Download Canadian National Clean Plant Program

The Future of Post Entry Quarantine:
Canadian National Clean Plant Program
Dr. Michael Rott, Canadian Food Inspection Agency (CFIA)
Sidney, BC, Canada.
© 2007 Her Majesty the Queen in right of Canada
(Canadian Food Inspection Agency), all rights reserved. Use without permission is prohibited.
Overview
• What is a National Clean Plant Program (NCPP)
• A model: US Clean National Clean Plant Network
• Canadian Imported material: what is required
• Time Line – illustration and explanations
• Current approaches – Testing technologies
• Advances in testing
• Model for the implementation of NCPP
• What we need to get there
• Benefits
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What is a National Clean Plant Program
(NCPP)
Goal:
To promote the production and use of pathogen-free,
healthy plant material for food crops in Canada
Framework:
A set of rules/regulations to govern the maintenance,
testing, propagation and distribution of pest and disease
free plant material from nuclear generation 1 material to
generation 4 material grown for retail.
Enabler: A lab network and testing technology to support
the Program
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A good model: US National Clean Plant
Network (NCPN)
•
2005: Idea initiated by grape and tree fruit industries
•
2008: Grape and fruit tree networks developed by stakeholders,
industry members, scientists and other interested parties
•
2009: NCPN created as a voluntary association of specialty crop
networks to promote pathogen-tested, healthy plant material
 United States Department of Agriculture –Animal and Plant
Health Inspection Service (APHIS)
 Agricultural Research Service (ARS)
 National Institute of Food and Agriculture (NIFA)
•
2010: berries, citrus and hops programs added
•
2016: US Farm Bill: invested XXXX$ in program
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US NCPN: Grapes
New, state-of-the-art facility, Foundation Plant Service, Davis CA
•
Regulates importation of grapevine material
•
Provides tested, clean material, using latest equipment and
techniques
Manage Russell Ranch: foundation material for pathogen-tested
US grapevine material
http://ncpngrapes.org
/
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The Canadian Situation: Imported material
Currently, propagative tissues of tree fruit, grapevines
and small fruit imported into Canada must be held
in post entry quarantine to ensure they are free
from disease and pests of concern.
This includes:
• Foreign material from non-certified sources
• Audit samples from approved certified sources
• Domestic material from plant breeding programs and
nurseries
Time line: Import of new cultivar from a noncertified source
6 – 12 years!!
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Why so long?
Current Testing Methods
Molecular and Serological Tests:
•
Virus specific PCR and ELISA
1-3 days to complete
Bioassay Tests:
•
Herbaceous bioassay
Nonspecific, 2-3 weeks to complete
•
Woody field and greenhouse bioassay*
Nonspecific, up to 3 years to complete
*International “Gold Standard”
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Until now: Canadian Situation:
• Canada does not currently have a
NCPP due to several challenges:
• Additional costs:
• to the public
• to growers
• Reluctance to increase regulatory
burden
• Requires a willingness from industry
stakeholders and government
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What is different now?
Technological Advances and Novel Applications
DNA sequencing: today a generally accepted a
way to ID an organism
e.g. “DNA Barcoding”
1st generation sequencing technology:
- laborious, slow, $$$
human genome: 13yrs, $3B
Next Generation Sequencing (NGS)
- faster, cheaper, automatable
 human genome: 1-2 days, <$5K
Metagenomics: use of NGS technology to ID
multiple species in a single sample
 detect multiple viral infections in plants!
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Small samples produce big data!
Tissue Types: bark/cambium, leaf
Tissue Amount: 1 - 5 g sample (individual/composite)
DNA extraction: manual/automated
Genomic “Libraries” – DNA that has been “Prepped”
for sequencing – all genetic material from the sample
Next Generation Sequencing: various systems
Reads 25-40 Gigabytes of data in <12h
Cost: $150/sample/test – includes above steps
Data analysis: Bioinformatics processes –
computational advances allow for
Computer facilitated analysis of data
i.e. easier to “find” detection targets!
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Other Benefits of NGS:
•
Samples processed in months vs years
•
Less expensive: 1/10th the cost/sample.
•
Or, 10x as many samples for the same cost.
•
As sensitive or more sensitive than conventional
•
More accurate
•
Greater specificity
•
Greater ability to detect new viruses
•
Replace the bioassay?
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Example: 2013 grapevine audit imports
• Approximately 2.5 million vines imported
• Center for Plant Health in Sidney receives 1800
vines for testing (0.07%)
• Samples are:
•
•
•
•
inoculated to 5 indicator plants
rub inoculated onto 3 herbaceous indicators
tested by PCR for 12 virus
tested by ELISA for 5 virus
• > 5200 individual tests are performed on these
samples over 3 years!!
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Example: 2013 grapevine audit imports
vines imported:
vines tested by CPH:
2.5 million
1800
Traditional tests: >5200 tests in 3 years
The future: using NGS, metagenomics and
bioinformatics approaches:
90 -180 NGS tests
+ Confirmatory testing (PCR or ELISA)
IN 4 – 8 months
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CFIA Programs that could be modernized
through a NCPP:
Export Certification Programs:
•
Canadian Fruit Tree Export Program (CFTEP) for Malus,
Pyrus, Chaenomeles and Prunus (D-08-05)
•
Plant Protection Export Certification Program for Grapevine
Nursery Stock, Vitis spp. (D-97-06)
Import Programs: Post Entry Quarantine
•
To prevent introduction of plant viruses/virus-like diseases in
tree fruit, grapevines & small fruit.
Other activities:
•
Viral elimination, maintenance of clean stock
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NCPP Vision:
Harmonize with Canadian National Import and Export Programs
•
new test methods based on NGS
Harmonize with USA
•
North American Plant Protection Organization (NAPPO)
• USA National Clean Plant Network (NCPN)
Harmonize Internationally
•
International Plant Protection Convention (IPPC)
• EUPHRESCO Network for Phytosanitary research
coordination and funding
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Supporting Research: Current, Next, Future….
NGS validation & Generation 1 nuclear repository
• Re-test current grapevine and tree fruit export repository by NGS
• Validate NGS for plant viruses
• Develop NGS methods for grape fungal pathogens
NGS Tech transfer to 3rd party diagnostic lab
• Testing need for strawberry plant exports
www.cscr.in
Methods for Curating Gen 1 nuclear material
www.biw.kuleuven.be
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Research: Current, Next, Future….
Viral Elimination:
• Heat therapy
Plant Propagation
• Meristem culture
• In vitro cultures
• Chemotherapy
• micropropagation
• Cryotherapy
• Micrografting
• Micrografting
• Others
• Others
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Go from this:
6–12 years
…….to this:
Negative
released to
importer
(4 plants)
Imported
material to
CPH.
Virus free
material released
to importer
(4 plants)
4-6 years
Viruses
testing
program
(4-8
months)
Positive
Virus
elimination
program
(1-2 years)
Micropropagation
(1-1/2
years)
First crop
(2 years)
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Benefits to Canada establishing a NCPP
• Help maintain the highest standards for Canadian food production
while improving competitiveness of the Canadian Agro-Foods Sector
• Facilitate access to new material to Industry while reducing the
reliance on imported and potentially infected material
• Provide protection to production systems and to farms, nurseries,
and orchards while promoting trade
• Help prevent the introduction and spread of potentially harmful plant
pests and diseases in Canada
• An integrated consortium of laboratory expertise linking university,
AAFC, CFIA and the various industry sectors
Acknowledgements
Funding
Genomic R&D Initiative:
“Protection of Canadian biodiversity
and trade from the impacts of global
change through improved ability to
monitor invasive alien and
quarantine species”
Canadian Safety and Security
Programs:
CSSP-2014-TA- 2123
CSSP-2015-TA-2124
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© 2007 Her Majesty the Queen in right of Canada
(Canadian Food Inspection Agency), all rights reserved. Use without permission is prohibited.
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