A New DNA-Based Tool to Detect and Monitor Forest Pests

By Emmanuelle Brière
June 2012

Scientists are looking to genomics to more quickly detect forest pathogens and monitor their propagation.

An oak infected by sudden oak death, a disease caused by the pathogen Phytophthora ramorum.

The most well-known forest pests currently infesting Canadian forests are undoubtedly insects such as the brown spruce longhorn beetle, the mountain pine beetle and the emerald ash borer. But these insects are not the only threat to our forests. Forest pathogens can also be devastating pests. Most of these pathogens are fungi that attack trees and can lead to major epidemics in forests.

It is very difficult to detect and monitor these pathogens. To date, their presence has mainly been signalled by the damage they cause. In many cases, however, a pathogen may be present in significant quantities without causing any obvious symptoms, which increases the risks of transmission.

This is why Richard Hamelin, a researcher in forest pathology and genomics at Natural Resources Canada (NRCan), is developing a DNA-based diagnostic tool. “We proposed to develop a faster, more reliable diagnostic tool that will better detect pathogens and prevent their dissemination,” explains Richard. To carry out the project, Genome Canada has recently awarded Richard and his team a $4.25 million grant.

Genomics-based Tool

Over the next three years, Richard and his team will decode the complete genome of various fungi that have different characteristics, such as virulence. By comparing the genomes, they will be able to identify the genes associated with these characteristics. The genes will become the basis for a DNA “fingerprint” common to the pathogens. The end result will be a detection tool that can be applied to detect and track pathogens.

The advantage of this approach is that it offers the possibility of predicting the pathogenicity of fungi according to their genomic profile. The researchers will then be able to discover and identify new pathogens that were previously unknown.

The Chosen Diagnostic Tool: A Biochip

Until now, only one pathogen could be identified at a time through laboratory experimentation. The new tool will be able to detect several pathogens simultaneously from samples taken directly from the environment. This will be made possible through the development of a biochip with thousands of nanocavities 10,000 times smaller than a drop of water, each containing a DNA probe. The probes will be able to recognize the genes of the pathogens, making it possible to detect several at once. In addition to increasing detection capacity, the method will reduce the error rate.

Technology Transfer

A major component of the project is the technology transfer of the tools. To accomplish this, project partners from the Canadian Food Inspection Agency (CFIA) and FPInnovations will work toward validating the tools and comparing their performance with diagnostic tools currently in use. “We are constantly on the lookout for new diagnostic methods and this genomics project permits us to strive to be leaders in this area,” says Stephen Brière, head pathologist at the CFIA.

One of the uses planned by the CFIA is the certification of imported products to better protect forests against new invasions. The team will also work with export companies toward certifying product safety and facilitating exports to countries protected by quarantines.

To read about related articles, see Forest Disturbances

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