Genomics Research and Development Initiative Annual Performance Report 2018–2019

 

Alternate format:  Genomics Research and Development Initiative - Annual Performance Report 2018–2019  (PDF, 2.08 MB)

About the initiative

Federal science departments and agencies collaborate on genomics research projects through the Genomics R&D Initiative to address issues that matter to Canadians. This document reports on the progress of 64 research projects, including the interdepartmental Antimicrobial Resistance and Metagenomics-Based Ecosystem Biomonitoring projects.

Prepared by: The working group for the Genomics R&D Initiative.
For additional information: Dr. Anne-Christine Bonfils

Executive summary

The Government of Canada’s Genomics Research and Development Initiative (GRDI) enables common approaches and collaboration on genomics research across federal science departments and agencies with the overarching aim of addressing issues that matter to Canadians. The Government of Canada has funded the GRDI in 3- to 5-year cycles from 1999 until March 2019, when it renewed the initiative on an ongoing basis.

The GRDI generates high-quality, genomics-based research and development (R&D) solutions for use in federal laboratories to support regulatory, public policy and operational mandates in socially and economically important areas such as health sciences, food safety, natural resource management, agriculture and aquaculture sector sustainability and competitiveness, and environmental protection. GRDI-funded projects focus on departmental mandates and federal government priorities, are strategically aligned with departmental objectives, and involve strong collaboration with universities and private sectors.

About this report

The 2018–2019 GRDI Annual Performance Report follows the Performance Measurement Framework that the interdepartmental GRDI Working Group developed in 2015. It profiles the initiative and planned results by department, draws connections to departmental objectives and program alignment architectures, and presents governance, coordination and accountability structures. Further, it reports on GRDI performance for 2018–2019 in terms of interdepartmental governance, research and development, and knowledge and networks. Appendix A presents summary statistics as well as a narrative account of research and development achievements for the period.

GRDI performance in 2018–2019

Fiscal 2018–2019 marked the last year of Phase VI of the GRDI. The initiative continued to support mandated research within participating departments and facilitated structured, interdepartmental collaboration. Phase VI also involves 2 highly coordinated interdepartmental shared priority projects: the Antimicrobial Resistance (AMR) and Metagenomics Based Ecosystem Biomonitoring (EcoBiomics) projects that will extend to 2020-2021.

Achievements this period include:

  • Agriculture and Agri-Food Canada (AAFC) deposited genome sequences of cultivars and wild relatives of wheat, barley, and oat in a public database for breeder-friendly gene marker development.
  • Canadian Food Inspection Agency (CFIA) enhanced its capability of using next-generation sequencing technology to detect tuberculosis and brucellosis in infected cattle.
  • CFIA developed an automated bioinformatics work flow management system for the detection of African swine fever virus and other priority viruses for emergency preparedness measures.
  • CFIA developed and validated quality assurance metrics in support of food safety programs and produced the Record of Genomic Analysis (ROGA) featuring a standardized, user-friendly reporting format meeting the needs of the end-user community (i.e., Food Safety Science Directorate, risk assessors and recall specialists).
  • CFIA implemented the FoodPort cloud-based analytical service, an easy-to-use platform that enables users to access the CFIA’s bacterial genomics data with minimal training.
  • Fisheries and Oceans Canada (DFO) developed and validated cutting-edge environmental DNA (eDNA) tools to support the department’s resource management decisions.
  • DFO used next-generation sequencing to resource profile Arctic char, chinook and Atlantic salmon, and Atlantic cod.
  • Health Canada (HC) led the publication of consensus opinions on procedures and strategies used for toxicology testing and risk assessment by the International Workshop on Genotoxicity Testing working group.
  • HC participated in the drafting of the Environmental Health Criteria Document under the World Health Organization (WHO)/ International Programme on Chemical Safety, which provides principles and methods to assess the risk of immunotoxicity associated with exposure to nanomaterials.
  • The National Research Council of Canada’s (NRC) commercial partner, Forbius, has conducted clinical assays with a molecule developed with support from the GRDI and acquired under licence from the NRC.
  • The NRC comprehensively profiled global gene response to low temperatures in spring and winter wheat.
  • Natural Resources Canada (NRCan) contributed to accelerate end-users’ spruce breeding programs by one generation, allowing improved spruce stocks to be planted much earlier, more than doubling the net economic output value compared to conventional breeding.
  • The Public Health Agency of Canada (PHAC) validated field-deployable sequencing technology for the quick and reliable detection of numerous viruses including enteroviruses, Zika, Ebola and Lassa directly from clinical samples. The information is important when trying to understand the spread of a virus during an outbreak and when decisions are made to deploy vaccines, since some vaccines do not work on closely related viruses.
  • PHAC developed genomic sequencing methods and analytical tools to address gaps in national surveillance of drug resistance, level of pathogenicity, and person-to-person transmission of nonenteric bacterial pathogens.

Addressing issues that matter to Canadians

In 1999, the Government of Canada launched the Genomics Research and Development Initiative (GRDI) to establish and maintain core genomics R&D capacity in federal departments and agencies. This report details the performance of the participating departments and agencies on 61 research projects under the GRDI, including the 2 shared priority projects (SPP): the Antimicrobial Resistance (AMR) project and the Metagenomics-Based Ecosystem Biomonitoring (EcoBiomics) project.

Each year, the GRDI delivers $19.9 million in funding across:

  • Agriculture and Agri-Food Canada (AAFC)
  • Canadian Food Inspection Agency (CFIA)
  • Environment and Climate Change Canada (ECCC)
  • Fisheries and Oceans Canada (DFO)
  • Health Canada (HC)
  • National Research Council of Canada (NRC)
  • Natural Resources Canada (NRCan)
  • Public Health Agency of Canada (PHAC)

GRDI-funded projects focus on departmental mandates and federal government priorities, are strategically aligned with departmental objectives, and involve strong collaboration with universities and private sectors. This includes upholding regulatory, public policy and operational mandates in important areas such as health, food safety, natural resources management, environmental protection, and the sustainability and competitiveness of Canada’s agriculture sector. The 2 shared priority projects (AMR and EcoBiomics) are highly coordinated interdepartmental projects that address shared priorities and common goals.

The 6 phases of the GRDI

The federal government invested $393.3 million into the GRDI between 1999 and 2019 to fund 6 phases:

  • $55 million for Phase I (1999–2002)
  • $59.7 million each for Phases II (2002–2005), III (2005–2008), IV (2008–2011) and V (2011–2014)
  • $99.5 million for Phase VI (2014–2019)
Table 1: Funding allocations ($000)
Department/agency Phase 1
1999 – 2002
Phase II
2002 – 2005
Phase III
2005 – 2008
Phase IV
2008 – 2011
Phase V
2011 – 2014
Phase VI
2014 – 2019
Agriculture and Agri-Food Canada 17,000 18,000 18,000 18,000 15,300 22,200
Canadian Food Inspection Agency - - - - - 3,600
Environment and Climate Change Canada 3,000 3,000 3,000 3,000 2,550 4,000
Fisheries and Oceans Canada 2,500 2,700 2,700 2,700 2,295 3,600
Health Canada / Public Health Agency of Canada 10,000 12,000 12,000 12,000 10,200 16,000
National Research Council of Canada 17,000 18,000 18,000 18,000 15,300 22,200
Natural Resources Canada 5,000 6,000 6,000 6,000 5,100 8,000
Shared Priorities - - - - 8,955 19,900
Medical Research Council Footnote 1 500 - - - - -
Total 55,000 59,700 59,700 59,700 59,700 99,500

All departments have leveraged the GRDI funds with allocations from their A-base resources and from successful collaborations. Table 2 provides an overview of resources invested in 2018–2019 in support of GRDI projects and demonstrates that non-GRDI funds represented 1.7 times the GRDI investments. Additional in-kind investments 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 2018–2019 ($000)
Department/agency GRDI NON-GRDIFootnote 2 Total
National Research Council of Canada 4,440 6,245 10,685
Agriculture and Agri-Food Canada 4,440 9,249 13,689
Health Canada 1,600 2,234 3,834
Public Health Agency of Canada 1,600 2,325 3,925
Natural Resources Canada 1,600 4,262 5,862
Environment and Climate Change Canada 800 1,615 2,415
Fisheries and Oceans Canada 720 234 954
Canadian Food Inspection Agency 720 3,177 3,897
Shared priority project
Antimicrobial Resistance 1,884 3,238 5,122
Metagenomics Based Ecosystem Biomonitoring 1,874 1,005 2,879
Coordination and Common Functions 222 45 267
Total 19,900 33,629 53,529

Planned results for 2018–2019

As reported in the NRC’s Departmental Report on Plans and Priorities Supplementary Table for the GRDI, the participating departments established a collective set of planned results for 2018–2019:

  • using genomics to significantly increase Canada’s share of global wheat production
  • using genomics to improve the value of Canadian crops and agri-products
  • using genomics for food safety, animal health and plant protection
  • genomics knowledge and advice for the management of fisheries and oceans
  • genomics-based tools and technologies for responsible environmental decision-making
  • genomic knowledge for the Canadian health regulatory system
  • commercially-relevant advances in genomics R&D related to human health
  • concerted interdepartmental research along shared priorities and common goals on issues that are beyond the mandates of single departments
  • genomic knowledge for forest regeneration and protection
  • genomics knowledge to strengthen public health programs and activities related to the prevention and control of infectious disease

The participating departments and agencies developed research plans and activities to deliver on these planned results. Descriptions of these plans and activities follow.

Agriculture and Agri-Food Canada

AAFC will use its GRDI funding to advance Canadian Crop Genomics Initiative priorities as well as enable industry to take advantage of innovations. Activities will fall under 2 broad themes:

  • biodiversity, gene mining and functional analysis—develop value-added traits (e.g. seed quality) for the highly competitive marketplace as well as make Canada’s crop production more resilient against potentially catastrophic abiotic and biotic stresses to maximize sector profitability
  • improved access to biological materials and data sets—make plant breeding more efficient, laying the scientific foundation for major advances in priority trait development and delivery for industry

Canadian Food Inspection Agency

The CFIA’s genomics research will enhance the capacity and ability to regulate pests and pathogens by focusing on 2 thematic areas: detection and isolation, and identification and characterization. Research under these themes aligns with the Agency’s 3 business lines:

  • animal health—support management of public health risks associated with the transmission of zoonotic diseases as well as reportable and emerging animal diseases
  • food safety—enhance compliance testing, source attribution and risk profiling while enabling enforcement of Health Canada risk assessment standards
  • plant health—advance early detection and rapid response capabilities, and inform regulatory decision-making regarding regulated plant pests and commodities in the agriculture and forestry sectors

CFIA will also conduct research to harmonize genomics activities across its 3 business lines with the aim of improving the transfer of technology and tools between the business lines and making genomics tools more accessible to CFIA scientists.

Environment and Climate Change Canada

ECCC will continue to apply its GRDI funding under the Strategic Technology Applications of Genomics in the Environment (STAGE) program with the following priorities:

  • ecotoxicology—establish toxicology endpoints for micro-organisms, chemicals of concern and emerging stressors, and predict the mode of action of chemicals of concern and their effects on organisms
  • wildlife conservation—understand how genes interact within flora and fauna in response to environmental conditions, and track disease in wildlife
  • environmental monitoring—develop indicators (e.g. gene expression profiles for key species) of ecosystem health in priority ecosystems (e.g. Great Lakes and St. Lawrence), and track pathogen sources
  • compliance and enforcement—analyze flora and fauna to identify individual species, determine parentage and ascertain geographic origin

This work will support ECCC’s obligations under the Fisheries Act, the Canadian Environmental Protection Act, and programs including the Chemicals Management Plan.

Fisheries and Oceans Canada

Genomics-enabled research within DFO will continue to align with 3 key themes:

  • protecting fish species and promoting sustainable harvesting—develop and apply leading-edge genomics tools to accurately identify species, populations and stocks for fisheries management, and conserve vulnerable stocks, at-risk species and aquatic biodiversity
  • safeguarding Canadian fish and seafood products—develop innovative genomics techniques to detect, monitor and minimize the impact of pathogens (e.g. infectious salmon anemia virus) to safeguard the health of Canada’s aquatic resources and secure Canada’s fish and seafood export markets
  • maintaining healthy and productive aquatic ecosystems—develop and apply new genomics tools to monitor, mitigate and restore aquatic ecosystems (e.g. aquatic invasive species, marine protected areas)

This research will support fisheries managers, who increasingly rely on innovative genomics and bioinformatics technologies to inform resource management and conservation decisions across DFO sectors and programs. Genomics can inform fisheries, biosecurity, and aquaculture applications by clearly defining population or stock structure, tracing migratory fish back to rivers of origin, and distinguishing escaped farmed fish, wild fish, and hybrids.

Environmental DNA (eDNA) refers to molecules of DNA that are shed by organisms into their environment that can be collected in a simple water or sediment sample and analyzed to infer species presence. Genomics approaches, including environmental DNA, can enhance management outcomes through increased efficiency and sensitivity such as early detection and mitigation of aquatic invasive species and monitoring of species at risk, as well as tracking the impacts of climate change on species distributions in real time.

Health Canada

Genomics research at HC will continue to focus on 4 priority investment areas to strengthen the department’s regulatory role:

  • supporting regulatory knowledge on therapeutics and biologics—inform and support regulatory decisions throughout the biotherapeutic product life cycle
  • supporting regulatory knowledge on food safety and nutrition—enable detection and characterization of foodborne micro-organisms; enable characterization of health effects of food contaminants (e.g. fungal toxins, anthropogenic contaminants and seafood toxins), food allergens, nutrients, novel foods or food ingredients, and prebiotics and probiotics; and develop markers of health status and disease (e.g. cancer, diabetes, obesity, allergies and cardiovascular disease) in the context of nutrition, micro-organisms, allergens and food contaminant exposure
  • protecting human health from potential adverse effects—protect Canadians against potential negative impacts of environmental contaminants, radiation, consumer products and pesticides
  • researching the socio-ethical impacts of genomics technologies, outputs and products—develop approaches for the responsible integration of genomics for societal benefit, accounting for ethical, legal and socio-economic considerations

National Research Council of Canada

GRDI investments will support NRC programs that require genomics-related activities to help industry and the federal government pursue strategic national priorities with the support of mission-oriented research and technology deployments. In 2018–2019, these will be:

  • the NRC’s contribution to the Canadian Wheat Alliance, which aims to improve the yield, sustainability and profitability of wheat for the benefit of Canadian farmers and the economy through improved breeding efficiency; reduced losses from drought, heat, cold and diseases; and more efficient nutrient use
  • Biologics and Biomanufacturing program, which aims to cover all aspects of biologic development—from discovery up to pre-clinical testing—in collaboration with industry partners

The NRC’s Senior Executive Committee approved implementation of these programs after careful deliberation and a rigorous assessment process.

Natural Resources Canada

NRCan’s Canadian Forest Service will focus on applying genomics knowledge to promote the competitiveness of Canada’s forest sector, including:

  • forest generation—develop innovative genomic applications to accelerate production of higher quality fibre to realize economic and environmental benefits for Canada
  • forest protection—develop innovative genomic diagnostic tools to enable rapid detection and management of invasive insects and diseases that threaten the health and ecological integrity of Canadian forests, the forest sector and forest communities

Public Health Agency of Canada

GRDI research activities at PHAC apply “-omics” technologies to generate new knowledge to support public health decision-making and create tools to enhance disease prevention and control. These technologies support:

  • prevention and control of priority pathogens
  • response to antimicrobial resistant pathogens
  • infectious disease surveillance
  • public health security measures

The knowledge genomic approaches generate supports more detailed risk analyses, as well as the identification and development of new intervention points for infectious disease control and prevention

Shared priorities

The Antimicrobial Resistance (AMR) project is a key component of the Federal Action Plan for Antimicrobial Resistance and Use in Canada. AAFC is the project coordinator, and CFIA, HC, the NRC and PHAC are all involved. The project will add to the understanding of the critical activities that contribute to antimicrobial resistance development. It will also shed light on critical exposure pathways through which antimicrobial bacteria reach humans, which could help validate economically sustainable technologies, practices, and policies to mitigate the development of antimicrobial resistance.

AAFC also coordinates the Metagenomic-Based Ecosystem Biomonitoring (EcoBiomics) project, which involves CFIA, DFO, ECCC, the NRC, NRCan and PHAC. The collaborating parties will develop advanced genomics tools to assess freshwater ecosystem biodiversity and water quality in lakes and rivers, evaluate the health of soil essential to the productivity of agricultural and forestry systems across Canada, and investigate land remediation for the oil and mining sectors. The project will support environmental responsibility, secure market access for resource products and improve social license for economic development in Canada.

How the GRDI supports federal government priorities

One of the GRDI’s primary aims is to help participating departments and agencies make evidence-based regulatory and policy decisions called for by their respective mandates. It also seeks to support development of new policies and standards, as well as the ability to anticipate and respond to the needs of Canadians in the areas of public health, the economy, agriculture, fisheries and aquaculture, and the environment. Based on these aims, GRDI-funded projects focus on advancing departmental mandates and objectives as well as federal government priorities.

Going forward, the GRDI will support the goals of Canada’s Innovation and Skills Plan to make Canada a world-leading centre for innovation, to help create more well-paying jobs, and to help strengthen and grow the middle class. It will also help anticipate and respond to the needs of Canadians through genomics-related innovation opportunities in health, agri-food, clean technology, digital industries and clean resources.

Department-specific details follow.

Agriculture and Agri-Food Canada

AAFC uses the GRDI funding to develop and strengthen the Canadian Crop Genomics Initiative with investments into plant genomics and by forming multidisciplinary teams across Canada that focus on promoting the sustainability and competitiveness of the country’s agriculture sector.

Canadian Food Inspection Agency

Genomics research outcomes support commodities and resources regulated under CFIA’s program activities, including those of its food safety, animal health and zoonotic, and plant resources programs. CFIA’s GRDI program targets the development and application of genomics tools for the rapid detection of food pathogens, plant pests and animal disease agents. This enables the agency to respond effectively to regulatory needs in food safety, ensure compliance, maintain consumer confidence, and minimize animal and plant disease incursions.

Environment and Climate Change Canada

The genomic research priorities under ECCC’s STAGE program contribute to monitoring and understanding Canada’s ecosystem, helping to assess risks posed by chemical pollutants to wildlife and migratory birds, and delivering practical applications that support regulatory compliance and evidence-based decision-making related to risk mitigation and conservation efforts.

Fisheries and Oceans Canada

Genomics research is building the scientific knowledge base and expertise necessary to support priorities for fisheries management and ocean conservation and protection. At DFO, activities under the GRDI support genomics research for 2 of the 4 core responsibilities of the department’s program alignment architecture. The department coordinates genomics research nationally through its Biotechnology and Genomics Program.

Health Canada

GRDI-funded research generates regulatory knowledge that contributes to the appropriate management and communication of health risks and benefits associated with food, products, substances and environmental factors. The knowledge and tools genomics research generates ultimately support departmental efforts to respond to current and emerging health issues under the aforementioned strategic outcome as well as the “Canadian Health System Policy” program activity.

National Research Council of Canada

The NRC’s research aligns with Government of Canada strategic outcomes and federal priorities as well as the NRC’s business processes. The GRDI at the NRC contributes to research programs that focus on improving Canadian wheat and developing new biologics.

Natural Resources Canada

The GRDI has helped NRCan’s Canadian Forest Service generate important data, infrastructure and partnerships that deliver practical applications. This foundation supports NRCan’s efforts to make Canada’s natural resource sectors globally competitive, the program activity “Innovation for New Products and Processes,” and the intended outcome “Advancing Forest Product Innovation.”

Public Health Agency of Canada

PHAC uses GRDI funding to support the development of innovative tools that apply genomic and bioinformatic technologies for more effective public health interventions. The GRDI also generates leading-edge scientific knowledge to support public health decision-making and program development. It also facilitates integration of reliable and current information into public health decision-making and interventions across Canada by driving collaboration and knowledge exchange among public health professionals working at all levels of government as well as with non-governmental organizations. These functions directly support the Agency’s program of Laboratory Science Leadership and Services.

Governance, coordination and accountability

Accountability can make it challenging to manage shared programs that have a collective sense of purpose because departments are vertically accountable for delivering on their mandates and spending resources. The NRC established an interdepartmental governance framework for previous phases of the GRDI to ensure sound management. The same framework will be used to oversee the collective coordination for the current phase.

The GRDI governance structure includes 3 main elements (with support from ad-hoc advisory committees as needed):

  • Assistant Deputy Minister Coordinating Committee (ADM CC)
  • Interdepartmental GRDI working group
  • a coordination function
Assistant Deputy Minister Coordinating Committee

Chaired by the NRC, the interdepartmental ADM CC includes ADMs from each of the GRDI-funded organizations and guest representatives from Innovation, Science and Economic Development Canada (ISED) and Genome Canada. The committee typically meets 3 times a year at the call of the chair—more often when the need for decision-making warrants. The ADM CC is responsible for:

  • determining the overall strategic direction of the GRDI
  • approving investment priorities
  • ensuring effective priority-setting mechanisms are established for the GRDI
  • ensuring federal government objectives and priorities are addressed
  • ensuring common management principles are implemented
  • ensuring collaborations between organizations are pursued wherever relevant and possible
Interdepartmental GRDI working group

The interdepartmental working group, chaired by the NRC with membership at the director level from all participating departments and agencies and ISED, supports the work of the ADM CC. Its mandate is to support the ADM CC’s strategic priority setting and overall management of the GRDI with recommendations and strategic advice. The working group meets about every 2 months—more often as ADM CC’s needs for recommendations and advice warrant. The working group is responsible for:

  • providing direction to GRDI activities related to operational delivery, implementation planning and investment priority setting
  • supporting evaluation and reporting requirements related to the GRDI
Coordination function

Housed at the NRC, the coordination function:

  • provides GRDI-wide program coordination, communication, networking and outreach support (including support to the ADM CC and the GRDI working group),
  • provides transparent and effective communication to departments regarding the planning cycle, process requirements, financial administration and other project management requirements
  • supports shared priority project planning and implementation
  • helps establish GRDI-wide research priorities
  • facilitates interdepartmental project development and peer review,
  • ensures shared priority project management plans and funding agreements are in place
  • supports performance management, reporting, evaluation and communications

The GRDI coordination function is made possible by the funding set aside for shared priority activities.

GRDI Performance Measurement Strategy Framework

GRDI Phase VI uses an updated version of the Horizontal Performance Measurement Strategy developed for Phase V. This version covers fiscal years 2014–2015 to 2018–2019 and formalizes the roles and responsibilities of the 8 participating departments and agencies to promote effective monitoring and evaluation. These updates align with the Policy on Evaluation (2009) and associated Guide to Developing Performance Measurement Strategies (May 2010), as well as the policy and the associated instructions to departments for developing a management, resources and results structure (March 2013).

Appendix B includes an overview of the Performance Measurement Strategy Framework, as well as a logic model that reflects the overall objectives for the GRDI: the uptake and application of the knowledge and tools it generates for policy and regulatory decisions, key public policy priorities, and private sector innovation.

How the GRDI performed in 2018–2019

The NRC recorded the performance of the GRDI for 2018–2019 in 3 areas:

  • interdepartmental governance
  • research and development
  • knowledge and networks

Interdepartmental governance

Coordinated management approaches

The NRC provided ongoing coordination in 2018–2019, the last year of Phase VI, including timely secretariat support to GRDI departments and agencies and the implementation of GRDI governance, management and operating processes. A key activity of the interdepartmental working group and the ADM CC was to plan the renewal of funding beyond March 2019 with the development of options for rebranding and strengthening the initiative. Steps were then taken to extend the current GRDI model in agreement with guidance provided by Deputy Ministers, and the Government of Canada renewed the GRDI on an ongoing basis. Other activities included supporting the implementation of the AMR and EcoBiomics projects, reporting on performance of the GRDI, and implementing the Management Response and Action Plan resulting from the 2016 evaluation report. Communications materials were developed to present key impacts deriving from GRDI research: a brochure, 2 infographics, sample success stories, a kit folder, and a presentation booth.

Shared priorities

Phase VI shared priority projects continued to implement their approved project management and science plans. Project leads held regular teleconferences with project participants, theme leads met bi-weekly, and all principal investigators met monthly.

The Management Advisory Committees of both shared priority projects met on January 11 and 16, 2019 for the EcoBiomics project and on January 24, 2019 for the AMR project, including some members of the Scientific Advisory Boards. Project-specific annual workshops took place in 2019 (EcoBiomics in Ottawa, March 19-20, and AMR project in London, Ontario, June 26-27) to update participants on project progress and coordinate activities for the coming year. Key end users and science advisors participated in the annual workshops and were engaged throughout the year. Both teams updated their Knowledge Translation plans, approved by the ADM CC.

Research and development

The GRDI Performance Measurement Strategy Framework measures all activities surrounding the actual conduct of research and development, the transfer of technologies and results to stakeholders for uptake and application, and the communication of these results. All these areas are critical to ensuring GRDI-funded projects make an impact.

Annex 2 lists the direct scientific outputs for 2018–2019 and quantitative performance indicators by department/agency for:

  • scientific contributions (key scientific contributions demonstrating leadership, other scientific contributions, research tools and processes)
  • knowledge translation and mobilization (contributions to scientific networks)
  • collaborations
  • communications products
  • end-user engagement and knowledge transfer activities
  • research and technical personnel

Annex 3 provides highlights of the results achieved in 2018–2019 against planned results, while Annex 4 presents a list of research tools and processes developed under the GRDI.

Several GRDI scientists received recognition of the excellence of their research, as shown in Table 3.

Table 3: GRDI participant recognition for research excellence
Recipient(s) Prize/award/recognition
Therese Ouellet (AAFC) The publication ‘Transcriptome Dynamics Associated with Resistance and Susceptibility against Fusarium Head Blight in Four Wheat Genotypes. BMC Genomics 19:642’ was one of top 3 downloaded papers in BMC Genomics in 2018
A. Bahadoor (AAFC) The publication ‘Bahadoor, A. et al. Gramillin A and B: Cyclic lipopeptides identified as the nonribosomal biosynthetic products of Fusarium graminearum. Journal of the American Chemical Society 140: 16783-16791’was highlighted as a JACS Spotlight article
(https://pubs.acs.org/doi/full/10.1021/jacs.8b12815)
Mary Miltenburg
(graduate student with Dr. Subramaniam, AAFC)
First place winner of the poster session at the Joint Ninth Canadian Workshop on Fusarium Head Blight and Fourth Canadian Wheat Symposium, Nov. 2018. Winnipeg
Kristina Shostak
(graduate student with Dr. Subramaniam, AAFC)
Second place winner of the poster session at the Joint Ninth Canadian Workshop on Fusarium Head Blight and Fourth Canadian Wheat Symposium, Nov. 2018. Winnipeg
Ian Bradbury (DFO) 3-year Cox Fisheries Scientist in Residence Award from Dalhousie University for 2017–2020
Pooja Sridhar
(graduate student with Dr. Subramaniam, AAFC and Dr. Michele Loewen, NRC)
Second place winner of oral presentation at the Joint Ninth Canadian Workshop on Fusarium Head Blight and Fourth Canadian Wheat Symposium, Nov. 2018. Winnipeg
Carole Yauk (HC) ADM and DM Award of Excellence in Science at Health Canada for outstanding work in genomics
Carole Yauk (HC) Editor’s Choice paper award (featured on front cover, publicized and free open access – value $3K USD): Corton JC, Williams A, Yauk CL. Using a gene expression biomarker to identify DNA damage-inducing agents in microarray profiles. Environ Mol Mutagen. 2018 Dec; 59(9):772-784. doi: 10.1002/em.22243. Epub 2018 Oct
Carole Yauk (HC) Elected in-coming president of the Environmental Mutagenesis and Genomics Society
Dele Ogunremi (CFIA) Scientific Excellence, CFIA Science Branch award for active participation in the 2018 genetically
Catherine Soos et al.(ECCC) Third place award for the best student poster at the Annual Graduate Student Poster Competition of the Western College of Veterinary Medicine, University of Saskatchewan
Catherine Soos et al.(ECCC) First place for the best student poster at the Graduate Student Poster Competition at the Saskatchewan Structural Sciences Centre Open House, University of Saskatchewan
Hezhao Ji (PHAC) University of British Columbia Science Co-op Supervisor Recognition Award 2018 for supervising Mr. Chao Chun Liu during 2 co-op terms
Robert Penner (PHAC) Outstanding Research Communication Award, Festival for Undergraduate Research, University of Alberta, for work identifying hepatitis C virus genetic recombinants using the Ultra L protocol
Marisa Rankin (PHAC) First place at the Clive Kingsbury Poster Competition, April fifth Ontario Food Protection Association Spring Technical Meeting, Mississauga, for poster entitled ‘Increasing Traceability of Salmonella Enteritidis using Single Nucleotide Variant Subtyping based on Population Structure’
Celine Nadon, Gary Van Domselaar and WGS Implementation Team (PHAC) 2018 Dr. Lucil Dutil Memorial Award in Applied Science

Knowledge and networks

Knowledge translation and mobilization activities are essential to maximizing the GRDI’s value and applying the research and tools it generates to commercial and public-good objectives as the initiative matures. These activities include the development of scientific networks, communications products, end-user engagement activities, science policy integration, science advice, protocol transfer, field trials, outreach activities, and more. Activities like these ensure research is relevant by creating opportunities to understand the needs of end users and share the results of GRDI projects with them.

Examples of knowledge and networks activities completed in 2018–2019 follow.

Antimicrobial Resistance project

The leading-edge software and datasets developed by the AMR project have been adopted as a central component of a new research project funded by Genome Canada under the 2019 call for Large Scale Applied Research Projects on agri-food.

Members of the AMR project are well connected to domestic and international initiatives, for example providing science advice for the Joint Programming Initiative on AMR (JPIAMR), chairing the Transatlantic Taskforce on Antimicrobial Resistance (TATFAR) Action Item 1.5 - Collaborate on implementation of the Guidelines for Risk Analysis of Foodborne Antimicrobial Resistance prepared by Codex Alimentarius, and chairing the expert meeting of the United Nations Food and Agriculture Organization / World Health Organization on foodborne antimicrobial resistance: Role of environment, crops and biocides.

EcoBiomics project

Members of the EcoBiomics project engaged regularly with water quality monitoring program end users in ECCC and the Ontario Ministry of Environment to ensure EcoBiomics water sampling was integrated with priority federal and provincial programs in the Great Lakes. Researchers also continued discussions on protocols for implementing genomic monitoring and selecting candidate genomic observatories with ECCC’s National Water Quality Monitoring Program and the Canadian Aquatic Biomonitoring Network (CABIN). They co-led the project “Sequencing the Rivers for Environmental Assessment and Monitoring” that brings science to citizens and that involves the University of Guelph, ECCC, and the World Wildlife Fund.

They participated in international working groups (e.g. International Bio-economy Forum, Genomic Standard Consortium, Earth Biome Initiative); provided science advice on microbiome-based data management at the kick-off meeting of the MicrobiomeSupport project (European Cooperation in Science and Technology (COST) Action) in Vienna, Austria; organized conferences such as the annual meeting of the Society of Canadian Limnologists, in London, ON, and the annual meeting of the Biodiversity Information Standards (Taxonomic Databases Working Group), in Ottawa, ON; co-chaired a special metagenomics session with the Ontario Ministry of Environment; presented the EcoBiomics project at the 2018 Conference of the International Association of Great Lakes Research held in Toronto; served on the Health Canada federal/provincial committee revising the Canadian Recreational Water Quality Guidelines and recommended to incorporate metagenomics considerations in the management of beaches and other recreational waters.

The Global Omics Observatory Network (GLOMICON), a task group jointly created by AAFC and the EcoBiomics project under the Earth Observations Biodiversity Observation Network (GEO BON) expanded considerably and developed a website (www.glomicon.org) and a discussion board.

Dr. Donald Buckingham, Chief Executive Officer of the Canadian Agri-Food Policy Institute, led a policy-focused discussion at the March 2019 EcoBiomics annual general meeting.

Agriculture and Agri-Food Canada

AAFC organized the joint conference of the Fourth Canadian Wheat Symposium and the Ninth Canadian Workshop on Fusarium Head Blight (https://www.cwfhb-cws.com), November 19-22, 2018, reaching out to an audience of more than 150 participants including government scientists, academia, industry, and many sector organizations.

AAFC Ottawa Research and Development Centre hosted the annual Oat Day on July 18, 2018.

AAFC scientists also participated in the Prairie Pest Monitoring Network Annual Meeting (March 26, 2019) – “Genetic diversity and population structure of wheat midge (Sitodiplosis mosellana)in western Canada”.

Several new collaborations were established (e.g. with United States Department of Agriculture (USDA)/Kansas State University; the University of Manitoba; with scientists in Spain, Italy, Germany, Brazil, and the United Kingdom).

Canadian Food Inspection Agency

CFIA scientists have enhanced their capacity to improve management, analysis and interpretation of genomics data. This includes data gathering from public databases to design assays and to perform comparative genomics, incorporating better and faster tools for computing-intensive processes, and streamlining workflows through in-house scripts that automate time-consuming steps. Knowledge and tools generated from genomics research ultimately support the Agency to fulfill its mandate to protect food safety, plant and animal

Fisheries and Oceans Canada

During 2018-2019, DFO scientists developed innovative fisheries genomics tools including a novel remote in-field environmental DNA (eDNA) sampling device, genome-wide panels for key commercial fish species including Atlantic cod, Atlantic salmon, chinook salmon, and Arctic char to provide strong scientific evidence for conservation and management decisions, and the application of eDNA for early detection of aquatic invasive species and at-risk species. DFO transferred the knowledge that these tools generated and provided science advice for evidence-based decision making through networks of international and Canadian partners including the International Council for the Exploration of the Sea as well as Canada’s Nisga’a, Gwich’in and Sahtu First Nations communities, whose livelihoods depend on the fisheries.

Health Canada

HC scientists participated in a number of knowledge translation and mobilization activities related to the GRDI in 2018–2019. A scientist chaired the working group of the International Workshops on Genotoxicity Testing to develop consensus opinions on the use of high-content data in genotoxicity assessment. Another scientist participated in drafting the Environmental Health Criteria Document (Principles and Methods to assess the risk of immunotoxicity associated with exposure to nanomaterials) produced by the International Programme on Chemical Safety of the World Health Organization, and chaired specific chapters. This scientist also provided expert advice on experimental designs and sample collection for toxicogenomics studies for 3 EU2020 research consortia.

Several scientists serve as advisors to international organizations on the use of genomics technology to assess risks associated with chemicals, including:

  • the Organization for Economic Cooperation and Development’s Extended Advisory Group on Molecular Screening and Toxicogenomics
  • WHO’s International Programme on Chemical Safety
  • European Centre for Ecotoxicology and Toxicology of Chemicals
  • International Life Sciences Institute Health and Environmental Science Institute Genetic Toxicology Technical Committee
  • European Union’s Horizon 2020 project consortium

In the area of stem cells, a scientist participated in a bilateral meeting with cell therapy stakeholders, regulators and policy makers from Health Canada to discuss regulatory issues regarding the use of stem cells and gene therapies as medicines in Canada.

National Research Council of Canada

In 2018-2019, the NRC’s Biologics & Biomanufacturing program held the National Biomanufacturing Summit in Montreal, during the International Biotechnology Symposium (IBS2018).

Researchers under the NRC’s Canadian Wheat Improvement flagship program contributed to the:

  • International Wheat Yield Partnership for research of photosynthetic efficiency in wheat
  • Wheat initiative led by the Institut national de la recherche agronomique as part of an expert working group on adaptation of wheat to abiotic stress
  • FusResis Consortium to develop enhanced Fusarium resistance in wheat
  • International pan-genome (10+) sequencing effort
  • Wheat initiative-sponsored meiosis and recombination collaborative research partnership
  • International wheat genome sequencing initiative
  • Wheat transcriptome atlas coordinated by international initiative and publication of second article in Science August 2018 issue
  • International collaboration group on cereal recombination
  • International Rye Genome Sequencing Consortium
Natural Resources Canada

NRCan researchers continue to accelerate the translation of genomics research to develop tools for use in mapping and monitoring the spread of forest invasive alien species and to transfer these technologies and tools to end-users. NRCan has also finalized 4 outward material transfer agreements for continued research on Asian gypsy moth. Metagenomics tools were used in the field to assess the impact of disturbances on forest ecosystems and to improve land reclamation strategies. In 2018, researchers were invited to present their research across North America, Europe, and Asia on the development of applications to increase fibre supply and quality, to enhance the early detection of invasive forest pests, and to support more effective disease management in Canada’s forests. Researchers hosted a workshop with USDA Animal and Plant Health Inspection Service personnel on the application of their molecular assays in the United States. Finally, a traceability system for large-scale white spruce seedling production was newly established in a provincial nursery.

Public Health Agency of Canada

GRDI projects undertaken at PHAC include engagement with national and international partners. For instance, PHAC researchers have developed enhanced tools for detecting and characterising foodborne pathogens in partnership with established national surveillance networks FoodNet Canada and PulseNet Canada. These tools are now routinely used by these national surveillance networks. Similarly, genomics-based tools for controlling and reducing antimicrobial resistance were developed in close collaboration with the national antimicrobial resistance surveillance networks: 1) the Canadian Nosocomial Infection Surveillance Program and 2) the Canadian Integrated Program for Antimicrobial Resistance Surveillance. These partnerships between genomics researchers and surveillance epidemiologists have maximised the impact of GRDI projects through sample and knowledge sharing, and through the transfer of research results to practical use.

Internationally, researchers collaborated with the WHO to share knowledge and technological approaches for eradicating the measles virus, and for detecting drug-resistant human immunodeficiency viruses. Researchers also contributed to enhancing the global surveillance of rubella virus and antibiotic-resistant gonorrhoea in conjunction with partners from the WHO.

Nationally, researchers created a plan to enable the adoption of enhanced proteomic methods for the rapid detection of bacterial pathogens in clinical settings. The genomic tools developed for the detection and characterisation of foodborne bacteria were transferred for the characterisation of the bacteria that cause tuberculosis. Researchers also shared the data and tools produced by GRDI projects with academic researchers involved in Genome British Columbia and Genome Canada research projects.

Scientists serve nationally and internationally on several advisory boards that support the prevention and control of infectious diseases:

  • Committee for next-generation, extended and whole genome sequencing for measles and rubella, working group of the WHO Measles and Rubella LabNet
  • WHO Global HIV Drug Resistance Network Steering Committee and Research Innovation Working Group
  • Committee for International Genomics Standards for Salmonella
  • Federal Food Safety Sciences Committee on implementation of genomic standards in food safety
  • PulseNet Canada Steering Committee
  • International Shiga-toxin producing E. coli Genomics Working Group
  • International committee on in-silico E. coli serotyping, as developer of the tool and allele database
  • Scientific advisory board for the INNUENDO consortium funded by the European Food Safety Authority, which aims to develop an analytical platform for the integration of genomics in the surveillance of foodborne pathogens
  • International working groups for whole-genome multi-locus sequence typing for Salmonella and campylobacter
  • GenEpiO consortium currently developing an ontology for genomic epidemiology proposed as the international standard
  • Global Microbial Identifier Consortium

Appendix A - Supplemental performance details

Annex 1: 2018–2019 GRDI projects and allocations from GRDI funds

GRDI funds ($) Project title
Shared Priority Projects
1,883,640 Antimicrobial resistance (AMR)
1,874,160 Metagenomics based environmental biomonitoring (EcoBiomics)
Agriculture and Agri-Food Canada
86,500 Mining legume genomes for attributes of sustainable nutrient (nitrogen) acquisition through symbiosis
417,000 Camelina sativa as a 21st century clean energy crop for Canada
1,225,530 Targeting resistance and susceptibility genes and dissecting infection mechanisms through genomics for durable Fusarium and rust resistance in cereals
186,600 Gene-for-gene mediated resistance to midge in canola and wheat
1,136,250 Advanced genomics strategies to capture novel genetic diversity for oilseed crop improvement
1,126,600 Genetic and epigenetic variants of Canadian cereal crops for breeding and functional analysis
220,530 Improving soybean for Canadian agriculture: management of biotic stresses and symbiotic microbes
Canadian Food Inspection Agency
70,000 Application of whole genome sequencing for molecular epidemiological investigations of bovine tuberculosis in Canada and for the high throughput discovery of novel diagnostic antigens for Mycobacterium bovis and Brucella abortus
130,000 Enhancing the CFIA’s genomic capabilities for detection and characterization of high consequence known and unknown/unexpected animal viruses and their vectors/reservoirs
200,000 Whole genome sequencing technologies as tools for the detection, isolation, identification and characterization of pathogens in support of Canadian food inspection objectives
200,000 Detection and identification of plant pests and plants with novel traits using next generation sequencing
70,000 Development of diagnostic sequencing methods to monitor, detect and characterize RNA viruses of food, animals and plants, following viral contamination or infection
50,000 Development of infrastructure and bioinformatics tools to support genomics activities in CFIA’s food, plant and animal business lines
Environment and Climate Change Canada
100,844 Hybrid data generation from traditional and DNA-based biomonitoring
49,868 Metabolomics for predicting the mode of action of chemicals of concern in aquatic organisms
64,274 Viable pathogen identification using DNA sequencing technology in microbial risk assessment
65,936 Rapid assessment of algal community composition and harmful blooms using DNA barcoding and remote sensing
72,031 Toxicogenomic solutions for assessing exposure and effects of environmental contaminants in wildlife
45,435 Metagenomic profiling of river water quality for watershed protection
49,868 Environmental DNA – improving inference through validation studies.
83,113 Development of next-generation genomic tools to investigate cumulative effects of urban pollution and natural stressors in 2 sentinel fish species.
55,409 Transcriptomic analyses of the ecotoxicological effects of nanomaterials on microorganisms.
64,385 Measuring genome health in wildlife populations
25,820 Application of genomics to assess the impact of harvest and other mortality sources on vulnerable populations of North Atlantic murres
55,409 Development and validation of metabolomics techniques to evaluate impacts of large-scale environmental changes on stress responses in wildlife
25,488 Population genetic structuring in a widely-distributed Pacific coast seabird
Fisheries and Oceans Canada
251,218 Genomic analysis of spatial stock structure of Arctic char
75,868 Investigating population structure and connectivity of Atlantic cod in the western Atlantic using next generation sequencing
91,093 Detecting aquatic organisms ‘in the field’ using environmental DNA methods
164,169 Parentage-based tagging of chinook salmon in British Columbia
100,358 Rapid and sensitive eDNA methods for early detection and mitigation of aquatic invasive species and monitoring of aquatic species at risk
Health Canada
394,000 An integrated systems biology approach to investigate immunopotentiation induced by respiratory syncytial virus vaccines
200,000 Development of genomics biomarker to provide mechanistic context and data in support of human relevance for chemicals inducing cellular stress responses
360,000 Identification of biomarkers for the standardization and risk assessment analysis of mesenchymal stem cell-based health products
80,000 MicroRNA profiling of serum and milk from toxicological studies of natural and anthropogenic chemicals as an endpoint for comparative assessment with apical endpoints within the benchmark dosing framework
39,000 Safety of prebiotics in infants
189,000 Systems biology informed structure-activity relationships to predict pulmonary pathology induced by nanomaterials
188,000 The coming revolution: next generation sequencing detection of de novo mutations in the offspring to identify germ cell hazards
National Research Council of Canada
888,000 Biologics and biomanufacturing program: development of support technology
3,552,000 Wheat improvement flagship (enhancing Fusarium and rust tolerance; genomics-assisted breeding; abiotic stress; seed development)
Natural Resources Canada
61,273 Accelerating the discovery of insect volatile attractant molecules with genomics
147,277 An early detection tool for emerald ash borer and ash resource protection
317,037 Applied genomics for tree breeding and new applications
64,191 Development of metagenomic and bioinformatics tools to facilitate processing of trap captures
113,788 Developing molecular and environmental genomic approaches for microbial and invertebrate communities to assess ecosystem integrity in forest management
163,894 Developing the next generation biosurveillance tools for tracking and preventing forest pest invasions
87,533 Genomics-assisted tree breeding for improving remediation of disturbed forest ecosystems
204,091 Innovative land reclamation approaches following oil sand mining: Improving phytoremediation tree-soil microbes interactions
83,070 Spruce budworm eco-genomics: from population dynamics to population suppression
81,200 Tools for enhanced molecular detection of Asian gypsy moth and identification of their geographic origins
Public Health Agency of Canada
185,000 BioTools for the predictive genomics of priority foodborne pathogens
125,000 Implementation of genome-based analyses to “One Health” surveillance of enteric disease
90,000 PulseNet Canada: model framework development for genomic technology delivery in a laboratory network
34,000 Single nucleotide variant subtyping of Salmonella Enteritidis and Salmonella Heidelberg
100,000 Field deployable genomic sequencing for pathogen identification using the MinION
125,000 Mass spectrometry technology development
328,000 Improving surveillance of non-enteric bacterial pathogens by whole genome sequencing
100,000 Bridging the epidemiological gap for priority Salmonella serovars through genomic characterisation and nomenclature development
353,000 Revolutionizing molecular viral characterisation strategies in support of enhanced outbreak investigation and surveillance in the next generation sequencing era

Annex 2: Quantitative indicators for performance measurement

Scientific contributions

Scientific contributions include scientific information and publications produced, accepted, in press, or published (including online) in 2018-2019. They include contributions from any project team member as long as they relate to the GRDI project. They also include contributions deriving from a previous phase of the project, if produced in 2018-2019. They do not include submitted papers or publications in draft form, nor contributions that were reported in previous years.

Key scientific contributions demonstrating leadership
Number of key scientific contributions
  AAFC CFIA DFO ECCC HC NRC NRCan PHAC AMR EcoBiomics Total
Publications in refereed journals 51 48 19 42 27 47 21 16 38 6 315
Publications in refereed conference proceedings 10 14 0 0 2 5 4 1 135 1 52
Books (edited, written) and book chapters 4 3 0 0 0 1 0 1 3 0 12
Invited presentations 31 25 7 17 15 17 22 20 16 18 188
International conference presentations 14 7 1 19 7 15 17 20 20 8 128
Editorial posts for national and international journals (excludes peer reviewers) 14 9 0 0 5 1 4 0 3 0 36
New genomics-related databases or libraries 10 8 0 6 5 8 0 2 2 5 46
Awards, prizes 5 1 1 2 3 2 0 4 2 1 21
Total 139 115 28 86 64 96 68 64 99 39 798

Other scientific contributions

Number of other scientific contributions
  AAFC CFIA DFO ECCC HC NRC NRCan PHAC AMR EcoBiomics Total
Technical reports 1 261 1 1 0 0 0 0 1 0 265
Other publications (ex. abstracts, notes, industry magazines, etc.) 5 3 2 6 3 2 2 4 1 3 31
Poster presentations at conferences 54 21 0 36 20 18 3 5 17 4 178
National conference presentations 14 14 1 6 2 20 13 1 2 6 79
Deposits in genomics-related databases or libraries 9 19 2 15 5 1388 5 34 362 2 1841
Total 83 318 6 64 30 1428 23 44 383 15 2394

Research tools and processes

Research tools and processes include those produced in 2018-2019, deriving from previous phases of the GRDI if produced in 2018-2019, as well as produced in previous years if they have been improved since last reported on.

Number of research tools and processes
  AAFC CFIA DFO ECCC HC NRC NRCan PHAC AMR EcoBiomics Total
Research tools 14 29 8 17 12 19 8 34 14 6 161
Research processes 13 25 10 11 5 11 5 8 12 2 102
Total 27 54 18 28 17 30 13 42 26 8 263

Knowledge translation and mobilization

Knowledge translation and mobilization activities include the development of scientific networks, communications products, end-user engagement activities, science policy integration, science advice, transfer of protocols, field trials, outreach activities, etc. They ensure that research remains relevant to solve specific problems by maximizing opportunities to understand the needs of targeted end-users and active dissemination of GRDI results to them.

Contributions to scientific networks

Number of contributions to scientific networks
  AAFC CFIA DFO ECCC HC NRC NRCan PHAC AMR EcoBiomics Total
Participation in government meetings/seminars/advisory panels related to regulations or policy in Canada and internationally 1 9 12 16 12 9 7 3 14 3 86
Participation in national or international genomics-related committees 1 8 10 11 4 8 3 15 10 0 70
National or international genomics research peer review committees served on 2 0 0 2 3 5 1 5 1 1 20
Participation in national conferences 29 4 1 3 0 16 1 0 1 1 56
Participation in international conferences 33 3 2 2 3 8 1 2 10 2 66
Total 66 24 25 34 22 46 13 25 36 7 298

Collaborations

Collaborations by department/agency, expressed in terms of number of individual research collaborators in 2018-2019 from an organization 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 research collaborators
  AAFC CFIA DFO ECCC HC NRC NRCan PHAC AMR EcoBiomics Total
Canadian universities 31 10 34 37 9 5 25 10 29 23 213
International universities 29 1 15 14 4 1 9 6 4 3 86
Other international research organizations 5 1 10 4 2 1 18 6 3 2 52
Other Canadian research institutions 1 0 2 4 0 6 0 1 2 0 16
Private sector 6 1 3 11 4 4 2 0 2 1 34
Other government departments 17 12 2 18 16 1 13 6 16 10 111
Other public sector organizations such as provinces, municipalities, and non-governmental organizations 1 6 11 1 0 0 12 18 2 3 54
Total 90 31 77 89 35 18 79 47 58 42 566

Communications products

Number of communication products
  AAFC CFIA DFO ECCC HC NRC NRCan PHAC AMR EcoBiomics Total
Media interviews 13 0 7 0 0 1 5 3 4 0 33
Press releases 1 0 0 0 0 2 0 1 2 0 6
Newspaper and magazine articles 9 1 7 0 0 4 0 1 0 1 23
Community presentations 2 0 1 2 4 0 0 3 5 2 19
Brochures, fact sheets, web pages 0 1 0 3 2 10 0 1 3 0 20
Total 25 2 15 5 6 17 5 9 14 3 101

End-user engagement and knowledge transfer activities

Number of outreach activities
  AAFC CFIA DFO ECCC HC NRC NRCan PHAC AMR EcoBiomics Total
End-user consultations 5 17 3 6 13 0 0 25 5 2 76
Public meetings 2 0 2 0 0 0 2 1 1 0 8
Science advice, including to senior management 11 7 5 11 4 1 8 0 12 0 59
Outward material transfer agreements 4 0 0 0 0 1 4 1 1 0 11
Transfer of standard operating procedures 1 12 2 2 1 0 0 2 4 1 25
Disclosures 0 0 0 0 0 41 0 0 0 0 41
Active patents, patent applications, patents issued 0 0 0 0 0 21 0 0 0 0 21
Licenses issued 0 0 0 0 0 16 0 0 0 0 16
New formal collaborative agreements / standard operating protocols 1 2 0 1 0 0 1 0 2 0 7
Knowledge transfer workshops with stakeholders/end-users 8 2 4 11 12 1 2 2 3 3 48
Requests for research results, papers, collaborations 27 13 0 6 3 not tracked 2 3 25 5 84
Total 59 53 16 37 33 81 19 34 53 11 396

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 in 2018–2019, including but not exclusive to personnel financed through GRDI funds

Number of research and technical personnel
  AAFC CFIA DFO ECCC HC NRC NRCan PHAC AMR EcoBiomics Total
Research scientists 47 20 16 29 14 62 27 31 38 30 314
Research professionals 3 21 22 12 18 7 15 41 25 14 178
Research technicians 36 17 19 19 11 137 15 12 20 19 305
Post-doctoral/visiting fellows 4 1 14 9 3 0 3 4 5 6 49
Graduate students 19 4 5 12 3 0 9 6 23 1 82
Undergraduate students 16 9 1 8 1 1 1 6 12 2 57
Administrative officers 0 0 1 1 0 0 1 1 2 0 6
Total 125 72 78 90 50 207 71 101 125 72 991
Total estimated full-time equivalents 40 19 28.9 34.6 19 71.4 37.6 27.3 38 41.5 357.3

Annex 3: Highlights of results achieved in 2018–2019

Interdepartmental research along shared priorities and common goals

Metagenomics-Based Ecosystem Biomonitoring (EcoBiomics) Project

Participating departments/agencies: AAFC, CFIA, ECCC, DFO, NRC, NRCan, PHAC
Scientific coordination: ECCC, AAFC
Project management: AAFC

Water and soil biodiversity are paramount to sustain diverse ecosystem services and economic activities across Canada. Genomics tools are the only tools available to characterize this complex biodiversity. The EcoBiomics project enables a more comprehensive perspective of water and soil as living systems by developing advanced genomics tools to:

  • assess freshwater ecosystem biodiversity and water quality in lakes and rivers,
  • evaluate the health of soil, which is essential to the productivity of agricultural and forestry systems across Canada, and
  • investigate soil remediation for the oil and mining sectors.
Project highlights:
  • Coordination across 7 federal departments and agencies was achieved through the use of the bioinformatics platform hosted on the General Purpose Science Cluster (GPSC) in Dorval for metagenomics data analysis.
  • The Sequence Database (SeqDB), which manages genomic data and metadata, has been enhanced to support standardized sequence submission to the NRC Saskatoon facility, customized to support metagenomic workflows, and upgraded to add functionality for environmental metadata capture and reporting. It is now used by all EcoBiomics participants to store and track DNA sequences.
  • Standardized methods for sample collection, nucleic acid extraction methods and Polymerase Chain Reaction (PCR) were developed to assess the diversity of bacterial, algae, fungi, and invertebrates in soil and water. These will be published as standard operating procedures (SOPs).
  • Scientists collected more than 7,450 soil, water and invertebrate samples across Canada for centralized Illumina MiSeq (metabarcoding) /HiSeq (metagenomics) DNA sequencing at the NRC in Saskatoon. Millions of DNA sequences were generated for harmonized bioinformatics analyses of these samples.
  • Spatial variability of the aquatic microbiome in the Thames River/Lake Erie water continuum showed changes in relative abundance of phyla along the water continuum and shifts in cyanobacterial communities.
  • Biomarkers were developed to monitor soil microorganisms that can help accelerate the return of perturbed mining and oil sand sites to resilient and functioning ecosystems.
Antimicrobial Resistance (AMR) Project

Participating departments/agencies: AAFC, CFIA, HC, NRC and PHAC
Scientific coordination: AAFC
Project management: AAFC

The project will add to understanding of the critical activities that contribute to antimicrobial resistance development. It will also shed light on critical exposure pathways through which antimicrobial bacteria reach humans, which could help validate economically sustainable technologies, practices and policies to mitigate the development of antimicrobial resistance.

Project highlights:
  • The CFIA was able to add surveillance for AMR genes in their routine genetic analysis of pathogenic bacteria such as disease-causing types of E. coli and Salmonella.
  • Researchers continued progress on targeted isolate sequencing using Illumina technology. Whole genome sequences for over 3,640 bacterial isolates were completed this year and provided to project partners through the IRIDA platform that had been developed under the GRDI Food and Water Safety project. They also continued the deployment of long-read nanopore sequencing technology to close whole genomes, including plasmid DNAs, of 559 isolates. A bioinformatics pipeline with new software and algorithms was developed and validated to analyze the ‘resistome’.
  • The sensitivity of AMR gene detection in metagenome samples was improved by 200-fold and new plasmids carrying AMR genes were characterized.
  • Researchers discovered that compounds from purified cranberry and blueberry extracts could help fight bacterial and viral infections in chickens and help chickens mount a stronger immune response against viruses. Carvacrol (an essential oil in oregano) and citral (present in the oils of several plants such as lemon myrtle and lemongrass) were shown to help improve gut health and prevent gut disease in chickens.
  • Researchers found that the Enterococcus bacteria commonly harboured in cattle are different from the species that are a health threat for humans, and that AMR Enterococcus found in humans was associated with antibiotics not used in beef production.
  • Researchers found that Extended Spectrum Betalactamase producing Salmonella, which are resistant to fourth generation cephalosporins, were generally different in food and humans.
  • Researchers showed that antibiotic resistance genes in soils increased in abundance following fertilization with organic matter from food waste compost or yard waste compost, and demonstrated the transmission of AMR through Enterobacteriaceae.
  • Researchers continued to develop a suite of risk science tools including: 1) an integrated assessment model, 2) risk profiles, 3) a threat assessment, and 4) a quantitative microbial risk assessment to evaluate how antimicrobial resistance moves from farm to fork.
  • Anaerobic digestion of manure showed potential to eliminate AMR bacteria — with the added benefit of generating clean burning biogas and providing producers with a new revenue stream.
  • Bacteria from conventional swine setting were shown to be resistant to a larger number of antibiotics than the isolates originating from antibiotic-free pigs.
  • The integrated assessment model was expanded to a greater number of scenarios including data from Canadian surveillance and to incorporate whole genome sequencing data. Risk profiles were produced using the international standard guidelines from Codex.

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

Over the years, the NRC has used GRDI support to apply genomics and other 'omic technologies to advance multiple projects, with the overall objective of improving cancer treatment.

Better cancer targets for smarter therapies

Acute lymphocytic leukemia (ALL) is the most frequent pediatric cancer, with 1,200 Canadian children diagnosed every year. Despite the great progress achieved over the last 40 years, with cure rates now exceeding 85%, refractory or relapsed ALL still constitutes a dismal prognosis. Indeed, ALL is the second cause of disease-related death in children. This poor outcome reflects the lack of unique treatment that specifically target relapsed ALL. NRC scientists are tackling this challenge by using pooled shRNA/CRISPR genome-wide screening strategies in primary samples and ALL cell lines to identify clinically-relevant relapsed ALL therapeutic targets. After validating the most promising targets using orthogonal approaches, these will be funneled through our monoclonal antibody production pipeline and developed into lead therapeutic candidates. This project is being carried out with scientists and clinicians at the Centre Hospitalier Universitaire Ste-Justine in the context of an NRC Collaboration Centre.

A high performance expression platform for production of cost-effective therapies

Antibodies and other protein-based therapeutics are large, complex molecules that have to be reliably manufactured at scale to enable clinical testing and ultimately, commercialization. The NRC’s Chinese hamster ovary cell production platform has been a cornerstone of our biomanufacturing strategy and is currently being used internally as well as by multiple external partners. The NRC’s proprietary cell line has been fully sequenced and this genomic information is being used as the basis for understanding production characteristics. A pooled genome wide-screening with a CRISPR/Cas9 system is underway to identify candidate genes which function to enhance productivity and robustness. Cell engineering approaches will then be used to improve the platform’s performance.

Improving Canada’s health regulatory system

Assessing the safety of prebiotics for infants

Maternal milk contains a wide variety of carbohydrates that are not digested in the small intestines of infants but pass into the large intestines, where they serve as an energy source for the developing bacterial community. Some infant formulas contain easily fermentable carbohydrates to mimic this function. There is a large body of scientific literature linking these carbohydrates to gut bacteria composition, immunological function and gastrointestinal disease. For this reason, it is important to assess the short- and long-term effects of fermentable carbohydrates on the developing gut bacteria of infants.

HC researchers are studying the impact and long-term effects of dietary fermentable carbohydrates on the gut bacterial community of weaning rats. Published methods for assessing gut barrier integrity either do not work or are poor approximations. Using a rat model, the group has developed a method for properly identifying associations between physiological outcomes and microbiome composition.

This project has already increased awareness among HC regulators of the physiological outcomes that are potentially associated with consuming fermentable materials, especially as they apply to infant formula. This work confirms the safety of rapidly fermented oligosaccharides in infant formula, and the statistical methods developed for assessing bacterial community composition are being applied at HC bureaus.

Measuring the health effects of fungal toxins and chemical contaminants in food with microRNA

MicroRNA (small, non-coding RNA) is important for regulating gene expression and translating genes into protein products. HC researchers have identified and characterized microRNA molecules found in rodent serum and milk (surrogate tissues) that are associated with dietary exposure to fungal toxins and chemical contaminants detected in foods.

HC researchers have developed methods for screening microRNA and relate it to gene expression from that same tissue. This has provided insight into the mechanism of action of the targeted fungal toxins and anthropogenic chemicals. The screening of microRNA in serum from treated rodents translates to methods of detection of toxicity in humans. The use of surrogate tissue such as serum and milk to detect changes in circulating microRNA levels would enhance the ability to detect and respond to the presence of anthropogenic toxins in food consumed by Canadian populations.

Predicting pulmonary pathology induced by nanomaterials

Nanomaterials are tiny materials measuring less than 100 nanometres that can induce harmful effects in animals. In the first study of its kind, HC researchers are combining toxicogenomics and computational tools to identify and analyze the potential toxic effects of different classes of nanomaterials on lung cells and tissues.

HC researchers used gene expression data collected the first 4 years in a case study to demonstrate the applicability of toxicogenomics to rank the potency of nanomaterials to induce lung inflammation and lung fibrosis (manuscript recently published). The results show the limitations and the opportunities of using pathway perturbations to rank or order the toxic potency of nanomaterials. In addition, a 17-gene classifier was established that is predictive of lung fibrosis in mice following exposure to nanomaterials. The classifier is being further validated in multiple exposure models.

Toxicogenomics gene expression data was used by an international academic research group to develop classification‐based cytotoxicity nanostructure–activity relationship models. The findings were presented at several international meetings and workshops.

Understanding the respiratory syncytial virus vaccine

The respiratory syncytial virus is a highly contagious virus that infects the respiratory tracts of infants and young children. It is the most common cause of bronchitis. There are currently no approved vaccines for the prevention of this infection, largely due to a lack of understanding of both the disease and the critical elements for evaluating the efficacy and safety of vaccines.

This project aims to assess the safety and efficacy of candidate vaccines. Scientists have identified toxicity associated with certain forms of candidate vaccines and the underlying mechanism of toxicity.

HC researchers have developed a preclinical animal study model to investigate the mechanisms underlying vaccine-induced adverse reactions. This model is now being used for the study of vaccine induced toxicity and development of relevant tools for the evaluation of next generations of vaccines. They have also developed methodologies to analyze biomarkers to assess vaccine-induced toxicity.

Using next-generation sequencing to detect de novo mutations to identify germ cell hazards

HC researchers are using genomics technologies to analyse chemically induced de novo mutations in the offspring of exposed fathers in both laboratory animals and humans. A de novo mutation is a genetic change that appears for the first time in a family member and that can be associated with a diverse array of human diseases.

The research team applied advanced genomic technologies to measure heritable genome changes affecting large sections of the genome in mouse offspring of males exposed to benzo(a)pyrene, a common environmental pollutant. The analysis of approximately 350 samples showed a significant increase in the occurrence of these large-scale events in the offspring of mice exposed to benzo(a)pyrene.

The analysis of whole genome sequencing from 6 mouse families (exposed male, unexposed female and 3 offspring) also showed a significant increase in single base changes in the sequence of the DNA in the offspring of exposed males. It also showed benzo(a)pyrene induced mutations in germ cells that are transmitted to the offspring.

A power analysis was conducted to establish the best experimental design for detecting mutations in studies with human families.

Standardizing and assessing the risk of stem cell-based health products

Stem cells have a tremendous potential to treat diseases for which there are no cures. Stem cells from adults are a particularly promising source as they circumvent the social and ethical issues associated with the use of embryo‑derived cells. The use of adult stem cells in a health care environment is not without health risks. HC is responsible for the evaluation of the safety and efficacy of stem cell-based health products and therapies.

The Biologics and Genetic Therapies Directorate of HC uses GRDI funding to develop diagnostic tools that will allow thorough evaluations of the risks and benefits associated with the therapeutic use of adult stem cells. This program will provide a means to standardize mesenchymal stem cell-based health products using biomarkers that are directly linked to product safety and potency. The knowledge and tools generated from this work will benefit both federal regulatory agencies and their stakeholders by improving methods for the manufacturing and regulatory evaluation of health products based on mesenchymal stem cells.

Assessing the health effects of chemicals

Traditional toxicology tests that evaluate the health effects of chemicals are both time consuming and expensive. HC researchers are developing and validating genomics-based toxicology methods that promise to save time and money. The new methods can predict whether a chemical will cause DNA damage or other adverse genetic effects.

The researchers applied genomics signatures (patterns of gene expression changes) to identify agents that cause various toxic effects. The team previously successfully validated a signature that predicts the ability of chemicals to damage DNA in cultured cells relevant to humans. These signatures provide important tools to rapidly assess large numbers of toxicities in parallel. This project’s highlight is the validation of a specific genomic signature (TGx-DDI) for use by any laboratory.

HC researchers demonstrated how to combine different sources of toxicogenomic information for mode of action and potency assessment. A milestone relating to regulatory acceptance was the launch of the Organisation for Economic Cooperation and Development's project on genomic data analysis frameworks. A first draft framework was produced and is in review by an expert working group.

A HC first was the completion of the Task Force on Scientific Risk Assessment's report on toxicogenomics. The report was endorsed at the executive committee level and published in public literature.

A sub-group of the International Workshops on Genotoxicity Testing led by HC’s Principal Investigator published consensus opinions on the use of high-content and high-throughput data sources for genotoxicity assessment.

Strengthening public health programs

Controlling and preventing foodborne illness

PHAC research addresses the critical need for innovation in pathogen detection and characterization to improve the identification of outbreaks, as well as accurate and timely source attribution. GRDI researchers have developed a suite of genomic epidemiology tools to enhance the prevention and control of foodborne illness. The surveillance programs of FoodNet Canada and the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS) monitor foodborne pathogens and the use of and resistance to antibiotics in the food chain. These programs monitor various points along the “farm-to-fork” continuum: farms, surface waters, food production and public health laboratories. The new genomic tools produced by GRDI research is being used to increase their ability to identify risk factors, sources of exposure, virulence factors, determinants of AMR and transmission dynamics along the food chain of E. coli, Salmonella and Campylobacter. As a result, GRDI research is strengthening the capacity of these programs to identify the sources of foodborne illness and generate risk assessments that lead to risk reduction measures. New genomic tools for the detection and characterisation of foodborne pathogens have also been implemented by PulseNet Canada to allow the outbreak detection system to more effectively detect and respond to outbreaks of foodborne illness.

Detecting and determining the genomic epidemiology of priority pathogens

Because DNA is the common code for the genomes in all living organisms, the tools developed to analyse the DNA of one organism can also be used to study the genome of other unrelated organisms. Exploiting this principle, researchers at PHAC have spun off the tools used to analyse outbreaks of foodborne bacteria and are adapting them to the study of tuberculosis outbreaks. In doing so, they have by-passed a lengthy and costly research phase by leveraging a proven tool that will allow public health epidemiologists to better track and understand the spread of tuberculosis in Canada.

Rapid identification, close surveillance and effective outbreak response are essential to preventing and controlling viral diseases. Genomics researchers at PHAC are developing advanced bioinformatics technologies that will be implemented into federal laboratory services that respond to HIV-1; hepatitis A, B and C viruses; influenza virus; and measles virus. They are also developing a series of laboratory processes and bioinformatics tools that will revolutionize our existing molecular viral characterization strategies. These tools will enable more informative disease surveillance and timely disease outbreak investigations. This work will also provide the core infrastructure extendable to other viral pathogens, facilitating the adoption of whole genome sequencing as a routine technology for the protection of public health.

Canadian, American and European scientists have worked together to establish a national mass spectrometry database that supports diagnostic laboratories across Canada. Mass spectroscopy is a new technology in clinical laboratories that is able to identify infectious disease pathogens rapidly, accurately and inexpensively. Work conducted by the GRDI is increasing the capacity of this new clinical tool to identify uncommon and rare bacterial directly in the hospital, thereby increasing the capacity of this powerful new technology to enable a rapid and effective clinical response.

New genomic tools to characterize bacterial pathogens and study their routes of transmission

Clostridium difficile — In ground-breaking research, GRDI investigators in partnership with provincial public health and academic colleagues, have found that asymptomatic colonization by C. difficile is a key factor contributing to cases of clinical C. difficile infection emerging during hospitalisation. Importantly, this work will stimulate a re-evaluation of the mechanisms and relative contribution of hospital acquired C. difficile infection in relation to the role played by asymptomatic community associated infection. This new understanding of the importance of community associated C. difficile infection strengthens our understanding of transmission routes and will contribute to efforts to reduce its occurrence in Canadian hospitals.

Neisseria gonorrhoeae — Researchers have developed a method to carry out whole genome sequencing of N. gonorrhoeae directly from leftover urine samples collected by clinics. This is an important tool needed to provide information on disease causing bacteria that will not otherwise be captured now that culture-independent diagnostic testing methods are being used. The expected long-term public health outcomes will include improved N. gonorrhoeae outbreak response, enhanced antimicrobial stewardship, and better understanding of N. gonorrhoeae dissemination and AMR transmission.

Streptococcus pneumoniae and Haemophilus influenza — Whole genome sequencing typing methods have been developed to characterise these infectious pathogens that improve diagnostics, typing, including antibiotic resistance profile, and our understanding of their transmission pathways.

Increasing Canada’s share of global wheat production

The Canadian Wheat Improvement flagship program, funded in part by the GRDI, is the NRC’s contribution to a large-scale research alliance established to improve the yield, sustainability and profitability of Canadian wheat for the benefit of Canadian farmers and the Canadian economy. The flagship program ended in March 2018 but several projects continued. The Canadian Wheat Alliance includes major contributions by the NRC, AAFC, the University of Saskatchewan and the Government of Saskatchewan.

This program has developed strong expertise in genomics and developmental aspects relevant to performance and yield in wheat.

Improving breeding practices

Researchers are working on improving a number of necessary resources including genomic sequences and annotation, large collections of genetic markers, high-throughput genotyping and the development of new populations for wheat breeding.

High-throughput DNA sequencing has become an essential molecular tool affecting all aspects of biological research. Hundreds of gigabytes of data are being delivered by the advanced sequencing instruments on a daily basis. Researchers are tasked with converting this data into knowledge and creating a coherent biological picture by filtering, assembling and interpreting sequencing information. In modern biological research, bioinformatics has become an indispensable tool for managing and analyzing data. We have developed a number of data analyses pipelines/workflows for genome, transcriptome and proteome sequencing as well as genotyping by sequencing applications.

Scientists have established a multiple genotyping and bioinformatics platform to support Canadian wheat researchers and breeders with a range of applied genomic techniques. These include marker-assisted selection, gene pyramiding, association mapping and high-density genetic map generation. The genotyping platform is based on targeted resequencing strategies including the reduced exome capture for wheat, repetitive amplicon sequencing and a variation of region-specific extraction sequencing. It has decreased the costs of genotyping, improved accuracy and decreased bias.

Stettler is an awned, semi-dwarf Canadian Western Red Spring wheat variety with very high grain yield, high grain protein potential and strong straw, and well adapted across the grain growing areas of western Saskatchewan and Alberta. In consultation with AAFC wheat breeders, the team selected this variety for whole genome sequencing as a part of a Canadian pan genome sequencing project. A hybrid genome sequencing approach, involving Illumina short read, Oxford Nanopore long read and 10x Chromium linked read sequencing approaches combined with Chicago scaffolding (Dovetail genomics), has generated sequence information equivalent of approximately 100 fold coverage of the estimated 17 Gb genome. A hierarchical assembly approach was used to establish a draft genome assembly of Stettler.

The transfer of high-value target loci from genetically diverse wild relatives to adapted elite cultivars is key to the future of wheat breeding. Pairing and recombination between chromosomes of the wild donor and those of cultivated crops result in such gene introgressions. Scientists have developed advanced genetic and genomic resources to characterize natural variation and enhance the rate of meiotic recombination to create novel gene combinations for crop breeding.

The NRC in Saskatoon has established a breeder-friendly gene editing toolkit comprising web-based gRNA designer (https://crispr.bioinfo.nrc.ca/WheatCrispr/), a functional expression vector system and a novel microspore-based haploid gene editing system. This gene editing platform is being utilized to develop improved crop germplasm with desired end-use quality.

Enhancing Fusarium and rust resistance

Researchers have developed breeder-friendly genetic markers and quantitative trait loci (QTL) for dissecting the genetic architecture of complex traits in wheat, including for abiotic stress tolerance, grain development, and for the major wheat diseases Fusarium head blight (FHB) and rust disease resistance, which together account for $200 million in annual losses in Canada. To date, hundreds of genetic markers of resistance and new lines of wheat showing increased FHB or rust resistance have been delivered to wheat breeders. Breeders are now using marker-assisted selection and rapid introgression methods developed at the NRC to produce germplasm with increased FHB resistance.

Improving wheat productivity under conditions of abiotic stress

Scientists have developed genetic markers and advanced wheat lines for several abiotic stress-related genes, including traits for drought, heat and cold tolerance. They have also developed a framework map of markers associated with physiological traits affecting drought tolerance including root traits, photosynthesis and a number of yield-contributing traits. They established a standardized whole phenology platform and used it to discern genetic differences between wheat lines as well as identify superior lines with better root systems and greater photosynthetic efficiency.

Developing new wheat lines to improve performance and yield

Wheat as a crop faces several challenges, including yield gaps and low economic returns. To address these challenges, scientists at the NRC have significantly advanced their understanding of the gene targets and regulatory networks that influence photosynthetic efficiency and grain development in wheat. They have established a comprehensive gene expression atlas for grain development. Scientists have also created new wheat lines with more tillers, high vegetative biomass, upright leaf architecture, high photosynthetic efficiency and several desirable spike traits, providing a unique resource for wheat improvement breeding programs.

Increasing the value of Canadian crops and agri-products

Genomics research is playing a key role in ensuring the continued profitability of the agriculture and agri-food sector. The GRDI at AAFC supports 7 GRDI-mandated projects. Examples of results and outcomes from these projects follows.

Durable Fusarium and rust resistance in wheat

AAFC scientists have identified novel proteins involved in the biosynthesis pathway of Fusarium mycotoxins and elucidated the structure of 2 cyclic grammilin lipopeptides shown to be potent phytotoxins and virulence factors in maize, however not in wheat.

Over 200 perennial lines of intermediate wheat grass (Thinopyrum intermedium) were characterized for overwintering survival and response to different pathogens (stripe rust, tan spot, Fusarium head blight) in Lethbridge and Winnipeg. From these, 282 unique putative resistance genes were identified, and 66 were characterized, that could provide novel sources of resistance for wheat. Crosses between selected lines of intermediate wheat grass and wheat have been initiated and will continue under different germplasm development projects in the coming years.

The AAFC Ottawa Research and Development Centre has developed a platform to screen novel adjuvants and fungicides that could target several pathogens relevant to the agricultural sector, providing foundational tools and processes for further progress in wheat science, innovation, breeding and cultivar development.

Breeding midge-resistant wheat and canola

The swede midge (Contarinia nasturtii) is a serious pest of brassica vegetables and canola in Ontario and Quebec and now poses a significant threat to canola production in the prairie region. Crop losses when there are swede midge infestations are as high as 85% in Canada and 100% in Europe. The orange blossom wheat midge (Sitodiplosis mosellana) is a major pest of Canadian wheat, accounting for annual losses of $60-120 million. Since 2010, several varieties of resistant spring wheat have been released that carry an R gene from winter wheat (Sm1). Sm1 is the only known wheat midge resistance gene and the probability of “breakdown” is high.

This project has conducted the most in-depth examination of the genomics of swede midge and orange blossom wheat midge to date and has provided details of their interaction with host plants at the molecular level. Midge larvae were collected from the field and laboratory colonies and techniques established to finely dissect larval salivary glands. The entire suite of genes expressed in these glands was catalogued using next generation sequencing. This information is now being used to identify genes encoding salivary ‘effector’ proteins that may interact with the host plant to modify its physiology or to initiate a defense response leading to host plant resistance. The complete genome sequence of swede midge was sequenced and assembled for future work on this insect. Finally, a Brassica napus diversity collection was screened for interactions with swede midge, leading to the identification of several more tolerant lines.

Exploiting DNA diversity for AAFC cereal research

Understanding genetic diversity is essential for basic and applied genomic research. AAFC is developing a user-friendly database to support the rapid deployment of DNA assays for plant variety development and to provide a foundational resource for discovering the causal genetic factors of adaptive plant traits.

In the project’s first year, AAFC researchers assembled and sampled more than 600 varieties of germplasm in wheat, oat and barley, representing diversity in wild and cultivated forms of each crop. The researchers used a method called “exome capture” to isolate and sequence the DNA from tens of thousands of genes from 200 of these varieties. They then developed a wheat database that provides access to DNA sequence differences in each gene. This database has enabled researchers to identify highly predictive DNA markers that will be used to improve disease resistance in Canadian wheat breeding programs. In the second year of the project, AAFC scientists have sampled deeply and broadly at a genome sequence level, the gene diversity in Canadian cultivars and wild relatives of wheat, barley and oat.

The results of this work are now deposited in a database for each crop, where they can be accessed as DNA variants relative to the position of a gene on a complete genome sequence. There will be many spin-offs from this work for germplasm enhancement and variety development through AAFC-industry partnerships. The data resource that has been developed has positioned AAFC scientists to proactively follow up and deploy marker-based assays for virtually any gene target found to be relevant or desirable for selection in a breeding program.

Capturing novel genetic diversity for oilseed crop improvement

Exploiting genetic variation is the central tenet of plant breeders’ efforts to optimize crops for yield, quality traits and sustainable production in the face of disease and environmental stresses. However, plant breeding practices in canola have resulted in a general lack of genetic variation in current germplasm, limiting the ability of breeders to effectively address new production challenges. AAFC researchers are addressing this issue by working toward the following goals:

  • define the genomic nature of available variation
  • identify favourable gene variants and corresponding molecular markers for desirable traits
  • develop and establish molecular strategies to accelerate combining of such traits in elite varieties
  • facilitate targeted gene adaptation through gene editing technologies

By defining available genetic variation and providing genetic tools and foundational knowledge to expedite the establishment of desirable traits in canola, this project aims to accelerate the genetic improvement of the crop and secure the sustainable production and profitability of Canada’s $19 billion canola industry.

Specifically, AAFC scientists have developed an exome capture array and developed a web-based interface for designing guide RNAs to target genes in Brassica napus reference genome (CanolaCRISPR) in collaboration with the NRC in Saskatoon.

Developing clean energy crops

Canada’s Clean Energy Strategy currently under development will undoubtedly include biofuel crops. Camelina is marketed as a bio-diesel and aviation fuel feedstock. Researchers are exploring its genetic variation and agronomic characteristics (tolerance to abiotic stress, disease resistance, and seedling vigour), seed size, and protein quality. They also seek to better understand economic opportunities for this emerging clean energy crop. The adoption of camelina in Canada could 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.

Identifying virulence effectors that trigger cultivar-specific immunity to soybean root rot

Soybean is an important Canadian crop ($2.8 billion in farm cash receipts in 2016), but root and stem rot disease caused by the pathogen Phytophthora sojae still lead to $50 million in crop losses annually. This pathogen has shown an ability to rapidly develop resistance to the available treatment options, reducing their effectiveness over time. AAFC studies interactions between soybean and P. sojae and has identified a gene that is tightly linked to reduced rates of infection and disease from P. sojae that can be used for the development of more resistant soybean varieties.

Reducing the need for fertilization through a symbiotic microbiome

One of the central societal challenges for the twenty-first century will be to mitigate the environmental and economic costs of excessive fertilization, such as increased air and water pollution, reduced biodiversity and increased human health risk.

Using cutting-edge technologies, AAFC scientists explore natural systems to capture and deliver nutrients to plants through the study of beneficial, nitrogen-fixing rhizobial bacteria. Specifically, they investigated plant attributes that mediate the development of nodules, the root-derived accommodation structures of leguminous plants that host the symbiotic bacteria. Using a forward genetic approach along with next-generation RNA sequencing, they were able to identify a new locus (SUNERGOS1) and characterized a novel family of transcription factors, called STYs, and documented that these transcriptional regulators were critical for root nodule formation.

This adds to the understanding of symbiosis by defining new, relevant plant genes and the associated processes that mediate nodule formation, thus advancing the long-term goal of using beneficial plant-microbe interactions for sustainable crop productivity.

Enhancing forest generation and protection

In 2018-2019, the GRDI continued to fund 10 multi-year projects to develop the genomics knowledge base that can be used to protect Canada’s forests, improve tree generation efforts to respond to a changing climate, support land restoration efforts, detect pests earlier, and support disease management efforts.

Identification of genes controlling desirable attributes in economically important tree species

Genomics tools and genomic resources were developed for well-established spruce breeding programs to maximize the return on spruce reforestation activities. Spruces are a significant contributor to Canada’s forest sector and are the most common reforested tree species across Canada. GRDI research, in close collaboration with federal, provincial, and industry partners, continues to support the development of tools to enhance breeding programs and genomics-improved spruce stock. Researchers also built and validated genomic selection models for advanced-breeding populations, focusing on targets for wood quality, growth, and weevil resistance in field conditions. The same work led to a unified approach with dendroecology and quantitative genetics to assess tree sensitivity to climate.

Early detection of forest invasive alien species

Surveillance of forest insects and pathogens is increasingly important in the wake of global trade and climate change. Research has focused on early detection and the reliable identification of invasive alien species to prevent the introduction, guide mitigation efforts and reduce spread across the country. In 2018-2019, research validated a suite of assays for the detection of fungal pathogens responsible for white pine blister rust, the butternut canker and for the insects such as the Asian gypsy moth. DNA libraries were generated and a pilot study was initiated to demonstrate the proof of concept and optimization of metagenomics and bioinformatics tools.

Emerald ash borer

Ash is a significant component of the deciduous forests spanning eastern Manitoba to the Atlantic provinces but remains at risk from the devastating effects of emerald ash borer. This is partially due to a lack of an accurate, sensitive and scalable early detection tool, combined with the absence of resistance displayed by native ash. Research has determined the function and origin of 2 digestive enzymes that are involved in emerald ash borer host exploitation and that could be targeted for the control of larvae. Research continues to focus on sequencing the assembly of the emerald ash borer genome to help identify the genetic causes of this insect’s prolific presence in its new environment.

Spruce budworm

Spruce budworm population genomic structure analyses conducted at the continental level were completed. The assembly of the spruce budworm genome reached a new height with the most recent draft featuring 30 scaffolds (= 30 chromosomes). Research also identified an outlier gene whose allele frequency varies significantly across the Ontario landscape. The gene in question encodes a juvenile hormone carrier protein paralog that may play a role in the induction of diapause.

Tree resistance to white pine blister rust

White pines are economically and ecologically important to Canadian forest communities and industries, but are highly susceptible to white pine blister rust. GRDI research revealed diversity of resistance genes among white pine species and developed genomics-based tools for speeding up forest breeding and conservation. Researchers applied the tools in breeding programs and demonstrated the efficiency of these tools in prediction and selection of white pine resistance to white pine blister rust in British Columbia and Alberta. They continue to work collaboratively to identify resistance germplasm with novel genes for the restoration of forests disturbed by white pine blister rust.

Evaluating insect volatile attractant molecules with genomics

GRDI funds supported a study on the isolation and characterization of odorant receptors from multiple invasive and native species of beetles that are, or could be, threats to Canadian forests and Canadian trading partners. This research makes use of innovative genomics approaches such as transcriptomics of adult insect antennae for the quick identification and screening of insect active compounds, which is both faster and complementary to classical (i.e. live-insect based) approaches.

Improving land reclamation following oil sands mining

Genomics tools were used to better understand the important interactions between trees and the soil microbiome. In Fort McMurray, Alberta, an industrial-scale pilot project focused on genomics tools to speed up the reclamation of oil sands sites. Researchers explored the dynamics of tree and plant community establishment and succession on different reclamation treatments, comparing natural tree stands before and after disturbances.

Assessing the integrity of ecosystems in forest management

Metabarcoding tools were evaluated as a method for biomonitoring the diversity of microarthropod, which are ubiquitous and ecologically significant in terrestrial environments. It was found that the inclusion of locally derived specimen barcodes to reference libraries significantly improved the quality of metabarcoding data. These results will improve the cost efficiency of incorporating soil faunal biodiversity into forest sustainability assessments.

Managing fisheries and oceans

Genomics and eDNA applications in fisheries and aquatic ecosystem research is an emerging field that broadens the capacity to address questions in fisheries management. Genomic approaches bring a new paradigm for fisheries management by making it possible to integrate adaptive diversity to understand fundamental aspects of fisheries resources, which is particularly important in the face of climate change and changes in trophic communities.

The GRDI has supported several multi-year projects (through Phases I–VI from 2011 to 2019) that relate to how teams identify stocks or populations, manage mixed-stock fisheries, protect aquatic animal health, manage invasive species, protect threatened or endangered species, predict and plan for climate change impacts on species, design marine protected area networks and manage aquaculture. Examples of results and outcomes from these projects follows.

Analyzing spatial stock structure of Arctic char (Salvelinus alpinus) in Labrador

Arctic char is a freshwater and anadromous Arctic salmonid with a long history of commercial and subsistence fisheries. However, little is known to inform management decisions related to commercial and First Nations fisheries. Scientists and collaborators characterized Arctic char population structures using genome-wide scans and genetic markers. These investigations provided an unprecedented understanding of population structure and provide strong science advice to inform decisions related to the sustainable exploitation of this valuable arctic species under a changing climate.

Using environmental DNA methods to detect and mitigate aquatic invasive species and monitor aquatic species at risk

Using eDNA in water samples to detect species can support traditional field surveys for aquatic species management and conservation, particularly for hard-to-find cryptic species. This project developed, evaluated and optimized eDNA-based tests for more than 20 aquatic invasive species as well as for the at-risk Brook Floater. It generated a rapid and sensitive new tool to monitor important aquatic species and create distribution maps for the Brook Floater as well as ecologically and economically damaging invasive species. These resources will allow conservation workers to develop more efficient management and conservation strategies.

Using next-generation sequencing to investigate Atlantic cod population structure and connectivity in the western Atlantic

Atlantic cod fisheries used to have enormous commercial value, but overfishing led to depleted stocks. Despite management efforts, populations have not recovered. This project aimed to solve management issues by identifying factors involved in stock recovery. Atlantic cod populations were genetically characterized through a comprehensive sampling of spawning areas in Canada and the United States. Population structures and connectivity were assessed at the Canada-US border and the northern Gulf of St. Lawrence. This project validated existing management units, and helped design alternate units to improve fishery management in both Canadian and United States waters.

Using environmental DNA methods to detect aquatic organisms in the field

Scientists used newly developed, easy-to-use, portable qPCR instruments for eDNA analysis for real-time, in-the-field detection of aquatic invasive species, species at risk or other species important for fisheries. Scientists developed methodologies for zebra mussel, a recent invasive species in Manitoba, and they tested the transferability of these methods to other aquatic organisms (e.g. freshwater finfish). The work proved useful for programs with monitoring requirements in remote areas or for point-of-need locations (e.g. shipping ports, inspection sites), enabling community-based approaches to support government monitoring and managing of important aquatic organisms.

Using parentage-based tagging of Chinook salmon in British Columbia

Scientists collaborated with salmon enhancement programs to develop a genomics-based alternative to the expensive and impractical coded-wire-tag program that is currently used to monitor hatchery contributions to Chinook salmon stocks. By genetically identifying all individuals used as hatchery broodstock, the age, origin, and parents of hatchery-born fish returning from their marine migration can be identified. Combining this technology with other innovations in the future will provide test fisheries with hand-held field devices that will enable them to determine the identity of a fish down to the parent. This non-invasive technique will provide much more information than the current program in an easier and less costly manner, to provide science advice for salmon enhancement and conservation management.

Promoting responsible environmental decision-making

Genomics-based tools and technologies for responsible environmental decision-making

The research cycle of 2016-2019 encouraged projects focused on the development of genomics tools and approaches to support pollution prevention, regulatory compliance and enforcement, wildlife management, and risk assessment of potentially toxic substances.

The 4 priority research areas are described below.

Improving understanding of ecotoxicology

Efforts were undertaken to improve the efficiency and accuracy of models to predict the effects of chemical exposure by building a better understanding of the molecular mechanisms underlying the toxicological effects of chemicals in both wildlife and aquatic life. For instance, genomics tools and approaches are in development to examine the impact of existing and emerging chemicals (i.e., their transport, fate, effects, and associated risks) on the biology and physiology of organisms as well as on biodiversity and ecosystem functions. Research focused on assessing the effects of exposure to chemicals of concern (including individual chemicals and complex mixtures) in avian, mammalian and aquatic species.

In 2018-2019, 2 new ToxChip PCR arrays for 2 Arctic-breeding avian species (thick-billed murre and black guillemot) were developed in support of conducting strategic environmental assessments in the Baffin Bay/Davis Strait. These ToxChips are useful for determining the impacts of resource development transportation and hotspot identification of contaminated sites in the Great Lakes, Pacific Coast, and Oil Sands Region.

Monitoring ecosystems

Activities also focused on understanding and monitoring aquatic and land-based ecosystems. For example, research focused on extending an established method for recovering biodiversity information from bulk environmental samples. In 2018-2019, a large-scale field experiment was conducted in the Miramichi watershed to demonstrate whether the prevalence of invertebrates observed through meta-barcoding can be used to infer patterns of fish abundance.

Between 2016 and 2019, over 245 environmental samples were collected from Lakes Erie, St. Clair, Winnipeg, Georgian Bay, and the Thames River. Data analyses for these samples are underway to identify biogeographic patterns and conditions under which phytoplankton species typically occur and thrive.

Enhancing wildlife conservation

Genomic techniques were developed to better understand wildlife species and how they are responding to changes in their habitats due to disturbances, including climate change and natural resource development. For example, scientists are using genomics to study the impacts of cumulative stress associated with large scale environmental changes (e.g. climate change and pollution) in wildlife populations such as arctic nesting eiders.

Over the course of the project, specific metabolites in the blood of birds have been identified which are important in chronic or long term stress. Early results have indicated that arctic nesting common eiders show increased stress responses with increasing arctic temperatures. Also, tree swallow nestlings developing in oil sands area have shown changes in stress and immune responses compared to birds away from oil sands areas. These results from these efforts will support the management of wildlife species and increase our understanding of how populations adapt to changes in their environment.

Improving compliance and enforcement

Scientists are developing various innovative methods and tools to support the enforcement of regulations to protect the environment and wildlife from pollution, wildlife trafficking and other threats, and to support regulatory monitoring programs. For example, genomic markers are under development to inform the harvest management of murre colonies in the North Atlantic.

This year, population modeling for murre colonies was completed and published by ECCC and Danish colleagues. The report indicated that Canada may still have a role in conserving these colonies and this work will be a contributor in negotiations to set an international harvest management strategy for Atlantic murres.

Improving food safety, animal health and plant protection

Characterizing foodborne pathogens through genomics databases

This project aims to develop genomic databases of known food-borne pathogens that will allow the CFIA to deliver a highly responsive, risk-based food inspection system. Scientists are working to create a database of food-borne pathogens and develop tools with enhanced capacity to detect the presence of microbial hazards in the food supply. Processes for rapid sequencing of foodborne bacteria have been developed and incorporated into the maintenance of this CFIA resource. Sequence data from metagenomics samples including beef, pork and produce have been mined to help inform the development of improved methods for detection of pathogens from foods. Automated bioinformatic processes for rapid sequence analysis, including quality assurance, have been developed to ensure the curation of the pathogen collection is ongoing with the highest data reliability.

Over the last 6 years, the CFIA food microbiology laboratories have sequenced over 9,000 bacterial isolates, including a collection of over 3,000 foodborne pathogens from inspection and surveillance samples. This whole-genome sequence database represents a valuable asset for the CFIA that can be mined in support of research and diagnostic objectives.

Through complementary investments by the Canadian Safety and Security Program, the GRDI, and Food Safety Modernization, CFIA scientists have developed a process to isolate genomic DNA from single colonies, sequence it, and produce high-resolution characterization of bacterial pathogens that has the potential to replace lengthy biochemical characterization, molecular and serological typing procedures widely used in food-testing laboratories.

Strengthening animal health diagnostic tools

This project aims to enhance the CFIA’s ability to acquire, manage, analyze and use genomic data to identify pathogens and disease vectors/reservoirs important to animal health. Progress this fiscal year includes:

  • implementing new wet bench methodologies and bioinformatics pipelines to acquire, assemble and annotate genomic sequences of high-priority known priority, unknown or unexpected pathogens and differentiate disease vectors from closely related species
  • enabling new capabilities to automate the management, analysis and utilization of sequence data for the rapid detection and identification of high priority animal viruses
  • sequencing a diverse collection of more than 1200 diagnostic, surveillance, outbreak, and archived research samples representing more than 50 viral species, including complete/near complete mitochondrial genomes of a number of disease vectors and reservoirs

In addition, the Ottawa Fallowfield Laboratory created the reference genomic database of Mycobacterium bovis strains isolated between 1985 and 2016 from Canadian livestock and wildlife, and harmonised whole genome sequencing-based epidemiological investigations of bovine tuberculosis outbreaks with the USDA. Exploring the genome sequences of Mycobacterium bovis isolates has facilitated the discovery of 4 novel protein candidates for the serological diagnosis of tuberculosis in cattle. Through the development of new, user-friendly methods for rapid detection and typing of high priority pathogens and vectors, this project is working to enhance CFIA’s capability to prepare for and respond to high priority, new, emerging, and re-emerging animal health threats.

Detecting and identifying invasive plants, plant pests and plants with novel traits

The CFIA is developing capacity for DNA barcoding and next-generation sequencing to enhance CFIA regulatory plant health responsibilities in the areas of detection and identification of invasive plants, regulated plant pests and pathogens, and plants with novel traits. Researchers have acquired materials and samples, and are using bioinformatics tools to create sequencing data storage. The development of methods for the targeted sequencing of plants with novel traits continued and metagenomic sequencing data from spore and insect traps, pollen sampling and baiting plates were analysed to detect potential forest invasive alien species and weed seeds. Several standard operating procedures and bioinformatics pipelines were developed and transferred to CFIA diagnostic laboratories. More specifically, fungus identification assays targeting Lachnellula species and Fusarium species were developed and transferred. Next-generation sequencing technology was also used to detect and confirm viruses and viroids in potato. This procedure significantly reduced the time needed for various regulatory testing, including quarantine testing of foreign potato germplasm. Results from this project support the diagnostic activities of the CFIA to regulate the environmental presence and release of invasive plants, plant pests and plants with novel traits.

Developing genomics and bioinformatics tools

Research groups from the plant and food business lines have developed collaborations with AAFC to enhance CFIA-wide access to bioinformatics support. The use of common platforms for genomics and bioinformatics work will ensure that efforts are not duplicated and that automated genomics analysis can be integrated into CFIA’s diagnostic arsenal to support a wide range of mandated activities.

The CFIA’s list of regulated pests includes many RNA viruses that infect plants and animals. Scientists in all 3 of the CFIA’s business lines are working to develop, improve, adapt and harmonize next-generation sequencing methods and pipelines to identify and characterize known or unknown RNA viruses. Different approaches were developed for the detection of RNA viruses depending on whether the virus was able to replicate in the matrix (e.g. plant viruses in plant material) or not (e.g. zoonotic viruses as non-replicating contaminants in food). Significant improvements were made to the workflow Virtool, originally designed for the detection of plant viruses and viroids. The changes provide for an unlimited number of reference libraries for plant and animal viruses. A new data interpretation analysis tree was also developed to ensure more consistent and defined data interpretation.

Scientists also focused on regulated bacterial organisms that pose human health risks and are infectious to both plants and animals. They have developed automated bioinformatic pipelines for the analysis of both long-read and short-read whole genome sequencing data, which are universally applicable to many different bacterial species including foodborne pathogens. Processes for generating and analyzing shotgun and targeted metagenomics sequence data have also been developed to study, for example, the influence of commensal bacteria on the detection of regulated organisms.

A database incorporating over 10,000 sequences generated by multiple CFIA labs has been developed, including best practices for tracking sequence information, sample identification, and quality assurance. Automated bioinformatic processes for rapid sequence analysis and quality assessment have been and implemented in a cloud-based environment: the CFIA FoodPort, which: 1) stores and allows access to sequence data and metadata associated with bacterial isolates; 2) allows labs to submit new sequencing data for analysis; and 3) has a variety of analytical tools available enabling users with any level of expertise to do custom analyses of the bacterial isolate sequence data. The use of a cloud-based platform allows accessibility, flexibility, and security while avoiding the purchase, installation, and maintenance of local high-performance servers.

Annex 4: Research tools and processes produced by the GRDI

Research tools

  • CO1 Classifier v3: a CO1 reference set that can be used with the RDP classifier to make high throughput CO1 metabarcode taxonomic assignments (Porter and Hajibabaei, 2018; Wang et al., 2007), developed for academic use (EcoBiomics)
  • Custom CO1 Classifier v2.1: A CO1 reference set that can be used with the RDP classifier to make high throughput CO1 metabarcode taxonomic assignments (Hoage, 2018 Master’s Dissertation; Wang et al., 2007), developed for academic use (EcoBiomics)
  • 18S Classifier v3: An 18S reference set that can be used with the RDP classifier to make high throughput 18S metabarcode taxonomic assignments (Wang et al., 2007), developed for academic use (EcoBiomics)
  • NRC pipeline - AmpliconTagger: an integrated pipeline for marker gene amplicon sequence data processing geared for HPC environments. Tremblay, (2019) (EcoBiomics)
  • NRC LIMS dataDownloader: software that explores the NRC-LIMS website, downloads all sequence files for the EcoBiomics project, and stores metadata in a sqlite database. The tool is also capable of identifying duplicated or reprocessed sequence runs, and only downloads data that has not been retrieved before (EcoBiomics)
  • Reference Data Manager: automated system that obtains, updates, and manages reference datasets from well-known public repositories such as GenBank. The software is freely available to the research community as a whole on GitHub (EcoBiomics)
  • A multiplex PCR assay for detection of AmpC-like beta-lactamase blaCMY-2 and glutathione S-transferase fosA7 genes conferring resistance to cephalosporins and fosfomycin (AMR)
  • A visual heat map analysis tool (in-house programing with SAS software) was developed using data from over 10,000 isolates to determine hotspots of Extended Spectrum Betalactamase enterobacteria in the swine production continuum (sows, suckling piglets, weanling piglets, growing pigs, finishing pigs and carcasses from the longitudinal study on conventional and antibiotic-free farms) (AMR)
  • Integrated Assessment Model of Antimicrobial Resistance (IAM.AMR) to incorporate and account for data describing the ecology and epidemiology of AMR creating a framework to estimate AMR along the various dissemination pathways and assess the relative contribution of each pathway (AMR)
  • Quantitative Microbial Risk Assessment (QMRA) of Ceftiofur-resistant Salmonella Heidelberg in broilers (AMR)
  • Spfy v6.3.1: an integrated graph database for real-time prediction of bacterial phenotypes and downstream comparative analyses, including anti-microbial resistance and predictive marker discovery for virulence and AMR (AMR)
  • Phylotyper v0.11: : prediction of gene subtypes from genome sequence data, including AMR genes (AMR)
  • Metagenome_Resistome analysis pipeline: culture-independent analysis of relevant samples (feces, soil, waste water) subjected to shotgun metagenomics sequencing to characterize the resistome and bacterial communities found across production systems (AMR)
  • StarAMR v0.5.1: tool integrating the functionalities of ResFinder and PointFinder for the prediction of antimicrobial resistance in bacterial genome sequences based on the presence of genes and point mutations (AMR)
  • PhenoRes v2693e07: tool for the prediction of minimum inhibitory concentration (MIC) for 13 antimicrobials in Salmonella based on machine-learning analysis (AMR)
  • AMR Summary/Plasmid borne identity: a tool for determining whether AMR genes are chromosomal or plasmid borne (AMR)
  • The Salmonella in silico Typing Resource (SISTR): platform for in silico prediction of serovar and advanced subtyping via core genome multi-locus sequence typing analysis for Salmonella enterica (AMR)
  • Core genome Multi-Locus Sequence Typing schema for Salmonella Heidelberg: a tool for generating genome-based subtyping data from whole genome sequencing data for Salmonella Heidelberg to investigate population structure (AMR)
  • BARISTA (Bayesian allele recovery in Sequence Typing Analysis): a tool for recovery of missing/incomplete allelic data in population structure analyses aimed at examining AMR gene transmission patterns (AMR)
  • MOB-suite: software tools for clustering, reconstruction and subtyping of plasmids from draft genome assemblies (AMR)
  • CRISPR vectors constructed for site-specific modification of wheat genes (AAFC)
  • Wheat plants with CRISPR-engineered sequence modifications at alleles of 2 candidate FHB susceptibility genes (AAFC)
  • Candidate genes tightly linked to wheat 2DL QTL for FHB resistance (valuable markers for tracking the QTL in breeding programs) (AAFC)
  • Toolbox components to increase CRISPR efficiency and reduce costs for wheat gene editing (e.g. fluorescent tagging method to simultaneously detect gene editing in each of the 3 wheat genomes) (AAFC)
  • Transcriptomic evidence for genes associated with 2 FHB resistance QTLs in the wheat mapping population Wuhan 1 X Nyubai (AAFC)
  • 9 families with smaller 7EL fragments (with robust FHB resistance) introgressed from a wild wheatgrass into wheat (AAFC)
  • Lines of intermediate wheatgrass (Thinopyrum intermedium) with identified winter hardiness and resistance to FHB, tan spot, and/or stripe rust (AAFC)
  • Reference databases in wheat, oat, and barley containing DNA sequence variants in captured genes (exons) and adjacent regions (AAFC)
  • A new capture-based genotyping-by-sequencing assay (Rapture) for oat (AAFC)
  • Full exome capture design for use in diploid, tetraploid, and hexaploid oat (AAFC;
  • Material from reciprocal crosses between elite Canadian wheat lines and 4 selected synthetic wheat line form from crosses between Aegilops tauschii and Triticum turgidum (AAFC)
  • Chromosome conformation capture array for wheat (AAFC)
  • Nimblegen/Roche exome capture array for Brassica napus (AAFC)
  • CanolaCRISPR – web-based interface for designing guide RNAs to target genes in Brassica napus reference genome, in collaboration with the NRC in Saskatoon (AAFC)
  • Protein microarray technique for screening immunogenic proteins from bacterial pathogens (CFIA)
  • An E. coli expression system for the production of recombinant proteins secreted by bacterial cells into the culture medium (CFIA)
  • Python script for converting a GenBank file to a feature table to be used for providing annotations to sequence submissions to the National Center for Biotechnology Information (NCBI) (CFIA)
  • Git version control for all bioinformatics pipelines and applications (CFIA)
  • Continuous Integration (CI) automated software testing of bioinformatics pipelines and applications (CFIA)
  • Protocol for nucleic acid extraction from formalin fixed tissue (CFIA)
  • New PCR primer pools for foot-and-mouth disease virus diagnostics (CFIA)
  • Open source Neptune program for identification of genetic markers (CFIA)
  • Workflow for avian influenza virus genome assembly, variant calling, phasing, subtyping, sequence data quality control, and high-level report generation for Illumina sequencing data (CFIA)
  • Workflow for classical swine fever virus, foot-and-mouth disease virus, Ebola virus genome assembly and analysis from IonTorrent AmpliSeq data, applicable to other pathogens (CFIA)
  • Pipelines for rapid-sequence analysis of Nanopore data for rabbit haemorrhagic disease virus (CFIA)
  • Pipelines for rapid-sequence analysis of Nanopore data for African swine fever virus (CFIA)
  • Pipelines for metagenomic detection, classification and characterization of known, unknown and unexpected viruses in complex samples including building and testing of taxonomic classification databases and testing of different combinations of open source software and approaches for finding viral sequences in metagenomic sequence data (CFIA)
  • GeneSeekR analytical pipeline: real-time whole-genome sequencing and analysis of food-borne pathogen isolates (CFIA)
  • Direct sequencing protocol using the Ion Torrent platform for detecting bacterial contaminants of food (CFIA)
  • GMOseqr: a pipeline script that utilizes BLAST plus and other bioinformatics tools to identify transgenic elements and event junctions in data sets generated with next-generation DNA sequencing (CFIA)
  • Adapter Kmer Alignment Trim: a cross-platform software designed to eliminate the partial adapter sequences and other noise sequences from the next-generation sequencing data (CFIA)
  • Amplicon mapper: bioinformatics analysis application for screening next generation sequencing data for specific plant species barcode sequences (CFIA)
  • Updated Virtool diagnostic tool for the detection of plant viruses (CFIA)
  • CFIA FoodPort: cloud-based genomics portal pilot project that: 1) stores and allows access to whole genome sequence data and metadata associated with bacterial isolates; 2) allows labs to submit new sequencing data for analysis; and 3) has a variety of analytical tools available enabling users with any level of expertise to do custom analyses of the bacterial isolate sequence data (CFIA)
  • Redmine Automator: web-based interface to automatically submit requests for supported bioinformatic analyses (CFIA)
  • PointFinder Redmine Automator: performs detection of AMR in draft genome assemblies (CFIA)
  • AMRSummary Redmine Automator: performs AMR detection using the ResFinder database, as well as plasmid prediction using MOB-suite on FASTA files. The pipeline creates a report combining and summarising the outputs, allowing for the rapid prediction of plasmid-borne AMR sequences (CFIA)
  • ConFindr Redmine Automator: identifies intra-species and inter-species contamination in raw reads, which can cause misassemblies and erroneous downstream analysis (CFIA)
  • GeneSeekr Redmine Automator: marker discovery in FASTA files that supports the following analyses: genomically-dispersed conserved sequences (GDCS), Genesippr, multi-locus sequence type, ResFinder (identifies acquired antimicrobial resistance genes), ribosomal multi-locus sequence type, serosippr (calculates the serotype for Escherichia), sixteenS (determines closest 16S match), and virulence (CFIA)
  • PlasmidBorne Identity Redmine Automator: allows for rapid prediction of plasmid-borne sequences (CFIA)
  • PrimerFinder: performs in silico PCR analyses on FASTA and FASTQ formatted files (CFIA)
  • Prokka Redmine Automator: fully annotates draft bacterial genome in about 10 minutes on a typical desktop computer. It produces standards-compliant output files for further analysis or viewing in genome browsers (CFIA)
  • Sipprverse Redmine Automator: conducts a suite of analyses to detect gene targets in raw FASTQ reads (CFIA)
  • Science advice framework (decision tree) for Program Managers regarding eDNA results (DFO)
  • Validated stress-specific biomarkers for application on salmon Fit Chips (DFO)
  • Sequences for 22 primer pairs for the amplification of tetramer microsatellite loci in narwhals (DFO)
  • Ion Torrent workflow for next generation sequencing of narwhal and beluga (DFO);
  • New R software package called HYBRID_DETECTIVE designed for the statistical treatment of hybrid identification, simulation of hybrids, estimation of the accuracy and efficiency of putative panels and of the hybrid origin of experimental data (DFO)
  • Baseline single nucleotide polymorphism (SNP) allele frequencies for wild and farmed Atlantic salmon from both Newfoundland and Maritimes (DFO)
  • A panel of primers that produces 390 amplicons for chinook salmon in a single polymerase chain reaction (DFO)
  • Hatchery Brood Full Parental Genotyping process: stock identification of chinook salmon to specific hatcheries and release years for DFO Hatchery managers and stock assessment staff (DFO)
  • An online, cloud-based data analysis tool as part of a project with Genome Canada – EcoToxXplorer.ca – to support the evaluation of toxicogenomics data derived from ToxChips and other transcriptomic platforms (ECCC)
  • Flow cytometric micronucleus assay in cultured avian cells: in vitro test for the ability of chemicals to induce DNA damage (micronuclei) in cultured avian cells (ECCC)
  • Flow cytometric DNA damage and repair assay in cultured avian cells: in vitro test for the ability of chemicals to induce DNA damage (DNA repair enzymes and cell cycle regulation) in cultured avian cells (ECCC)
  • Flow cytometric blood micronucleus assay for avian embryos: used to measure the induction of DNA damage (micronuclei) in avian embryos (ECCC)
  • DNA methylation epiTYPER assay for bank swallows: epigenetic regulation of a gene related to stress response (glucocorticoid receptor) (ECCC)
  • Refined in vitro biomarker for use in human health risk assessment through the US FDA biomarker qualification program and the Health and Environmental Sciences Institute (HC)
  • Redesigned BMDExpress, a tool for high-throughput analysis of toxicogenomic dose-response data (https://www.sciome.com/bmdexpress/) (HC)
  • Method of isolation of extracellular vesicles from conditioned media from human mesenchymal stem cells and proteomics and RNA-based isolation approaches (HC)
  • Method of enriching glycoproteins from human mesenchymal stem cells and extracellular vesicles (HC)
  • Method of protein isolation for whole cell lysates from human mesenchymal stem cells for use in proteomics-based analyses (HC)
  • Bioinformatics pipeline for applying Next Generation Sequencing to simultaneously sequence large numbers of barcoded mutant LacZ genes for elucidating and comparing mutagenic mechanisms of various agents and improved evaluation of genotoxins (HC)
  • Animal models for the evaluation of vaccine-induced adverse reactions (vaccine-induce pulmonary pathology) (HC)
  • Assays for the evaluation of immune response and adverse reactions (published in peer-review journals) (HC)
  • Lung disease signatures (markers of human health effects, gene expression fingerprints), optimization of animal exposure protocols, statistical normalization algorithms, identification of microarray data analysis tools, standard operating protocols for microscopic detection of engineered nanomaterials in tissues after exposure, and guidance documents to employ genomics for the assessment of risks posed by engineered nanomaterials (HC)
  • Elucidated mode of action of known fungal toxins and anthropogenic chemicals (HC)
  • Method to identify changes in bacteria associated with physiological and metabolic outcomes (HC)
  • Procedure to identify the limits of taxon assignment for bacterial identification using next generation sequencing (HC)
  • High-Throughput Genotyping platform for wheat capable of simultaneously profiling SNP markers (NRC)
  • Breeder-friendly diagnostic markers for rust-resistance genes (NRC and AAFC)
  • 2 breeder-friendly Fusarium head blight-resistance molecular markers developed (NRC)
  • Genes exhibiting extreme heat tolerance when highly expressed in wheat in growth chamber conditions (NRC)
  • Identified markers for glaucousness, root proliferation, height, and seed size in wheat (NRC)
  • Signalling factors involved in abiotic stress response in wheat for drought, heat, or cold tolerance (NRC)
  • Gene targets for photosynthetic efficiency in wheat (NRC)
  • Gene expression atlas for wheat seed development (NRC)
  • Galaxy Bioinformatics platform for wheat sequence data analysis (NRC)
  • Genomic tools for enhancing the frequency of meiotic recombination and CRISPR/Cas9-based gene editing in wheat (NRC)
  • Pan genome sequencing of Canadian wheat - Genome sequence assembly of Stettler, a popular Canadian wheat variety (NRC)
  • A bread wheat Nested Association Mapping population – a valuable genetic and germplasm resource for wheat improvement (NRC)
  • Valuable pre-breeding germplasm for future Canadian wheat breeding programs (NRC)
  • A breeder-friendly gene editing platform for crop plants (NRC)
  • An integrative wheat bioinformatics portal as a primary access point for information and bioinformatics resources developed in-house and from third party (NRC)
  • An RNAseq data analysis workflow in the Galaxy platform; Meiotic transcriptome atlas in wheat (NRC)
  • Pairing homoeologous 1 (Ph1) – deletion mutants (NRC)
  • Genomic resources (breeder-friendly genetic markers and quantitative trait loci) vital for dissection of genetic architecture of complex traits in wheat (NRC)
  • Novel method for the production of pure Cas9 protein reducing the overall process to a single day (NRC)
  • Advanced genetic and genomic resources to characterize natural variation in wheat (NRC)
  • Genomic selection models for advanced-breeding populations of targets for wood quality, growth, weevil resistance, in operational conditions (NRCan)
  • Unified approach with dendroecology and quantitative genetics to assess tree sensitivity to climate (NRCan)
  • Traceability system developed for large-scale production of white spruce in provincial nurseries (NRCan)
  • Sequencing and assembly of spruce budworm and gypsy moth genomes (NRCan);
  • Detection assays for poplars and pines rusts (NRCan)
  • Detection assays for Phytophthora species (NRCan)
  • Molecular approach to the identification of the geographic origins of gypsy moth samples intercepted at North American ports (NRCan)
  • Molecular assay for the detection of Asian gypsy moths in bulk pheromone trap samples (NRCan)
  • The Salmonella In Silico Typing Server (SISTR) (http://lfz.corefacility.ca/sistr-app): a bioinformatics resource for multiple rapid Salmonella subtyping required for epidemiological analysis (PHAC)
  • Panseq (http://lfz.corefacility.ca/panseq) for the pan-genomic analyses of closed and draft genomic sequences (PHAC)
  • SuperPhy (http://lfz.corefacility.ca/superphy) online predictive genomics platform for near real-time analyses of thousands of genome sequences (PHAC)
  • Spfy (https://lfz.corefacility.ca/superphy/spfy/) for near real-time analyses of thousands of genome sequences with results that are understandable and useful to those in the fields of clinical medicine, epidemiology, ecology, and evolution (PHAC)
  • Phylotyper (https://github.com/superphy/insilico-subtyping) to predict biological subtypes from gene sequence data (PHAC)
  • Ectyper (https://github.com/phac-nml/ecoli_serotyping) to predict serotypes and identify known Escherichia coli virulence factors within whole-genome sequence data (PHAC)
  • Feht (https://github.com/chadlaing/feht): a commandline program to automatically identify markers predictive of groups (PHAC)
  • BIO-HANSEL: an in silico analytical tool to subtype S. Enteritidis and S. Heidelberg strains using raw Illumina sequencing data or unfinished genomic sequences (PHAC)
  • RNAse-H dependent PCR (IDT Inc.) for detection of single nucleotide variants of S. Heidelberg strains using raw Illumina sequencing data or using unfinished genomes (PHAC)
  • EpiQuant for comparisons of the strength of epidemiological and genetic relationships between bacterial isolates (PHAC)
  • CrowBAR v.0.9 to support pathogen characterisation from unfinished data (PHAC)
  • Neisseria meningitidis Bacterial Isolate Genome Sequence database (BIGSdb) to upload whole-genome sequencing data to the online system and interrogate against data stored in this public database enabling investigation of N. meningitidis local epidemiology and outbreaks (PHAC)
  • Pipelines for emerging pathogen detection developed using ultrafast k-mer based methods (PHAC)
  • Neptune: a bioinformatics tool for the rapid discovery of signature sequences in pathogen genomes (PHAC)
  • National MALDI Database (NMD): a database containing the spectra of rare and unusual, but clinically relevant bacteria, as well as species that are under-represented in the commercial Bruker Daltonic databases, providing fast, accurate and cost-effective identification of those pathogens locally, rather than having to be sent to a reference centre (PHAC)
  • Protocol for serum extraction and HBV DNA amplification for Illumina MiSeq ultra-deep sequencing to inform HBV outbreak investigation in order to understand transmission and risks (PHAC)
  • One-tube multiplex real time PCR protocol for influenza viruses to assess the potential benefits of implementing a whole genome sequencing approach in routine influenza A surveillance in Canada (PHAC)
  • Protocol for PCR amplification of the full genome of both seasonal and pandemic influenza A viruses (PHAC)
  • Long-range PCR amplification of hepatitis C virus genomes from patient samples that provides viral genomic information important for genotyping, surveillance and for informing patient antiviral therapy (PHAC)
  • Hepatitis C virus and HIV Next Generation Sequencing by Capture Probe Enrichment applicable for use for any virus of any size but is particularly adept at dealing with high heterogeneity viruses (PHAC)
  • Long-range PCR amplification of hepatitis A virus genomes from patient samples for studying putative transmission clusters (PHAC)
  • Measles virus template enrichment for improved whole genome sequencing from <10% to ~60% on clinical specimens (PHAC)
  • BEAST analysis for distinguishing measles virus endemic transmission from separate importation events (PHAC)
  • “Winnipeg Consensus” on bioinformatics strategies for next generation sequencing-based HIV drug resistance data analysis for HIV drug resistance surveillance and clinical monitoring (PHAC)
  • Publically available amino acid variant reporting format for next generation sequencing-based microbial sequence analysis for HIV drug resistance testing has been made publically available (https://github.com/winhiv/aavf-spec) now adopted by many data analysis pipelines worldwide (PHAC)
  • Quasitools: a suite of publically available tools to analyze viral quasispecies sequencing reads generated by next-generation sequencing (https://github.com/phac-nml/quasitools) (PHAC)
  • Quasitools complexity: software that measures the complexity of viral quasispecies using indices proven adequate to measure species diversity in ecology. These complexity indices may be used to research the evolution of a viral quasispecies within an infected individual (PHAC)
  • Quasitools distance: a new methodology and software to measure evolutionary distances between viral quasispecies (PHAC)
  • Quasitools quality: a tool to perform basic quality control on viral quasispecies sequencing reads that improves the accuracy of analyses (PHAC)
  • msaboot: a multiple sequence alignment tool to generate resampled multiple sequence alignments for use in robust phylogenetic tree construction (PHAC)
  • R2DO (Response to Disease Outbreak): a series of connected software that generates clusters from quasispecies sequencing reads to generate epidemiology hypotheses (PHAC)
  • Identifying Amino Acid Mutations in Influenza NGS Data: a series of connected software that identifies and reports amino acid mutations in influenza virus next generation sequence data to rapidly identify evolution in seasonal influenza (PHAC)

Research processes

  • A process integrated into the EpiQuant tool for quantifying the strength of epidemiological relationships between bacterial isolates: this process allows users to generate a quantitative measure of epidemiological similarities between bacterial isolates based on 3 basic epidemiological meta-data fields: source of isolation, location of isolation, date of isolation (AMR)
  • A validated pipeline for pre-processing of whole genome sequencing data, allowing users to take raw sequencing reads and prepare it for downstream analyses (AMR)
  • A framework for assessing the stability of clusters of isolates in bacterial populations comparing results from different molecular sub-typing methods to identify stable clusters that can form the foundation of nomenclature systems for tracking strains of interest in genomic epidemiology, and to identify clusters that are undergoing diversification such as in the case of outbreaks (AMR)
  • A mouse model for studying horizontal transfer of antimicrobial resistant genes in the intestine: horizontal transfer of plasmids encoding for β-lactamase resistance was established between 2 E. coli strains in mouse gut under antibiotic selective pressure. This mouse model will assist the evaluation of factors contributing to horizontal gene transfer for use in AMR risk assessment and risk management (AMR);
  • Validated bioinformatics analysis pipeline to determine the microbiome and resistome of a wide variety of environmental metagenomes (AMR)
  • Risk profiles of Ceftiofur-resistant Salmonella Heidelberg and of Carbapenem-resistant Escherichia coli of shrimp and salmon origin, synthesizing the current state of knowledge and identifying risk management options (AMR)
  • AMR Threat Assessment: a process to evaluate semi-quantitatively the potential contributions to AMR human exposure through the food chain (AMR)
  • Methods for metagenomics analysis of samples: including for targeted shotgun metagenomics using AMR target capture from metagenomics samples using the MyBaits kits (i.e. capture probe-based) and 16s rDNA metagenomic analysis (i.e. barcode-based) to understand the impact of gut microbiota on the development of infection by antimicrobial resistant bacteria and the horizontal transfer of resistance genes in the mouse gut (AMR)
  • Workflows for genomic characterization of microbial samples including: a workflow for high-throughput DNA extraction and sequencing (WP1.0); a protocol for optimization of DNA extractions for long-read sequencing using the Nanopore MinION platform; a workflow for hybrid DNA assembly using Illumina and long-read sequencing; a workflow for genome assembly QA/QC of AMR resistant food pathogens; a workflow for integration of mobilome (MOB-suite) and resistome (starAMR) workflows using the Galaxy platform (AMR)
  • Genome Analysis and Multiplex PCR Method for the Molecular Detection of Cephalosporins - Fosfomycin Resistant Salmonella enterica serovar Heidelberg (AMR)
  • Identification of primary AMR drivers in agricultural non-typhoidal Salmonella enterica serovars using machine learning (AMR)
  • Biological confinement procedures at the piggery including spatial organization and procedures for animal keepers to avoid bacterial contamination between pens, different treatment groups and with other off-project animals housed in the piggery (AMR)
  • Molecular assay information and protocols (EcoBiomics)
  • Efficient homogenisation method for the handling of large samples of solid material for DNA extraction following the PowerSoil nucleic acid extraction Protocol (EcoBiomics)
  • RenSeq analysis of 16 Thinopyrum intermedium lines exhibiting fungal pathogen resistance to reveal R gene candidates (AAFC)
  • Transcriptomic (RNASeq) analysis of dissected tissues comparing resistant Tenacious and susceptible Roblin wheat (AAFC)
  • 5 subnetworks and 8 novel proteins within the FuNTAP network of interacting proteins involved in mycotoxin biosynthesis (AAFC)
  • Metabolomic profiling (UPLC-HRMS) of 12 F. graminearum and 23 F. avenaceum strains (AAFC)
  • Structural elucidation of 2 novel F. avenaceum secondary metabolites (AAFC)
  • Genome sequences assembled for 15 F. avenaceum strains (AAFC)
  • Updated SNP discovery pipeline for polyploids (AAFC)
  • Validated haplotype-based genotyping-by-sequencing analysis for genomic selection and gene association analysis (AAFC)
  • Characterized chromatin structure of Chinese Spring using ChIP (AAFC)
  • Characterized methylome of Chinese Spring using WGBS (AAFC)
  • Nucleosome positions in Chinese Spring using Mnase-Seq (AAFC)
  • Genotyped parental diploid, tetraploid and synthetic hexaploid material using the wheat SNP array (AAFC)
  • Characterized phenotypes of diploid, tetraploid and synthetic hexaploid wheat for morphology and flowering time (AAFC)
  • Combination of in vivo cloning, in vitro transcription-translation, and protein microassay as a high throughput strategy for diagnostic and vaccine antigen discovery (CFIA)
  • Synthesis of cDNA for Next Generation Sequencing (CFIA)
  • Next generation sequencing of RNA viruses using MyBaits probe capture method (CFIA)
  • Next-generation sequencing of DNA viruses using MyBaits probe capture method (CFIA)
  • Illumina – 16S Metagenomic next-generation sequencing library preparation (CFIA)
  • Operation and maintenance of the AB Library Builder System (CFIA)
  • Ion Torrent template preparation using OneTouchTM 2 & Ion ES instruments (CFIA)
  • Ion Torrent - preparation of amplicons for library construction (CFIA)
  • Isolation of viral DNA from cell culture samples (CFIA)
  • Isolation of viral DNA from tissues (CFIA)
  • Isolation of viral nucleic acids from tissues using triphasic reagents (CFIA)
  • Protocols for species confirmation and microbial contamination screening (CFIA)
  • Protocol for Nanopore sequencing of African swine fever virus (CFIA)
  • Protocol for Nanopore sequencing of foot-and-mouth disease virus (CFIA)
  • Protocol for Nanopore sequencing of vesicular stomatitis virus (CFIA)
  • Protocol for Nanopore sequencing of avian influenza virus (CFIA)
  • Protocol for Nanopore sequencing of swine vesicular disease virus (CFIA)
  • Protocol for targeting sequencing of African swine fever virus genomes (CFIA)
  • Protocol for targeted sequencing of mitogenomes and assembly (CFIA)
  • SerotypeFinder: integration of Centre for Genomic Epidemiology serotyping tool for E. coli in GeneSeekR pipeline (CFIA)
  • Real time Whole Genome Sequence analysis of food-borne pathogen isolates using a bioinformatics pipeline named GeneSeekR (CFIA)
  • Prophage sequence typing procedure for Salmonella (CFIA)
  • Prophage sequence typing procedure for Listeria monocytogenes (CFIA)
  • Whole genome procedure using the Ampliseq tool to identify the presence of virulence genes in microbial isolates (CFIA)
  • PCR-based serotyping method for characterization of L. monocytogenes isolates (CFIA)
  • Procedure for end-user specific eDNA assay in Biomeme portable qPCR instrument (DFO)
  • eDNA sampling strategies and procedures (DFO)
  • Bioinformatic pipeline to discover and validate biomarkers associated with stressors across multiple microarray studies (DFO)
  • Mapping of 5 salmon microarray platforms to the Atlantic salmon genome (cGRASP 16K and 32K, Koop 44K, Traits, SIQ) (DFO)
  • Targeted enrichment with Agilent SureSelect to re-sequence portions of genes represented by probes on different microarray platforms (DFO)
  • Identification of 158 genes highly associated with smoltification processes across species and study systems (DFO)
  • Identification of 139 genes highly associated with thermal response and tolerance across species and study systems (DFO)
  • Identification of 40 of genes predictive of salmon morbidity (imminent mortality) (DFO)
  • High quality SNP determination for genotyping of chinook salmon (DFO)
  • Hatchery Brood Full Parental Genotyping: by genotyping hatchery broodstock, all juveniles released are genetically marked, enabling identification of hatchery and year of release (DFO)
  • Transient transfection method for human mesenchymal stem cells (HC)
  • Protocols for assays used in the analyses of mucosal immune responses in animals (HC)
  • Protocols for the identification of biomarkers in immune cells involved in vaccine-induced host reactions (HC)
  • Comparative analysis of the classical toxicology endpoints and toxicogenomic data to provide more comprehensive data sets to assist regulatory toxicology evaluators (HC)
  • SNP discovery approaches for wheat, including an automated DNA extraction and SNP analysis platform (NRC)
  • Data analysis pipeline that integrates quantitative trait locus and expression quantitative trait locus mapping methods (NRC)
  • Metabolomics methods for experimental analysis of wheat infected by fungi (NRC)
  • Marker-assisted selection and rapid introgression methods to produce wheat germplasm with increased Fusarium head blight resistance (NRC)
  • Optimised methods for gene editing (NRC)
  • Pan genome of Canadian wheat; mapping structural variation (NRC)
  • Optimized method for single cell sequencing in plants (NRC)
  • A well-rounded research program to study diseases and pest in wheat (NRC)
  • A cost-effective microbial community profiling platform based on cpn60 gene UT region PCR amplicon sequencing (NRC)
  • Novel root systems architecture for phenomics platforms (NRC)
  • Targets identified for photosynthesis improvement (NRC)
  • Improved laboratory and field protocols for soil and fauna assessment (NRCan)
  • Standard operating procedures for the maintenance of insect cell lines (NRCan)
  • Rapid rust-resistance prediction without inoculation in BC western white pine seed families using marker-assisted selection tools (NRCan)
  • Asian Gypsy Moth (AGM) TaqMan Detection Workshop. Part I: Detection from egg mass samples (NRCan)
  • Asian Gypsy Moth (AGM) TaqMan Detection Workshop. Part II: Detection from bulk pheromone trap samples (NRCan)
  • Improved analysis of whole genome sequencing data from highly clonal bacterial pathogens (PHAC)
  • A knowledge translation pathway to provide comprehensive training and ongoing support to provincial public health and federal food safety laboratories that will introduce whole genome sequencing into routine surveillance and outbreak response by the PulseNet Canada network (PHAC)
  • A process for quantifying the strength of epidemiological relationships between bacterial isolates enabling the use of genomic data by federal and provincial epidemiologists working to track the source of infectious pathogens (PHAC)
  • Salmonella and Campylobacter core genome multi-locus sequence typing pipelines that allow for rapid phylogenetic analysis of draft whole genome sequencing assemblies and rapid assessment of assembly quality (PHAC)
  • A framework for assessing the stability of clusters of isolates in bacterial populations used to identify stable clusters for tracking strains of interest in genomic epidemiology and to identify clusters that are undergoing diversification such as in the case of outbreaks (PHAC)
  • An analytical process to analyse N. meningitidis genomic epidemiology using the Bacterial Isolate Genome Sequence database (BIGSdb) (PHAC)
  • A process for shotgun metagenomics sequence library preparation for various complex biological specimens and target pathogen types (PHAC)
  • A rapid mass spectroscopy method for the identification of 7 toxins from 5 bacterial groups, enabling clinical diagnostic laboratories to more rapidly and accurately identify bacterial toxins in patients (PHAC)
  • Methodologies to rapidly obtain S. pneumoniae genome sequence data from clinical specimens including data on drug resistance and pathogenicity (PHAC);
  • A genomic typing method for H. influenzae to support genomic epidemiology and identification of antibiotic resistant clones (PHAC)
  •  A method for the PCR amplification of seasonal and pandemic influenza A viruses (PHAC)
  • Long-range PCR amplification of hepatitis C virus genomes from patients (PHAC)
  • A method for hepatitis-C virus next generation sequencing by capture probe enrichment (PHAC)
  • A method for hepatitis-A virus next generation sequencing by capture probe enrichment (PHAC)
  • A method for hepatitis-B virus next generation sequencing by amplicon-based sequence analysis (PHAC)
  • Protocols for PCR amplification and next generation sequencing of HIV-1 protease, reverse transcriptase and integrase genes to analyze human immunodeficiency virus resistance for both research and surveillance purposes (PHAC)
  • An improved method for measles virus whole genome sequencing using enrichment of virus nucleic acids (PHAC)
  • A new Multiple Experiment Viewer (MeV) sequence analysis protocol to distinguish endemic transmission from separate importation events (PHAC).

Appendix B - Performance Measurement Framework overview

A horizontal Performance Measurement Strategy was developed for Phase VI of the GRDI. This document covers fiscal years 2014–2015 to 2018–2019 and formalizes the roles and responsibilities of the 8 departments and agencies involved in the Initiative to support effective monitoring and evaluation activities.

The logic model presented in Figure 1 reflects the overall objectives for the GRDI:

Through the GRDI, 8 federal science departments and agencies collaborate in the field of high-impact genomics research to address biological issues that are important to Canadians, focusing on the innovative and regulatory role of federal government research and operational mandates in important areas such as safe guarding health, food safety, sound management of natural resources, a sustainable and competitive agriculture sector, and environmental protection.

A number of activities are conducted to reach this objective, focused on: research and development activities; coordination of research, reporting and management activities; collaboration among stakeholders to access world-class research infrastructure and networks; and 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 for interdepartmental collaborations, scientific information and publications, research tools and products, and a highly skilled workforce. As immediate outcomes, these outputs will provide: structured collaboration mechanisms among participating departments and agencies; enhanced scientific leadership to support federal governmental mandates and priorities; knowledge, tools and advice for policy and regulatory decisions, as well as for the development of innovative tools and processes.

Intermediate outcomes consist of positioning federal science departments and agencies as genomics research leaders; use of research results by government policy makers and regulators for better informed evidence-based regulatory, policy, and resource management decisions; and use of research results by stakeholders to support innovation in Canada. Ultimately, the GRDI would be one of the factors contributing solutions to issues that are important to Canadians, and to the Government of Canada Outcomes: Healthy Canadians; Strong economic growth; An innovative and knowledge-based economy; and A clean and healthy environment.

The GRDI comprises 3 important program elements:

  • Interdepartmental governance—While good management is an important aspect of any government program, it is particularly important for the GRDI because of the number of departments and agencies involved and the diversity of their respective mandates. It is thus important that practices put in place support effective departmental and interdepartmental coordination and provide a well-structured framework to clarify expectations and foster strategic approaches. It is critical that departmental and shared priorities be well defined so that the projects are selected to ensure federal government-wide priorities for genomics research information are addressed. Phase V of the GRDI demonstrated the viability of a truly interdepartmental approach and the ability of GRDI participating departments/agencies to work together, foster synergies, and add value to existing departmental resources. Phase VI builds on this successful model.
  • Research and development—Research and development is the central component of this initiative to respond to priorities, support federal governmental mandates, inform policy and regulatory decisions, and foster innovation. All activities surrounding the actual conduct of research and development; reporting and management activities; building a highly qualified work force to ensure enhanced scientific leadership in support of federal government mandates and priorities; collaboration to access world-class research infrastructure and expertise, and dissemination and transfer of research results are all critical to ensuring progress towards outcomes.
  • Knowledge and networks— To maximize the value of the GRDI and move that value to users for commercial and public good applications as the Initiative matures, knowledge translation and mobilization activities are required. These include the development of scientific networks, communications products, end-user engagement activities, science policy integration, science advice, transfer of protocols, field trials, outreach activities, etc. They ensure that research remains relevant to solve specific problems by maximizing opportunities to understand the needs of targeted end-users and active dissemination of GRDI results to them.

Table 4 outlines the performance indicators, sources and responsibility for the outcomes outlined in the logic model (Figure 1) 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 contribution of the GRDI to the Government of Canada Outcomes, as attribution becomes challenging. Rather, it will focus on the achievement of immediate and intermediate outcomes, and assess whether it is reasonable to expect that the achievement of these outcomes would contribute to the Government of Canada 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 agencies, and are not included as indicators of performance.

Figure 1: Logic Model for the interdepartmental Genomics Research and Development Initiative Phase VI

Through the GRDI, eight federal science departments and agencies collaborate in the field of high-impact genomics research to address biological issues that are important to Canadians, focusing on the innovative and regulatory role of federal government research 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.

Logic Model for the interdepartmental Genomics Research and Development Initiative Phase VI
Long description of the Figure 1: Logic Model for the interdepartmental Genomics Research and Development Initiative Phase VI

The Government of Canada contributes targeted funding of $19,900,000/year to the Genomics Research and Development Initiative (GRDI). GRDI departments and agencies also contribute existing funds (salaries, infrastructure, and operational budgets) and resources leveraged from collaborators.

With these inputs, the GRDI undertakes a number of research and development activities, coordinates reporting and management activities, collaborates among stakeholders to access world-class research infrastructure and networks, disseminates research results, and translates knowledge into commercial and public good applications.

From these inputs and activities come several outputs, including interdepartmental governance (such as coordinated management approaches for project selection and management, planning meeting and workshop reports, project charters and plans, and annual performance reports); research and development (such as scientific information, advice and publications, and research tools and processes); and knowledge and networks to transfer and mobilize knowledge (such as communication products, scientific networks, and end-user engagement activities).

These outputs lead to several immediate outcomes. For example, interdepartmental governance leads to structured collaboration among participating department/agencies. Research and development and knowledge transfer efforts lead to enhanced scientific leadership and research results that are available to government policy makers and regulators to support government mandates and priorities, including innovation in Canada.

These immediate outcomes lead to several intermediate outcomes. For example, federal science departments and agencies are positioned as genomics research leaders. In addition, research results are used to inform government regulatory, policy, and/or resource management decisions. Furthermore, research results are used by stakeholders to support innovation in Canada.

Finally, the immediate and intermediate outcomes of the GRDI contribute to the Government of Canada's desired outcomes, including healthy Canadians, strong economic growth, an innovative and knowledge-based economy, and a clean and healthy environment.

Table 4: Program Performance Measurement Strategy Framework

Area Indicator Methodology / Source Frequency Target Footnote 3 Date to achieve target Responsibility
Project information developed by all participating departments/agencies towards the start of every phase (Descriptive, within departments/agencies)
  • Project titles and summary descriptions (key objectives and impact areas)
Financial information reported annually by all participating departments/agencies (Descriptive)
  • Internal funding leveraged from A-base resources
  • Other funding by collaborators (OGDs; universities; international organizations; private sector; etc.)
  • In-kind contributions by collaborators
End-users determined by all participating departments/agencies at project planning stage (Descriptive)
  • List of stakeholders and end-users available for each research project (including contact information)
Outputs

Interdepartmental governance

Coordinated management approaches

% of processes, templates and guidelines for interdepartmental shared priority projects approved by ADM CC Processes (e.g. for collective decisions on priorities and projects) and documents (e.g. Project Charter template and annexes) approved by ADM CC. Source: meeting minutes Once per phase 100% March 2016 NRC secretariat and departments / agencies
% of departments /agencies sharing information on management approaches for mandated research projects Departmental processes in place and shared in GRDI Best Practices Document Once per phase 100% September 2014 Departments / agencies
% of publicly available GRDI-level annual performance reports completed GRDI Annual Performance Report approved by ADM CC and published online Annual 100% September of following fiscal year NRC secretariat
% of project performance reports completed for internal management Project performance reports produced according to department/agency requirements Annual 100% September of following fiscal year Departments / agencies

Research and development

Scientific contributions

# of key scientific contributions by type demonstrating leadership Annual reporting in project reports (e.g. publications in refereed journals, publications in refereed conference proceedings, book chapters, invited presentations, etc.) Annual Within the range recorded for Phase V (1,472, avg. 490/yr.) Footnote 3 By end of phase Departments / agencies
# of other scientific contributions by type Annual reporting in project reports (e.g. technical reports, poster presentations, deposits in genomics related databases or libraries, etc.) Annual Within the range recorded for Phase V (1,445, avg. 482/yr.) Footnote 3 By end of phase Departments / agencies
# of research tools produced
# of research processes produced
Reporting of tools and processes produced in project reports Annual Within the range recorded for Phase V (283, avg. 94/yr.) Footnote 3 By end of phase Departments / agencies

Knowledge and networks

Knowledge translation and mobilisation initiative

# of contributions to scientific networks by type Annual reporting in project reports (e.g. participation in meetings related to regulations or policy, participation in national or international research committees, etc.) Annual Within the range recorded for Phase V (252, avg. 84/yr.) Footnote 3 By end of phase Departments / agencies
# of research collaborations by organization type Annual reporting in project reports (e.g. universities (Canadian and international), other research organizations private sector, etc.) Annual Within the range recorded for Phase V (1,101, avg. 367/yr.) Footnote 3 By end of phase Departments / agencies
# of communications products by type Annual reporting in project reports (e.g. media interviews, press releases, newspaper and magazine articles, brochures, web pages, etc.) Annual Within the range recorded for Phase V (241, avg. 80/yr.) Footnote 3 By end of phase Departments / agencies
# of projects that included end-user engagement activities Annual reporting in project reports Annual 100% By end of phase Departments / agencies
Immediate outcomes
Structured collaboration among participating departments / agencies % of GRDI shared priority projects managed using interdepartmental governance structures Meetings of project management teams and ADM CC, decisions recorded in meeting minutes Once per phase 100% By end of phase NRC secretariat
and
departments / agencies
% of resources allocated to interdepartmental collaborations Funding allocations approved by ADM CC and transferred by the NRC to participating departments /agencies according to formal Project Charters Annual 20% By end of phase NRC secretariat
# of departments involved in shared priority projects Shared priority project planning meetings, Project Charters Once per phase At least 3 per project By end of phase Departments / agencies
Enhanced scientific leadership in support of government mandates and priorities # of research and technical personnel Annual reporting in project reports (e.g. research scientists and professionals, post-doctoral fellows, students, etc.) Annual Within the range recorded for Phase V (2,410, avg. 803/yr.) Footnote 3 By end of phase Departments / agencies
Research results are made available to government policy makers and regulators to support government mandates and priorities % of projects leading outreach activities for disseminating results to identified end-users Annual reporting in project reports (e.g. end-user consultations, workshops, transfer of methods and protocols, science advice, etc.) Annual 100% By end of phase Departments / agencies
Research results are made available to stakeholders to support innovation in Canada # of transfer activities by type Annual reporting in project reports (e.g. collaborative agreements, workshops, material transfer agreements, standard operating procedures, disclosures, patents, etc.) Annual Within the range recorded for Phase V (398, avg. 133/yr.) Footnote 3 By end of phase Departments / agencies
Intermediate outcomes
Federal science departments and agencies are positioned as genomics research leaders Scientific production and impact in genomics Evaluation Every 5 years On par or better than other genomics researchers in Canada By end of phase Evaluators
Research results are used to inform government regulatory, policy, and/or resource management decisions Case analysis of examples where risk assessment, regulatory, policy, and resource management decisions have been informed by GRDI research (federal, provincial, municipal) Evaluation Every 5 years n/a (qualitative/descriptive) By end of phase Evaluators
Research results are used by stakeholders to support innovation in Canada Case analysis of examples where innovative tools and processes have been adopted in Canada based upon GRDI research (# of people interviewed who have used GRDI research) Evaluation Every 5 years n/a (qualitative/descriptive) By end of phase Evaluators

Appendix C - List of acronyms

AAFC
Agriculture and Agri-Food Canada
ADM
Assistant Deputy Minister
ADM CC
Assistant Deputy Minister Coordinating Committee
ALL
Acute lymphocytic leukemia
AMR
antimicrobial resistance
BIGSdb
Bacterial Isolate Genome Sequence database
CABIN
Canadian Aquatic Biomonitoring network
CFIA
Canadian Food Inspection Agency
CIPARS
Canadian Integrated Program for Antimicrobial Resistance Surveillance
COST
European Cooperation in Science and Technology
CRISPR
clustered regularly interspaced short palindromic repeats
DFO
Fisheries and Oceans Canadas
DNA
deoxyribonucleic acid
ECCC
Environment and Climate Change Canada
EcoBiomics
Metagenomics-Based Ecosystem Biomonitoring
eDNA
environmental DNA
FHB
Fusarium head blight
GEO BON
Earth Observations Biodiversity Observation Network
GLOMICON
Global Omics Observatory Network
GPSC
General Purpose Science Cluster
GRDI
Genomics Research and Development Initiative
HC
Health Canada
HIV
human immunodeficiency virus
ISED
Innovation, Science and Economic Development Canada
IRIDA
Integrated Rapid Infectious Disease Analysis
JPIAMR
Joint Programming Initiative on AMR
NRC
National Research Council of Canada
NRCan
Natural Resources Canada
OECD
Organization for Economic Cooperation and Development
PCR
polymerase chain reaction
PHAC
Public Health Agency of Canada
qPCR
quantitative polymerase chain reaction
QTL
quantitative trait locus
R&D
research and development
RNA
ribonucleic acid
SNP
single nucleotide polymorphism
SOP
standard operating procedure
SPP
shared priority project
STAGE
Strategic Technology Applications of Genomics in the Environment
TATFAR
Transatlantic Taskforce on Antimicrobial Resistance
USDA
United States Department of Agriculture
WHO
World Health Organization