ontario farms (https://www.milk.org/corporate/pdf/media-ontariomilkindustry.pdf, site accessed December, 2018). Canadian dairy genetics exports are also a growing source of revenue, rising 45% during the last decade to a total value of $155.2M in 2017; in particular, semen sales rose by 80% ($127M in 2017) (http://www.dairyinfo.gc.ca, site accessed December, 2018). The Semex Alliance, which is owned by three well-established Canadian genetics organizations, delivers innovative genetic solutions both within Canada and globally. With its headquarters in Guelph Ontario, Semex is well aware of the importance of addressing the anticipated environmental changes associated with climate change.
Dairy cow performance (such as growth, milk production, and reproduction), as well as animal welfare and health, can be strongly influenced by air temperature, humidity, and other climatic factors. Genetic selection plays a key role in breeding livestock that can better cope with changing climate, and more specifically, tolerate extreme temperatures and humidity and changes thereof. This project will provide novel and innovative methods for genomically selecting robust dairy animals which are resilient to environmental stressors, such as extreme hot/cold temperatures, while maintaining health, production, and reproductive efficiency. This proof-of-concept project integrates phenotypic data collected using automated sensor technologies with high-throughput genotypes of dairy cows through application of machine-learning algorithms to identify the underlying associations therein. In this way, a sustainable and economically profitable genomics-derived process for identifying healthy, fertile, resilient animals for use in genomic selection programs will be demonstrated and ready for large-scale realization, thus strengthening Ontario’s leadership in this field.
Academic Lead: Milad Eskandari, Assistant Professor, University of Guelph
Industry Lead: Jeff Reid, General Manager, SeCan
Soybean (Glycine max) is an important source of high-quality dietary protein throughout the world and a major crop grown in Ontario with just over 3.0 million acres planted in 2018 and farm revenue exceeding $1.6 billion. The food-grade soybean industry in Ontario is globally recognized for its high quality seeds. In an increasingly competitive market, the key factor for continuing the success and further expansion of food-grade soybean production in Ontario is to increase seed yield in new food-grade cultivars while improving or maintaining important seed composition traits such as protein concentration.
Despite the success in developing high-yielding soybean cultivars using conventional breeding methods in last two decades, the average protein concentration, in general, has been declining in commercial cultivars over the time due mainly to the negative phenotypic relationship between seed yield and protein content. Current genomics-based innovations and technologies, fortunately, provide opportunities to shift this negative correlation resulting in further improvement in profitability of food-grade soybean industry in Ontario.
This collaboration between the soybean breeding program at the University of Guelph, Ridgetown Campus, and SeCan will accelerate the development of high-yielding soybean cultivars with value-added traits and improve the genetic gain for these target traits. This will be accomplished through the development and implementation of genetic and genomics-assisted tools and an unprecedented eight-parent MAGIC (Mutli-parent Advanced Generation Inter-Cross) soybean population. The specific deliverables to be achieved within 2 years of the completion of the project are:
- Ontario-adapted food-grade soybean cultivars and germplasm with increased yield and improved seed quality
- Genetic and genomics-assisted breeding tools for accelerating the development of new cultivars
The aim of this project and the team is to translate these deliverables into commercial food-grade soybean cultivars by the year of 2024.
Academic Lead: Ray Lu, Associate Professor, University of Guelph
Industry Lead: Dave Vanderbroek, CEO, Alliance Genetics Canada
The pork industry is a vital sector of Canadian economy, which exported $4.6 billion in 2017 (Canadian Pork Council, 2018), with Ontario being the biggest pork production province in Canada. There are 1,192 farmers who market 5.41 million hogs in the province (Ontario Pork, 2018). From the 300,000 breeding sows, 15% of born piglets will not survive till weaning, 50% of which (or 650,000 piglets) die from crushing or savage by the sows, resulting in ~$12.9 million loss to the Ontario pork industry each year. Animal stress and the related sow behaviours are believed to play a significant role in piglet survival and overall growth performance. A reduction of 10% of piglet loss due to the stress-related crushing or attack from the sow (“savaging”) would bring about $1.3 million savings to Ontario pork industry annually; it would also represent an improvement in animal welfare which has become increasingly important for the growth and sustainability of the pork industry.
Decades of production trait-driven genetic breeding may have been at the expense of other traits such as animal behaviours. In this proposal, we will validate our discovery of stress genes in pigs and identify beneficial genetic variations/DNA markers with the goal of lowering sow stress through breeding. With the help of our industry lead, Alliance Genetics Canada (one of the biggest breeding companies in Ontario), and our collaborator, Canadian Centre for Swine Improvement (which has broad connections with breeders and producers), we will make the lower stress DNA markers and/or breeding stocks available to other pig farmers in Ontario.
Metabolomic-based strain selection of microbial bioinoculants which alleviate impacts of drought stress in crop production
Academic Lead: Neil Emery, Professor, VP research & Innovation, Trent University
Industry Lead: Kelly Tanaka, CSO, NutriAg Ltd
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.
A genomics-derived assay for rapid determination of Eimeria spp. oocyst viability: Improving coccidiosis management in the poultry industry
Academic Lead: John R. Barta, Professor, University of Guelph
Industry Lead: Jennifer Brisbin, R&D Project Lead, Ceva Animal Health Inc.
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.
Application of genomic-based technologies to improve the rate of genetic gain in Ontario winter wheat breeding
Academic Lead: Elizabeth Lee*, Professor, University of Guelph
Industry Lead: Josh Cowan, Manager, Research & Innovation, Grain Farmers of Ontario
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.
Development of an omics-driven beer yeast performance database to support the Ontario craft brewing industry
Academic Lead: George van der Merwe, Associate Professor, University of Guelph
Industry Lead: Richard Preiss, Co-founder/Co-Owner, Escarpment Laboratories
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.
Academic Lead: Praveen Saxena, Professor, University of Guelph
Industry Lead: Barb Yates, Agronomist, Ferrero Canada
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.