Genomics
for Agriculture
& Agri-Food
Ontario’s Strategic Opportunity
Ontario’s Strategic Opportunity
Ontario’s agriculture and agri-food sector is critically important to all of us — as individuals and as a society. We rely heavily on the sector, not only to feed, nourish and employ us, but also for a wide variety of industrial bioproducts. We count on farming and processing technologies that contribute to Ontario’s and Canada’s economic development, protect the environment, mitigate and adapt to climate change, and promote human health and wellness as well as animal welfare.
Rapid advancements in genomics-based innovations and technologies provide significant opportunities to advance Ontario’s agriculture and agri-food sector.
Ontario’s agriculture and agri-food sector is strong and growing. However, the demands and challenges the sector is faced with are also growing.
In the context of enhancing a socially and environmentally responsible industry, genomics-based innovations and technologies provide significant opportunities to advance Ontario’s agriculture and agri-food sector. Genomics technologies coupled with precision agriculture methodologies and artificial intelligence will revolutionize the sector.
Ontario’s agriculture and agri-food sector is large and highly diverse. At $37.6B1, it accounts for approximately one third of the total GDP generated by the sector in Canada.
One in every eight jobs in Ontario currently comes from the agriculture and agri-food sector which includes input and service suppliers, primary agricultural producers, industrial bioproducts manufacturers, transporters and distributors, food and beverage processors, food retailers and wholesalers, and foodservice providers.
Ontario’s agriculture and agri-food sector is well-positioned for significant growth.
The promise of genomics technologies is to improve the efficiency, quality and yield of crop and livestock development. ‘Omics technologies also enable the analysis of unintended changes in new crop varieties and livestock breeds that result in new cultivars, regardless of the techniques used to develop them — whether through conventional crossbreeding or genetic engineering.
Communications to educate and engage the public about beneficial new technologies is essential to ensure both social acceptance and sector growth.
The rapid advancement of the Ontario agriculture and agri-food industry is largely due to uptake of new technologies, such as new cultivars, vaccines, improved agronomic practices, and advanced mechanization. There is considerable opportunity and need for genomics technologies to further advance the sector. However, the uptake of new technologies by developers and growers requires their confidence that the application will be socially accepted and result in a positive economic and/or environmental benefit.
It must be recognized that — despite the scientific rigour of development and the high quality safety and efficacy standards involved with regulatory reviews in Canada — the application of genomics innovations in the agriculture and agri-food sector can be a source for public concern. Communications to educate and engage the public about beneficial new technologies is essential to correct misperceptions and ensure both social acceptance and sector growth.
Agriculture and agri-food sector focused genomics R&D involves public, not-for-profit and for-profit private organizations working collaboratively provincially, across the country and around the world.
Ontario has established stellar agriculture and agri-food research and innovation capacity in academia, in government and in the private sector. Ontario benefits from:
Genomics-based technologies, coupled with precision agriculture methodologies and artificial intelligence, will revolutionize the agriculture and agri-food sector. These opportunities and advances are linked with and will have positive impacts for other priority sectors across Ontario and around the world.
Climate change along with year-to-year variability in weather patterns will have a major impact on agricultural production. A major focus of genomics R&D is on adaptation to and mitigation of the impacts of climate change.
Adaptation — It is expected that most regions of Canada will warm during the next several decades, which will result in increased greenhouse gas (GHG) level emissions. This can have both positive and negative impacts on agricultural production. For example:
Biodiversity is the basis of resilient agriculture. It includes all species of crops and domesticated livestock and the variety within them − as well as all of the ecosystem services, such as soil and water conservation, maintenance of soil fertility and biota, and pollination − all of which are essential to sustain agriculture and human well-being.
In addition to sustaining livelihoods, biodiversity is essential to:
Biodiversity genomics is a relatively new field that can be defined as the use of DNA, as part of a larger framework of integrated data, to answer questions about the diversity and processes that govern the patterns of life on the planet, and how they change. It enables us to discover new species, detect invasive species, and protect and minimize the loss of existing populations and species.
Applications of genomics approaches and technologies offer numerous beneficial impacts. However, in order to flourish, genomics innovations must be addressed in the context of ethical and policy questions because its applications can directly affect the environment, and both human and animal health and nutrition for worse or for better.
There is a need to educate and engage the public at large about advances in genomics, including the ethical, legal and social implications that they pose.
Policies need to be socially acceptable in order to be sustainable and effective. This means that policies should be informed by the views of a public that is accurately informed. Therefore, there is a need to educate and engage the public at large about the basics of genomics and the advances being made, including the ethical, legal and social implications that they pose. Policy making must incorporate an ongoing analysis of public perception of genomics to ensure that it constructively addresses areas of public concern and the apprehensions of society towards genomics-based applications.
With this in mind, Genome Canada and the Genome Centres have created significant expertise in Canada through the funding of integrated GE3LS studies—the Ethical, Environmental, Economic, Legal, and Social aspects of genomics. GE3LS studies investigate questions at the intersection of genomics and society. They provide stakeholders the insights needed to anticipate impacts of scientific advances in genomics, avoid pitfalls, and cultivate success.
We are entering the Fourth Industrial Revolution − where the speed of current breakthroughs is unprecedented and emerging technologies are being rapidly developed and converging across numerous fields, including biotechnology, robotics, artificial intelligence, nanotechnology, and quantum computing.
Rapid advances using existing knowledge, along with new discoveries that cannot be anticipated at this time, will undoubtedly take place. This revolution will fundamentally alter the way we live, work and relate to one another.
Ontario, with its abundant human and natural resources, its diversified economy, and its stable institutions and political systems, has the current capacity and potential to participate and lead with advances in ‘omics research and their application to the agriculture and agri-food sector.
Increased investment in agriculture and agri-food genomics R&D, coupled with an ongoing commitment to technology development, communications, application, and commercialization, can play an increasingly important part in wealth and job creation in Ontario. This effort can capitalize on Ontario’s diversity in agricultural products, on its innovation and manufacturing capacity, and on its varied, well-educated, and multi-talented workforce.
This report recommends six rich domains for genomics-based research and innovations that build upon identified strengths and opportunities to advance Ontario’s agriculture and agri-food sector.
Ontario’s agriculture and agri-food sector is critically important to all of us — as individuals and as a society. We rely heavily on the sector, not only to feed, nourish and employ us, but also for a wide variety of industrial bioproducts. We count on farming and processing technologies that contribute to Ontario’s and Canada’s economic development, protect the environment, mitigate and adapt to climate change, and promote human health and wellness as well as animal welfare.
Rapid advancements in genomics-based innovations and technologies provide significant opportunities to advance Ontario’s agriculture and agri-food sector.
Ontario’s agriculture and agri-food sector is strong and growing. However, the demands and challenges the sector is faced with are also growing.
In the context of enhancing a socially and environmentally responsible industry, genomics-based innovations and technologies provide significant opportunities to advance Ontario’s agriculture and agri-food sector. Genomics technologies coupled with precision agriculture methodologies and artificial intelligence will revolutionize the sector.
Genomics-based innovations and technologies can contribute to:
Based on a thorough review of the sector and extensive stakeholder consultations, this Sector Strategy Report presents a set of recommendations to ensure the continued sustainability and accelerated growth of Ontario’s agriculture and agri-food sector over the next decade.
Ontario’s agriculture and agri-food sector is large and highly diverse. At $37.6B1, it accounts for approximately one third of the total GDP generated by the sector in Canada.
One in every eight jobs in Ontario currently comes from the agriculture and agri-food sector which includes input and service suppliers, primary agricultural producers, industrial bioproducts manufacturers, transporters and distributors, food and beverage processors, food retailers and wholesalers, and foodservice providers.
Ontario’s primary agriculture is strongest in livestock, field crops and horticulture. Although most farms produce field crops, the dairy sector dominates farm receipts, followed by soybeans, horticultural crops, corn, pork and poultry. There is also a growing demand for Ontario’s agricultural feedstocks for bioproducts.
With 14 million residents, and 150 million more people within a day’s drive, Ontario’s agriculture and agri-food sector has tremendous opportunities to produce products that appeal to a wide range of tastes and lifestyles.
Fast facts — Ontario’s agriculture and agri-food sector:
1 All data based on 2016
Ontario’s agriculture and agri-food sector is well-positioned for significant growth.
Current trends represent both challenges and opportunities for the sector:
The impact of international trade agreements, fluctuations in farmland prices and currency exchange rates, and changes in weather patterns and consumer demands also represent both challenges and opportunities for the sector. However, Ontario’s agriculture and agri-food sector has traditionally been very resilient with a strong history of early adoption of technological advances dating back to the establishment of the Ontario Veterinary College in 1862 and the founding of the Ontario Agricultural College in 1874.
Advances in genomics and the application of these innovations will play a key role in the growth of Ontario’s agricultural and agri-food sector. New technologies such as artificial intelligence, big data analytics, ‘omics and gene editing technologies, will help reshape and accelerate productivity of the sector.
Genomics provides new approaches to achieve results that have been the ongoing goals of crop breeding since the 19th century, such as:
Field Crops — Genomics approaches are already well established in the development of Ontario’s major field crops such as soybean, corn and wheat. The public sector in Ontario has a strong history in field crop cultivar development. Since the 1980s, conventional plant breeding has been aided by marker-assisted selection, enabling prediction-based development of crop cultivars which are licensed to various domestic seed companies. In addition to strengthening our own capacity in Ontario and Canada, this provides opportunities to license Ontario’s innovations to large foreign-based companies. A recent example includes the Canadian-developed disease-resistant White Russet™ potatoes which are being commercialized in the USA.
Horticulture — Currently, most of the development of new horticulture cultivars is being done by a few multinational companies outside of Canada. However, thanks to institutions such as the Vineland Research and Innovation Centre and the University of Guelph, Ontario now has the capacity and is beginning to do more of this development and application itself. For example, in 2017 we saw: the introduction of the Cold Snap™ Pear; the Ontario-bred Guelph Millennium asparagus become a $30 million crop; and the Canadian Shield Rose — bred for our difficult climate and released to celebrate Canada’s 150th anniversary. Genomics technologies will continue to enhance and accelerate the ability of Ontario’s growers to successfully produce superior crops.
Pollinators — There is increasing need for, and interest in, the role genomics can play to understand and mitigate the negative impacts on pollinators, such as honeybees, leafcutter bees and bumblebees — which are essential for agriculture. In response to this need, genomics research and development in Canada has focused on improving colony health and resilience, and reducing the need to import queen bees, thereby guarding against the inadvertent introduction of Africanized bees. Other examples of how genomics innovations and technologies can enhance crop breeding and production can be found in the sector strategy report.
Genomics provides new tools and approaches to improve livestock breeding, with a focus on:
Disease Prevention & Resistance — Advances in genomics are aiding in identification and the development of livestock breeds with stronger immune systems. For example, recent successes include pig breeding with resistances to Porcine Reproductive and Respiratory Syndrome and to the African Swine Fever virus. Another example of the successful application of genomics is the development of the High Immune Response (HIR™)/ Immunity+ technology by Dr. Bonnie Mallard at the University of Guelph. This new technology can identify cattle with naturally optimized immune responses, enabling breeders to select cattle that will have about half the average disease occurrence and also have a better response to vaccinations for improved disease management.
Antimicrobial Resistance — There is increasing concern about the adverse impacts of antimicrobial agents in veterinary medicine and livestock production resulting in resistance to antibiotics in animals and humans. Application of genomics sciences and technologies is foundational to the discovery and development of effective alternatives to antibiotics that include careful consideration of the health, safety and wellbeing of livestock. Examples include improving animals such as pigs’ immune responses through microbiome manipulation to enable the reduction or elimination of antibiotic use at weaning, and assessing the impact of gut microflora on the nutrition, feed conversion and health of poultry in an antimicrobial-free environment.
Point-of-Care Diagnostic Tools — Genomics technologies for the diagnosis of the cause of infection in real time would enable a veterinarian to recommend timely care, such as prescribe a specific antimicrobial, recommend no treatment if the prognosis for recovery is good, or administer a biologic or alternative treatment that is targeted to the infection – all of which would benefit the overall agriculture and agri-food sector.
Other examples of how genomics innovations and technologies can enhance livestock breeding and production can be found in the sector strategy report.
Genomics is providing better tools for understanding microorganisms and microbiomes to help achieve agriculture and agri-food sector goals, such as:
Soil Microbiomes — Genomics technologies are aiding in the understanding of complex interactions between microbe-plant, microbe-microbe and the microfauna in soil microbiomes. Understanding soil microbiomes will enable improved agronomic performance of both individual crops and different crop species in rotation. For example, breeding a cereal cultivar and a legume cultivar in rotation can improve complementary benefits for the overall performance of the agroecosystem.
Diet Optimization — There is growing recognition that diet affects the composition and metabolic activity of the human gut microbiota impacting health. Genomics technologies have greatly advanced our understanding of this area and provides opportunities to develop products with improved macronutrients to optimize diets for both human and livestock populations.
Food & Beverage Processing — Microorganisms play an important role in fermented food and beverage products. Genomics technologies are being applied to increase understanding of the associated microorganisms in both plant-based products such as yeast leavened bread, pickles, brewing and winemaking, and animal-based products such as yogurt and cheese. This is providing opportunities to improve food and beverage processing systems with real-time quality control as well as health benefits to consumers with prebiotics and probiotics.
Other examples of how genomics innovations and technologies can advance the agriculture and agri-food sector can be found in the sector strategy report.
Genomics is providing opportunities to further develop and expand Ontario’s bioeconomy, particularly in the bioproducts and bioprocessing sectors, with new technologies aimed at:
Feedstock — Genomics is playing a key role in moving from petroleum based feedstock to renewable biomass feedstock. Ontario’s agriculture sector has already been producing feedstock, such as corn and soybean, for industrial purposes. Genomics has helped drive this by developing breeds of corn specifically for industrial use, notably by boosting yields to drive economical use.
Bioenergy — Genomics technologies can be used to optimize fermentation processes that produce bioenergy, including biofuels and renewable natural gas. This represents a significant opportunity for greater efficiency. For example, it is estimated that 37% of Ontario-produced corn is used for ethanol production and other industrial purposes, making bio-based feedstock a major source of revenue for Ontario growers.
Eco-Friendly Biochemicals — Recent advances in genomics have allowed for the engineering of microorganism metabolism to produce a wide variety of biochemicals that can directly replace their petroleum-based equivalents − reducing emissions. For example, BioAmber, an industrial biotechnology company located in Sarnia, is now successfully manufacturing succinic acid from sugar sources for use in polymers, resins and solvents, which materially decreases the carbon footprint.
Other examples of how genomics can advance the agriculture and agri-food sector and further develop Ontario’s bioeconomy can be found in the sector strategy report.
Agriculture and agri-food sector focused genomics R&D involves public, not-for-profit and for-profit private organizations working collaboratively provincially, across the country and around the world.
Ontario has established stellar agriculture and agri-food research and innovation capacity in academia, in government and in the private sector. Ontario benefits from:
Climate change along with year-to-year variability in weather patterns will have a major impact on agricultural production. A major focus of genomics R&D is on adaptation to and mitigation of the impacts of climate change.
Adaptation — It is expected that most regions of Canada will warm during the next several decades, which will result in increased greenhouse gas (GHG) level emissions. This can have both positive and negative impacts on agricultural production. For example:
Advances in genomics accelerate our understanding and the development of solutions for sustainable crop and livestock production that can adapt to the effects of climate change and the resulting impacts on our environment.
Mitigation — Canada’s Nationally Determined Contribution is to reduce economy-wide GHG emissions by 30% below 2005 levels by 2030. Therefore, R&D efforts in the agriculture and agri-food sector must focus on reducing greenhouse gas emissions and increasing carbon capture.
To that end, researchers at the University of Guelph and their collaborators at Benson Hill Biosystems have identified genes related to seed yield in different plants that can be incorporated into canola to significantly enhance its sustainability and productivity. This is achieved by increasing photosynthetic capacity and carbon capture without negatively impacting seed quality to produce game-changing varieties of canola for producers across Ontario and Canada.
More information about how genomics can help the Ontario’s agriculture and agri-food sector adapt to and mitigate the impacts of climate change can be found in the sector strategy report.
Biodiversity is the basis of resilient agriculture. It includes all species of crops and domesticated livestock and the variety within them − as well as all of the ecosystem services, such as soil and water conservation, maintenance of soil fertility and biota, and pollination − all of which are essential to sustain agriculture and human well-being.
In addition to sustaining livelihoods, biodiversity is essential to:
Biodiversity genomics is a relatively new field that can be defined as the use of DNA, as part of a larger framework of integrated data, to answer questions about the diversity and processes that govern the patterns of life on the planet, and how they change. It enables us to discover new species, detect invasive species, and protect and minimize the loss of existing populations and species.
Ontario is a world leader in biodiversity genomics due to the work carried out at the University of Guelph’s Centre for Biodiversity Genomics (CBG) where the global DNA barcoding initiative began.
DNA barcodes use a small fragment of an organism’s DNA to identify the species to which the organism belongs. They are powerful tools, which can be used to help catalogue biodiversity and advance understanding of the distribution and interactions among species. This technology is applied to develop solutions ranging from breeding better plants, protecting and improving human and animal health, and detecting marketplace food fraud, to enabling more effective control of invasive pests.
A key component of social acceptance of genomics-based innovations relates to public confidence and trust in its regulatory institutions. Both Ontario and Canada have responsibilities for legislation and regulations pertaining to the agriculture and agri-food sector, and the two levels of government work together to meet the needs of the sector.
The Canadian Food Inspection Agency (CFIA) regulates agricultural products including plants, feeds, veterinary biologics and fertilizer supplements. Health Canada regulates foods, veterinary drugs and pest control products.
The Canadian model for regulation of agricultural products combines the use of existing legislation together with an evaluation focused on the characteristics of new agricultural products, rather than the means through which the product was developed. This model is consistent with an evidence-based approach and considered to be fairer and more efficient than other approaches. There appears to be a trend towards wider adoption of the Canadian model by regulators in other countries.
Genomics science aims to develop and apply new knowledge and expertise, and faster, more accurate, and cost-effective diagnostic technologies, tools and methods for detection, isolation, identification and characterization of new and emerging pathogens, pests, and invasive species relevant to agriculture and agri-food. The application of genomics technologies is already making a difference at the CFIA by providing knowledge to support more efficient and effective decision-making practices.
Historically, proprietary rights for agricultural innovations were considered non-existent since germplasm (the living tissue from which plants can be grown) was presumed to be a communal resource to be shared freely. It wasn’t until the 1960s with the implementation of the International Convention for the Protection of New Varieties of Plants that proprietary protection became available.
Issues related to intellectual property for agricultural innovations are complex. For example, there are situations where protective mechanisms meant to foster agricultural innovation conflict with germplasm sharing practices – and these differ from jurisdiction to jurisdiction. This makes it exceptionally challenging to navigate and work within the various domestic and international regimes to advance genomics innovations in agriculture.
The Canadian Intellectual Property Office is responsible for the administration and processing of the greater part of intellectual property in Canada. Its mandate is to deliver IP services, and to increase awareness, knowledge and effective use of intellectual property by Canadians.
Ontario Genomics, Genome Canada, and the other Genome Centres across Canada can play a key role in supporting research focused on resolving issues related to how regulatory and IP systems affect incentives for the development of products derived from agricultural genomics R&D.
In order to ensure social acceptance and the implementation of sustainable policies, advances in genomics need to be accompanied by proactive communications that effectively educate and engage the public at large. Communications must constructively address areas of public concern associated with these scientific advancements with a high level of openness and transparency about both the benefits and any balanced risks posed by their application.
In an era where so much policy relates to technological advances and the increased need and support for genomics-based applications, success in communications is essential to ensure a more informed public.
Communications will need to understand and address the varying interests and concerns of a variety of stakeholders − all with varying degrees of knowledge of genomics and agriculture – including everyday consumers, growers, suppliers, shippers, wholesalers, retailers, manufacturers, researchers, private investors, government and funding agencies. Communicators must be broadly accepted as being both knowledgeable and impartial.
People prefer to be informed through media that they use routinely and are comfortable with. Today, this includes traditional media such as radio and television broadcasts, books, newspapers and magazines, as well as a wide array of online and social media platforms. Consequently, connecting and engaging with target audiences is an increasingly difficult challenge – particularly where scientific and technological advances can be difficult to explain to a lay person. However, in an era where so much policy relates to technological advances and the increased need and support for genomics-based applications to ensure advancement of Ontario’s agriculture and agri-food sector, success in communications is essential to ensure a more informed and engaged public.
The success of genomics in agriculture and agri-food hinges on our ability to collect, store and analyze large amounts of data. With a highly creative, burgeoning AI sector, this is a significant opportunity for Ontario.
Big data refers to data sets with such large volume or complexity that they are difficult to process using traditional data processing applications. Big data infrastructure is a framework which is used for storing, processing, and analyzing big data. Big data analytics covers collection, manipulation, and analyses of massive, diverse data sets that contain a variety of data types including genomic data along with phenotypic and environmental data to reveal hidden patterns, cryptic correlations, and other intuitions on a big data infrastructure.
Big Data Management is a both a tremendous opportunity and a challenge for the future of Ontario’s agriculture and agri-food sector. It will be particularly important in advancing the emerging field of environmental DNA (eDNA) — genetic material obtained directly from environmental samples without any obvious signs of biological source material. It will also play an important role in the emerging fields of integrating genomics with precision agriculture — to develop crops with combinations of genes that lead to the best performance in specific environments — and phenomics — the measurement of change in response to genetic mutation and environmental influences — as well as many other areas. The availability of adequate human and machine capacity to carry out this work in a timely and efficient way needs to be addressed along with approaches to avoid duplication.
Data Sharing and the concept of open access to scientific data has both domestic and international development dimensions. Currently, genomics datasets are being published under an array of different access regimes, with inadequate agreement on appropriate protocols and standards to effectively govern access to the massive amount of data being generated. There is a need to ensure that stored data can actually be used to improve crops and livestock and also to ensure optimal benefits to developing nations while simultaneously securing much-needed revenue from newly developed technologies. This is an area that needs to be addressed through both national and international forums.
There are many areas of genetic and metabolic similarity among the species that comprise the renewable resources sectors. As a result, research on tree or fish genomics could contribute to advances in crop and livestock research and vice versa. Similarly, advances in understanding livestock microbiomes could contribute to a better understanding of human microbiomes.
Similarities and links among species provide a rich domain for multidisciplinary genomics research with potential opportunities for all of the renewable resource sectors.
The primary purpose of agriculture is to provide food for nutrition and wellness. Much of crop and livestock research has focused on output traits, such as flavour, texture and nutritional qualities − and input traits such as yield, performance and disease resistance. This is also true for aquaculture. Ontario has nutrition and dietetics programs at several universities in the province and, along with this, opportunities for multidisciplinary R&D using genomics-based approaches aimed at producing foods and diets with enhanced nutritional and health benefits, such as functional foods, nutraceuticals, and probiotics.
Additionally, genomics-based approaches can contribute to the management and reduction of antimicrobial resistance, which has important implications for both human and animal health. These similarities and links provide a rich domain for multidisciplinary genomics research and development with potential opportunities for all of the renewable resource sectors.
Technologies such as remote sensing, satellites, robotics and UAV (unmanned aerial vehicles), have driven farming into a digital age, where farmers are becoming inundated with large amounts of data about the environment and information about how crops are developing. In this era of digital agriculture, phenomics, has emerged as a new field of science concerned with the measurement of physical and biochemical traits belonging to a given organism as they change in response to genetic mutation and environmental influences.
Genomics tools coupled with big data and AI will enable rollout of new varieties of crops more quickly to feed our growing population in an ever-changing world.
Since no two agricultural environments are exactly alike, determining how to rollout successful new varieties of crops that will be subject to extreme weather conditions, climate change or changing soil conditions as well as weed, disease and insect pressures is a big challenge for plant breeders and farmers. Understanding how to manage an agricultural environment means taking hundreds, if not thousands of factors into account.
Big data and artificial intelligence are poised to help plant and livestock breeders develop programs and protocols to begin to inform farmers which breeds will be more successful in different types of environments. Breeders using genomic tools and AI will be able to test, validate in the field, and rollout new varieties of crops more quickly to enable farmers to feed our growing population in an ever-changing world.
The earth’s population is expected to increase from the current population of 7.6 billion to 8.6 billion in 2030, and 9.8 billion in 2050. To accommodate the increased demand for food, world agricultural production needs to rise by 50% by 2030. In 2015, United Nations members adopted the 2030 Agenda for Sustainable Development, which has 17 Sustainable Development Goals. The Government of Canada is committed to supporting the implementation of these goals. The goals most aligned with the agriculture and agri-food sector are:
In general terms, increased food production must largely take place on the same land area while using less water and coping with climate change impacts. Advances in crop genomics will be one of the best approaches available to increasing output per unit area and reducing input requirements while also dealing with adverse environmental conditions resulting from changes in global weather patterns and climate.
As Canada’s most populous province with a well-established agriculture and agri-food sector and the largest share of the national GDP, Ontario can play a key role in this international development initiative. Ontario is well positioned to provide food exports, food aid, and technology transfer, and to contribute by educating and training highly qualified personnel, including personnel with genomics expertise, as well as other forms of international development assistance.
Synthesis Agri-Food Network conducted a study in the fall of 2017, under the direction of Ontario Genomics, with the objective of identifying key areas of opportunity for Ontario’s agriculture and agri-food sector, as well as barriers to advance the sector, through the application of new technologies.
This study was comprised of interviews with both regional and global experts and group discussions with Ontario stakeholders – including participants from industry, academia, associations, not-for-profits and the provincial and federal governments.
Based on this study, nine key areas of opportunity and nine key barriers for Ontario’s agriculture and agri-food sector were identified as follows:
Many of these opportunities and barriers are interrelated and must be considered in conjunction with one another to optimize potential impacts for Ontario’s agriculture and agri-food sector.
For more information about the results and recommendations of this study, please refer to the sector strategy report.
This includes a focus on:
In terms of evaluating and making investments in programs, projects and other initiatives, this approach considers the impacts relative to the social, environmental, and economic benefits that can be reasonably expected for Ontario − both in the short-term and the long-term, and in the context of Ontario’s domestic and international roles
For more information about the results and recommendations of this study, please refer to the sector strategy report.
Augment multidisciplinary R&D using a systems biology approach with a focus on increased understanding of microbiomes and their interconnectivity to human health.
The human microbiome impacts health and disease and it is likely that much of this impact is mediated through diet. Growing evidence suggests that gut microbes influence what humans can extract from their diets, both nutritionally and energetically. Linking agriculture and agri-food genomics initiatives concerned with the chemical, microbiological and organoleptic (sensory attributes relating taste, colour, odour, and texture) attributes of food with research on diets and human nutrigenomics can have a profound impact for both agriculture and nutritional medicine.
This requires multidisciplinary research to integrate knowledge from diverse and highly complex biological systems − from the molecular, cellular, organismal and ecosystem levels − together with data into models of the system as a whole. It involves science and engineering that links computational analysis techniques with systematic biological experimentation.
Multidisciplinary research initiatives using a systems biology approach to increase understanding of all of the various microbiomes and their interconnectivity to human health provide strong potential to devise improved dietary recommendations at the population level, and eventually to develop diets tailored to individuals. This will result in enhanced disease prevention, increased longevity, and improved quality of life.
For more information, please refer to the sector strategy report.
Prioritize programs for sustainable agriculture and food that consider the economy, the environment, and society, for crop production and livestock performance.
Scientifically-based genetics research has for more than a century resulted in major advances in developing crop cultivars and livestock breeds with enhanced performance, resilience, disease resistance, and marketability—both for domestic and export markets.
Support should be given to genomics-based research and innovation programs with the greatest potential to meet Ontario’s priorities – such as increased efficiency of crop production and livestock performance − in the context of a sustainable agriculture and food system that takes into consideration the economy, the environment, and society.
For more information, please refer to the sector strategy report.
Develop rapid diagnostic methods to support regulation and trade, rapid disease detection and traceability in crops and livestock, and biologics to reduce the use of antimicrobials.
Genomics-based innovations can provide solutions for the challenges of greatest importance for Ontario. This includes rapid diagnostic methods to support regulation and trade, rapid disease detection in plants and livestock, and traceability, and biologics to reduce the use of antimicrobials for crops and livestock.
Improved Diagnostics
Genomics research and innovations can make importance advances within the next three to five years that will contribute to producing more accurate, rapid, and cost-efficient diagnostic tests for important crop and livestock diseases. This will assist with disease prevention and quarantine, assist traceability, and provide molecular tools to verify the nature and quality of domestic and exported products. Ontario can focus on supporting the precision and robustness of testing, decision-making, and regulatory approaches to advance Ontario’s agriculture and agri-food sector commodities and products.
Biologics
With increasing pressure on agriculture to reduce the use of antimicrobials, viable alternatives are needed. Agricultural and veterinary biologics provide new avenues in this regard. While achievements in this area will likely take place over a longer timeframe (five to fifteen years), it is an important field for investment. Current alternatives do not have the same efficacy as traditional antimicrobials and have a fairly long development time. Genomics research will enable the development of new and more effective tools such as vaccines, antibody products, in vitro diagnostic test kits, and novel gene therapies. These tools will help to increase knowledge of animal biology, microbiomes, and the immune system - which will lead to increased disease resilience in livestock, better disease management, more effective vaccines, and less use of antibiotics. Ontario can support targeted treatments that focus on biologics development relevant to key challenges impacting Ontario’s production systems and can be made available in a cost-effective manner to the industry.
For more information, please refer to the sector strategy report.
Enhance advanced manufacturing and processing systems for food and industrial bioproducts, including fermentation and traceability.
Genomics can play a key role in breeding crops and livestock with traits that make them more attractive for both food processing and the processing of non-food products, such as industrial bioproducts. Genomics-based approaches can also contribute to safety, optimization, fermentation, and quality control and assurance for processing systems for both food and industrial bioproducts.
Food processing
Crop diversification is expected to expand in Ontario both in terms of field crops and crops grown in protected environments to take advantage of market opportunities for new food products. Genomics advances can help to adapt and select new species and cultivars to local conditions, enable the incorporation of traits making them better suited to novel processing systems, and provide tools for traceability to help ensure that crop segregation is maintained when similar crops are developed for different uses. Genomics will also allow better understanding and optimization of the many plant and animal fermented food and beverage products. Diversification of animal products can also be expected to appeal to specialty markets for a diverse society. This diversification of crop and livestock products will help to further strengthen Ontario’s food and beverage manufacturing industry, replace imports and increase exports.
Industrial bioproducts
Building on its current bioindustrial infrastructure, Ontario has opportunities to use genomics technologies to develop crops with attributes tailored for use in Ontario-based processing and manufacturing facilities producing bioenergy, biomaterials, and biochemicals. In some cases, it will be necessary to segregate and trace crops intended for bioindustrial, biopharmaceutical and other non-food uses. Genomics can also help to develop tools to enable robust systems for segregation and traceability.
For more information, please refer to the sector strategy report.
Address barriers to the adoption of genomics innovations including issues related to data sharing, intellectual property, regulation and public acceptance.
There are several barriers to the adoption of genomics innovations that must be addressed in order to advance Ontario’s agriculture and agri-food sector. The most significant barriers include issues related to data sharing, intellectual property, regulation and public acceptance.
Public Acceptance
Genomics innovations, such as CRISPR, provide tremendous opportunities to advance the agriculture and agri-food sector. However, the application of genomics innovations will only succeed if they are deemed to be socially acceptable by the public at large. Genomics-based innovations require proactive communications, education and engagement to ensure their social license by an accurately informed public. This is especially important for developments related to food and health. For example, despite the tremendous benefits, sound science and assured safety of genetically modified foods, there is a significant anti-GMO movement. Innovations must have public acceptance to be commercially viable. In an era where so much policy relates to technological advances and the increased need and support for genomics-based applications to ensure advancement of Ontario’s agriculture and agri-food sector, success in communications is critical to ensure a more informed public.
Data Sharing, Intellectual Property, and Regulation
Issues related to data sharing, intellectual property and regulation are complex barriers to the application of genomics-based innovations. Given their interconnectivity, they must be addressed with a view to the impacts of one area on the other. Additionally, consideration must be given to the varying regimes from one jurisdiction to another to ensure the development of commercially viable commodities and products for export markets.
Ontario has access to resources and expertise that can enable it to play an important role both independently as well as in collaboration with the federal government and other provinces and territories, to advance both regional and national interests. Ontario must support work in collaboration with relevant Ministries, agencies, and institutions in order to facilitate a coordinated solutions-oriented approach to advance development of the agriculture and agri-food sector.
For more information, please refer to the sector strategy report.
Leverage Ontario’s strengths in computational biology and artificial intelligence to accelerate the development and application of agricultural genomics-based innovations.
A major challenge facing agricultural research is that the availability of genomics data for different commodities and products varies greatly. The ability and costs to link this data to other attributes required to improve prediction outcomes and increase sector efficiencies also vary widely. For major sectors like the dairy, poultry, hog, corn, wheat and soybean industries, there is a wealth of genomics data, compared with other crop and livestock species supported by smaller industries. Lowering the costs of acquiring and manipulating genomics data will help to level the playing field and should be a continuing priority to advance the sector.
Another priority for agricultural development is phenomics research, which is concerned with measuring trait changes in response to genetic mutations and environmental influences. The requirements for this research to be conducted − technologies for high-throughput phenotyping, conceptual, analytical and bioinformatics approaches that enable the use of high-dimensional data, and dynamic models that link phenomics across all levels – are advancing rapidly and becoming increasingly available. It is an opportune time to harness phenomics research to advance Ontario’s agriculture and agri-food sector.
Ontario’s public and private sectors now have strengths in computational biology and artificial intelligence that could be leveraged to advance agricultural research and development. For example, companies like the Vector Institute for Artificial Intelligence provide examples of how machine learning, as a powerful form of artificial intelligence, can find patterns in massive datasets and infer computer models of how cells read the genome and generate biomolecules. Big data analysis is becoming increasingly practical, with the potential to provide remarkable insights into the nature of complex systems to advance agricultural innovations.
For more information, please refer to the sector strategy report.