Genomics research offers new way to protect Canada's agricultural exports

A bulk carrier loaded with thousands of tonnes of rice arrives at the Port of Vancouver. Before it can be unloaded, the cargo must be checked to make sure invasive insect pests won't be coming into Canada along with the rice.

An inspector with the Canadian Food Inspection Agency (CFIA) spots some beetles in one of the bags of rice. They look like warehouse beetles—an insect that damages stored grain, but that is already widespread in Canada. A few more won't make that much difference.

On the other hand, they also look just like khapra beetles—a very destructive pest of grain and grain products, and considered one of the top 100 invasive species in the world. If they are khapra beetles, the shipment of rice must be destroyed or sent back where it came from.

At Agriculture and Agri-Food Canada (AAFC) in Winnipeg, Research Scientist and stored-product insect pest specialist Dr. Paul Fields says making a positive identification of these insects is not easy. "They're only a couple of millimetres long and telling one from the other involves counting the sensory pores on their inner lip, " says Dr. Fields. "Even a trained expert may not be able to say for sure which is which—and a mistake in either direction could prove costly. "

A risk to trade

Dr. Fields notes the same thing can happen in reverse—an inspector in another country could mistake a more-or-less harmless species of beetle in a shipment of Canadian grain for a quarantine species. "The shipment would be turned away, " says Dr. Fields. "And the other country might ban all shipments of grain from Canada until we can prove the beetle is actually not a species of concern. "

Dr. Fields is a member of a research team overseen by Dr. Kevin Floate, an AAFC Research Scientist in Lethbridge. The team has succeeded in developing a genomics-based identification tool that would allow anyone with a few basic lab skills to tell the bad bugs from the not-so-bad bugs.

The bar code approach

"DNA bar-coding has been around for awhile, " says Dr. Floate. "Basically, you find a section of DNA where differences exist among the species of interest. You then sequence the DNA of the unknown sample and compare it to a library of sequences from known species to identify your sample, much like a grocery store scanner reads a bar code."

Along with accuracy, DNA bar-coding also allows for the identification of a species while it's still in the larval or even egg stage—no more waiting for it to turn into an adult to see what it is.

Validating the test

Dr. Floate says a big part of this project was making sure they were using the right section of DNA for the bar code. "There are small differences in the DNA for populations of the same insect species in different parts of the world, but we need differences large enough to reliably distinguish among insect species, " says Dr. Floate. "So far, we have compared the DNA of more than 200 populations of insects from 57 different species in 24 different countries—so we know the bit of DNA we're using for our bar code is going to provide accurate results. "

Taking it to the next level

Dr. Floate's team is now in the final stages of developing a multiplex-PCR test. "Using the sequence differences between species in our barcode, we snip out DNA fragments of different lengths. We then compare the length of the DNA fragment from the unknown sample against the length of the corresponding DNA fragment from 3 to 5 known species. " In fact, the team is developing three of the multiplex-PCR tests—each one will be used for a different group of closely-related species.

Importantly, the test is fast as well as accurate. "We don’t need to wait a week for the results of DNA sequencing and we don’t need to wait for days or even weeks for an expert to identify a particular species of insect, " says Dr. Floate, "You'd have an answer within a single day. "

Valuable research

Dr. Floate says this project—which represents the work of a scientific team from AAFC labs across Canada, collaboration with the CFIA and others—is an excellent example of the value of the Government of Canada's Genomics Research and Development Initiative (GRDI).

"Wheat alone is a multi-billion dollar concern in Canada. If a quarantine pest like the khapra beetle were to become established here, we'd be very limited in where we could sell our wheat, " says Dr. Floate. "Thanks to the funding we've received through GRDI, we've been able to demonstrate a simple, effective and inexpensive way to better protect our wheat and other crop exports. "