Protecting PEI potatoes
On a late autumn day in 2000, a grower on Prince Edward Island noticed some strange-looking potatoes among the thousands rolling up into his harvester. Suspicious, he pulled a few of the odd ones off the conveyer and turned them over to the Canadian Food Inspection Agency (CFIA). The news was not good—potato wart disease.
Potatoes with the fungus are safe to eat, but the effects on the appearance of the potato are so extreme, it is doubtful anyone would even try—they are unmarketable. For a province that relies heavily on the industry for its economic well-being—potatoes are a billion-dollar business in PEIFootnote 1—this was bad news indeed.
Almost immediately, to protect its own potato industry, the United States closed its border to imports of both table and seed potatoes from PEI. It would not re-open for eight months. Potato growers in PEI lost an estimated $70 million in sales. Together with the impact on employment and other economic activity, the total cost to the provincial economy was estimated as high as $280 million.Footnote 2
Outbreak or isolated incident?
Before the border could be re-opened to PEI potatoes, Canada had to prove to the U.S. that potato wart fungus was not widespread—that the discovery was an isolated incident and the disease could be contained.
Soil samples were collected from potato fields around the province and checked for the spores that spread the fungus. The CFIA opened three new laboratories on the island and hired a battery of people to run the tests—every sample, 600,000 of them, had to be looked at through a microscope.
It was the only test available at the time and it took months to get through all the samples. On top of that, the test was challenging for diagnosticians. Soil is filled with spores from a variety of fungi, most of which are harmless, but which can look remarkably alike, even under a microscope. The risk of a "false positive" that could extend the border closure was considered high.
Looking for a better test, and knowing that Agriculture and Agri-Food Canada (AAFC) had been involved in genomics research, CFIA officials approached researchers at AAFC for help.
Within six weeks of that initial contact, a team led by AAFC research scientist Dr. André Levesque developed a genetics-based test that was used to double-check any positive results that came from the microscopic examination of the soil samples.
"The test we developed used what is called the bar-code approach," says Dr. Lévesque. "Basically, we look at a few sections of the DNA of the suspected positive spore and compare those to a few sections of the potato wart DNA. If they don't match, we can rule out potato wart."
Fast forward to 2012
Using the DNA-based test to demonstrate that the fungus was isolated to a very small section of just one potato field was a key factor in the success of Canada's efforts to negotiate the re-opening of the U.S. border to PEI potatoes in April of 2001. Years later, access to a refined version of the same test was important in keeping the border open when potato wart was detected in two other fields in PEI in 2012.
Dr. Guillaume Bilodeau, Research Scientist at the CFIA Plant Protection Laboratory in Ottawa, says that since the first incident in 2000, projects funded by the Government of Canada's Genomics Research and Development Initiative (GRDI) and related research supported by the Canadian Safety and Security Program have enabled construction of a database of DNA bar codes from a whole range of organisms, including many strains of the potato wart fungus.
"This funding also provided for increased access to bioinformatics to analyse genomic sequences for the database," says Dr. Bilodeau. "While we continue to refine our testing, this new genomics capacity enabled us to prove that the detection of potato wart in 2012 was almost certainly not a new outbreak, but an isolated case of the same strain detected in 2000. We were also able to offer the proof very quickly, thanks to the speed and accuracy of the next-generation sequencing technologies we have access to today."
Setting the standard
Comparing the two cases, Dr. Lévesque says there is no question the GRDI played a part in protecting the PEI potato industry from another major economic blow in 2012. "It's also significant that the test for potato wart developed here in Canada is now used by the United States Department of Agriculture."
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