For Official Use DSTI/STP/BNCT(2015)4

Organisation de Coopération et de Développement Économiques Organisation for Economic Co-operation and Development 12-May-2015 ______English - Or. English DIRECTORATE FOR , TECHNOLOGY AND INNOVATION COMMITTEE FOR SCIENTIFIC AND TECHNOLOGICAL POLICY For Official Use DSTI/STP/BNCT(2015)4

Working Party on , Nanotechnology and Converging Technologies

OMICS-TECHNOLOGIES FOR SUSTAINABLE PRODUCTION OF BETTER FOOD FOR BETTER NUTRITION

Results of a survey

18-19 May 2015

OECD Headquarters, Paris, France

The project started under Programme of Work and Budget (PWB) 2013-2014, Output Result 3.2 on Science, technology and innovation (STI) and green growth: Industrial and environmental biotechnology for sustainable growth. A survey was conducted as one input to that output result. This paper discusses the findings of that survey and will inform PWB 2015-2016. Delegates to the Working Party on Biotechnology, Nanotechnology and Converging technologies are invited to: - Discuss this draft survey report on the “Omics technologies for sustainable production of better food for better nutrition”; and - Provide comments in writing by 15 June 2015.

For further information, please contact: Kathleen D'Hondt; Email: [email protected]

English English JT03376073

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DSTI/STP/BNCT(2015)4

TABLE OF CONTENTS

OMICS-TECHNOLOGIES FOR SUSTAINABLE PRODUCTION OF BETTER FOOD ...... FOR BETTER NUTRITION ...... 3 The role of ‘’-technologies in food and nutrition ...... 3 Survey results ...... 6 Technological trends and industrial applications of omics technologies for better food and nutrition .... 6 Policies and programmes devoted to mics technologies for better food and nutrition ...... 9 Enabling framework for sustainable production through omics technologies ...... for better food and nutrition ...... 14 Conclusions ...... 15 ANNEX 1 ...... 16

Boxes

Box 1. GRDI's priorities of Agriculture and Agri-Food Canada ...... 11 Box 2. Canada Programming ...... 13

Tables

Table 1 Enabling framework for sustainable production through omics technologies for ...... better food and nutrition ...... 15

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OMICS-TECHNOLOGIES FOR SUSTAINABLE PRODUCTION OF BETTER FOOD FOR BETTER NUTRITION

The role of ‘omics’-technologies in food and nutrition

1. Population growth, climate change, resource depletion, human health and nutrition, and sustainability are all issues with which the world is grappling, issues that are placing a growing strain on available resources. Producing more high quality and safe food on less land with less environmental impact will be one of the greatest challenges of the twenty-first century. Advances enabled by ‘omics’- technologies1 are supporting production through agriculture, animal husbandry and aquaculture in being better positioned to master these challenges.

2. Omics-technologies are powerful tools, particularly in combination with advanced molecular and breeding techniques. By increasing consistency and predictability, in particular, has the potential to make conventional breeding and advanced breeding techniques more efficient and precisely targeted. Indeed, genomics and other omics-technologies such as and provide information that is fundamental to understanding genes and their function. Opportunities offered by the application of omics-technologies for food production include:

 Understanding defence mechanisms and disease pathways in crops, livestock, poultry and marine organisms to make them better able to deal with the presence of current and emerging pests and diseases;

 Improving the detection of invasive pathogens, insects, weeds and toxins through the development and use of molecular tools;

 Preventing disease, improving the efficiency of feed utilisation and reducing wastes (including manure and greenhouse gases) through the better understanding of, for example, the interaction between the gastrointestinal and livestock host;

 Optimising yield (without compromising nutritional attributes) through measures to increase the resistance to disease, insect pests, drought, flooding and temperature extremes and other challenges posed by climate change;

 Extending the shelf and eating quality of foods, thereby potentially reducing food waste;

 Optimising crop values and traits in livestock, poultry or marine organisms (fish, shellfish, algae…) by using the technology to identify the origins of certain traits and breeding for those

1 Omics-technologies regroup the technologies supporting the study of groups of biological molecules, in particular the genome, but also the , the , the and the and interactions between molecules such as interactomics, epigenomics and may include also microbiomics in which the whole (symbiotic) microbial environment is studied. ‘Omics’ also refers to the integrative collective technologies used in a systems approach to explore the roles, relationships, and actions of these various types of molecules often in high throughput applications.

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specific traits and attributes that have high value food, nutrition, health applications or lead to new biobased products;

 Accelerating the growth of yield potential and optimal nutritional composition (especially micronutrient and content where applicable) in food produced;

 Promoting an ecosystem approach by studying the soil ecosystem to better understand interactions between plants and soil microflora that can be used in order to sustainably intensify crop production;

 Supporting human health by enabling the production of food with enhanced food safety, nutrition and functional attributes, and addressing specific health concerns through increased availability of high quality food products; and

 Breeding for traits that will lessen the production footprint on the environment, such as through adaptation for minimum tillage production to reduce greenhouse gas emissions or herbicide tolerance to reduce the use of crop protection materials, or by reducing livestock or aquaculture greenhouse gas emissions.

3. Omics-technologies may in the future also be combined with emerging approaches like synthetic to use available genetic building blocks to create "bespoke" or "built for purpose" non-food crops including marine organisms, like algae, for applications such as biofuels and biobased products.

4. In addition, developments in lead to deeper insights of how genomic and other omics information can be used in an integrated manner to address ambitious goals of higher and more sustainable production.

5. Overall, omics-technologies for food production can bring opportunities for investments with potential benefits for human health and nutrition, deliver better solutions for environmental needs and climate change. Globally there is a capacity engaged in using those techniques in the agri-food and other food production sectors to help address major social, economic and environmental challenges in the context of the development of a sustainable bioeconomy.

6. The project that started in 2014 focusses on the applications of omics-technologies for food production. The project builds on the Bioeconomy 2030 report2 where it relates to the application of biotechnology to agriculture and food production. In the context of discussions around the global capacity for omics-research and development (R&D) for food production and how these are governed and regulated, countries are seeking to share their knowledge and experience with other OECD-member countries and with non-member countries. It is an opportunity to reflect on what to anticipate about what the future holds for likely applications of omics for food production3 and the role they can play in the sustainable intensification of global agriculture, aquaculture and livestock husbandry.

2 OECD (2009), Bioeconomy 2030 – Designing a Policy Agenda, OECD, Paris. 3 Delegates will note that the OECD’s Working Group on Harmonisation of Regulatory Oversight in Biotechnology of the Environment Directorate deals with the environmental risk/safety assessment of transgenic plants and other genetically engineered organisms including GMOs.

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7. The project focuses on food produced through agriculture, livestock breeding and husbandry and aquaculture. It will also consider food research and development, food processing through biotechnology and its impact on food quality, nutritional value, human nutrition and health and well-being as well as contributions to the development of novel foods and new biobased products.

8. The project has four main objectives:

 To review the current technological trends and industrial applications of omics-technologies in food production;

 To explore and report on the current status of omics-R&D for food production and identify enabling programmes and policies, public engagement and communication activities, in OECD and, where possible, other countries;To discuss scenarios for the future of omics for food production; and

 To address, as appropriate and in light of the work in this area by other groups within the OECD and elsewhere, the implications of omics-technologies on and for food security and safety. This includes consideration of possible harms and benefits of new breeding and selection technologies for food and feed production and possible effects on the nutritional value.

9. Last year, as a first step, the Organisation for Economic Co-operation and Development (OECD), together with the Human Genome Organisation (HUGO), organised a workshop on “Genomics for Better Food and Nutrition” in Geneva on 29 April 2014. The event was a three hour session and took place in the context of the Human Genome Meeting 2014 (http://www.hgm2014-geneva.org/). The objective of the workshop was to review some of the latest advances in omics-technologies in relation to food, in both OECD and emerging economies, and to look at the related policy implications. A workshop report (DSTI/STP/BIO(2014)12) was finalised last year and presented to the Working Party on Biotechnology in December 2014.

10. Discussions at the workshop also led to the design of the survey as a next step in the development of the project. The survey was sent to the WPB member delegations in 2014. Responses were collected until the end of the year. The survey tried to collect information on:

 Technological trends and industrial applications of omics-technologies for food production;

 Policies and programmes devoted to omics for food production (including research funding programmes and outreach activities, for example);

 Enabling frameworks for sustainable production through omics-technologies for better food and nutrition, such as those covering human resources, infrastructure, intellectual property, international collaboration, investment / financing and public engagement / communication.

11. This report summarises the results of the survey. The survey is added in Annex 1 of this report.

12. Annex 2 gives an overview of the definitions of the different omics-technologies mentioned.

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Survey results

13. Eight countries (Belgium, Canada, Czech Republic, Italy, Korea, Luxemburg, Portugal, Spain) and BIAC responded to the questionnaire.

Technological trends and industrial applications of omics technologies for better food and nutrition

14. The first part of the survey addressed the technological and industrial applications of omics technologies for better food and nutrition. In summary, there was almost unanimous agreement that omics technologies in general are important and used for primary production purposes in agriculture, for livestock breeding and aquaculture. These technologies are used in addition for postharvest applications and processing for food production, novel food development and to improve nutritional value. Important applications of these technologies are related to ensuring food safety and security or to trace the origin of food.

15. All of the common omics technologies that were listed are used for agriculture, animal breeding or for aquaculture. The most important technologies were considered to be genomics, proteomics, , Marker Assisted breeding and the use of biomarkers and QTL mapping.

16. Some of the omics technologies listed are used for relatively new applications, such as the use of to assess meat quality or the use of metabolomics to establish soil health. and microbiomics are increasingly used to study and analyse the livestock rumen microflora. While epigenomics allows to analyse the effects biotic and abiotic conditions on gene expression which may have yield and quality consequences of the food product.

17. One respondent referred to the use of fluxomics for postharvest storage applications and quality management. Fluxomics refers to a range of methods in experimental and computational biology that attempt to infer or predict the rates of metabolic reactions in biological systems. It is connecting omics information to phenotypes and relies on the critical link between genes, and the observable phenotype.

18. Omics technologies are a combination of powerful tools that have the potential to increase yields through higher net volume production in general, but also through increasing resistance to all kinds of biotic and abiotic stresses. Respondents envisioned that a combination of genomics, proteomics and metabolomics and marker assisted breeding are most important technologies to achieve these goals. It is the combination of genomics to proteomics and metabolomics that enable the selection of desirable phenotypes. Marker Assisted Breeding is much more efficient and can reduce classical breeding time by half or more.

19. In addition, these technologies are also essential when addressing the causes of climate change crucial as also greenhouse gas emission may be lowered through the use of omics technologies. Indeed, omics technologies are also available to make biofuel production more efficient through the use of better adapted enzymes or by making bioresources more accessible to be used for biofuel production. The same approaches are at the basis of innovative developments leading to biobased products and chemicals.

20. Omics technologies are expected to have a continued and increasing importance in the future and will be used for all major applications related to food production. Several countries estimate that these technologies will not only be used for the more traditional crops, but also for new or less traditional food resources in the future.

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Agricultural production

21. It is striking that 85% of our global human food calories are delivered by only twelve plant and eight animal species. Wheat, rice, maize (corn), millet, and sorghum provide nearly all (70%) of the food energy (calories) and up to 90% of all protein consumed by the world's population. In addition, the number of both crop and animal species and varieties that are used for primary production, is becoming more limited. Most of crop varieties are optimised for cultivation in more temperate climate zones. Given that the climate is changing, these traditional crops may become less suitable for high yield production. Broadening the germplasm based on the available biodiversity is becoming a priority to deal with upcoming challenges related to climate change and optimise yields.

22. Biodiversity refers to the number or variety of plants and animals in an ecosystem. A gene pool is the complete set of unique alleles in a species or population. So, when there is diversity in the gene pool, there is difference in the characteristics of species. New traits and characteristics can be selected from the global biodiversity gene pool of a species. For example, to deal with new pest attacks, disease resistance genes can be identified from such gene pools and by omics technologies be integrated in the crop variety. Other traits related to drought resistance, water or salt tolerance, etc can be found in the globally available gene pool. The combination of omics technologies ensures a powerful toolbox to address new challenges ahead. These technologies are likely to significantly impact primary production systems a lot in the near future and are expected to ensure a more sustainable production, higher yields and higher nutritional value products.

23. However, it is expected that although the basis for global calorie food supply will increase, respondents believe the absolute number of crops that deliver most food calories will not significantly change. It is expected though that the yield of these crops will increase, together with their nutritional value. In line with gradual climate changes, the traits of these crops will be changed, to keep an optimised yield. Increasing the germplasm from related wild species, will open more variety in the available traits.

24. In addition, several countries expect that orphan crops will become more important as future food resources. Orphan crops still need to go through selection and breeding cycles to optimise production, and may open new opportunities for food production. Most countries indeed expect that omics technologies will become more important for the breeding of orphan crops next to traditional crops. Orphan crops listed with promising potential in the future include cassava, millet, sorghum, eggplant, pulses, coffee, coco, ancient grains, and banana. In addition, it is expected that also fruits like apple, pear, tomato, berries, citric species, melon and trees in general will be subject to new trait development with omics technologies. Only Korea and Luxemburg foresee to be working only on the more traditional crops and have no focus on orphan crops. In Korea apart from rice, also pepper, radish and soybean are most focussed on.

25. An important new development may come from expanding the cultivation of C4 plants. C4 plants have a photosynthetic cycle which is less energy consuming than C3 plants and therefore produce more efficiently. C4 plants have a competitive advantage over plants possessing the more common C3 carbon fixation pathway under conditions of drought, high temperatures, and nitrogen or CO2 limitation. The C4 pathway has been development over 50 times independently throughout evolution. All genes implicated in the C4 pathway identified so far exist also in C3 plants, just their regulation seems to be different. This would imply that it is fairly easy to switch on a C4 photosynthesis pathway in C3 plants. Projects are ongoing to turn C3 plants into C4 plants, in particular in rice is an ambitious projects started in 2008. C4 plants may become more significant in the future for more efficient food supply.

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26. Rapeseed or canola and other Brassica species are subject to a complete suite of genomics to enhance its oil profiles and improve its meal quality for example, to extent its used for fish feed in aquaculture.

Meat dairy production

27. In Canada omics technologies are expected to become most powerful tools for intensive applications for dairy and meat production from sheep, beef cattle and pork. Like in agriculture omics technologies provide selection tools for new traits with respect to meat or milk quality or disease resistance. In addition genomics are used for traceability or parentage verification, Genomics information for breeding purposes has revolutionised the cattle industry. Genomics technologies are also used to improve cattle health and welfare, for the rapid sampling and detection of E. coli in meat, and for Listeria detection and surveillance. Lipidomics are used to establish for meat or milk quality. Omics technologies are also used to establish the microbiotic gut flora of cattle and the impact of feed on greenhouse gas emissions.

Aquaculture

28. In contrast to expectation in agriculture, it is expected that the number of species from aquaculture contributing to food calories will significantly increase. As the proportion of wild capture fisheries will decline, more diverse species from aquaculture will become increasingly important. In the Canadian fishery, almost all species of commercial importance are considered for genomics research, including marine mammals and fish such as Atlantic salmon, rainbow trout, and shellfish species such as blue mussels, oysters and clams. Emerging or underutilised species that are expected to become more important in the future include arctic char, Coho salmon, brook trout, whitefish, cod, eels, tilapia, sablefish, sturgeon, shellfish such as abalone, geoduck clams, and invertebrates such as sea cucumber. Omics technologies in this field are next to the use for breeding purposes, also used for pathogen detection, quality assessments or feed optimisation.

Novel foods, nutraceuticals, nutritional value food safety, pest protection

29. Omics technologies are also used in general for improving or assessing the nutritional value of food, for the production of micronutrients and bioactives or for the development of novel foods. Some respondents mentioned the importance of insects as new sources of nutrients. Applications are in addition available to address food safety or to determine the origin of food or guarantee its origin. Omics technologies are powerful tools for the detection of pathogens for animals, plants, fish and shellfish and to guarantee food safety.

30. Almost all respondents indicate there is also a focus on omics technologies for the production of biofuels or biobased products. Omics technologies in addition may be used to increase the biobased product development. In Canada, two other Brassiceae, Camelina sativa and Brassica carinata, are used for the production of industrial lubricants and biofuels.

31. Canada in addition indicated that omics technologies are also employed to gather molecular characterisation data for the purposes of informing the regulatory analysis of genetically modified plants; to understand migration, biodiversity and population dynamics as well as to understand interactions between fisheries and aquaculture in fisheries and wild stock management,; in bee breeding for research on disease resistance traits and bee health; and to provide support to policy and regulatory decisions (e.g. quarantine, toxicology, food safety).

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Omics technologies for diet and health

32. Omics technologies are also very powerful tools to study the impact of diet on health (Q8). Research in this field is ongoing in all countries that responded. Relevant technologies in this field include , metabolomics, high throughput PCR arrays, transcriptomics of culture assays, epigenomics to establish changed DNA methylation patterns in response to certain diet or nutrient intake. Biomarkers for nutrition are being identified, in addition to their relation to oxidative stress and inflammation..

33. Recently, new insights on the impact of diet on the gut microbiome have been collected. This has only become possible with a metagenomics approach.

Policies and programmes devoted to mics technologies for better food and nutrition

34. The second part of the survey collected information on the policies and programmes in place in the different countries that support the use of and developments with respect to omics technologies for food production.

35. Only three countries (CA, ES, KR) report to have policies/ programmes in place to support the development of better food and nutrition through omics technologies. These programmes include focus on agriculture, livestock breeding and aquaculture. In agriculture the focus is mainly on molecular breeding, stress tolerance and plant genomics. For livestock breeding and aquaculture these programmes contribute to the improvement of health and productivity. More than the other fields, the issue to secure biological resources is considered to be very important in aquaculture.

36. In Spain, the State Research and Innovation plan which runs from 2013 to 2016 in implemented by annual calls for proposals which have a standard duration of three years. This plan also supports the development of novel foods or the focus on the link between diet and health.

37. In Korea there is significant government support to address diet and health issues. To get better insight in the link between diet and health is the core focus of the Center for Food and , which was established in 2008 by the Ministry of Education, Science and Technology and the Korea Science and Engineering Foundation.4

38. Programmes focussing on aquaculture are coordinated by the Korea Institute of Ocean Science and Technology (KIOST).5 Supports encompasses all aspects of marine science, and has as a main objective to secure biological resources.

39. In Canada the development of sector strategies is funded by Genome Canada, which is a not-for- profit organisation that acts as a catalyst for developing and applying genomics and genomic-based technologies to create economic and social benefits for Canadians.6 It invests in large-scale science and technology that involves academic, industry and government partners. These sector strategies map out how key sectors of the Canadian economy can further leverage the transformative power of genomics and related disciplines, to their advantage. They were developed through national steering committees of

4 http://genome.neocorea.net/eng/01_about/scheme.asp 5 http://eng.kiost.ac/kordi_eng/main/ 6 http://www.genomecanada.ca/en/sectorstrategies/

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industry, academic and government representatives and the consultative process included workshops with wide representation from across the country.

40. For each sector, the challenges being faced are described as well as the role of genomics in mitigating the challenges and creating opportunities. The strategies include next steps toward success with roles for government, industry, producers and academia. Building upon the input received through the sector strategy process for the agri-food and fisheries and aquaculture sectors, In June 2014 Genome Canada launched its competition with the theme of “Genomics and Feeding the Future”, which aims to support large-scale applied research projects focused on using genomic approaches within the agri-food and fisheries/aquaculture sectors to address challenges and opportunities related to global food safety, security and sustainable production. In Canada the policies do not include the development of novel foods or focus on diet and health.

41. Three countries (CA, ES, LU) report to have dedicated R&D programmes to support the use of omics technologies for better food and nutrition. In addition to that, Canada and Spain also has a dedicated programme to support the use of omics technologies for better food and nutrition for the industry.

42. Also a major industrial food company, as a BIAC representative, responded to the questionnaire and reported to have major dedicated R&D programmes in support of developing better food and nutrition through the use of omics technologies. This R&D programme focusses on less traditional crops such as coffee, coco for producing countries.

43. In Spain the Ministry for Economy and Competitiveness allocated a budget for R&D programmes that support omics technologies for better food and nutrition of EUR 255 million.7,8 The programme runs over three years and is reserved for CSIC, the Spanish National Research Council, universities and INIA, the National Institute for Research and Technology in Agriculture and Food.

44. The National Fund for Research in Luxemburg supports research projects that focus on omics technologies for better food and nutrition up to EUR one million.9

45. In Canada, since 1999, a total yearly budget of CAD 19,9 M is allocated for federal research laboratories, through the Genomics Research and Development Initiative (GRDI).10 For agriculture the budget received by Agriculture and Agri-Food Canada from the GRDI to support its research activities under the Canadian Crop Genomics Initiative, Quarantine and Invasive Species, and Food and Water Safety Projects amounts to approximately CAD 5.5 million per annum. Funding has been provided for periods of 3-5 years since 1999. The current cycle will end in March 2019. The main focal areas for agricultural research are summarised in Box 1.

7 http://www.mineco.gob.es/portal/site/mineco/idi 8 http://www.inia.es/IniaPortal/verPresentacion.action 9 http://www.fnr.lu/ 10 http://grdi-irdg.collaboration.gc.ca/eng/about/

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Box 1. GRDI's priorities of Agriculture and Agri-Food Canada

• Biodiversity, gene mining and functional analysis: to develop value-added traits (e.g. seed quality) for the highly competitive marketplace, enhancing the resiliency of Canada’s crop production in the face of potentially catastrophic abiotic and biotic stresses, and to maximize profitability for the sector.

• and physical tools: ensuring that scientists can maximize the opportunities presented by genomics-based research (e.g. identification and characterization of genes coding for desirable traits related to seed quality or disease resistance).

• Improve access to biological materials and data sets: to enhance the efficiency of plant breeding to lay the scientific foundation for major advances in the development and delivery of priority traits identified by industry (e.g. disease resistance). Expected outcomes include the accelerated commercialization of new crops and crop varieties, leading to a resilient and competitive sector.

• Enhance our capacity to identify organisms from all life stages (especially regulated quarantine pests in imported commodities) through the development of new genomics tools for efficient detection of quarantine and invasive species; thus substantially bolstering Canada’s operational strategy for both prevention and effective eradication or mitigation of new invaders that can affect food production and quality;

• Enhance our understanding of risks associated with international trade through a much deeper assessment of biodiversity in commodities;

• Protect Canadians against false positives in export commodities, i.e. native but innocuous species that are mistaken for quarantine species, thus protecting our crop exports;

• Provide baseline data for long term monitoring of the effects of climate change on native and invasive species that can affect food production and quality;

• Develop new multidepartmental data repositories and data analysis tools that can be used for developing detection as well as control tools of invasive species that can affect food production and quality.

• Enhance food and water safety by developing and demonstrating the improved utility, increased speed and reduced cost of genomics-based methods for pathogen isolation, detection and characterisation;

• Develop federally integrated systems to manage, store and provide open access to genomic data and related information from food and water-borne pathogens that also supports the development and application of genomic based methods to formulate more discriminatory risk assessment criteria and superior means to accurately identify the source of a given pathogen.

46. For aquaculture the aim is to strengthen food and water safety in Canada. A budget of CAD 720K per year is allocated to researchers of the Canadian government for the period from April 2014 to March 2019.11 The main focus of this programme is to enforce aquatic profiling, to promote aquatic animal health and aquatic ecosystems health. Additional programmes to support research and development for aquaculture are available. Research funded through these programmes use omics technologies as platform technologies and can indirectly benefit that food and nutrition without necessarily being the main focus. These programmes include:

11 http://grdi-irdg.collaboration.gc.ca/eng/about/success_stories/fws.html

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 Aquaculture Collaboration Research and Development Program (ACRDP);12

 National Aquatic Animal Health Program;13

 Atlantic Cod Genomics and Broodstook Development Project by Genome Atlantic;14 and

 Genomic Research on Atlantic Salmon by GenomeBC.15

47. In addition to the dedicated programmes described, Genome Canada has a suite of programs that support genomics R&D in Canada across all sectors, including in support of industry. The programs most relevant to the support of ‘omics-technologies for better food and nutrition are summarised in Box 2.

12 http://www.dfo-mpo.gc.ca/science/enviro/aquaculture/acrdp-pcrda/index-eng.htm 13 http://www.dfo-mpo.gc.ca/science/aah-saa/National-Aquatic-Animal-Health-Program-eng.html 14 http://www.genomeatlantic.ca/projects/view/8- 15 http://www.genomebc.ca/research-programs/projects/fisheries-aquaculture/completed/genomics-research- atlantic-salmon-project-grasp/

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Box 2. Genome Canada Programming

 Large-Scale Applied Research Project Competition on Genomics and Feeding the Future;16 It aims to support projects focused on using genomic approaches within the agri-food and fisheries/aquaculture sectors to address challenges and opportunities related to global food safety, security and sustainable production, and thereby contribute to the Canadian bioeconomy and the well-being of Canadians. All projects must clearly demonstrate end-user engagement in the development and execution of the research plan in order to help ensure receptor uptake of the research.. Examples of end-user organizations include breeders’ groups, industry and industry associations, government departments and regulatory agencies, and producer organizations.

 Budget: CAD 90 million comprised of CAD 30 million from Genome Canada, CAD 5 million from Western Grains Research Foundation and CAD 55 million from project co-funders such as provincial governments, industry, universities and private foundations

 Timeframe: Program was launched in June 2014. Approved projects are expected to start in October 2015 with terms of up to 4 years.  Genomics Innovation Network:17 Genome Canada’s mission includes a commitment to provide researchers across Canada access to leading edge technologies in all genomics-related fields. Beginning in 2015, Genome Canada will fulfil this part of its mandate through a network of genomics technology innovation centres collaborating across Canada, the Genomics Innovation Network (GIN). Each member of the GIN, to be designated as a Node, will provide researchers (including those in agriculture and aquaculture) access to high throughput genomic technologies, such as DNA sequencing, RNA expression, protein identification and quantitation, and metabolomics, as well as new method and protocol development, data analysis and bioinformatics. Each Node will also assist researchers in the development of research proposals by providing advice on appropriate technologies, study design, data analysis and bioinformatics that improve the quality of the research.

 Budget: CAD 32 million comprised of CAD 16 million from Genome Canada, and CAD 16 million from Node co-funders such as provincial governments, industry, universities and private foundations

 Timeframe: Program was launched in June 2014. Approved Nodes are expected to start in April 2015 with terms of two years.  Genomic Applications Partnership Program18 aims to stimulate partnering of academic researchers with industry and other “users” of genomics (industry, government, non-profit or other organizations) to translate innovations that are expected to have considerable economic and social impacts within the near term. Applications from any area, including agriculture and aquaculture are eligible. While the Genome Canada funds cannot flow to most users (e.g., industry), the project must be driven by a user need (“user-pull”).

 Budget: CAD 111 million comprised of CAD 37 million from Genome Canada CAD 37 million from the user partners (industry or other) and CAD 37 million from other project co-funders.

 Timeframe: Program launched in 2013. Competitions were planned every six months until the funds are exhausted. There are currently sufficient funds to hold competitions until the fall of 2015. Approved projects have terms of up to three years.

48. In addition to the national programmes, different regions and provinces support R&D in the sector via a number of other programmes and mechanisms. For instance, in western Canada, Genome

16 http://www.genomecanada.ca/en/portfolio/research/2014-competition.aspx 17 http://www.genomecanada.ca/en/portfolio/research/genomics-innovation-network.aspx 18 http://www.genomecanada.ca/en/portfolio/research/genomic-applications-partnership-program.aspx

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British Columbia supports the application of genomics in partnership with companies in the Agrifood sector through the Strategic Opportunities Fund for Industry (SOFI)19 and the Proof-of-Concept program (POC).20 These programs provide matching funds for projects of up to CAD 1 million in size. The Alberta based food metabolome project, which was funded in 2012, provides another example.21

49. The national government has a number of dedicated programmes to support innovation in the industry, although not specifically addressing the use of omics technologies.

 Agriculture and Agri-Food Canada AgriInnovation Program22 is targeted at industry and its main focus is to accelerate the pace of innovation by supporting research and development activities in agri-innovations and facilitating the demonstration, commercialization and/or adoption of innovative products, technologies, processes, practices and services. The aim is to enhance economic growth, productivity, competitiveness, adaptability and sustainability of the Canadian agriculture, agri-food and agri-based products sector and assist in capturing opportunities for the sector in domestic and international markets.

 Budget: CAD 468 million over 5 years

 Timeframe: 5 years ending in March 2018

 Canada’s Natural Research Council’s Industrial Research Assistance Program (IRAP)23 is focussing towards small and medium enterprises and was implemented since in the 1950s.

Enabling framework for sustainable production through omics technologies for better food and nutrition

50. Finally the survey also addressed the enabling framework that is responsible or required for future developments in this field (table 1).

51. Public financing and infrastructure were identified by the respondents as being the most important conditions to support the use of omics technologies for better food and nutrition. All respondents agreed that public financing could be improved in their countries. Except for one respondent there was general agreement that also private investments should be increased. The infrastructures needed to be improved for seven out of the nine respondents.

52. Surprisingly consumer acceptance was at the bottom of the list of enabling framework conditions that were considered to be important for the development of better food and nutrition through omics technologies. A single respondent also reported consumer education, science communication and government policy as important enabling conditions that need improvement.

19 http://www.genomebc.ca/research-programs/opportunities/current-funding-competitions/sofi/ 20 http://www.genomebc.ca/research-programs/opportunities/current-funding-competitions/proof-of-concept- poc/ 21 http://bio.albertainnovates.ca/media/41490/i2-2012-david-wishart-what_s-in-food.pdf 22 http://www.agr.gc.ca/eng/?id=1354301302625 23 http://www.nrc-cnrc.gc.ca/eng/irap/index.html

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Table 1 Enabling framework for sustainable production through omics technologies for better food and nutrition On a scale of 1 (most important) to 5 (least Please tick which of these framework important), please indicate how important the conditions need to be better developed in different framework conditions are for the your country development of better food and nutrition through the use of omics-technologies. Skills/education 2 2 3 5 1 1 1 2 1 X X X X X X X IP 4 5 4 3 1 3 3 3 X X X X Infrastructure 2 4 4 1 1 1 1 1 X X X X X X X Public financing 1 1 1 5 2 1 1 1 1 X X X X X X X X X Private investments 3 1 1 3 1 2 2 2 1 X X X X X X X X Public acceptance 3 2 5 2 2 1 2 2 X X X X X X Other, 3 X Consumer education

Science communication 2 3 X

Government policy 1 X

Conclusions 53. In general and not surprisingly, omics technologies are considered to be powerful platform technologies and are expected to be become even increasingly important in the future for the production of food. It is the multitude of available complementary technologies that will allow to increase yields to produce more on less land, with less input of water and agrochemicals in a manner that is more sustainable. These conditions have to be met while the current climate is changing so that selection of crops for optimised yields is needed. 54. Increasing the germplasm based on the available biodiversity is considered an essential approach to ensure sufficient production. Using the biodiversity in addition allows to find and introduce new traits into traditional crops. Such new traits allow to find new ways to deal with biotic and abiotic stress conditions. 55. Marker Assisted Breeding, the use of biomarkers and other omics technologies are also increasingly crucial for selection and breeding of livestock, for meat or dairy production. 56. It is expected that for the food supply aquaculture will become more important in the future as wild catch of fish and shell fish is expected to be decreasing. More species will be studied for use in aquaculture, and omics technologies will also become increasingly important for aquaculture, for selecting best traits, for health protection or for safety assessment of the production. 57. Although there is a trend for the development of novel food and nutraceuticals, surprisingly, the respondents had no dedicated programmes in place to support these developments. Nevertheless, there are important developments ongoing internationally to support this field and to get a better insight in the link between diet and health, among others through the influence of diet on the gut microbiome. The gut-brain axis is believed to play a crucial role in lifelong health and wellbeing. Omics technologies are powerful tools to study this and for the first time to start understanding this complex interplay. It is believed that this may ultimately lead to personalised diet or disease prevention through diet. 58. To support further development in this field the respondents indicated that most importantly there is a need for sufficient investments and funding, in addition to top of the line research infrastructure.

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ANNEX 1

OECD WPB Survey on “Omics-technologies” for better food and nutrition

Scope

Producing more high quality and safe food on less land with less environmental impact will be one of the greatest challenges of the twenty-first century. Advances enabled by “omics-technologies” are supporting production, through agriculture, animal husbandry and aquaculture, thereby enabling society to be better positioned to master these challenges.

Omics-technologies (e.g. genomics, metabolomics, transcriptomics, proteomics, etc.) are powerful tools - particularly when used in combination with advanced molecular and breeding techniques. They have the potential to make conventional breeding and advanced breeding techniques more efficient and precisely targeted, to bring benefits for human health and nutrition, and to help to address environmental needs and climate change.

It is striking that only twelve plant and eight animal species provide about 85% of our global human food calories. Wheat, rice, maize (corn), millet, and sorghum provide nearly all (70%) of the food energy (calories) and up to 90% of all protein consumed by the world's population. In addition, the number of both crop and animal species varieties that are used for primary production, is becoming more limited.

Biodiversity refers to the large number or variety of plants and animals in an ecosystem. A gene pool is the complete set of unique alleles in a species or population. So, when there is diversity in the gene pool, there is difference in the characteristics of species. New traits and characteristics can be selected from the global biodiversity gene pool of a species. For example, disease resistance genes can be selected from such gene pools. Omics-technologies are likely to significantly impact primary production systems a lot in the near future and may lead to more sustainable production, higher yields and higher nutritional value products.

Purpose

This survey aims to collect information on the status of omics-technologies for better food and nutrition. It should provide evidence on:

 application areas of omics-technologies for better food production and higher value nutrition;  country approaches to support the use of omics-technologies for better food and nutrition; and  enabling framework for sustainable production through omics-technologies for better food and nutrition.

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Guidelines

This questionnaire should be completed by representatives of national governments, ministries or their agencies and returned to the OECD Secretariat not later than 30 September 2014. Please send completed questionnaires electronically to the following contact at the OECD WPB Secretariat:

Ms. Kathleen D’Hondt, OECD Email: [email protected] Tel: +33 1 45 24 98 12 REQUEST FOR INFORMATION

Details of the primary contact person in the responding country.

Country:

Your name:

Your organization:

Your position:

Area of responsibility:

Telephone number:

E-mail address:

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Note: Double clicking on a check box should bring up a Check Box Form Field Options box. The default value is “Not checked”. If you wish to check the box, select the second option, “Checked”.

Part I. Technological trends and industrial applications of omics-technologies for better food and nutrition

Q1. In which application areas omics-technologies are used in your country? Please tick all that apply. Please note that “agriculture”, “livestock breeding” and “aquaculture” are considered primary production systems, whereas “food production” refers to any applications or processes after harvesting. “Novel food development” refers to the development of dietary supplements or nutraceuticals.

Agriculture Livestock breeding Aquaculture Food production Novel food development Improve nutritional value Other, please specify, ……………………………………………………………………..

Q2. Which technologies are used in the application areas you indicated above? Please tick all that apply and indicate for which application area(s) from the list above.

Marker assisted breeding, for application area(s) ………………………………………….. QTL mapping, for application area(s) ……………………………………………………… Biomarkers, for application area(s) ………………………………………………………… Genomics, for application area(s) ………………………………………………………….. Transcriptomics, for application area(s) …………………………………………………… Proteomics, for application area(s) ………………………………………………………… Lipidomics, for application area(s) ………………………………………………………… Metabolomics, for application area(s) ……………………………………………………... Microbiomics, for application area(s) …………………………………………….……….. Epigenomics, for application area(s) ………………………………………………………. Other, please specify, ……………………………………………………………………..

Q3a. For which outcome areas are omics-technologies most important? Please tick all that apply.

Yield increase Increasing pest resistance Increasing disease resistance Increasing drought/water resistance

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Reduction of greenhouse gas emissions Reduction of use of agrochemicals Contributing to biodiversity Biobased products development Biofuels development Increasing the shelf life of food Increasing nutritional value Food waste reduction Other, please specify. ………………………………………………………………………

Q3b. Which are the three most important omics-technologies from Q2 to advance the outcome areas you indicated above?

1. …………………………………………………………………………….…………………

2. ……………………………………………………………………………………………….

3. …………………………………………………………………………….…………………

Q4. Which application area(s) will benefit most in the future from omics-technologies in your country? Please tick all that apply.

Agriculture Livestock breeding Aquaculture Food production Novel food development Improve nutritional value Other, please specify, …………………………………………………………………….. Please indicate which crops or other organisms will be most focused on in your country.

………………………………………………………………………………………………………………… ………………………………………………………………………………………………………………… ………………………………………………………………………………………………………………… …………………………………………………………………………………………….………………… ………………………………………………………………………………………

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Q5. Will the focus in the future be exclusively on traditional crops/species or will also orphan crops/species are taken into consideration?

Traditional crops/species only Traditional crops/species and orphan crops/species Orphan crops/species only If relevant, please indicate which orphan crops or other species will be most focused on. ………………………………………………………………………………………………………………… ………………………………………………………………………………………………………………… ………………………………………………………………………………………………

Q6. Will the number of crops and other species that form the basis of the global calorie food supply in the future be altered? YES NO If so, how? ………………………………………………………………………………………………………………… ………………………………………………………………………………………………………………… ………………………………………………………………………………………………

Q7. Will the availability of biodiversity and the total gene pool become more important in the future?

YES NO If so, how? ………………………………………………………………………………………………………………… ………………………………………………………………………………………………………………… ……………………………………………………………………………………………….

Q8. Are omics-technologies used to study the impact of diet on health in your country?

YES NO If YES, which technologies are used? ………………………………………………………………………………………………………………… ………………………………………………………………………………………………………………… ………………………………………………………………………………………………

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Part II. Policies and programmes devoted to omics-technologies for better food and nutrition

Q9. Do you have policies and/or programmes in place in your country for the development of better food and nutrition through omics-technologies?

YES NO If YES, indicate which primary production systems are addressed through these policies. Please tick all that apply and indicate website if available.

Agriculture; Website ………………………………………………………………………. Livestock breeding; Website ……………….……………………………………………….. Aquaculture; Website ……………………………………………………………………… What are the main goals of these policies?

With respect to agriculture?

 ..………………………………………………………………………………………… …………………………………………………………………………………………..  ………………………………………………………………………………………….. …………………………………………………………………………………………..  ………………………………………………………………………………………….. ………………………………………………………………………...... With respect to livestock breeding

 ..………………………………………………………………………………………… …………………………………………………………………………………………..  ………………………………………………………………………………………….. …………………………………………………………………………………………..  ………………………………………………………………………………………….. ………………………………………………………………………...... With respect to aquaculture

 ..………………………………………………………………………………………… …………………………………………………………………………………………..  ………………………………………………………………………………………….. …………………………………………………………………………………………..  ………………………………………………………………………………………….. ………………………………………………………………………...... Please indicate the budget and timeframe for the implementation of the policies in place, if applicable.

 Budget ……………………………………………………………………………………....  Timeframe ………………………….………………………………………………………

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Do these policies address also the development of novel food?

YES NO NOT APPLICABLE

Do these policies also address diet and health issues?

YES NO NOT APPLICABLE

Q10. Do you have dedicated R&D programmes in your country to support the use of omics- technologies for better food and nutrition?

YES NO If YES, please indicate

 Website ………………………………………………………………………………………..  Main focus and main stakeholders ………………………………………………………….  Budget24 ………………………………………………………………………………………..  Timeframe25 ……………………………………………………………………………………

Q11. Do you have dedicated support programmes for industry in your country to support the use of omics-technologies for better food and nutrition?

YES NO If YES, please indicate

. Website ……………………………………………………………………… . Main focus and main stakeholders ………………………………………… . Budget1 ………………………………………………………………………. . Timeframe2 ……………………………………………………………………

24 If available, please provide the budget associated with the programme and indicate the associated timeframe. 25 If available, please provide the timeframe associated with the programme.

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Part III. Enabling framework for sustainable production through omics-technologies for better food and nutrition:

Q12. Please indicate which of the framework conditions listed below are important to create the right enabling framework to use omics-technologies for the production of better food and nutrition.

On a scale of 1 (most important) to 5 Please tick which of these (least important), please indicate how framework conditions important the different framework need to be better conditions are for the development of developed in your country better food and nutrition through the use of omics-technologies. Skills/education IP Infrastructure Public financing Private investments Public acceptance Other, please specify …………………………….. …………………………….. …………………………….. …………………………….. …………………………….

Other trends and technologies in your country that are important to develop better food and nutrition through omics-technologies.

Please state here all other relevant information that is important in exploring and understanding current and upcoming trends based on omics-technologies to develop better food and nutrition in a sustainable way.

………………………………………………………………………………………………………………… …………………………………………………………………………………………….………………… ………………………………………………………………………………………………………………… ………………………………………………………………………………………………………………… ………………………………………………………………………………………………………………… ………………………………………………………………………………………………………………… ………………………………………………………………………………………………………………… ………………………………………………………………………………………………………………… …………………………………………......

THANK YOU FOR COMPLETING THIS QUESTIONNAIRE

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ANNEX 2: GENOMICS AND –OMICS TECHNOLOGIES DEFINITIONS

Omics-technologies regroup the technologies supporting the study of groups of biological molecules, in particular the genome, but also the proteome, the transcriptome, the lipidome and the metabolome and interactions between molecules such as interactomics, epigenomics and may include also microbiomics in which the whole (symbiotic) microbial environment is studied. ‘Omics’ also refers to the integrative collective technologies used in a systems approach to explore the roles, relationships, and actions of these various types of molecules often in high throughput applications. More specific definitions of the major technologies mentioned are listed below.

Genomics is a discipline that applies recombinant DNA, DNA sequencing methods, and bioinformatics to sequence, assemble, and analyse the function and structure of (the complete set of DNA within a single cell of an organism). Genomics was a relatively unknown discipline until widespread publicity was created around the Human (HGP), which was declared complete in April 2003.26

Transcriptomics is the study of genes being expressed at any given time under given conditions. The transcriptome is the complete set of transcripts in a cell, and their quantity, for a specific developmental stage or physiological condition (Wang et al., 2009).

Proteomics is the large-scale study of proteins, particularly their structures and functions, and the proteome is the entire set of proteins produced or modified by an organism or system. Proteomics lagged behind genomics for a long time due to technical difficulties, but has progressed radically in recent years and is now on a par with most genomic technologies in throughput and comprehensiveness (Mann and Kelleher, 2008).

Metabolomics refers to the comprehensive analysis of all low-molecular-weight primary and secondary metabolites present in and around cells growing under defined physiological conditions (Mashego et al., 2007). It is emerging as a rapidly developing field of research with the promise to speed up the functional analysis of genes of unknown function.

The above are listed in order of “information flow”. The metabolome is the final downstream product of gene transcription. Additionally, as the furthest downstream product, the metabolome is closest to the phenotype of the biological system being studied (Horgan and Kenny, 2011).

Metagenomics is the application of modern genomics technologies to microbial communities in their natural environments, bypassing the need for culturing (Röling et al., 2010). The vast majority of bacterial life, for example, remains unculturable using available methods (Amman et al., 1995). For almost the entire history of as a discipline, perhaps 90-99% of the diversity of has been a complete mystery. Metagenomics is uncovering this biodiversity at an unprecedented rate.

Marker assisted breeding or selection27 is the process used in plant and animal selection and breeding whereby a marker (morphological, biochemical or one based on DNA/RNA variation) is used for

26 http://web.ornl.gov/sci/techresources/Human_Genome/index.shtml 27 http://en.wikipedia.org/wiki/Marker-assisted_selection

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indirect selection of a genetic determinant or determinants of a trait of interest (e.g. productivity, disease resistance, abiotic stress tolerance, and quality). It is an indirect selection process where a trait of interest is selected, not based on the trait itself, but on a marker linked to it. The assumption is that the marker used for selection associates at high frequency with the gene or quantitative trait locus (QTL) of interest, due to genetic linkage (close proximity, on the chromosome, of the marker locus and the disease resistance- determining locus). The majority of MAS work in the present era uses DNA-based markers. However, the first markers that allowed indirect selection of a trait of interest were morphological markers. Markers may be:

 Morphological - These markers are often detectable by eye, by simple visual inspection. Examples of this type of marker include the presence or absence of an awn, leaf sheath coloration, height, grain color, aroma of rice etc. In well-characterized crops like maize, tomato, pea, barley or wheat, tens or hundreds of genes that determine morphological traits have been mapped to specific chromosome locations.  Biochemical - A protein that can be extracted and observed; for example, isozymes and storage proteins.  Cytological - The chromosomal banding produced by different stains; for example, G banding.  DNA-based or molecular - A unique gene (DNA sequence), occurring in proximity to the gene or locus of interest, can be identified by a range of molecular techniques such as RFLP, RAPD, AFLP, DAF, SCAR, microsatellite, or single-nucleotide polymorphism (SNP) detection.

Modern breeding uses molecular markers to track the genetic makeup of plants during the variety development process.28 A molecular marker is a genetic tag that identifies a particular location within a plant’s DNA sequences. Markers can be used in transferring a single gene into a new cultivar or in testing plants for the inheritance for many genes at once. Markers can be based on either DNA or proteins. Both DNA- and protein-based markers have been widely used in plant breeding, but DNA-based markers by far predominate. Greater numbers of DNA-markers can be identified to cover all regions of an organism’s DNA, and they are not based on the developmental stage of the plant as many protein-based markers are. DNA-based markers can be derived from seeds or seedlings in rapid screening tests performed by automated robotic systems. Plants lacking the desired traits can be eliminated before moving on to more expensive or lengthy greenhouse or field trials. It provides a dramatic improvement in the efficiency with which breeders can select plants with desirable combination of genes.

QTL mapping:29 A quantitative trait locus refers to the location of a specific gene that affects a measurable or quantifiable trait. These traits are typically affected by more than one gene, and also by the environment. Examples of quantitative traits are plant height (measured on a ruler) and body weight (measured on a balance).

The assumption is that the marker used for selection associates at high frequency with the gene or quantitative trait locus (QTL) of interest, due to genetic linkage (close proximity, on the chromosome, of the marker locus and the disease resistance-determining locus).

28 http://www.seedquest.com/keyword/seedbiotechnologies/primers/varietydevelopment/markerassistedbreeding.htm 29 http://www.isaaa.org/resources/publications/pocketk/19/default.asp

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Lipidomics is the large-scale study of pathways and networks of cellular in biological systems (Wenk, 2005). The word "lipidome" is used to describe the complete profile within a cell, tissue or organism. Lipidomics research involves the identification and quantification of the thousands of cellular lipid molecular species and their interactions with other lipids, proteins, and other metabolites. Investigators in lipidomics examine the structures, functions, interactions, and dynamics of cellular lipids and the changes that occur during perturbation of the system.

Epigenomics is the study of the complete set of epigenetic modifications on the genetic material of a cell, known as the epigenome. Epigenetic modifications are reversible modifications on a cell’s DNA or histones that affect gene expression without altering the DNA sequence (Russell 2010 p. 475).

Microbiome is the collective genomes of a community of microbes (composed of bacteria, bacteriophage, fungi, protozoa and viruses).

Fluxomics refers to a range of methods in experimental and computational biology that attempt to infer or predict the rates of metabolic reactions in biological systems (Winter and Krömer, 2013). This includes a number of different methods, broadly divided into stoichiometric and kinetic paradigms.

References

Amann, R.I., W. Ludwig, and K.H. Schleifer, 1995. “Phylogenetic identification and in situ detection of individual microbial cells without cultivation.” Microbiological Reviews 59, 143-169.

Horgan, R.P. and L.C. Kenny, 2011. “SAC review. ‘Omic’ technologies: genomics, transcriptomics, proteomics and metabolomics.” The Obstetrician & Gynaecologist 13, 189-195.

Mann, M. and N.L. Kelleher, 2008. “Precision proteomics: The case for high resolution and high mass accuracy”. Proceedings of the National Academic of 105, 18132-18138.

Mashego, M.R., K. Rumbold, M. De Mey, E. Vandamme, W. Soetaert and J.J. Heijnen, 2007. “Microbial metabolomics: past, present and future methodologies”. Biotechnology Letters 29, 1–16.

Röling, W.F.M., M. Ferrer and P.N. Golyshin, 2010. “Systems approaches to microbial communities and their functioning”. Current Opinion in Biotechnology 21, 532–538.

Russell, P.J., 2010 ‘’iGenetics’’. 3rd ed. San Francisco: Pearson Benjamin Cummings.

Wang, Z., M. Gerstein and M. Snyder, 2009. “RNA-Seq: a revolutionary tool for transcriptomics.” Nature Reviews Genetics 10, 57–63.

Wenk, M.R., July 2005. "The emerging field of lipidomics". Nature Reviews Drug Discovery 4, 594–610.

Winter, G. and J.O. Krömer, 2013. “Fluxomics – connecting ‘omics analysis and phenotypes”. Environmental Microbiology 15, 1901–1916.

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