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The Genomics R&D Initiative coordinates federal science departments and agencies in the field of genomics research. Its strategic goal is to contribute solutions to biological issues that are important to Canadians, focusing on the role of federal government research

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Executive Summary

The Genomics R&D Initiative (GRDI) is a federal program that coordinates science departments and agencies in the field of genomics research to contribute solutions to issues that are important to Canadians. The GRDI’s overarching goal is for federal laboratories to deliver and apply high quality, genomics-based R&D solutions to uphold regulatory, public policy, and operational mandates of Canada’s government in important areas such as health care, food safety, sound management of natural resources, a sustainable and competitive agriculture sector, and environmental protection, with strong collaborations with university and private sectors.

The GRDI has been funded for three-year cycles: Phase I (1999-2002), Phase II (2002-2005), Phase III (2005-2008), Phase IV (2008-2011), and Phase V (2011-2014). Since the initiative was first funded in 1999, it has delivered insights into pests and diseases for Canada’s important crops (wheat, soybean, canola); contributed to water, forestry and fisheries management; identified cancer genetic signatures that allow better targeted treatments; contributed to the development of international standards for the use of toxicogenomics in regulatory policy; developed novel methods for the rapid identification of human and plant pathogens; and secured a large number of national and international collaborations. Phase V (2011-2014) continues to support mandated research in participating departments. It also supports two highly coordinated interdepartmental projects along shared priorities and common goals: 1) Strengthening Food and Water Safety in Canada through an Integrated Federal Genomics Initiative; and 2) Protection of Canadian biodiversity and trade from the impacts of global change through improved ability to monitor invasive alien and quarantine species.

This Annual Performance Report for 2012-2013 follows the Performance Measurement Framework that was developed for the GRDI in 2011. It presents the GRDI program profile and planned results, its links to departmental objectives and program alignment architecture, its governance, coordination and accountability structures. It then reports on performance for 2012-2013 in terms of governance, research and development, and maintenance of capacity. Annexes present summary statistics as well as a summary narrative account of R&D achievements for 2012-2013.

Practical Applications

Since the implementation of the GRDI in 1999, participating departments and agencies have built a solid genomics research capacity and have gone a long way to deliver on the initiative’ stated objectives, as confirmed by two independent evaluations (2006 and 2010) and an audit by the Office of the Comptroller General (2012). Examples of practical applications that have resulted from GRDI research follow.

Government policy makers and regulators have used GRDI research results for evidence-based regulatory, policy, and resource management decisions:

  • Genomics datasets were developed by GRDI scientists and are used operationally by federal regulators at Fisheries and Oceans Canada for the most intensive real-time management of mixed-stock fisheries in the world, thus greatly increasing the effectiveness of conserving threatened Pacific salmon while sustainably harvesting more abundant stocks.
  • Novel strains of avian influenza virus were identified in Newfoundland birds and an inventory of the virus distribution was transferred by GRDI scientists to the province of Newfoundland and Labrador as an invaluable source of information for supporting mitigation decisions should an emergency outbreak arise in the wild or in the poultry industry.
  • Using toxicogenomics tools, GRDI scientists assisted the City of Montreal (one of the world’s top three municipal effluent emitters) select a new wastewater treatment system. Results showed that ozonation effectively reduced target levels of bacteria while breaking down many other contaminants, and the city invested in an ozonator facility. Another GRDI project showed the relative effectiveness of wastewater treatment systems of twelve other municipalities, to be used as a guide by municipal decision-makers when new treatment systems need to be introduced.
  • GRDI scientists developed test methods that show the impact of various dosages of chemicals with much greater accuracy than conventional methods, and as a result were invited to join the Organization for Economic Cooperation and Development (OECD) group that sets international standards for the use of toxicogenomics in regulatory policy.
  • Campylobacter is responsible for over 400,000 cases of food poisoning every year and the leading cause of bacterial gastroenteritis in Canada. GRDI scientists developed an innovative generic fingerprinting method for rapid identification of Campylobacter strains, and transferred it to the British Columbia Centre for Disease Control and to the Canadian Food Inspection Agency (CFIA). This approach provides results in a matter of hours rather than days; it enables front-line regulators to pinpoint where specific strains originates, and from there, look for ways to reduce their transmission.
  • Sudden oak death is a fungal disease that could pose a significant economic risk to Canada if it entered the country and attacked hardwood forests. Also, Canada exports some $5.5 billion worth of lumber and hundreds of millions of dollars in ornamental plants every year and major trading partners restrict imports of wood and plant materials from countries where the disease has been found. Since plants can be infected long before they show any symptoms, CFIA inspectors who survey the disease have relied on laboratory tests that can take as long as a month to produce results. Today, a new test developed by GRDI scientists that is much more sensitive and provides results in as little as 24 hours is used operationally by the CFIA, as well as by the United States Department of Agriculture. Agencies in the United Kingdom and France are taking steps to adopt the test as well.
  • Genomics data has allowed GRDI scientists to distinguish the subspecies and populations of northern Dolly Varden charr as distinct groups. This research has resulted in the listing of northern Dolly Varden as a ‘species of concern’ in Canada, re-opening of the Big Fish River fishery, and partnerships with the Fisheries Joint Management Committee and Gwich’in Renewable Resources Board for genetic analysis to assist them with assessing the stability of their fisheries.
  • Knowledge generated from genomics research on redfish has provided new scientific advice for fisheries managers, recommending that the Acadian redfish and deep water redfish be managed as separate resources. The research also helped play a role in the Committee on the Status of Endangered Wildlife in Canada’s assessment of the status of deep water redfish as threatened in the Northwest Atlantic (2010), and facilitated a collaborative partnership with redfish harvesters to identify the redfish species being caught in the Laurentian Channel in the Gulf of St. Lawrence, where a moratorium on the redfish fishery has been in effect since 1995.

Private and public stakeholders involved in the innovation continuum in Canada have adopted innovative or improved tools and processes using GRDI research results:

  • The balsam fir sawfly has been a problem for decades in Eastern Canada, reaching epidemic proportions since the early 1990s and posing a significant threat to the forest industry of the province. Based on research conducted by GRDI scientists, a baculovirus that specifically attacks the balsam fir sawfly was registered and licensed to Forest Protection Limited of New Brunswick for commercial use. More than 50 000 hectares of infested forest have since been treated with the virus as part of operational forest insect pest control programs by the Newfoundland and Labrador Department of Natural Resources and by the New Brunswick Department of Natural Resources. A new company, Sylvar Technologies, was formed to produce and commercialize the virus under the trade name Abietiv. Recognizing the value of its technology and research capabilities, Andermatt BioControl, a major biotechnology company based in Switzerland, acquired majority ownership of Sylvar in 2011.
  • GRDI scientists found a new and unique bacterial marker that distinguishes fecal contamination from seagulls, a serious source of pollution around the Great Lakes. This marker has changed how Canadian municipalities manage their beaches, as it allows more targeted and cost-effective solutions for the cleanup of pollutions sources, and is now being used around the world. The US Environmental Protection Agency presented its Scientific and Technical Achievement Award in 2010 to the scientists for this breakthrough work.
  • Fusarium head blight, a fungal disease that has caused Canadian wheat producers more than $1.5 billion in lost income since the mid-1990s, produces mycotoxins causing serious illness in people or animals who consume infected wheat. With support from the GRDI, scientists have developed a library of genes identifying those that are used by the fungus to produce a number of mycotoxins, as well as when they are produced and under what conditions. This is part of a global research effort that now provides the most complete and accurate sequencing of the fungus, accessed by the international research community to explore how to block infection.
  • Canada’s forest industry plants an estimated 650 million trees every year. Long-term tree breeding programs help companies choose the best seedlings for planting. GRDI scientists are identifying genetic markers associated with the most valuable traits. With them, breeders will be able to tell at the seedling stage whether a tree has inherited desired traits that could otherwise be measured only when the tree has reached maturity, decades later. This research is already contributing to tree breeding programs of provincial governments in Quebec and Newfoundland and Labrador, and has been recognized by a forest industry representative as the ‘some of the most positive developments we have seen in the field’.
  • Marker-assisted breeding techniques developed by GRDI scientists for wheat have become integrated into a large-scale research alliance established with the common goal of improving the yield, sustainability, and profitability of Canadian wheat for the benefits of the Canadian farmers and the economy. The Canadian Wheat Alliance includes major contributions by the National Research Council of Canada, Agriculture and Agri-Food Canada, the University of Saskatchewan, and the Province of Saskatchewan, as per a formal agreement signed in 2012.
  • The antibody library developed and characterized by GRDI scientists has attracted three Canadian companies to collaborate for the development of the next generation of targeted therapy of cancers based on antibody-drug conjugates (ADC). One of these companies, AvidBiologics, announced that “this partnership transforms AvidBiologics into a leading ADC company with one of the most compelling pipelines in the industry worldwide.”

Acronyms

AAFC Agriculture and Agri-Food Canada
ADC Antibody-Drug Conjugates
ADM Assistant Deputy Minister
ADM CC ADM Coordinating Committee
CEPA Canadian Environmental Protection Act
CFIA Canadian Food Inspection Agency
CFS Canadian Forest Service
CIHR Canadian Institutes of Health Research
CWA Canadian Wheat Alliance
DFO Fisheries and Oceans Canada
DNA Deoxyribonucleic Acid
EC Environment Canada
eQTL Expression Quantitative Trait Loci 
FTEs Full Time Equivalents
FWS Food and Water Safety
GRDI Genomics Research and Development Initiative
HC Health Canada
HIV Human Immunodeficiency Virus
IHNV Infectious Hematopoietic Necrosis Virus
IT Information Technology
mRNA Messenger RNA
NGO Non-Governmental Organization
NGS Next-Generation Sequencing
NRC National Research Council
NRCan Natural Resources Canada 
OECD Organization for Economic Cooperation and Development
PCR Polymerase Chain Reaction
PHAC Public Health Agency of Canada 
PMF Performance Measurement Strategy Framework
PWEF Photonic Wire Evanescent Field 
QIS Quarantine and Invasive Species
qPCR Quantitative PCR 
QTL Quantitative Trait Locus
R&D Research and development
RAD Restriction Site Associated DNA
RNA Ribonucleic Acid 
RNAi RNA Interference
S&T Science and Technology
SE Salmonella Enteritidis 
SNP Single Nucleotide Polymorphism
SOP Standard Operating Procedure
SSC Shared Services Canada
STAGE Strategic Technology Applications of Genomics in the Environment
STEC Shiga-toxin Producing
TB Tuberculosis
VTEC Verotoxigenic Escherichia coli
WG Working Group

Genomics R&D Initiative – Program Profile

The GRDI was established in 1999 to establish and maintain core genomics R&D capacity in federal departments and agencies and provides $19.9M/year, based on a three-year cycle, to: Agriculture and Agri-Food Canada (AAFC); Environment Canada (EC); Fisheries and Oceans Canada (DFO); Health Canada (HC); Public Health Agency of Canada (PHAC); National Research Council (NRC); and Natural Resources Canada (NRCan).

Projects funded under the GRDI are focused on departmental mandates and government priorities, and are strategically aligned with the objectives of the departments. They seek to uphold regulatory, public policy, and operational mandates in important areas such as health, food safety, sound management of natural resources, a sustainable and competitive agriculture sector, and environmental protection, with strong collaborations with university and private sectors.

New to this phase of the GRDI (2011-2014), is the mobilization of resources for concerted research on issues that are beyond the mandates of single departments. It supports highly coordinated interdepartmental projects along shared priorities and common goals. Two projects were identified for priority action: 1) Strengthening Food and Water Safety in Canada through an Integrated Federal Genomics Initiative; and 2) Protection of Canadian biodiversity and trade from the impacts of global change through improved ability to monitor invasive alien and quarantine species. All GRDI participating departments, as well as the Canadian Food Inspection Agency, have the opportunity to participate in these shared priority projects.

Resources

Table 1: Funding Allocations ($000)
Department/Agency Phase I
1999-2002
Phase II
2002-2005
Phase III
2005-2008
Phase IV
2008 - 2011
Phase V
2011 - 2014
Agriculture and Agri-Food Canada 17,000 18,000 18,000 18,000 15,300
Environment Canada 3,000 3,000 3,000 3,000 2,550
Fisheries and Oceans Canada 2,500 2,700 2,700 2,700 2,295
Health Canada / Public Health Agency of Canada 10,000 12,000 12,000 12,000 10,200
National Research Council Canada 17,000 18,000 18,000 18,000 15,300
Natural Resources Canada 5,000 6,000 6,000 6,000 5,100
Shared Priorities - - - - 8,955
Medical Research CouncilFootnote 1 500 - - - -
Total 55,000 59,700 59,700 59,700 59,700

All departments have levered the GRDI with allocations from their Abase resources and from successful collaborations. Table 2 provides an overview of resources invested in 2012-2013 in support of GRDI projects, and shows that non-GRDI funds represented more than twice the GRDI investments. Additional in kind investments estimated to more than $4 million included the sharing of technology platforms, materials, and expertise with a variety of collaborators in research areas that cut across traditional departmental sectors.

Table 2: Overall Investment in support of GRDI projects in 2012-2013 ($000)
Department/Agency GRDI Non-GRDI Total
National Research Council 4,800 10,089 14,889
Agriculture and Agri-Food Canada 4,800 3,223 8,023
Health Canada 1,600 1,409 3, 009
Public Health Agency Canada 1,600 3,954 5,554
Natural Resources Canada 1,600 2,815 4,415
Environmental Canada 800 2,090 2,890
Fisheries and Oceans Canada 720 1,626 2,346
Shared Priority Project
Quarantine and Invasive Species 1,862 3,037 4,899
Food and Water Safety 1,805 3,613 5,418
Coordination and Common Functions 313 87 400
Total 19,900 31,943 51,843

Planned Results

As part of NRC’s 2012-2013 Report on Plans and Priorities supplementary tables for the GRDI, the participating departments established a collective set of planned results:

  • Concerted interdepartmental research along shared priorities and common goals on issues that are relevant to the mandates of multiple departments;
  • Commercially-relevant advances in genomics R&D related to human health;
  • Using genomics to improve the value of Canadian crops;
  • Genomics knowledge and advice for the management of fisheries and oceans;
  • Genomic knowledge for the Canadian health regulatory system;
  • Genomic knowledge for forest generation and protection;
  • Genomics knowledge to strengthen Public Health programs and activities related to infectious and chronic disease; and
  • Enhance Environment Canada's applications of genomics-based tools and technologies for responsible decision-making.

To deliver on these planned results, departments and agencies have developed the following research program plans and activities:

Agriculture and Agri-Food Canada

Projects supported by the GRDI at AAFC will continue to align with the Canadian Crop Genomics Initiative, with some expansion into additional key crop kinds and related activities. Investments will continue to be made in three main areas 1) biodiversity, gene mining and functional analysis for the identification and extraction of genes for desirable traits; 2) delivery of genomics discoveries through bioinformatics and physical tools in order to improve access to both biological materials and data sets, and to assist and accelerate the adoption and commercialization of new technologies; and 3) enhanced efficiency of plant breeding. The program will continue to focus on addressing biotic and abiotic stress through functional genomics of disease and insect resistance and tolerance to stress such as cold, enhanced quality attributes in cereals, oilseeds and legumes, as well as platform technologies.

Fisheries and Oceans Canada

Genomics-enabled research within DFO will continue to be aligned within the following themes: 1) Genetic Profiling of Aquatic Resources: DFO has responsibility for providing scientific advice and research for over 650 fish, invertebrate, and mammal species. There is enormous potential for the development of genomic tools relevant to those species under management, and particularly those that are of management concern; 2) Research and Development of Genomic Approaches for Aquatic Animal Health Diagnostic Tools to Protect Aquatic Ecosystems: Aquatic animal health research under this theme includes the genomics research concerning the health of aquatic animals that fall under DFO legislative authority. Further research incorporating genomics approaches to aquatic animal health will better position Canada to respond and manage aquatic animal resources, particularly under changing environmental conditions; and 3) Aquatic Ecosystem Health: Genomics approaches offer opportunities for increasing our understanding of the aquatic ecosystem, and are anticipated to be an important tool for applying an ecosystem approach to managing aquatic resources and healthy and productive aquatic ecosystems.

Environment Canada

The GRDI is delivered through the Strategic Technology Applications of Genomics in the Environment (STAGE) program at Environment Canada. The STAGE program develops genomics-based tools and technologies to support EC’s policy development, regulatory decision making, and enforcement. EC will continue to show leadership in environmental genomics and foster collaboration in other departments and external institutions.

Genomics research supports the department’s Strategic Outcomes: Canada’s Natural Environment is Conserved and Restored for Present and Future Generations and Threats to Canadians and their Environment from Pollution are Minimized, by assisting in the delivery of EC's obligations as a signatory of, and regulator for, major environmental legislation and agreements such as the Fisheries Act, the Chemical Management Plan, and the Canadian Environmental Protection Act.

In order to support the strategic outcomes of the department, STAGE research priorities for 2012-2014 are as follows: Strengthen predictive models (e.g., tools to address the transport, fate, effects and risks of existing and emerging chemical, biological, and physical influences on organisms, biodiversity, ecosystem function, and water availability); Understand and monitor ecosystems (tools to understand and monitor aquatic and land-based ecosystems); Understand cumulative risks/impacts (e.g., tools to understand and predict cumulative impacts on, and risks to, ecosystem health from multiple stressors interacting over time); and Manage environmental risks (e.g., tools to manage environmental risks of chemical, biological, physical, and genetic pollutants).

Health Canada

Genomics research will continue to focus on four priority areas of investment for strengthening the department's regulatory role: 1) Regulatory knowledge on therapeutics and biologics: Studies will be conducted for the identification of biomarkers associated with the safety evaluation of health products; 2) Regulatory knowledge on food safety and nutrition: Genomics research will be undertaken to detect food-borne contaminants, to characterize the health effects of food contaminants, nutrients, novel foods/food ingredients, and pre- and pro-biotics for enhanced regulatory decisions, and to develop biomarkers to monitor cellular and physiological responses in the context of nutrition and disease susceptibility of defined populations; 3) Regulatory knowledge to protect human health from potential adverse effects of environmental contaminants, consumer products, and pesticides: Research will focus on effectively and efficiently assessing the hazards of environmental contaminants, occupational health hazards, pesticides, and consumer products; and 4) Research on socio-ethical impacts of genomics technologies and products: Bioethics and benefit-sharing best practices will be developed for genetic research, with studies pertaining to ethical, legal, and social issues of genomics to address the use of DNA samples for research purposes.

National Research Council

NRC is changing the way it does business by placing a much greater effort on engaging the private sector and public collaborators in strategic R&D. This approach is market-driven with a focus on understanding and addressing real industry issues such as increasing innovation capacity, reducing risk in early stage technology development, and facilitating the development and deployment of innovative products, processes and services for targeted markets. As part of the transformation, NRC uses a program-based management model with industry-focused programs and projects. These programs are agile and multi-disciplinary in nature, with sufficient critical mass to address the technology needs of existing and emerging sectors and deliver economical and immediately applicable solutions to technical and business challenges affecting the competitiveness of Canadian industry.

NRC-GRDI programs follow NRC’s approach to program-based R&D which first requires a clear statement of the strategic business need for such a program. This is accomplished via a well-prepared program business case, and the subsequent program business plan. These take into account the market opportunity, the requirements of both internal and external stakeholders, as well as NRC’s competencies in this field. Later in the process, a program management plan is created which translates the business need into clearly defined program goals and deliverables. For NRC-GRDI, investments are made in program areas requiring genomics-related activities to help industry and government tackle strategic national priorities through mission-oriented research and technology deployment. The current focus of NRC-GRDI supported programs are in: 1) Canadian Wheat Improvement; and, 2) Biologics and Subsequent Entry Biologics.

Natural Resources Canada

Genomics research addresses the challenges faced by Canada's forest sector by using that knowledge for commercial innovation. Canada's capacity and expertise in forest genomics will address the needs of the forest sector by: 1) identifying genes of commercially important traits such as wood quality, growth and resistance, giving tree breeders the ability to select superior trees in seedlings as young as a year; 2) the production of innovative molecular technologies that will allow the identification or diagnosis of potentially invasive pests; 3) furthering our understanding of the interactions between hosts and pests or hosts and beneficial microorganisms for the development of environmentally-friendly forest management approaches, including biological control methods; and 4) investigating bioenergy solutions via improved feedstock and/or novel enzymatic processes and associated value-added bioproducts.

Public Health Agency of Canada

For Phase V, PHAC has selected research projects that target high priority issues in the areas of infectious and chronic diseases. Projects related to infectious diseases address priority issues such as increasing our knowledge related to the emergence of drug-resistant bacterial pathogens, and related to emerging and re-emerging pathogens such as Ebola virus and Mycobacterium tuberculosis. PHAC also directs GRDI support to the priority area of food safety, enabling the public health networks that monitor and respond to food-borne pathogens to deploy innovative tools for rapid and accurate characterization of pathogens leading to improved responses to food-borne pathogens. In addition, PHAC researchers are creating automated bioinformatics processes for genomic sequence analysis. The tools produced will provide PHAC researchers, public health partners and federal researchers in other government departments with methods needed to accommodate burgeoning genomic data that can now be generated more rapidly than it can be analysed. The effect of nutritional status on the development and outcome of chronic diseases is being investigated by other GRDI supported projects at PHAC. In particular, researchers are investing the effect of vitamin D status on the development of type-2 diabetes and the role that variation in folate metabolism plays in risk of chronic disease. The GRDI projects at PHAC apply genomics approaches to generate leading edge knowledge to inform public health decisions and to develop innovative tools in response to the public health needs of the federal government and of our provincial partners.

Shared Priorities

The project Protection of Canadian biodiversity and trade from the impacts of global change through improved ability to monitor invasive alien and quarantine species (the Quarantine and Invasive Species project) aims at developing diagnostic tools based on DNA barcoding for the early detection, surveillance and management of hundreds of species, focusing on those that are or quarantine concern. It is coordinated by AAFC and involves CFIA, DFO, EC, NRCan, and NRC. The project Strengthening Food and Water Safety in Canada through an Integrated Federal Genomics Initiative (the Food and Water Safety project) aims at developing increased speed and reduced cost of genomics‐based methods for pathogen isolation, detection and characterization; and developing a federally integrated database to manage, store and provide access to genomic data and related information from food and water‐borne pathogens, focusing on Escherichia coli and Salmonella Enteritidis. It is coordinated by HC and involves AAFC, CFIA, EC, NRC, and PHAC.

Alignment with Government Priorities

The GRDI seeks to support increasingly complex federal evidence-based regulatory and policy decisions required by the respective mandates of participating departments and agencies, as well as the development of new policies and standards, within the realm of the specific role of federal research as presented in the current federal science policy framework (S&T Strategy, 2007), and focusing activities in areas where government is best able to deliver results. It also seeks to support the ability to anticipate and respond to the needs of Canadians in relation to areas of government responsibility for public health, the economy and the environment. For example, research funded by the GRDI has: 1) allowed genomics datasets to be developed and used for the most intensive real-time management of mixed-stock fisheries in the world, thus greatly increasing the effectiveness of conserving threatened Pacific salmon while harvesting more abundant stocks sustainably; 2) led to the development of methods to detect microbial contamination of water to aid municipal and provincial governments in the management of water resources; and 3) produced a Salmonella identification method that reduces costs by 70% and identification time from 4 days to 7 hours. Provincial and municipal governments are also users of GRDI knowledge for the management of public resources.

Projects funded under the GRDI are focused on departmental mandates and government priorities, and are strategically aligned with the objectives of their respective departments.

All research and innovation activities at AAFC (including those of the GRDI) directly support the achievement of prioritized research outcomes. Funding from the GRDI has enabled AAFC to develop and strengthen the Canadian Crop Genomics Initiative through investments in plant genomics and the formation of multi-disciplinary teams across Canada. Under the agriculture portfolio, CFIA will contribute to shared projects to support its regulatory mandate, and will benefit from interdepartmental integration of common functions.

National coordination for genomics research at DFO is provided by the Biotechnology and Genomics Program. The Biotechnology and Genomics Program supports genomics research for Economically Prosperous Maritime Sectors and Fisheries and Sustainable Aquatic Ecosystems, two of the three Strategic Outcomes of the Department’s Program Alignment Architecture. Genomics research is building the scientific knowledge base and expertise necessary to support priorities for fisheries and oceans management.

Genomic R&D activities funded by GRDI at EC support its three Strategic Outcomes. Environmental genomics R&D activities deliver practical application that contribute to evidenced-based decision making for the risk assessment of chemicals; a better understanding of populations of wildlife that are at risk and migratory birds; and a better understanding and monitoring of Canada’s ecosystems.

The GRDI at HC contributes to the generation of knowledge that is required for the effective regulation of health and food related technologies. The Departmental Science Plan describes the contribution of genomics research towards improving policy development and regulations, informing and engaging the public on emerging technologies and supporting HC’s efforts in harmonizing policies nationally and internationally. The GRDI addresses a number of strategic objectives under the Program Activity of Emergent Health Issues.

NRC-GRDI programs support one of NRC’s two Strategic Outcomes: Advancements in the development and deployment of innovative technologies in targeted Canadian industries and national priority areas in support of federal priorities in innovation and S&T, and to the Program Activity Health and Life Sciences Technologies. This is accomplished by contributing to research programs that focus on improving Canadian wheat, and on developing new biologics and subsequent entry biologics.

At the Canadian Forest Service (CFS) of NRCan, the GRDI has developed the foundation for contributing to the Strategic Outcome Economic Competitiveness and to the Program Activity Economic Opportunities for Natural Resources. It contributes to the CFS Intended Outcome: Advancing Forest Product Innovation. Resulting from this foundation are important amounts of data, infrastructure, and collaborations that are delivering practical applications.

Within PHAC, projects funded by the GRDI support the over-arching strategic outcomes of promoting health, reducing health inequalities, as well as preventing and mitigating injuries and disease. Researchers create innovative tools that apply genomic and bioinformatic technologies for more effective public health interventions targeting infectious and chronic diseases. In addition, the GRDI generates leading edge scientific knowledge to support public health decision making and program development. By driving collaboration and knowledge exchange among public health professionals working in federal, provincial, territorial, municipal and non-government organisations, the GRDI facilitates the integration of reliable and current information into public health decision making and interventions at all levels across Canada. The development and application of leading-edge public health science and of tools to provide specialized laboratory testing and reference services that will contribute to better public health and improved responses to emerging health risks fall directly within the Program Activity of Science and Technology for Public Health.

The federal science policy framework is currently provided by Mobilizing Science and Technology (S&T) to Canada’s Advantage (hereafter referred to as the S&T Strategy), a strategy released by the Federal government in May 2007 that is committed to position Canada for global knowledge leadership. The GRDI contributes to the three S&T advantages for Canada outlined in the S&T Strategy (knowledge, people, entrepreneurial) with its focus on knowledge generation for evidence-based decision making, the recruitment and training of highly skilled personnel, and major collaborative relationships with academia and the private sector to deliver concrete results. It is also congruent with the vision presented in the S&T Strategy of what research should be pursued inside federal laboratories. It generates knowledge that helps support governmental mandates, formulates standards and regulations, facilitates evidence-based decision making and policy development, and develops novel applications related to key federal public-policy objectives in all life science sectors. Transformational research aims to support the competitive needs and economic viability of Canadian enterprises, including small and medium-size enterprises. The GRDI supports federal regulators in their evaluation of genomics data, as well as outreach activities to facilitate access to clear and accurate information on genomics R&D.

Governance, Coordination and Accountability

Departments are vertically accountable in terms of authority to deliver on their mandate and to spend resources. Accountability is thus often viewed as a challenge to the management of shared programs that have a collective sense of purpose. Indeed, programs involving more than one department to jointly pursue common objectives present unique complexities for setting priorities and sharing resources.

To ensure sound management of the GRDI, the interdepartmental governance framework established under the leadership of NRC for previous phases of the GRDI will continue to oversee the collective coordination of the GRDI. The governance structure for GRDI includes three main elements: an ADM Coordinating Committee, an Interdepartmental GRDI Working Group and a Coordination Function, with support from Ad Hoc Advisory Committees when particular needs for expert advice arise.

ADM Coordinating Committee (ADM CC)

An interdepartmental ADM CC, chaired by the lead agency (NRC) with membership at the ADM-level from each of the organizations receiving funding, the CFIA, and guest representatives from Industry Canada and Genome Canada. It is responsible for the overall strategic direction for the GRDI and approval of investment priorities. It ensures that effective priority setting mechanisms are established for the GRDI, and that government objectives and priorities are addressed. The Committee also ensures that common management principles are implemented and collaborations between organizations are pursued wherever relevant and possible. It typically meets three times a year at the call of the Chair, more often when warranted by specific needs for decision-making.

Interdepartmental Working Group (WG)

An interdepartmental GRDI WG supports the work of the ADM CC. It is chaired by the lead agency (NRC) with membership at the Director level from all participating departments/agencies, the CFIA, and Industry Canada. The mandate of the WG is to provide recommendations and strategic advice to the ADM CC regarding strategic priority setting and overall management of the GRDI. The WG is responsible for providing direction to GRDI program activities related to operational delivery, implementation planning and investment priority setting. The WG also supports evaluation and reporting requirements related to the GRDI. It meets about every two months, more often when warranted by specific needs for recommendations and advice, as well as to develop the GRDI Annual Performance Report.

GRDI Coordination Function

The Coordination Function for the GRDI is housed at NRC, the GRDI lead agency. It provides GRDI-wide program coordination, communication, networking and outreach support. This includes support to the ADM CC and the GRDI WG, transparent and effective communication to departments of the planning cycle, process requirements, financial administration and other project management requirements, and support for interdepartmental shared project planning and implementation. This function is also responsible for conducting studies and analyses to serve as input to determination of GRDI-wide research priorities, and providing management and administration support, as well as support for performance management, reporting, evaluation, and communications. It will be funded through the shared priorities portion of the GRDI.

Advisory Function

An advisory function is required, especially when it comes to engaging stakeholders and potential end users to address needs in the planning stages, and to seek strategic advice on priorities. The GRDI uses several means of seeking expert input: planning workshops; one to one meetings with stakeholders and end-users; or by convening ad hoc committees when particular needs arise (for example, to advise on common functions for the GRDI).

Performance Measurement Strategy Framework

Consistent with the concept of modern comptrollership that focuses on results-based control systems, a horizontal Performance Measurement Strategy Framework was developed for the GRDI in 2011 to formalize the commitment of the eight departments and agencies involved in the GRDI regarding the common measurement and accountability requirements associated with this Initiative. An overview of the Performance Measurement Strategy Framework is provided in Appendix B, as well as the logic model that reflects the overall objectives for the GRDI, leading to the uptake and application of the knowledge and tools it generates for policy and regulatory decisions, for addressing key public policy priorities, as well as for supporting private sector innovation.

Performance

Governance

Fiscal year 2012-2013 was the second year of Phase V programs.

GRDI Interdepartmental Coordination

Ongoing coordination was provided by NRC, including timely secretariat support to GRDI departments and agencies and the implementation of the GRDI governance framework, management and operating processes that were put in place for Phase V. Two meetings of the ADM Coordinating Committee and 9 meetings of the GRDI WG were held to allow for timely collaborative decisions.

A communication strategy for the GRDI was finalized and approved by the GRDI ADM CC at their 26 June 2012 meeting and a communication working group created under leadership of NRC communications. This group led the design and completion of an end-user survey to assess their level of awareness of the GRDI, to be used as a baseline to evaluate the effectiveness of future communications activities. An updated version of GRDI web site was launched in January 2013 to comply with the new Government of Canada Web standards.

The implementation of shared priority projects was supported: funding was made available to participating departments based on the approved Project Charters; a stakeholder review was completed in June 2012, bi-annual progress reports were presented to the ADM CC (June and December 2012), and a mid-term performance review was completed in March 2013. The mid-term review independent expert panels highlighted the importance of the shared priority research projects and the effectiveness of the interdepartmental approach to build synergies, maximize resources, and transfer results to end-users. A bioinformatics workshop was held in October 2012 to strengthen collaborative relationships between GRDI scientists and the Science Portfolio of Shared Services Canada to support GRDI computing requirements.

The GRDI Performance Measurement Strategy was implemented with the finalization and approval by the ADM CC of the Annual Performance Report for 2011-12, input into NRC’s Departmental Performance Report and Report on Plans and Priorities, as well as the continued implementation of the Management Response and Action Plan to act on recommendations from the 2010 evaluation.

The Office of the Comptroller General included the GRDI in its Horizontal Internal Audit of Compliance with the Policy on Management, Resources and Results Structures in August 2012. It concluded for the GRDI that: roles and responsibilities were well defined; accountability structures adequately designed; horizontal initiative activities monitored; and that the results of the overall initiative were reported publicly. No recommendations for improvement were addressed to NRC.

Mandated Research

Departments and agencies frame their GRDI program within the scope of existing program areas aligned with their respective Strategic Outcomes, Activities, and Sub-Activities defined in their Program Alignment Architecture. Continued support was provided to Phase V projects based on adequate performance. These projects were selected based on their contribution to identified priorities where federal scientists had distinct expertise, using balanced portfolio approaches, following formal approval processes.

Shared Priorities

Both shared priority projects have identified detailed governance structures in their Project Charters to ensure seamless integration and clear roles and responsibilities. These include Management Advisory Committees, comprising senior managers from each of the participating departments and agencies, a Science Advisory Board with members representing academia, government and industry, theme leaders, dedicated project managers, and overall leadership by Scientific Project Coordinators. Ongoing open communication was established through conference calls, emails, presentations, and regularly scheduled meetings, thus ensuring the sharing of update and decision-making fora. Web-based SharePoint sites were put in place for both projects to host the most current versions of all the project related documents for access by all project participants and advisory boards.

Research and Development

Research and development is the central component of this initiative to respond to priorities, support governmental mandates, inform policy and regulatory decisions, and foster innovation. All activities surrounding the actual conduct of R&D, the transfer of technologies and results to stakeholders for uptake and application, and the communication of these results are critical to ensuing impacts and are thus included in the performance measurement framework.

Direct scientific outputs for 2012-2013 and quantitative indicators for performance evaluation are enumerated in Annex 2 by department/agency, for: collaborations, scientific contributions, communications, knowledge and technology transfer, as well as research tools and processes. Highlights of the results achieved in 2012-2013 against planned results are provided in Annex 3, and Annex 4 presents a list of research tools and processes developed under the GRDI.

Awards and prizes were awarded to several GRDI scientists to recognize the excellence of their research:

  • Stephen Gleddie (AAFC) and Aiming Wang (AAFC) received Queen’s Diamond Jubilee medals for excellence in and contribution to agriculture;
  • Sean Kennedy (EC) received the Queen Elizabeth II Diamond Jubilee medal;
  • John Lawrence (EC) was awarded a Distinguished Visiting Scientist Fellowship from The Commonwealth Scientific and Industrial Research Organisation (CISRO) in Australia;
  • John Pezacki (NRC) received the Rutherford Memorial Medal in Chemistry from the Royal Society of Canada;
  • John Pezacki (NRC) received the Queen Elisabeth II Diamond Jubilee Medal for contributions to Canada;
  • Maureen O’Connor (NRC) won the Gervais Dionne award, which rewards the most promising technology;
  • Roger P. Johnson (PHAC) received the Queen Elizabeth II Silver Jubilee Medal for scientific research; and
  • Gary Van Domselaar (PHAC) received the Public Health Agency of Canada Research Merit Award.

Maintenance of Capacity

Highly Qualified Personnel

In 2012-2013, close to 900 persons were engaged in projects funded by the GRDI. The GRDI supported 715 scientific and technical staff, 67post-doctoral fellows, 106 students (PhD, MSc, BSc, and Co-op) and 5 administrative officers, representing 380 full time equivalents.

Facilities

Departments continued to invest in core infrastructure facilities and funding was allocated towards the purchase, maintenance and upgrading of laboratory equipment. For example:

At AAFC, contributions were made to the purchase and/or maintenance of a number of DNA sequencers. Other equipment that was supported or purchased included a Chemi Doc system, a Digital Droplet PCR, an Ultra-low freezer, and a 96-channel automatic pipettor. A console upgrade to a Bruker 500 NMR was made to improve sensitivity for secondary metabolite identification.

The HC core genomics laboratory maintains a state-of-the-science DNA microarray facility including: Agilent DNA microarray scanner and associated labware and software; Agilent Bionalyzer; Nanodrop spectrophotometer; two CFX real-time PCR machines; GeneSpring Gx microarray analysis software; Ingenuity Pathway Analysis; NextBio; and a core informatics platform including two high-end workstations (T7500) and three Dell R-900 servers. Support from the GRDI has allowed the leverage of internal funds to expand the facility and include next generation sequencing capabilities. The laboratory is now equipped with the Life Technologies Ion Proton and all required bioinformatics infrastructure (servers, operating systems, back-up and software) that will enable the evolution of genomics analyses from DNA microarrays to RNA-seq, ChIP-seq and full genome sequencing. International recognition of the high caliber of experiments conducted in the facility has also led to invited involvement in validation exercises for RNA-seq through ILSI-HESI.

GRDI funding in HC’s Food Directorate continued to expand capacity for genomics and proteomics data analyses and supported the maintenance of bioanalytical capacity in the Bureau of Food Surveillance and Science Integration. Non-capital items (part of operating expenditures), including computer hardware and software and application licenses were purchased to update and expand capacity for genomics data analyses. Two MacBook pro computer systems were purchased to enable NGS sequence data analysis and use of open-source unix-based software. Training was obtained for the Next-Generation sequencer (Illumina MiSeq). In addition, the Bureau of Food Surveillance and Science Integration was able to lend a 6-core 3.2GHz processor, with 12Gb DDR3 RAM and a 1 TB hard drive to help with bioinformatics-related work.

NRC has shifted the development and maintenance of genomics-related research equipment from its program-level investments to its Investment Plan (capital both >$250K and <$250K). Core infrastructure facilities such as DNA microarray and proteomics are now supported in this manner.

At EC, laboratory equipment was purchased including RT-qPCRs, 454-sequencer, growth chambers for algal/cyanobacteria culture collection, robotic work station for extraction, purification and enrichment of mRNA, chemiluminescence detector, and a confocal laser microscope. An Avian ToxPCR array was also developed for the National Wildlife Research Centre Molecular Toxicology Laboratory.

Infrastructure acquisitions for PHAC projects consisted of a Qubit 2.0 fluorometer and a high speed microplate shaker to support extensive RNA and DNA analyses. Two ViaFlo 96 automated high-throughput pipettors were also acquired, as were annual licenses for numerous genomics software applications. GRDI funds were used to directly support ongoing maintenance and support of over 1 million dollars of PHAC funded capital equipment, including flow cytometers, q-RT PCR machines, and diagnostic equipment. In addition, GRDI projects leveraged in kind use of PHAC funded capital equipment including state-of-the art computing infrastructure largely housed at the National Microbiology Laboratory, massively parallel sequencing infrastructure, and the proteomics core facility.

For the Quarantine and Invasive Species project, AAFC purchased new hardware infrastructure to support computation and storage and leveraged several local labs and stations to contribute to make a larger purchase for the benefit of the interdepartmental team. Numerous next-generation sequencing (NGS) analysis programs have been installed, and the team has set-up basic computational pipelines for genome re-sequencing, and RNA sequencing data.

Appendix A

Annex 1 – GRDI Projects and funding allocations from GRDI

GRDI funds ($) Project Title
Quarantine and Invasive Species
1,862,341 Protection of Canadian biodiversity and trade from the impacts of global change through improved ability to monitor invasive alien and quarantine species
Food and Water Safety
1,805,321 Strengthening food and water safety in Canada through an integrated federal genomics initiative
Agriculture and Agri-Food Canada*
1) Biodiversity, gene mining and functional analysis for the identification and extraction of genes for desirable traits, including mechanisms of plant resistance to biotic and abiotic stress and insect and pathogen virulence
260,169 Bertha armyworm (Mamestra configurata): genomics, population dynamics and biodiversity of pest and pathogens
214,997 Camelina - an integrated industrial oilseed crop platform for Canada
242,441 Defining molecular virulence in Fusarium and unique resistance mechanisms in wheat and maize towards reducing Fusarium mycotoxins in Canadian cereals
46,634 Exploitation and characterization of carbohydrate active enzymes from metagenomic and metatranscriptomic rumen samples
108,222 Exploiting wheat leaf rust fungus molecular resources to combat cereal rust diseases
248,214 Exploiting the biodiversity within the Brassica crops and exotic Brassicaceae
47,814 Fine mapping of the Sr9 stem rust resistance locus in wheat
41,403 Functional analysis of durable wheat rust resistance.
73,786 Genetic determinants of cultivar-specific virulence in the root rot pathogen Phytophthora sojae
57,694 Genetic characterization of the orange wheat blossom midge resistance gene Sm1
91,312 Genetics and genomics of symbiotic N2 fixation: all in the name of entry
153,704 Genomic-assisted strategies for evaluating and utilizing potato genetic resources
112,377 Genomics of multi-toxin synergies and interactions of Fusarium species in Canadian cereals to guide the development of resistant crops, mycotoxin monitoring, and hazard characterization
61,878 Next-generation genomics for oat improvement
107,025 Toward development of next generation resistance to soybean mosaic virus: genomics and genetics of soybean-virus interactions
2) Delivery of genomics discoveries through bioinformatics and physical tools in order to improve access to both biological materials and data sets, and to assist and accelerate the adoption and commercialization of new technologies
44,112 Prototyping the Microsoft surface for bioinformatics
3) Enhanced efficiency of plant breeding
187,588 Cell penetrating peptide transfection technology validation and deployment in Research Branch - Enabling functional genomics programs
248,260 Identifying and modulating determinants of DNA recombination to accelerate genetic improvement of crops
63,160 Managing crop reproduction
Environment Canada
113,400 Genomics research in support of risk assessments under the Canadian Environmental Protection Act of existing and new microbial substances
54,000 Metagenomic and DNA microarray characterization of water quality in shellfish areas monitored by Environment Canada
67,500 Development and validation of a crustacean microarray and correlation of gene expression profiles with traditional toxicological end-points for contaminant exposure
69,300 Avian toxicogenomics and adverse outcome pathways - New tools for risk assessment
100,800 Metagenomic tools for assessment and monitoring in aquatic ecosystems
33,800 Determining breeding source populations of purple sandpipers (Calidris maritima) wintering along eastern Canada and the northeastern United States
80,500 Use of high throughput genomics to predict the potential health effects of oil-sands contaminants on fish health
26,173 Genomic approach to toxic and harmful algal bloom prediction and management
35,100 Elucidating the relationship between toxicogenomic gene expression profiles and functional biological outcomes in underlying rainbow trout and neonate Daphnia magna
97,200 Evaluation of the toxicity of emerging contaminants in aquatic organisms using genomics
17,577 Testing the role of genetic variation in adaptation to climate change in Canadian seabirds
53,150 Using toxicogenomics in wood frogs and the adverse outcome pathway for environmental effects monitoring of oil sands industrial development
51,500 Novel stress biomarkers to study impacts of large-scale environmental changes on health of wildlife
Fisheries and Oceans Canada
66,101 Stock delineation of redfish (Sebastes mentella) based on genetic analyses of archived otoliths
192,668 Rapid SNP discovery and genetic mapping using next-generation sequencing: fostering the tools and expertise for genomic based management in model and non-model marine organisms
96,226 Development of molecular genetic markers for investigations into climate induced selection and usage in genetic mixed stock analysis of Atlantic salmon in the Northwest Atlantic
14,885 A genomic and telemetric approach to measure Atlantic cod population structure, and its application to Marine Protected Area effectiveness
144,167 Genomic characterization of physiologically compromised wild salmon
60,850 Identification and characterization of infectious hematopoietic necrosis virus carrier state in sockeye salmon using genomic tools
79,573 Arctic fish genomics as 'sentinels' of ecosystem integrity and change
65,530 Low pathogenic infectious salmon anemia virus variant in vivo: a comparative genomic study
Health Canada
194,000 Genomic characterization of clinically important foodborne isolates of Campylobacter and Listeria impacting public health
228,000 Immunotoxicogenomics and food allergy: developing a genomics assay to assess chemical food contaminants that modulate pathways leading to food allergy
220,000 Genomic characterization of tissues from P53+/- transgenic mice exposed to genotoxic and non-genotoxic carcinogens for developing short term cancer bioassays
150,000 Genomic analysis of mesenchymal stem cells to develop high throughput diagnostics for measuring the medicinal ingredient and tumourigenic contaminants in stem cell based health products
400,000 Integrating genomics endpoints into regulatory toxicology
258,000 Toxicogenomics for mixture toxicology: genomics-guided proteomic approach to identifying biomarkers of exposure and effect for carcinogenic complex mixtures in the environment
National Research Council
1,353,687 Wheat Improvement Flagship: Enhanced fusarium and rust tolerance
1,213,187 Wheat Improvement Flagship: Genomics-assisted breeding
1,234,118 Wheat Improvement Flagship: Abiotic stress
67,529 Wheat Improvement Flagship: Seed development
931,479 Biologics and Subsequent Entry Biologics: Development of support technology
Natural Resources Canada
448,000 Applied genomics for tree breeding and forest health
180,000 Spruce budworm eco-genomics: from population dynamics to population suppression
272,000 Genomics-enhanced next generation forest disease diagnostic and monitoring
38,000 Development of a method to detect mRNA by reverse transcription loop mediated isothermal amplification as an indicator of viability of pinewood nematode in wood products
216,000 Genomics of tree-microbe interactions
156,000 HApInomics: host, Agrilus planipennis integrative genomics
Public Health Agency of Canada
80,304 The modifying effect of genetic polymorphisms involved in folate and B12 metabolism on the relationship between folate/B12 intake and vitamin status
94,475 Prospect for proteomic biomarkers of inflammation to predict early risk of type II diabetes and to monitor response to nutritional intervention by vitamin D
92,654 New technology for HIV drug resistance testing – a model for integrating next generation sequencing and data analysis
94,475 Identification of targets to monitor the dissemination of carbapenem-resistance genes in enterobacteriaceae
141,712 The association of vitamin D insufficiency and related genetic variants with tuberculosis infection and disease in a Canadian cohort
132,265 Uncovering the signatures of Mycobacterium tuberculosis specific immune responses to distinguish active versus latent tuberculosis infection
85,027 Molecular characterization of Salmonella Enteritidis for surveillance and control of foodborne illness
94,475 Improving the accuracy of automated prokaryotic genome annotation
236,187 A rapid geno-serotyping tool for the classification of Salmonella serovars
283,423 High-throughput genomics and proteomics for public health molecular epidemiology: next generation laboratory workflow for the investigation and response to food and waterborne bacterial outbreaks and endemic disease
141,712 Application of comparative genomics to the identification of shiga-toxin producing Escherichia coli subgroups and pan-genomic markers frequently associated with human disease
*Non-pay operating expenditures only

Annex 2 – Quantitative Indicators for Performance Measurement

Research and Technical Personnel

Research and technical personnel by department/agency expressed in terms of number of persons engaged in projects funded by the GRDI. It includes everyone who worked on the project, including but not exclusive of personnel financed through GRDI funds.

Number of Research and Technical Personnel
AAFC DFO EC HC NRC NRCan PHAC QIS FWS Total
Research scientists 31 11 19 16 53 15 30 30 69 274
Research professionals 5 7 11 22 15 13 14 17 34 138
Research technicians 87 15 21 10 87 17 6 23 37 303
Post-doctoral/visiting fellows 10 1 7 6 20 15 3 5 0 67
Graduate students 26 2 5 3 0 5 3 2 6 52
Undergraduate students 0 2 10 1 3 4 9 25 0 54
Administrative officers 0 0 4 0 0 0 0 1 0 5
Total 159 38 77 58 178 69 65 103 146 893
Total FTEs 82.9 10.3 29.5 24 92.6 38.6 22.2 28.8 51.5 380.4

Collaborations

Collaborations by department/agency, expressed in terms of number of research collaborators. Research collaborators are considered to be collaborators from an organization that is different from that of the project’s lead scientist, and who are directly involved in the delivery of the project. The GRDI involves many research collaborative relationships among government-based science organizations, universities, industry, and other research institutes, both nationally and internationally.

Number of Collaborators
AAFC DFO EC HC NRC NRCan PHAC QIS FWS Total
Universities (Canadian) 12 6 26 7 9 9 14 12 1 96
Universities (international) 20 0 17 2 5 10 1 21 2 78
Other international research organizations 13 6 3 2 2 5 4 4 0 39
Other Canadian research institutions 5 1 5 0 2 1 0 4 0 18
Private sector 3 3 6 2 0 2 1 2 1 20
Other government departments 11 3 17 10 1 2 6 21 6 77
Other public sector organizations such as provinces and municipalities and NGOs 2 5 6 0 1 3 7 1 2 27
Participation in national or international genomics-related committees 9 0 3 3 0 3 0 2 5 25
National or international genomics research peer review committees served on 1 0 14 0 0 0 0 0 0 15
Total 76 24 97 26 20 35 33 67 17 395

Scientific Contributions by Department

Scientific contributions include scientific information and publications produced in 2012-2013, accepted, in press, or published, including online. They include contributions from any of the project team member as long as they are related to the GRDI project. They also include contributions deriving from a previous phase of the project, if produced in the fiscal year being reported on. They do not include submitted papers or publications in draft form. They do not include contributions that were reported in previous years.

Number of R&D Outputs
AAFC DFO EC HC NRC NRCan PHAC QIS FWS Total
Publications in refereed journals 61 13 20 17 9 42 12 16 4 194
Publications in refereed conference proceedings 7 - 1 6 0 5 8 0 2 29
Technical reports 0 1 5 0 0 0 2 0 1 9
Books (edited, written) 1 0 0 0 0 0 0 0 0 1
Other publications (ex. book chapters, monographs, abstracts, notes, etc. industry magazines) 12 1 4 0 0 21 3 1 1 43
Poster presentations at conferences 32 - 6 29 2 27 18 2 5 121
Invited presentations 19 12 9 8 0 20 6 12 16 102
National conference presentations 5 0 5 5 0 20 10 1 1 47
International conference presentations 31 2 7 11 3 9 8 3 4 78
Active participations in national conferences (organizer, chair, panel discussion etc.) 5 0 4 0 0 4 5 0 0 18
Active participations in international conferences (organizer, chair, panel etc.) 10 0 3 3 0 3 1 2 4 26
Editorial posts for national and international journals (excludes peer reviewers) 17 3 4 0 0 4 2 6 1 37
Deposits in genomics related databases or libraries 16 4 13 5 0 17 0 0 0 55
New genomics related databases or libraries 6 0 1 0 2 6 1 0 1 17
Awards, prizes 2 1 2 1 1 1 0 0 4 12
Total 224 37 84 85 17 179 76 43 44 789

Communications products

Number of Communications Products
AAFC DFO EC HC NRC NRCan PHAC QIS FWS Total
Media interviews 3 7 5 0 3 0 0 0 2 20
Press releases and announcements 1 0 1 0 1 0 1 0 0 4
Newspaper and magazine articles 6 2 0 0 17 0 0 0 0 25
Community presentations 0 0 1 0 0 0 0 4 0 5
Brochures, fact sheets, web pages 2 2 3 0 1 1 1 0 0 10
Total 12 11 10 0 22 1 2 4 2 64

Knowledge/Technology Transfer

Number of Knowledge/Technology Transfers
AAFC DFO EC HC NRC NRCan PHAC QIS FWS Total
Outreach activities 9 1 7 12 0 0 8 1 1 39
Material transfer agreements 27 0 0 0 9 0 0 0 1 37
Transfer of standard operating procedures 4 0 1 0 0 0 1 0 2 8
Disclosures 0 0 0 0 0 0 0 0 0 0
Active patents, patent applications, patents issued 16 0 0 1 0 0 0 0 0 17
Licenses issued 0 0 1 0 0 0 0 0 0 1
New formal collaborative agreements / standard operating protocols 0 1 3 0 0 0 0 0 0 4
Knowledge transfer workshops with stakeholders/end-users 1 1 7 0 0 0 0 18 2 29
Requests for research results, papers, collaborations 28 6 0 1 0 0 1 0 0 36
Total 85 9 19 14 9 0 10 19 6 171

Research tools and processes

Research tools and processes include those produced in 2012-2013, deriving from previous phases of the GRDI if produced in 2012-2013, as well as produced in previous years if they have been improved since last reported on.

Number of Research Tools and Processes
AAFC DFO EC HC NRC NRCan PHAC QIS FWS Total
Research tools 16 0 13 9 2 4 5 2 4 55
Research processes 8 0 10 3 5 3 7 2 1 39
Total 24 0 23 12 7 7 12 4 5 94

Annex 3 - Highlights of Results Achieved in 2012-2013

Concerted interdepartmental research along shared priorities and common goals on issues that are relevant to the mandates of multiple departments

Quarantine and Invasive Species Project

Protection of Canadian biodiversity and trade from the impacts of global change through improved ability to monitor invasive alien and quarantine species

Participating Departments/Agencies: AAFC, CFIA, EC, DFO, NRC, NRCan

Scientific Coordination: AAFC

Project Management: CFIA

The Quarantine and Invasive Species project is a collaborative effort by 28 Principal Investigators from six departments and agencies (AAFC, CFIA, DFO, EC, NRCan, NRC) focusing on the protection of Canadian biodiversity and trade from the impacts of global change through an improved ability to monitor invasive alien and quarantine species. These species can cause millions in economic losses, result in trade disputes and border closures, cause irreversible environmental damage, and require vigilance and rapid responses when such a species is newly detected in Canada.

Optimization and standardization of nucleic acid extractions

The objectives of this sub-project are to optimize and standardize methods for nucleic acid extraction for 1) preserved and archived tissues originating from the various federal collections and 2) bulk samples collected in the field for use in sensitive direct detection. Protocols for DNA extraction from the various samples have been tested or developed. PCR primers were optimized. A detection assay of DNA on bulk insect samples is being developed. The team has selected the best commercial kits for its purpose and published protocols for double stranded RNA extraction of plant viruses. The team has also generated a DNA extraction Standard Operating Procedure (SOP) for sampling plant material from herbaria. A microfluidic device prototype for the concentration of fungi of sizes ranging from 25 to 40 um has been developed and tested.

Barcoding of aquatic invasive species of highest risk to Canadian native fauna and trade

The general objectives of this sub-project are to generate research outputs and outcomes that will (1) enable enforcement by DFO of impending Aquatic Invasive Species regulations that will be part of a new or revised Fisheries Act; and (2) support EC’s primary responsibility areas of Ecosystem Sustainability – Protecting National Capital, and Environment Protection – Understanding Cumulative Risks. The focus is on generating reference DNA sequence datasets, first to attain molecular species identification capabilities for key aquatic invaders and then for use in the development of rapid and accurate molecular detection tools that will enhance Canada’s ability to prevent new aquatic invasions. The team has evaluated specimen quality and genes for barcoding and determined the need for additional freshwater fish sampling. Species on the list of potential invasive species and closely related species were also evaluated to ensure that banned species could be discriminated from other species. Several collaborations have been established to secure samples from reference collections. The team has established strategies and workflows for specimen processing in the lab and over one thousand parasites specimens have been sent for sequencing.

Barcoding of quarantine and invasive species in terrestrial ecosystems

This sub project focuses on species found in terrestrial ecosystems in Canada that are of quarantine significance and of economic importance to Canada, particularly to agriculture and forestry. Reliable taxonomies and rapid, accurate identification methods are central to early detection, monitoring and management of these quarantine and invasive species. The main objective is to generate DNA barcode libraries that will provide baseline identifiers for confirmation of identities. Second and possibly third barcode genes will be explored, particularly where they might help in increasing the detection resolution between closely related, recently radiated species. Laboratory protocols for the production of DNA barcodes were identified or developed and tested. A list of the non-native terrestrial arthropod species in Canada has been compiled and updated and nematode samples have been collected. Optimized protocols were used for DNA extraction from the AAFC Fungal Herbarium collection (obligate plant quarantine fungi) and a number of taxa have been sequenced. Cultures were obtained for ten most unwanted forest fungal pathogens, as established by NRCan, CFIA and Canadian forest pathologists, as well as of the quarantine agriculture fungi that were not in the AAFC Canadian Collection of Fungal Cultures, and their DNA was extracted. The team optimized the experimental conditions for rapidly determining the sequences of samples potentially contaminated with Phytoplasma spp using archived samples of known status. The team designed and optimized novel sets of universal primers for the different target groups. A virus collection has also been started and the collection of invasive plants from herbaria is underway. The detection of a new non-indigenous bark beetle in the forests of southwestern British Columbia has confirmed the establishment of the species in Canada and has been communicated to the CFIA, Canada’s quarantine regulatory agency.

Direct detection of quarantine and invasive species

In this sub-project, several themes have been developed to evaluate the application of next generation sequencing methods for the detection of diverse groups of invasive species from bulk environmental samples. Each theme addresses a real, practical need to either detect invasive species in a matrix not previously considered useable or to radically improve and expand on current detection methods with the ultimate goal of directly incorporating these new methods into federal government monitoring, surveying and diagnostic testing. The team obtained samples to determine the efficacy of next generation sequencing to identify species in bulk insect samples. Supplemental collections of bark and woodborers are currently being obtained through rearing of naturally attacked logs of five species of trees from coastal and interior of British Columbia. The team recovered more than 38 species of bark beetles from the 161,000 bark beetles identified to date. Nine individuals of a non-indigenous bark beetle new to British Columbia have also been identified. Construction of initial standardized samples of bark beetles for next generation sequencing has been completed. Aphid collection is underway. Sampling of viruses infecting fruit trees and grapevines was completed and double stranded RNA isolation has been completed. Nucleic acid extraction procedures have been identified that should allow reliable detection and identification of any viruses present in samples screened by next generation sequencing for alien invasive species.

Bioinformatics

The objective of this sub-project was to create a cyber-infrastructure platform to manage and analyse data generated by the other sub-projects. The goal is to have a biodiversity platform that includes the repositories and tools necessary to store information related to environmental samples and individual specimens, and provides the ability to design and execute automated analysis “workflows”, visualize the results, export data at any stage for external analysis and explore project metadata. This sub-project leveraged in-kind support for informatics, including core informatics staff, infrastructure, and applications established at AAFC based on past multi-departmental projects and recent professional staffing actions in biodiversity bioinformatics. As originally planned, external projects and tools were leveraged where components could be integrated into the biodiversity informatics platform. Work with Shared Services Canada (SSC) and AAFC Information Systems Branch staff to provide other government department collaborators with access to this environment, and to overcome IT policy challenges is ongoing. Standards required for the capture and management of specimen vouchers, DNA extraction and sequencing information were evaluated and implemented in a custom-made spreadsheet as an intermediate step until other federal collaborators are able to directly access the project database. Modifications required to permit the AAFC Specimen database to act as the repository for GRDI project data are nearing completion. Three sequencing platforms were used. For Sanger sequencing, protocols for the preparation and processing of individual targets for optimal PCR products have been developed and shared with the team, and samples are now being submitted by the team for sequencing on a routine basis. For 454 sequencing, the platform was upgraded and is available for planned target sequencing within the project. The longer length of sequence reads will provide significant additional resolving power to the data. For Illumina sequencing, the platform was upgraded to provide high volume (up to 600 Gb per run) in paired short read (2x100 bp) format, thus providing greater flexibility in scheduling sequencing runs. Protocols for preparation and processing of samples for sequencing have been disseminated to collaborators. The team has provided a series of technical full-day bioinformatics workshops to train collaborators.

Food and Water Safety Project

Strengthening Food and Water Safety in Canada through an Integrated Federal Genomics Initiative

Participating Departments/Agencies: AAFC, CFIA, EC, HC, PHAC and NRC

Scientific Coordination: HC

Project Management: HC

The Food and Water Safety project is a collaborative effort by six departments and agencies (AAFC, CFIA, EC, HC, NRC, and PHAC) to develop the tools and infrastructure needed to apply genomics-based methods for pathogen isolation, detection and characterization, focusing on verotoxigenic Escherichia coli (VTEC) and Salmonella Enteritidis (SE). It includes the development of an integrated federal system to manage, store and provide open access to genomic data, genomic-based methods to increase the discrimination of risk assessment criteria and improved identification of pathogen sources. Activities are organised under three major themes, (1) Isolation and Detection, (2) Information Generation and (3) Bioinformatics.

Isolation and Detection:

The main deliverable of this theme is to develop tools to isolate and detect VTEC from a variety of food, water and environmental matrices. All activities in 2012-2013 were on track. Good progress was made to finalize a procedure for the concentration and recovery of VTEC from ground beef and leafy greens. Progress was also made for differentiating live versus dead bacteria through the use of metabolic labeling combined with cell capture by antibody. This latter component is being integrated with the development of microfluidics- and photonic wire evanescent field (PWEF) waveguide sensor platforms to increase the sensitivity and reduce the time required for analysis. Work continued to adapt assays to several platforms with the potential to automate the assay procedure. A prototype for target concentration and capture based on magnetic separation in microfluidic devices was fabricated using low cost plastic materials. A centrifugal-based unit was also designed for the detection of multiple PCR amplification products by hybridisation. This design enables parallel processing of multiple targets and minimizes the volume of reagents and sample. A prototype has been fabricated and is currently being tested for hybridization efficiency.

Information Generation:

All activities in this theme were on track, despite delays related to strain selection, template preparation, and sequencing platform operations. Draft genome sequences were acquired for close to 220 VTEC and SE isolates, with additional prospectively-sampled strains expected to undergo whole-genome sequencing the following fiscal year. Sequence polishing and gap closure experiments for the selected subset of reference strains (11 VTEC and 9 SE strains) were initiated. Upon completion, these reference genomes will undergo full annotation of their gene products and detailed comparative genomic analyses. Environmental monitoring has detected non-O157 VTEC in three watersheds and two coastal regions. Many of these environmental isolates will be sequenced to investigate whether these strains pose a human health risk based on their genomic content relative to the genomes VTEC pathogen reference strains.

Bioinformatics:

Deliverables in this theme are centered on 1) the design and development of a computational platform for the storage, management, analysis, and reporting of microbial genomes and associated metadata; and 2) bioinformatics training workshops focusing on genomic epidemiology. Activities were on track for 2012-2013, except for delayed staffing due to restrictions linked to the Deficit Reduction Action Plan/Workforce Adjustment affecting all government departments. Full staffing except for one outstanding position was achieved in November 2012. Bioinformatics tools for large-scale storage and annotation of microbial genomes have been developed. The GView genome visualization tool has been modified to visualize up to several hundred microbial genomes and has an improved interface. Phylogenomics pipelines have been developed for closed genomes and draft genomes. A computational tool for in silico typing has been developed. An international consortium of subject experts for ontology engineering has been assembled and will meet in the third year of the project, and will guide database designs. Bioinformatics training activities are ahead of schedule: workshops have been developed and held for UNIX, Perl, and microbial informatics. A Genome Canada’s Bioinformatics and Computational Biology Large Scale Applied Projects competition proposal ($1.56M) to expand the ontology, tools, and training of this platform was awarded to Dr. Van Domselaar and co-applicants Dr. William Hsiao of the British Columbia Centre for Disease Control (BCCDC) and Dr. Fiona Brinkman of Simon Fraser University. This expansion of the platform will provide additional ontology development of epidemiology, additional platform functionality for pathogenomics analysis, and better integration with provincial Laboratory Information Management Systems and epidemiological database systems.

Commercially relevant advances in areas of genomics R&D related to human health

The antibody library developed and characterized by NRC scientists has become a valuable asset whereby three Canadian companies have entered in collaboration discussion with NRC to develop the next generation of targeted therapy for cancers – antibody-drug conjugates (ADC). In a January 2013 press release, one of these companies, AvidBiologics, announced that it is collaborating with NRC to expand its lead pipeline and that “This partnership transforms AvidBiologics into a leading ADC company with one of the most compelling ADC pipelines in the industry worldwide”.

Additionally, the genomics research conducted by NRC scientists in the field of anti-cancer antibodies has positioned NRC as a partner of choice in antibody-drugs characterization. This research expertise was critical in assisting the Canadian company Zymeworks in raising several rounds of financing and meeting its development milestones with its large pharma partner Merck. The lead scientist Maureen O’Connor of NRC has won the prestigious Gervais Dionne award in May 2012 for this work.

Using genomics to improve the value of cereal, canola and legume crops

A large-scale research alliance has been established with the common goal of improving the yield, sustainability, and profitability of Canadian wheat for the benefits of the Canadian farmers and the economy. The Canadian Wheat Alliance (CWA) includes major contributions by NRC, AAFC, the University of Saskatchewan, and the Province of Saskatchewan. A formal CWA agreement between the participants was signed on 6 September 2012. The Canadian Wheat Improvement flagship program, funded in part by GRDI, is NRC’s contribution to CWA. The CWA research institutions will work collaboratively towards the common goal, and also engage the private sector and other public institutions.

In 2012-2013, AAFC funded nineteen GRDI projects based on a call for proposals that was undertaken in 2011-2012. A number of these projects were based on previous activities under the GRDI, while some represented new areas of genomics research within the scope of the Canadian Crop Genomics Initiative, with some expansion into additional key crop kinds and related activities.

Biodiversity, gene mining and functional analysis for the identification and extraction of genes for desirable traits, including mechanisms of plant resistance to biotic and abiotic stress and insect and pathogen virulence

Reduction of rust disease incidence on cereals, even at moderate levels, will have a major impact on the economics of cereal production in Canada. Current estimated annual loss due to rusts is $200M. The primary defense against the wheat leaf rust fungus, Puccinia triticina, has been genetic resistance in the host plant. However, with the exception of the gene Lr34, many resistant genes have become ineffective over time. AAFC scientists are increasing our understanding of the effects of Lr34 expression and interaction with other resistance genes to create genetic tools and knowledge that will enable wheat breeders to achieve enhanced durable rust resistance.

Researchers are also using genomics to understand how the leaf rust pathogen acts on the wheat host. Recently gained knowledge emanating from the generation of genomic resources (complete genome sequences, expression of genes during infection, etc.) of wheat leaf rust, has led to the development of a specific antibody technique that can isolate highly pure fungal structures from infected wheat, allowing for large-scale protein analysis (proteomics) of the arsenal of virulence factors this fungus uses to cause disease and subdue its host. This technique has made possible a comparative and a genetic approach to identifying such fungal virulence factors in a segregating population. A transient reduction of disease was obtained by suppressing the fungal genes, using a gene silencing technology. This research, through its development of screening assays for field surveys, will assist in forecasting new, potentially harmful fungal introductions to North America, and will accelerate identification of wheat germplasm with increased or novel resistance against cereal rust diseases.

Stem rust can have major impacts on wheat yields. Resistance genes have effectively prevented another major epidemic from occurring since the last one in the 1950s, but the recent discovery of the highly virulent stem rust race Ug99 in Africa has reinforced the need to continue research to identify new resistance genes, understand the genetics and biology of resistance, and deploy resistance genes into new cultivars. Sr9 is a stem rust resistance gene that has seven alleles. The recently discovered seventh allele confers resistance to Ug99. This project has led to the construction of an improved genetic map of the Sr9 region and identification of flanking DNA markers. These outputs will support cloning of Sr9 which will provide significant insight into resistance gene specificity and could possibly result in our ability to engineer genes to confer broad-spectrum resistance in the future. Development of allele-specific markers for marker-assisted breeding will support the incorporation of the desirable allele into new stem rust resistant varieties of wheat.

Fusarium head blight in small grain cereals and gibberella ear rot in maize are devastating diseases resulting in low yielding, low quality, mycotoxin-contaminated grain, adversely affecting Canadian food safety and competitiveness. AAFC scientists are using genetics, genomics and proteomics tools to study host plant resistance and fusarium infection mechanisms. They have identified plant genes conferring susceptibility and next-generation sequencing is being applied to map resistance in wheat and maize. They have made significant progress towards characterizing fusarium genes involved in mycotoxin biosynthesis, regulation and pathogenicity. Development of stable plant resistance would greatly improve the economics for growers and contribute to decreasing mycotoxin levels found in Canadian cereals.

Work is also being done to improve our understanding of the competitive interactions between fusarium species found infecting Canadian wheat, and the impact this has upon total mycotoxin production. Focusing on species recommended by the Canadian Grain Commission, wheat heads were inoculated to evaluate fungal interactions, leading to gene expression profiling to monitor the impact of interspecific competition. Collaboration with the NRC Institute for National Measurement Standards has provided access to a state of the art mass spectrometry facility for secondary metabolite identification which accelerated the characterization of novel bioactive metabolites, some of which not previously described. This detailed evaluation of mycotoxin production from fungal isolates will guide the development of smart regulations, sampling methods and optimal timing of tests for quality and safety assurance.

The orange wheat blossom midge can cause annual losses of $60 to $300 million to wheat producers in Canada, depending on the severity of the infestation. The resistance gene Sm1, which inhibits larvae growth through antibiosis, has recently been incorporated into varieties that contain a blend of lines with and without the resistance gene. This blending is essential to preclude the development of insects resistant to Sm1. To that end, the wheat pedigreed seed industry needs molecular markers to identify lines with and without Sm1. Such markers would also be useful for wheat breeders to aid the incorporation of Sm1 into future varieties. Work at AAFC funded by the GRDI has led to the mapping of the Sm1 gene and development of several flanking markers.

The root rot disease pathogen causes millions of dollars of losses to soybean crop revenues each year. Currently, use of resistant varieties is the major means of addressing this disease. Genomics research has discovered molecular factors that determine pathogen virulence on soybean plants. This information will facilitate management of the disease and inform the development of resistant varieties.

Among the many viruses that infect soybean, the soybean mosaic virus is the most prevalent impediment to soybean production in Canada. Infection causes between 35% and 50% yield losses under natural field conditions, and up to 100% in severe outbreaks. The use of genetic resistance has been considered the most effective and sustainable approach to the control of this virus as it is environmentally-friendly and target-specific, and provides reliable protection without additional labour or material costs during the growing season. Based on results derived from earlier funding cycles of the GRDI, target-gene mutants were generated that are expected to provide new sources of resistance to the soybean mosaic virus, for use in soybean breeding programs.

Potato varieties with enhanced resistance to late blight will reduce the industry’s risk of catastrophic losses, reduce grower input costs, and lessen the impact of potato production on the environment by reducing chemical inputs. Genomic approaches to characterizing, identifying and capturing beneficial alleles from diverse germplasm sources are accelerating the development of resistant varieties. Improved DNA collection protocols have been developed and new data has been generated that will be used in a pilot genomic selection project.

The bertha army worm is one of the major insect pests of canola in western Canada causing estimated yield decreases of $10-$40 million per year, even when insecticides are applied at a cost of approximately $16.5 million. Genomics research is increasing our understanding of the genome and genetic variation of this pest species allowing us to explore the use of biologically-based rather than chemical control strategies. Novel strains of baculoviruses that attack bertha army worm have now been identified and sequenced, and several of these with high virulence will be used to investigate genes that may be exploited in novel insect control methods.

Traditional breeding approaches which continually select for a small number of traits, particularly when applied to crops that have quality constraints such as canola and wheat, have gradually narrowed the available genetic diversity to create effective genetic bottlenecks. The increasing world population will require an unprecedented increase in crop productivity to match future demand for food, fibre, fuel and additional bioproducts. Identifying and exploiting a diverse array of natural variation found within the wider crop germplasm base (including progenitor and wild species) is critical to ensure continued crop productivity and sustainability. Characterized germplasm with associated molecular tools is being generated, which will allow rapid deployment of identified favourable alleles in breeding programs for food and biorefinery crops.

Camelina sativa is an emerging industrial oilseed crop with the potential to yield a wide variety of bioproducts. The seed has potential uses for fish feed and unique seed protein products, while the straw shows promise as feedstock for bioethanol production and a source of industrial chemicals from the lignin. Camelina can benefit a wide range of stakeholders, including farmers, in that it can be grown on more marginal land in arid areas compared to other oilseed crops. It has potential to extend oilseed production by more than 2 million hectares, while offering significant economic and agronomic benefits, such as reduced input costs and better crop stress tolerance. The challenge is to integrate a cadre of desirable traits into the base camelina crop. At the core of the project is access to a large, genetically diverse, world collection of camelina that is being assessed for desirable traits using genomic tools. Among other things, research so far has indicated that it is possible to reduce levels of the antinutritional chemical sinapine in the seed through gene silencing. This has important implications for use of camelina as a fish feed.

Oat is an important crop in many regions of Canada and is part of a high-value commodity chain with documented benefits to human health. Maintaining or increasing oat production in Canada provides useful cropping alternatives, benefits industrial stakeholders, and generates interest in oat as a healthful food. Ongoing genetic improvement of oat varieties depends on genomic resources and innovations in molecular breeding that are competitive with, and complementary to, those in other crop species. Work on enhancing the genetic and physical maps of oat through the development of a direct sequence-based approach to genotyping, and through novel genomics-based approaches to understand the structure and origins of oat chromosomes, provided functional genetic assays that will be used by oat breeders to select superior oat varieties. This research directly complements work being conducted by collaborating researchers, and is pivotal to the ongoing contribution of genomics technologies to Canadian and international oat breeding programs.

Commercial agriculture is reliant on nitrogen fertilizers to boost crop yield. However, unintended impacts related to air and water pollution, reduced biodiversity and human health risk are one of the central environmental challenges for the twenty-first century. Legumes do not require nitrogen fertilizer because they are able to acquire their nitrogen from the air as the result of a symbiotic relationship with nitrogen-fixing soil bacteria. Transferring this ability to non-legume crops would be a transformational achievement for sustainable agriculture. Genomic research is allowing rapid identification and functional characterization of genes controlling the legume plant’s interaction with the soil bacteria – knowledge needed if this goal is to be achieved. As a result of this project, one of the essential legume genes required for rhizobial infection has been identified and a new regulatory paradigm for the process has been described.

Genomics is being used to identify new highly active enzymes from the rumen to enhance the sustainability and management of Canada’s environment and agriculture sectors. These enzymes could be used for feed additives, biomass conversion systems or other industrial uses. Samples have been taken from animals that vary in their ability to efficiently digest lignocellulosic material in the rumen to discover enzymes that are differentially expressed in the more efficient animals. The discovery of highly active enzymes has the potential to reduce feed costs by improving the nutritive value of fibrous forages, enhance productivity, and decrease environmentally detrimental outputs.

Delivery of genomics discoveries through bioinformatics and physical tools in order to improve access to both biological materials and data sets, and to assist and accelerate the adoption and commercialization of new technologies

The understanding of a genome’s function and relation to the genomes of other species is a highly complex and ongoing as new sequences become available. There is a need to invest in developing novel ways to interact with genomics data that has been generated to date and that which is in-progress (e.g. genome sequences and metagenomic profiles). Following significant advances in human-computer interactions, multi-touch and multi-person interactions are now possible to empower team-based collaborative interpretation of complex genomic and metagenomic data. The research team has evaluated a number of such analysis platforms (Microsoft Surface, GenGIS) and determined that that GenGIS was adequate to support the required team work.

Enhanced efficiency of plant breeding

Managing crop reproduction has a profound impact on the agricultural sector: it is essential for the development of hybrid crops, maintaining yields in a changing climate, addressing environmental and regulatory challenges, and limiting outcrossing. Pollination is controlled by complex pollen-stigma protein interactions, and pollen germination is susceptible to temperature stress. Pollen and stigma proteins important to pollination were identified and characterized, and the potential of specific carbohydrate metabolic enzymes to increase pollen tolerance to heat was demonstrated.

Genetic improvement of crops to overcome agronomic and environmental challenges of producers and address the quality and processing requirements of consumers and industry is key to maintaining a sustainable and profitable agricultural sector in Canada. Technologies developed from this research accelerate genetic improvement of crops by augmenting traditional breeding approaches and enabling precision genome editing. As a result, advanced germplasm can be generated more rapidly and more economically to meet the needs of producers, consumers and industry. Research focuses on characterising DNA recombination and repair processes in plants, and evaluating strategies to manipulate these processes. The project is a combination of applied efforts to evaluate and optimise strategies derived from preliminary results in earlier work, as well as studies of the biology of DNA recombination processes to discover new factors that could be used to enhance homologous recombination frequency in vegetative and meiotic cells. Investigations combine research using model systems, which enable more rapid assessment and establishment of experimental strategies, as well as implementation of some technologies in Brassica napus and Camelina sativa.

Cell-penetrating peptides are short strings of amino acids that can facilitate the movement across cell membranes of various molecules (from nanosize particles to small chemical molecules and large fragments of DNA) that would be otherwise unable to overcome the permeability barrier. The knowledge resulting from genomic studies, and the transfer of that knowledge into application in crop breeding programs, is highly dependent on the technological capacity to deliver nucleic sequences, or proteins such as nucleases, into cells. This research project builds on previous discoveries to further develop the technology to precision engineer the nucleus, chloroplasts and mitochondria in a cell and to validate and deploy it in a range of crops.

Genomics knowledge and advice for the management of fisheries and oceans

For Phase V of the GRDI, eight genomics research projects are underway at DFO to: increase understanding of the impacts of fisheries and/or potential for climate based selection on the population genetics and structure of Redfish, Atlantic cod, Atlantic salmon and Arctic fish; develop new genetic markers using next generation sequencing for the genomics-based management of aquatic resources; evaluate the immune response of salmon to non-pathogenic infectious salmon anemia virus and subsequent exposures to pathogenic strains; and characterize the genomics of infectious hematopoietic necrosis virus carrier state in Sockeye salmon and physiologically compromised Pacific salmon. Seven of the eight projects met the majority of their research milestones and are on-track to achieve their intended results; the objectives of one project were modified in response to unanticipated sampling problems.

Examples of the emerging results and outcomes of DFO’s genomics research projects from the previous GRDI phase include the following:

Discriminating capelin populations in the Northwest Atlantic

Capelin is a commercially exploited, key forage-fish species found in the boreal waters of the North Pacific and North Atlantic, with four capelin stocks assumed to inhabit the northwest Atlantic based on meristic, morphometric, tag returns, and seasonal distribution patterns. Researchers examined the population structure of capelin in the Canadian northwest Atlantic using genetic-based methods results suggest groupings that are somewhat different than the contemporary stock structure used for fisheries management and indicate that some changes in management practices may be required.

Host-parasite interactions: a functional genomics approach to characterizing salmonid responses to the salmon louse

This research was integrated into a Genome BC funded research project, Genomics in Lice and Salmon (GiLS). The combined research has contributed to unprecedented advances in sea lice genomics. Genomics tools including a novel 38K microarray and a suite of over 100 variable microsatellites as molecular markers for salmon louse were developed. These tools were applied to gene transcription analyses (microarray development and qPCR) and chemical interaction analyses which are fundamental to vaccine target identification, species and population analysis. Population-level analyses of salmon louse in British Columbia, and more widely within the Pacific and Atlantic Oceans, showed evidence of virtually unrestricted gene flow among populations within both Ocean basins, likely the result of parasitism on highly migratory salmonid hosts. Comparative infection experiments revealed evidence for a diversity of response mechanisms to salmon louse among salmon species and revealed insight into the early development of natural resistance.

Genetic monitoring and conservation of beluga whales in the Western Canadian Arctic

This project has investigated genetic stock structure in beluga aggregations in the Beaufort Sea to identify management units for monitoring the effects of human activity and the impacts of climate change. The areas used by summer aggregations of beluga in the Mackenzie River Delta have been designated as part of the Tarium Niryutait Marine Protected Area, with a conservation objective of maintaining the genetic fitness and integrity of beluga assemblages. Results suggest that there is a social structure within the Beaufort Sea stock of beluga whales. As belugas taken during the hunt in the Beaufort Sea have a very strong male bias, this dataset provides an opportunity to investigate the relatedness patterns in groups of male belugas.

Application of genetic markers to resolve species identification and population structure of aquatic invasive species

Population genetic patterns can shed light on many aspects of natural populations that are relevant to conservation, resource, or ecosystem management. Genomics methods were used to identify species of tunicates that invade British Columbia and Oregon and to characterize their populations. Population structures will be compared to invasion vector maps to better understand how this species may be spreading in the Pacific Northwest and what intervention options exist to limit its spread to new locations.

Microbial characterization of produced water and its influence on the microbial community in the marine environment around offshore oil and gas production platforms

Microorganisms play essential roles in global processes ranging from the recycling of matter in our air, water and soil, to causing or preventing disease in plants, animals, and humans. Until recently, we have lacked the tools to address fundamental questions about natural microbial population structures. The purpose of this project was to characterize the natural populations of microorganisms in the ecosystem around the Hibernia platform and in the produced water of the oil and gas production platforms. Key microorganisms were identified and quantified that may be used as tracer microorganisms for produced water. With improvements to detection methods, these particular signature microorganisms may be useful as markers to monitor the dispersion of produced water in the surrounding ocean. Knowledge gained from this project will be useful for the development of future protocols for regulatory and policy development.

Genomic knowledge for the Canadian health regulatory system

Genomic assessment of chemical food contaminants leading to food allergy

A cell culture assay was successfully developed to measure the effects of chemical contaminants on immune pathways related to food allergy. The assay was used to a known immunostimulatory chemical, a known immunosuppressant, and two different carbon-based nanomaterials that may contaminate foods. The results indicate that the immunomodulatory chemicals as well as the nanomaterials alter immune cell responses to an allergen. Using high-throughput plate-based PCR arrays, immune cells treated with nanomaterials were subjected to genomic analyses to link changes in immune function with changes in gene expression. Immune cells were also prepared for proteomic analyses using mass spectrometry techniques to determine changes in protein levels and post-translational alteration. Methods for protein extraction, purification and analyses are currently in progress, as well as studies in mice to confirm the cell culture results in whole animals. To date, the project deliverables against objectives are on target and a manuscript has been prepared that, once published, will be inform toxicologists and regulators.

Development of short term cancer bioassays using transgenic mice exposed to carcinogens

The isolation of microRNA from mouse organs treated with a variety of carcinogens has been completed. The profiling of these microRNAs is in progress and several manuscripts are in preparation.

Genomic approach for risk-benefit analyses of stem cell based health products

Stem cells are an emerging technology with a tremendous potential to treat diseases for which there are currently no cures. Stem cells from adults are a particularly promising source as they provide a means to avoid the social and ethical issues involved with the use of embryo derived cells. However, the use of adult stem cells in a health care environment is not without risk. It is currently the responsibility of Health Canada to evaluate these risks and ensure that stem cell-based health products are both safe and effective. Funding from the GRDI at HC supports the development of diagnostic tools that will allow thorough evaluation of the risks and benefits associated with the therapeutic use of adult stem cells. In the first two years of funding, HC has successfully utilized infrastructure and collaborations developed through GRDI to generate a list of candidate biomarkers that identify human stem cells that are both safe and effective for treating diabetes. The identified candidates are currently being validated to determine their capacity to discriminate human adult stem cells that can treat diabetes from those with the potential to form cancerous tumours. Successfully validated biomarkers will form the basis for the development of diagnostic tests for evaluating stem cell based health products.

Integrating genomics endpoints into regulatory toxicology

A cell culture methodology was developed to screen chemical agents for potential genotoxic (DNA damaging) mechanisms of action. The system has been tested on three chemicals thus far as proof of principle and is able to differentiate between known genotoxins and non-genotoxic agents. This project is one component of an international consortium that includes government, academic and industrial partners to develop new/improved regulatory toxicology methods that will advance toxicological risk assessment through collaborative harmonized efforts. A final validation of the system and formal qualification of the method will be sought from the United Sates Food and Drug Administration.

Two-year rodent cancer bioassays are currently the gold standard to test whether an agent causes cancer or not. These tests cost approximately $2 million and take about three years. Archival tissues preserved in formalin that are available from two-year cancer bioassays may be useful for the study of gene expression changes linked to cancer. A protocol to study gene expression in formalin-fixed tissues was optimized and applied to 16-year old archival rodent liver tissues from a cancer bioassay. Results showed that it was possible to measure the same molecular changes in these tissues as in freshly frozen samples. This protocol was published and will be used to explore whether genomics endpoints can be used in shorter-term (e.g., one or two month) experiments to predict cancer at the two-year time point, without the need to conduct more two-year cancer bioassay experiments.

Computational biology tools were developed to identify sites in DNA that interact with the thyroid hormone receptor. This work aims at understanding what genetic elements are controlled by the thyroid hormone, and facilitates the interpretation of molecular changes that are measured in animals exposed to chemical agents that perturb thyroid hormone levels.

Proteomic approach to identify biomarkers of exposure and effect of complex mixtures in the environment

The overall short-term objectives of the project is to employ in vivo mouse models to (1) establish gene/protein expression profiles of target tissues following exposure to complex mixtures and substances highlighted as priorities for concern and control; and (2) conduct proteomic analyses to identify biomarkers of exposure and adverse effects. A purified coal tar extract was obtained and experimental doses of tar were established for the studies. Gene expression profiling of organs from mice exposed to the substances was completed. Results to date indicate that multiple biological pathways were impacted, suggesting that quantitative risk assessment of complex mixtures need to account for several mechanisms of action.

Genomics knowledge to strengthen public health programs and activities related to infectious and chronic disease

Food-borne pathogens
Genomic characterization of foodborne isolates of Campylobacter and Listeria

The objectives of this HC project were modified for 2012-2013 to adjust for the late transfer of funds, which were allocated to the procurement of laboratory consumables, to contract sequencing services from the BC Genome Centre and to short-term contracts for technical assistance to isolate nucleic acids for sequencing from target Listeria and Campylobacter isolates. Two post-doctoral fellows were hired through the Natural Sciences and Engineering Research Council of Canada visiting fellowship program to carry out the bulk of the required analyses. Funds were also successfully obtained from the Chemical, Biological, Radiological-Nuclear, and Explosives Research and Technology Initiative (CRTI) Technology Acquisition grant to purchase a Next-Generation sequencer (Illumina MiSeq). Publically available data were used to develop a framework for bioinformatic analyses of whole genome data for assessing microbial typing methodology for Campylobacter and Listeria.

Development of rapid methods for molecular typing of Salmonella

Two complementary projects focus on the development of rapid methods to increase the efficiency of typing and characterization of Salmonella and thereby reduce the impact of outbreaks and burden of disease. The first approach involves an international collaboration between the Animal Health and Veterinary Laboratories Agency in the United Kingdom, the Austrian Institute of Technology in Austria, and the Laboratory for Foodborne Zoonoses, PHAC. These partners have conducted a multi-site validation of a Salmonella geno-serotyping array. Over 1800 Salmonella isolates were tested to assess repeatability, sensitivity, specificity and evaluate the utility of the array as a rapid alternative to the traditional method of serotyping.

In an alternative approach, comparative genomic fingerprinting and single nucleotide polymorphism assays have been evaluated for their capacity to provide rapid, reliable and high resolution molecular subtyping of S. Enteritidis. PHAC researchers have sequenced the genomes of 31 strains of Salmonella Enteritidis. The genomic data has been used to develop two rapid molecular methods to characterise the pathogen, comparative genomic fingerprinting and single nucleotide polymorphism (SNP) analysis. Testing has determined SNP analysis to be superior, enabling the high resolution discrimination between related and unrelated strains. A larger collection of related and unrelated strains will be used for more extensive evaluation of the panel of SNPs to confirm the potential of this method for high resolution subtyping of Salmonella Enteritidis. Success in this evaluation will provide a tool to greatly enhance response capacity of the public health and food safety systems and reduce the burden of illness due to Salmonellosis.

Genomic tools and methods to more accurately identify disease-associated E. coli strains

To date, genomic sequence data from nearly 200 E. coli O157:H7 strains spanning 1984-2013, including isolates from a high-profile beef recall event, have enabled the creation of a population framework of E. coli O157 from food-borne outbreaks and sporadic cases of human illness. BiologPM microarray testing is underway to investigate potential genotype-phenotype correlations. Other studies are investigating the environmental dynamics of E. coli strains in order to better understand the potential reservoirs of Shiga-toxin producing (STEC) E. coli commonly associated with human disease. Using genomic analysis software developed at PHAC and a database of more than 1000 genomic sequences, PHAC researchers are investigating the features of genomic regions most often associated with human disease and how they may contribute to human exposure and disease.

Other Infectious Pathogens

Pilot studies have indicated differences in the function of immune cells between active and latent tuberculosis (TB) infection and uninfected controls. The immune causes for the differences are being further investigated by detailed analysis of the T cells in the blood that have been activated specifically with TB antigens. In addition, the differences between latent and active infection groups will be investigated using proteomic and genetic methods. Other studies focus on identifying the role of vitamin D in controlling the risk for TB infection. Variations among the genes involved in vitamin D biology have been characterised in large populations of infected and non-infected individuals. Strikingly, variants were detected that were associated with resistance to becoming infected. These results are being replicated and fine mapped in a second larger case control sample from the same geographical and ethnic background. The main candidate genes resulting from this study will be sequenced and the rare polymorphism in this ethnically diverse sample will be tested for their impact on the TB phenotype on the background of known vitamin D serum levels. It is hoped that the results of these experiments will indicate how vitamin D controls risk of TB and its transmission. This will be one of the first examples of how a modifiable risk factor of a common disease and the host genetic background can be used jointly in improved disease control.

Antiretroviral therapy has dramatically decreased the morbidity and mortality due to HIV/AIDS. However, HIV drug resistance constitutes a major limitation to maximizing the clinical benefit of antiretroviral therapy. An up-to-date HIV drug resistance testing method that addresses these issues is urgently needed. By combining DNA sequencing, DNA barcoding and advanced bioinformatics technologies, PHAC researchers have created a method to establish a tagged, pooled pyrosequencing HIV drug resistance testing platform that covers all the viral genes targeted by antiretroviral therapy. In addition, an automated data analysis pipeline has been developed to support the technique. An internet-based HIV drug resistance analysis web server has been developed that takes the analyzed data and formats the results into reports that are accessible to clinicians. This web server will enable remote access to analytic results and allow users to upload data through internet, customize analysis settings, visualize and retrieve user-interpretable HIV drug resistance reports and related data sets. This final piece of the drug resistance platform is in the process of being implemented with clinician collaborators.

Bioinformatics Tools

To facilitate the rapid analysis of genomic sequence data, an automated genome annotation system is under development. The system has been evaluated for accuracy against several other popular automated genome annotation systems using the in-house manually annotated Streptococcus milleri group of genomes, and the ‘gold standard’ Chlamydia trachomatic genome. The expert system under development currently outperforms all tested genome annotation systems. Other researchers have created software, termed Panseq, to compare related bacterial genomic sequences. Panseq is publicly available on a website and as a stand-alone version. It now performs phylogenetic group comparisons with increased speed. Additionally the STEC genomic analyses platform has been expanded and a cloud service via the in-kind support of Cybera is being tested. That platform houses over 800 in-house and publicly available E. coli genomic sequences, as well as the analytical tools to perform epidemiological and comparative inquiries by users with and without bioinformatics training.

Genomic knowledge for forest generation and protection

Identification of genes controlling desirable attributes in economically important tree species

The genomics program at NRCan-CFS directs research towards the development of methods, tools and databases for the discovery of genes in forest trees coding for attributes favouring fibre quality and forest sustainability: phenology and growth; wood quality characteristics; resistance to biotic and abiotic factors; and adaptation to environmental change.

Molecular breeding programs will benefit from knowledge generated by NRCan-CFS scientists. Building on the association studies (i.e. correlation of marker presence with desired traits) performed in 2011-12 on spruce trees, it was shown that prediction accuracy and the resulting increase in genetic gain (i.e. tree improvement for specific traits) could be obtained when 500-700 makers were applied to pedigree material in the selection process. Selection of superior trees can thus be made within a period of two years instead of 20 years. Research is also underway to further understand which genes are involved in wood formation, specifically vascular tissue development. Also genes which are involved in budset can be ascertained by comparing those which are differentially expressed before and after budset.

Increased knowledge of genomics-based pest control and diagnostics

Research on genomics-based pest control products for species that are of economic importance involves searching for active ingredients, target sites, and new or improved strains for the development of environmentally benign pest control methods.

Spruce budworm is considered by many to be one of the greatest threats to our forests due to the periodic nature of its outbreaks, which can cause devastating damage and severe economic losses. Modeling their dispersal and the development of novel control options could offer forest managers new tools in the management of this pest.

Work in 2012-2013 focused on developing molecular markers for “residential” spruce budworm (that do not have the ability to disperse long distances) and “immigrant” spruce budworm (that have the potential to disperse hundreds of kilometers) from the same locality to examine dispersal characteristics such as distance, direction and dispersal rates, to name a few. In an effort to collect spruce budworm across its geographic range, specimens from “gaps” in the range were obtained to study of the population genetic structure. To elucidate the genes involved in diapause, a transcriptomics analysis continued that examined eggs, 1st instar and 2nd instar larvae. A number of potential targets for spruce budworm control via RNAi (a synthetic product that interferes with development) were identified. NRCan-CFS scientists are investigating the CfCDA2 gene which may induce abnormal moutling resulting in increased mortality.

Canada’s ash resources are threatened by the emerald ash borer. Three different approaches for potential control are underway at NRCan. Research is being performed towards the identification of genes essential in emerald ash borer development which could be used for control purposes. Genes relating to moulting and hormone receptors are the focus, as disruption of their proper function could result in stunted growth or death. A second approach involves the olfactory system. Understanding how the olfactory system operates, that is, what genes and proteins are involved, is critical to the development of optimal chemical lures. The final approach examines naturally occurring fungi which may be lethal to insects; to date 102 fungal strains have been obtained and are being examined.

NRCan-CFS scientists are working towards furthering our understanding of tree pathogen interactions: genes in fungi that may cause disease (pathogenicity genes) and genes in trees that may offer resistance. Research has focused on identifying and confirming these roles in specific genes. The identification of these types of genes could lead to the development of molecular markers that could be integrated into marker-assisted breeding programs. Three candidate genes showed significant association with quantitative disease resistance to blister rust in white pine. Furthermore, qualitative assays for resistance to white pine blister rust continue to be developed to decrease testing costs for white pine breeding programs.

For genomics data to be translated into DNA-based diagnostic tools, the genomic sequences of target pathogens, within three target pathogen groups, need to be obtained. The genome sequences for 21 pathogenic species have been generated. To reconstruct the epidemiology of invasive pathogens and to understand and predict migration pathways of invasive pathogens, knowledge of population genetic patterns is important. Pathogens can evolve rapidly and develop novel adaptation that could affect their ability to infect and spread. These adaptations will leave a signature in the genomes of pathogens, thus routes and patterns of migration can be inferred by these signatures. Population re-sequencing of the genomes of three targeted invasive pathogens was initiated in 2011-2012 and continued during 2012-2013 with the acquisition of samples from a wide variety of geographic and host sources. To design tools that answer end-user needs, a list of criteria was established in consultation with plant protection agencies to initiate the establishment of the list of the Top 50 most unwanted pathogens. Thus far, development and validation of assays for the Top 10 has been completed. This requires testing of samples against target species and close relatives.

Pine wood nematode is native to North America but its introduction overseas has caused devastation in pine forests. Internationally traded wood products may be subject to trade disruptions should dead nematodes be found in the wood. Accurate detection that differentiates between live and dead nematodes is essential. Scientists at NRCan-CFS designed and tested pine wood nematode specific primers. These primers were used in an assay optimized to test for living nematodes. In 2012-2013, the assay was validated on wood samples, showing its efficiency and specificity.

Investigation of bioenergy solutions via improved feedstock and/or novel enzymatic processes and associated value-added bioproducts

In an effort to improve biofuel production efficiency, as well as increase biomass quantity and quality, key genes are being investigated. Using activation-tagged poplar (i.e. gain-of-function mutations in poplar), gene clusters (less than 10kbp) have been identified which may positively impact bioenergy production and key traits such as biomass production, tree architecture and phenology. A functional gene approach was undertaken to identify specific genes that could facilitate biomass conversion. Genetic manipulation of poplar using enzymes was performed, targeting the bonds between cellulose and lignin. This alteration in wood fibre would require less energy and chemicals during processing.

Enhanced Environment Canada's applications of genomics-based tools and technologies for responsible decision-making

In 2012-2013, EC developed genomics tools and approaches that support the department in compliance promotion and enforcement, wildlife management, sustainability, pollution prevention, risk assessment of potentially toxic substances and the regulation of new and existing substances. Tools and approaches were also developed to advance environmental genomic capacity within the Department based on the four areas of research described below.

Strengthen predictive models

Genomic tools and approaches were developed to address the transport, fate, effects and risks of existing and emerging chemical, biological and physical influences on organisms, biodiversity, ecosystem function, and water availability. Research focused on modeling factors that affect microbial communities in water (such as toxic algae) in order to protect aquatic life and ensure sustainable water use. Developing an efficient and accurate model for the prediction of chemical exposure effects was also investigated through building a better understanding of the molecular mechanisms underlying the overt toxicological effects of chemicals in wildlife (e.g. avian species) and aquatic life. This research can assist in the development of regulatory criteria.

Understand and monitor ecosystems

The Department also focused its research into developing tools to understand and monitor aquatic and land based ecosystems. Tools and approaches were developed to determine the movement and habitat requirements of populations at risk; to monitor the toxicological impacts of substances released into the environment; and to monitor populations of wildlife exposed to stressors (e.g. chemicals, climate change, and oil sands development), including marine bird species like the Black legged Kittiwake, the Purple Sandpipers and Thick-Billed Murre and aquatic life such as fish and frogs.

Understand cumulative risk/impacts

Research was focused on the development of genomic tools to further our understanding and better predict cumulative impacts on, and risks to, ecosystem health from multiple stressors interacting over time on resident wildlife and aquatic life. Research explored how climate change and industrial development (e.g. oil sands) may be linked to cumulative impacts, such as the emergence of infectious diseases in wildlife populations and sublethal harm.

Manage environmental risks

Environment Canada’s research developed genomic tools to support the management of environmental risk of chemical, biological, physical and genetic pollutants. This research focused on the development of genomic tools, such as the development of a crustacean microarray, that could be used as a part of a regulation (e.g., CEPA, 1999 Disposal at Sea Regulations); help the Department to better perform its duties under the Fisheries Act by better delineating aquaculture and fish harvesting areas; and by assisting in the conservation of biodiversity by mitigating habitat fragmentation for wild populations.

Annex 4 – Research tools and processes produced by the GRDI

Research tools:

  • Microbial In Silico Typer software to simulate/predict the results of multiple molecular subtyping methods from draft-genome sequence data (FWS);
  • GView software to view, interact, investigate, and markup bacterial genomic sequence data (FWS);
  • GView Server, web site hosting commonly applied comparative analysis tools (FWS);
  • SNP Phylogenomics Pipeline software to extract phylogenetically informative SNPs from whole genome sequences, and use them to build a phylogenomic tree (FWS);
  • Magnetic capture hybridization and chip based microfluidic concentration to prepare samples for miniaturized DNA assays (QIS);
  • Phytophthora sojae avirulence genes Avr1d and Avr1c, determining strain specific compatibility to soybean cultivars (AAFC);
  • Plant transformation vectors for transient expression of proteins in plants to facilitate rapid characterisation of protein function (AAFC);
  • LIMS type system (LIIS database) for culture, sample and genomic information tracking for rumen enzymes (AAFC);
  • Transgenic wheat plants containing different lengths of Lr34 promoter driving a reporter gene (AAFC);
  • Methods to detect Enniatins in Fusarium cultures; description of novel Enniatin derivatives produced by fungi collected on Canadian wheat (AAFC);
  • Small RNA library and NGS sequencing data from Soybean Mosaic Virus infected soybean leaves (AAFC);
  • Mutagenized population of soybean to screen for target-gene mutants resistant to soybean mosaic virus (AAFC);
  • New comprehensive oat mapping database (AAFC);
  • Complete genome sequences of 18 new geographic isolates of Mamestra configurata nucleopolyhedrovirus from 2012 Bertha armyworm outbreak (AAFC);
  • Population genetic and genomic sequence resources of M. configurata (AAFC);
  • Multiplex PCR diagnostic system to distinguish bertha armyworm from other noctuid species commonly contaminating bertha armyworm pheromone traps (AAFC);
  • SNP genotyping, mutants and populations of wheat stem rust (AAFC);
  • Bioinformatics pipeline for assigning tetraploid genotypes based on raw Illumina Infinium SNP data and next-generation sequencing data (AAFC);
  • Antibody-based detection tool for the detection and recovery of E. coli VTEC pathogens from water (EC);
  • qPCR assays to detect fecal pollution from human, cattle, and seagull sources for municipalities near Great Lakes Areas of Concern (EC);
  • Avian Tox PCR array to screen chemicals for effects on mRNA expression across 36 genes (EC);
  • Agilent 44K chicken microarray for screening potential toxic effects of priority environmental contaminants in birds (EC);
  • Metagenomic and transcriptomic analysis tools to assess river microbial communities (EC);
  • Aligent 44 K chicken microarray used for screening for potential toxic effects of priority environmental contaminants (dioxin compounds) in birds, of use to risk assessors (EC);
  • Novel genomic method to predict the sensitivity of any avian species to dioxin-like compounds (EC);
  • In-situ incubation for growth and development of attached microbial communities (EC);
  • 10 variable microsatellite loci for Purple Sandpipers (EC);
  • 35 cyanobacteria strains were isolated from the Great Lakes and other focal water bodies (EC);
  • Diagnostic markers of reproductive impairment and acute toxicity of copper on Daphnia magna and Rainbow Trout (EC);
  • Complete genome sequence and Single Nucleotide Polymorphisms for Thick-Billed Murre (EC);
  • DNA sequence variation in Arctic Sea birds for 10 functional genes (EC);
  • Mitochondrial DNA and microsatellite DNA molecular marker variations of Canadian Herring Gulls (EC);
  • Sequence of clam leukemia retrovirus (EC);
  • Formic acid digestion method for the shotgun analysis of fish plasma proteins (EC);
  • Genomic library of trout brain transcripts (EC);
  • Library of white sucker liver transcripts (EC);
  • Genes for specific toxic responses for amphipods and lobster larvae (EC);
  • Genotype-phenotype association mapping and visualization tool package for QTL/eQTL mapping; and, GPA visualization tool for visualizing Genome- Transcriptome-Phenome Association (NRC);
  • Comparative Genomics tools for cereal nuclear genomes (NRC);
  • Molecular detection assays (qPCR) of 10 key forest pathogens (NRCan);
  • Fungal culture collection (NRCan);
  • Bioinformatics pipeline for identification of secreted proteins (NRCan); and
  • Bioinformatics pipeline for assay development workflow using genomic sequences (NRCan).

Research processes:

  • Genomics-based framework for the development and assessment of molecular subtyping methods to compare the performance of multiple subtyping methods using a number of objective and quantifiable criteria (FWS);
  • Automated methods (QIS);
  • Novel procedure for the isolation of DNA from water samples (QIS);
  • Methods to identify novel mycotoxins, and measure fungal interactions (AAFC);
  • Ethyl methanesulfonate (EMS) mutagenesis of in vitro shoots (AAFC);
  • Identification of target gene mutants using NGS (AAFC);
  • Adapted new “genotype by sequencing” technique and associated bioinformatics workflow (AAFC);
  • Improved DNA collection protocol using silica beads (AAFC);
  • Genomic regions associated with late blight resistance localized using association analysis (AAFC);
  • Small RNA profiling for virus detection and discovery (AAFC);
  • Optimized bioinformatic pipeline for analysis on RNA-seq data for Daphnia magna and Rainbow trout (EC);
  • Optimized procedures for harmful cyanobacteria bloom sampling extraction, detection, analysis, identification, source tracking, and evaluation of environmental effects (EC);
  • Recombinant expression system for Lr34 gene (NRC);
  • Data analysis pipelines that integrate QTL and eQTL mapping method in genotype-phenotype association mapping (NRC);
  • Methods for cell culture metabolomics and quantitative NMR metabolomics (NRC);
  • New analytical protocols for lipid and RNA extraction from wheat crown and leaf tissues (NRC);
  • Bioinformatics analysis pipeline for RNA-seq data (NRC);
  • Optimized procedure for DNA extraction from environmental samples (NRCan);
  • Optimized procedure for DNA extraction from herbarium specimens (NRCan);
  • Optimized RNA easy mini kit (Qiagen) extraction protocol resulting in 2X higher RNA yield (Reverse transcription loop mediated isothermal amplification protocol) (NRCan); and
  • Optimized whole genome amplification of a fungal pathogen using Multiple Displacement Amplification (NRCan).

Appendix B - Genomics R&D Initiative: Performance Measurement Framework Overview

In fulfillment of the requirements and guidelines of the Treasury Board, a horizontal Performance Measurement Strategy Framework (PMF) was developed for the GRDI in 2011. The PMF formalizes the commitment of the eight departments and agencies involved in the GRDI regarding the common measurement and accountability requirements associated with this Initiative. The PMF is based on a previous Results-Based Management and Accountability Framework that was developed in 2007 to address relevant conclusions and recommendations resulting from the formative evaluation of the GRDI completed in 2006. It also considers recommendations resulting from the impact evaluation that was completed in 2010.

The logic model presented in Figure 1 reflects the overall objectives for the GRDI, recognizing that there are significant differences in particular needs and priorities of each department, recognizing also that a proportion of the funds will be mobilized for coordinated interdepartmental projects along shared priorities and common goals, while the balance of resources will be used by departments and agencies to support their mandates and priorities.

A number of activities will be conducted to reach these objectives, focused on R&D activities and including research support related to management, coordination, evaluation, reporting, training, access to world-class research infrastructure and networks, strong collaborations, dissemination and transfer of research results, and translation of knowledge into commercial and public good applications.

These activities will generate outputs such as rigorous management processes, scientific information and publications, research tools and products, and a highly skilled workforce. As an immediate outcome, these outputs will be made available to support governmental mandates as well as horizontal integration. Intermediate outcomes will consist in uptake and application of the knowledge and tools generated by the GRDI for policy and regulatory decisions, for addressing key public policy priorities, as well as for supporting private sector innovation. Ultimately, the GRDI would be one of the factors contributing solutions to issues that are important to Canadians, resulting in improved human health; improved food safety and security; enhanced sustainability and management of the environment, agriculture, forestry and fisheries; and growth of S&T innovation.

The GRDI comprises three important program elements:

Governance:

While good management is an important aspect of any government program, it is particularly important to recognize for this initiative because of the number of departments involved. It is thus important that the practices in place support effective departmental and interdepartmental coordination. It is also critical that departmental and shared initiative priorities be well defined so that the projects are selected to ensure that government-wide priorities for genomics research information are addressed. Without this important program component, some of the outcomes and ensuing impacts may not occur or not be as successful. Future phases of the GRDI in particular seek to demonstrate the viability of a truly interdepartmental approach and the ability of GRDI participating departments/agencies to work together, show complementarities, add value to existing departmental resources, and build strong partnerships.

Research and Development:

Research and development is the central component of this initiative to respond to priorities, support governmental mandates, inform policy and regulatory decisions, and foster innovation. All activities surrounding the actual conduct of R&D, the transfer of technologies and results to stakeholders for uptake and application, and the communication of these results are critical to ensuring progress towards all outcomes and ensuing impacts.

Maintenance of Capacity:

Capacity building was the focus of earlier phases of this initiative and it is critical that this capacity continue to be maintained. The maintenance of a highly skilled workforce is essential for the federal labs to undertake the type of research projects required to ensure the success of the initiative as well as be credible participants in genomics research and applications. In order to continue to maintain the federal research capacity, it is also critical that the existing infrastructure be maintained and that new state-of-the-art infrastructure be acquired to ensure that federal labs can continue to play their role in genomics research to inform regulations, policies and other decisions. Without continued capacity maintenance, some of the outcomes and ensuing impacts may not occur or not be as successful.

Table 2 outlines the performance indicators, sources and responsibility for the outcomes outlined in the logic model presented in Figure 1 earlier which should be reported upon, either in the annual performance report or at the time of evaluation as appropriate. Evaluations will not attempt to measure the impact of GRDI against the long-term outcomes, as attribution becomes more tenuous. Rather, it will focus on the achievement of immediate and intermediate outcomes, and assess whether it is reasonable to expect that the achievement of intermediate outcomes would contribute to the achievement of the long-term outcomes.

As this is a horizontal Initiative including several departments and agencies, some descriptive information is also included in the Framework related to projects, financial support and stakeholders and end-users. This is intended to support consistent collection and reporting on GRDI activities within individual departments, and are not included as indicators of performance.

Descriptive information

  • Project Information developed by all participating departments/agencies every 3 years
  • Project titles and summary descriptions (key objectives and impact areas)
  • Financial Information reported annually by all participating departments/agencies
  • Internal $ leveraged from A-base resources
  • Other funding by collaborators (other government departments; universities; international organizations; private sector; etc.)
  • In-kind contributions by collaborators
  • Stakeholders and end-users determined by all participating departments/agencies every three years
  • List of stakeholders and end-users available for each research project (including contact information)

Figure 1: Logic Model for the interdepartmental Genomics R&D Initiative

Research supported by the GRDI seeks to uphold regulatory, public policy, and operational mandates in important areas such as health care, food safety, sound management of natural resources, a sustainable and competitive agriculture sector, and environmental protection, with strong collaborations with university and private sectors

Governance

Outputs
  • Project selection and performance management guidelines
  • Planning meeting and workshop reports
  • Project charters and plans
  • Annual Performance Reports at Initiative and department/agency levels
  • Forward-looking plans for future phases of the Initiative
Immediate Outcomes
  • Participating departments/agencies are working together to plan, set priorities, and implement coordinated management approaches
Intermediate Outcomes
  • Government policy makers and regulators have used research results for evidence-based regulatory, policy, and resource management decisions
  • Private and public stakeholders involved in the innovation continuum in Canada have adopted innovative or improved tools and processes using research results
Long-Term Outcomes
  • Improved human health in Canada
  • Enhanced sustainability and management of Canada’s environment, agriculture, forestry and fisheries sectors
  • Improved food safety and security in Canada

Research & Development

Outputs
  • For interdepartmental/agency shared priority research projects and departmental/agency mandate-driven research:
  • Scientific information and publications
  • Research tools and processes
  • Collaborations with university, private-sector, and other levels of government
  • Communication products
Immediate Outcomes
  • Government policy makers and regulators have access as appropriate to new knowledge, tools and advice generated by scientists for policy and regulatory decisions supporting government mandates and shared priorities
  • Private and public stakeholders involved in the innovation continuum in Canada have access as appropriate to new knowledge generated by scientists for the development of innovative or improved tools and processes
Intermediate Outcomes
  • Government policy makers and regulators have used research results for evidence-based regulatory, policy, and resource management decisions
  • Private and public stakeholders involved in the innovation continuum in Canada have adopted innovative or improved tools and processes using research results
Long-Term Outcomes
  • Improved human health in Canada
  • Enhanced sustainability and management of Canada’s environment, agriculture, forestry and fisheries sectors
  • Improved food safety and security in Canada

Maintenance of Capacity

Outputs
  • Highly skilled workforce
Immediate Outcomes
  • Government policy makers and regulators have access as appropriate to new knowledge, tools and advice generated by scientists for policy and regulatory decisions supporting government mandates and shared priorities
  • Private and public stakeholders involved in the innovation continuum in Canada have access as appropriate to new knowledge generated by scientists for the development of innovative or improved tools and processes
Intermediate Outcomes
  • Government policy makers and regulators have used research results for evidence-based regulatory, policy, and resource management decisions
  • Private and public stakeholders involved in the innovation continuum in Canada have adopted innovative or improved tools and processes using research results
Long-Term Outcomes
  • Improved human health in Canada
  • Enhanced sustainability and management of Canada’s environment, agriculture, forestry and fisheries sectors
  • Improved food safety and security in Canada

Program Performance Measurement Strategy Framework

Area: Project selection and performance management guidelines

Indicator 1

Templates and guidelines for priority setting, project selection and management processes produced for interdepartmental pilot projects

Frequency

Once per phase

Target

100% templates and guidelines approved

Responsibility

NRC Secretariat

Indicator 2

Templates and guidelines for priority setting, project selection and management processes produced for department/agency mandated research projects

Frequency

Once per phase

Target

100% templates and guidelines developed and shared with GRDI WG

Responsibility

Departments

Area: Planning meeting and workshop reports

Indicator

Percent of meeting and workshop reports completed and approved

Frequency

At time of meetings and workshops

Target

100%

Responsibility
  • NRC Secretariat
  • Departments

Area: Project charters

Indicator

Percent of project charters produced for approved interdepartmental pilot projects following appropriate templates and guidelines

Frequency

Once per phase, revised annually

Target

100%

Responsibility

NRC Secretariat

Area: Annual Performance Reports at Initiative and department/agency levels

Indicator
  • GRDI-level performance report produced
  • Departmental performance reports produced for the GRDI
Frequency

Annual

Target

100%

Responsibility
  • NRC Secretariat
  • Departments

Area: Forward-looking plans for future phases of the Initiative

Indicator

Next Phase plan produced based on updated environmental scans and needs assessment

Frequency

Once per phase

Target

Plan approved by ADM CC

Responsibility

NRC Secretariat

Area: Scientific information and publications

Indicator

Number of scientific contributions:

  • publications in refereed journals
  • publications in refereed conference proceedings
  • technical reports
  • book chapters
  • other publications
  • poster presentations at conferences
  • invited presentations
  • national conference presentations
  • international conference presentations
  • participations in national conferences
  • participations in international conferences
  • editorial posts for national and international journals
  • genomics related databases or libraries
Frequency

Annual

Target

Within the range recorded for Phase IV (1,871)*

Responsibility

Departments

Area: Research tools and processes

Indicators
  • Number of research tools produced
  • Number of research processes produced
Frequency

Annual

Target

Within the range recorded for Phase IV (30)*

Responsibility

Departments

Area: Collaborations with university, private sector, and other levels of government

Indicator 1
  • Number of participations in national or international genomics-related committees
  • Number of national or international genomics research peer review committees served on
Frequency

Annual

Target

Within the range recorded for Phase IV (97)*

Responsibility

Departments

Indicator 2

Number of formal research collaborations (i.e. established in funded project workplans) by organization type:

  • universities (Canadian and international)
  • other international research organizations
  • other Canadian research institutions
  • private sector
  • other public sector organizations such as provinces and municipalities (excluding other government departments)
Frequency

Annual

Target

Within the range recorded for Phase IV (792)*

Responsibility

Departments

Area: Communications products

Indicators

Number of communications products, including:

  • media interviews
  • press releases
  • community presentations (science fairs and events, schools)
  • brochures, fact sheets, web pages
Frequency

Annual

Target

Within the range recorded for Phase IV (151)*

Responsibility

Departments

Area: Highly skilled workforce

Indicators

Number of research and technical personnel:

  • research scientists
  • research officers
  • technical officers
  • research professionals (biologists, physicists, chemists, IT specialists)
  • post-doctoral fellows
  • visiting scientists
  • graduate students
  • undergraduate students
Frequency

Annual

Target

Within the range recorded for Phase IV (1,690)*

Responsibility

Departments

Area: Participating departments/agencies are working together to plan, set priorities, and implement coordinated management approaches

Indicator 1

Projects funded were selected based on agreed upon selection criteria

Frequency

Once per phase

Target

100%

Responsibility
  • NRC Secretariat
  • Departments
Indicator 2

Percent of resources allocated to interdepartmental collaborations established along shared priorities

Frequency

Annual

Target

Twenty percent of total GRDI resources allocated to collaborative projects for 2012-2013 and 2013-2014

Responsibility

NRC Secretariat

Indicator 3

Number of research projects involving three or more GRDI departments to address federal priorities

Frequency

Once per phase

Target

At least two

Responsibility

Departments

Area: Government policy makers and regulators have access as appropriate to new knowledge, tools and advice generated by scientists for policy and regulatory decisions supporting government mandates and shared priorities

Indicator

Number of outreach activities for disseminating results to end-users

Frequency

Annual

Target

Within the range recorded for Phase IV (27)*

Responsibility

Departments

Area: Private and public stakeholders involved in the innovation continuum in Canada have access as appropriate to new knowledge generated by scientists for the development of innovative or improved tools and processes

Indicator

Number of transfer activities:

  • outward material transfer agreements
  • transfer of standard operating procedures
  • disclosures
  • active patents, patent applications, patents issued
  • licenses issued
  • formal collaborative agreements / standard operating protocols
  • knowledge transfer workshops with stakeholders / end-users
  • requests for research results, papers, collaborations
Frequency

Annual

Target

Within the range recorded for Phase IV (339)*

Responsibility

Departments

Area: Government policy makers and regulators have used research results for evidence-based regulatory, policy, and resource management decisions

Indicator

Number of regulatory, policy, and resource management decisions informed by GRDI research

Frequency

Every 5 years

Target

At least ten regulatory, policy and resource management decisions informed by the last 5 years of GRDI research

Responsibility

Evaluators

Area: Private and public stakeholders involved in the innovation continuum in Canada have adopted innovative or improved tools and processes using research results

Indicator

Number of examples where innovative tools and processes have been adopted in Canada based upon GRDI research

Frequency

Every 5 years

Target

At least seven innovative or improved tools and processes adopted in Canada based upon the last five years of GRDI research

Responsibility

Evaluators

*Quantitative targets have been established based on GRDI Phase IV Annual Performance Reports between 2008 and 2011.

Footnotes

Footnote 1

Precursor to the Canadian Institutes of Health Research (CIHR) – one time allocation in fiscal year 1999-2000 to assist in the establishment and support of a Genome Canada Secretariat.

Return to footnote 1 referrer