Researchers are a step closer to having a portable, hand-held device and an array of tests that can positively identify species in the field, by their DNA.

This approach is already being used to try to reduce food fraud with species such as fish, which costs consumers millions of dollars a year and can compromise their health.

Researchers at the University of Guelph, where the initial specific tests used with this device were developed, think it will have many applications in the fruit and vegetable sector too, particularly for identifying and verifying pests.

Dr. Amanda Naaum is a senior research scientist with the university’s new spin-off company, TRU-ID. At the Building Canada sesquicentennial lecture series in Guelph in early November, she demonstrated how the portable device she’s working with can give users a yes-or-no reading for samples of species whose DNA sequences have been recorded in the university’s Barcode Of Life Database (BOLD).

The database contains the barcodes or gene sequences for 500,000 species. It’s been assembled over the past 15 years as part of an international effort to barcode all species on the planet, led by the groundbreaking research and development of Guelph’s Prof. Paul Hebert. DNA barcoding uses a very short genetic sequence from a standard part of the genome, the way a supermarket scanner distinguishes products using the black stripes of the Universal Product Code.

Naaum says onsite analysis with portable technology such as the BioMeme two3 molecular diagnostic device she’s using holds great promise. With just one swab from a sample, she can collect enough cells to run what’s called a real-time PCR analysis onsite, using a smart phone app as an interface. Real-time PCR uses a molecular probe to detect the presence of specific target DNA.

Here's how it works. DNA from a sample is placed in a tube with the molecular probe and other reagents that allow copying of a specific section of DNA, using cycles of heating and cooling. If DNA from a specific target (in this case, a specific species) is present in a sample, that section of DNA is copied. The probe generates fluorescence during this copying process. If that DNA is absent, no fluorescence is generated because no DNA is copied.

The app contains species-specific test information related to heating and cooling cycles needed to copy the target DNA. Naaum designs probes using sequences from BOLD as a reference that search for a specific region of DNA -- an even smaller portion of the DNA barcode -- that is unique to the target species.

In this way, samples can be rapidly screened in under two hours.

Naaum says food retailers could use the device onsite in their distribution warehouses to make sure the food shipments they receive are authentic, before they’re packaged for the public. Or, in the case of species like fish, which are currently the focus of her work, inspectors could take it dockside to test if initial labelling is accurate, before imports get repackaged and shipped widely.  

Naaum says portable species identification could be particularly helpful to find and differentiate apple aphid species. Two of these species, the green apple aphid (Aphis pomi) and the spirea aphid (Aphis spiraecola), look almost identical, but respond differently to pesticides and have different life cycles that may require spraying at different times. “It can be critical to differentiate which of the two species are present for effective management,” she says.

Rapid species-ID tests using real-time PCR are only going to allow screening for a specific target species. “You have to already know what you are looking for,” she says. But, she adds, in many cases, confirmation of a species is what’s really needed, and it’s possible to quickly screen for a few of them if there's more than one important target.

These tests can be run easily by non-experts, using simple kits that have all of the materials and instructions for identifying a specific species from DNA extraction to interpret results.

Naaum’s colleague Prof. Bob Hanner, of the Biodiversity Institute of Ontario, says a test for a poinsettia pest Bemisia tabaci developed back in 2014 by his graduate student Andrew Frewin is the kind of species identification that could be discovered by the Biomeme device.

“Knowing which biotype is present can help inform management decisions in commercial greenhouses to balance the use of pesticides and biocontrol agents most efficiently,” says Hanner. He’s inviting collaboration to address any early detection and identification issues faced by the fruit and vegetable industry.