DNA-based test helps protect Canadian forests

Sudden Oak Death (SOD) is not a serious problem in Canada, and we'd like to keep it that way.

The fungus-like disease is caused by a pathogen called Phytophthora ramorum and despite its name, it can infect and destroy a whole range of trees and other plants, from the stately Douglas fir to the ornamental rhododendrons found in gardens across Canada.

Since the mid-1990s, SOD is estimated to have killed more than a million trees along the central and southern coast of California, and it has spread northward through California and into OregonFootnote 1. The infection is also killing large numbers of trees in parts of the United KingdomFootnote 2 and has been found in a number of countries in Europe as well.

Prevention the best cure

The disease is almost impossible to control in nature so, for Canada and many other countries, the focus is on early detection and prevention. Plants and wood products from areas where the disease has been found are not allowed into Canada without a special certificate stating they are SOD-free. Similar restrictions apply to dozens of species of trees and plants that can carry the disease.

Along with routine inspections at the border, inspectors with the Canadian Food Inspection Agency (CFIA) survey plant nurseries and garden centres to check for SOD. Since plants can be infected for some time before they show any symptoms, inspectors take samples of leaves and soil to test for the pathogen.

"Unfortunately," says Canadian Forest Service researcher Dr. Richard Hamelin, "Conventional test methods can take as long as a month to produce a result — no one wants to quarantine a garden centre for a month while you wait for the test results. Conventional testing also produces a lot of 'false negatives', increasing the risk that the pathogen could spread."

Better protection for the forests and the economy

As more and more countries restrict imports of wood and plant material from countries where the disease has been found, SOD becomes a double threat for Canada. Beyond the destruction it could cause in our hardwood forests, Canada exports some $5.5 billion worth of lumberFootnote 3 and our multi-billion dollar horticultural industry exports hundreds of millions of dollars in ornamental plants every yearFootnote 4 — so the disease also poses a significant economic risk.

Today, Canada and other countries have a new line of defence against the pathogen responsible for SOD. A team of researchers led by Dr. Hamelin has developed a new, DNA-based test for the disease that's much more sensitive and provides results in as little as 24 hours.

"What we've done is identify portions of the pathogen's DNA that are unique to that pathogen," says Dr. Hamelin. "So, for example, to do the test, we would take a small piece of a leaf from a plant, and extract all the DNA that's in it. That sample would contain all kinds of DNA — from the plant, from all the other microbes and bacteria that are in the environment and of course, from the pathogen itself if it's there. Then, we go fishing in that little pool of DNA with a probe that recognizes the pathogen's unique DNA. If the pathogen is present, the probe reacts, and we know the plant is infected with SOD."

U.S. adopts Canadian method

The test developed by Dr. Hamelin and his colleagues has been used by the CFIA in Canada since 2006 and it is also part of the standard tests for SOD used by the U.S. Department of Agriculture. Agencies in the U.K. and France are considering adopting it as well.

At the CFIA's Ottawa Plant Laboratory, Director Linda DeVerno points out that it's unusual for the U.S. to adopt a Canadian plant pathogen test. "Most of the time, it's the other way around," says Ms. DeVerno, "So this is a bit of a coup for Canada. It's also important for our exports. Since the U.S. uses the same test, they are more likely to accept our certification that plants are SOD-free without question."

Crucial funding support

Dr. Hamelin's research was funded through the Government of Canada's Genomics Research and Development Initiative (GRDI). "GRDI funding was crucial — we couldn't have done this without it," he says. "The success of projects like ours shows the value of investing in genomics research, but it's a sizable investment — there was no way we could have funded this project through our regular budget."

Based on the achievements of the initial research project, Dr. Hamelin and his team have attracted additional funding from GRDI as well as other agencies, including Genome Canada, Genome BC, the CFIA and Forest Products International to work on developing similar DNA-based tests to provide fast, accurate identification of other pathogens that attack trees.

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