January 2026 | Canadian Food Inspection Agency | by Saanchi Singh
For many of us, weeds are simply an annoyance. Just unwanted plants that keep popping up in gardens, lawns or driveways, even if sprayed or pulled out. They are seen as little more than a cosmetic issue. However, in agricultural and trade contexts, weeds that are left unchecked – especially invasive plants – can grow to densities that pose biosecurity and economical challenges. They can reduce crop yields, spread plant diseases and disrupt ecosystems. Some even release toxins harmful to animal and human health. Weeds can have major impacts on the seed trade and grain export, too. Under Canada’s Weed Seeds Order, there is a zero tolerance for the 26 species classified as Class 1 Prohibited Noxious Weeds. If any of these species are found in a seed lot, those seeds cannot be legally sold, imported, or exported. Other countries have similar regulations for seed or grain import.
The problem with weeds
At every stage of their life, weeds have mechanisms that make their management extremely challenging. Weeds compete for light, water, and nutrients with crops like canola, wheat, and barley. They are also aggressive seed producers – a single plant of weedy pigweed can produce over 1 million seeds under optimal conditions.Footnote 1 These seeds can then get mixed with harvests, reducing seed or grain quality, and spreading long distances beyond their biological range to new territories. Seeds of weedy species can remain dormant and alive in the soil for years. For example, wild mustard seeds can stay dormant for up to 60 years!Footnote 2
Weed seeds also tend to have large germination windows. Some germinate before crop seed, which allows them to capitalize on available sunlight and water to grow taller. These taller weeds can then block younger crop seedlings from receiving sunlight, stunting their growth.
Although herbicides can be applied for weed management, seeds that germinate later can by-pass herbicide application or develop herbicide resistance. Wild oat is a weed that commonly grows in the prairies with wheat and canola and is resistant to many herbicides. Of the wild oat-infested fields surveyed in Western Canada, 69% are infested with herbicide-resistant wild oat.Footnote 3 This is a big problem, as invasive plants in crops and pastures alone cost around $2.2 billion each year in weed control and reduction in crop yields.Footnote 4
The seeds of invasive plants and weeds can spread and travel long distances if they’re mixed into seed or grain shipments, or by hitchhiking on vehicles, equipment, clothing, livestock (including their manure), and even pets. The most effective way to prevent the spread of weeds and invasives is to prevent the introduction of their seeds in our ecosystems from the start.
The challenges of weed seed identification
Identifying invasive weed seeds from other seeds is the key to preventing their introduction. However, seed identification is a big challenge in some cases, even for leading experts in the field. There are a lot of similarities between the seeds of many weeds, closely related non-weedy species, and crops. Advanced testing methods and tools can help improve the speed and accuracy of weed species identification.
Experts at the Centre for Seed Science and Technology at the Canadian Food Inspection Agency (CFIA) Saskatoon Laboratory provide seed identification services to ensure that seeds used and traded for planting, import and export meet regulatory requirements for safe trade, and do not cause the introduction or spread of weedy or invasive species. The Centre also includes the National Seed Herbarium, Canada's only reference collection of seeds for identification purposes. These experts in seed identification need to be able to detect and identify weed seeds in samples containing a minimum of 25,000 crop seeds based on physical traits alone.
Identifying weeds at the molecular level
The Molecular Identification Research Laboratory (MIRL) at the CFIA’s Ottawa Plant Laboratory, is working on developing innovative tools to assist in invasive weed seed identification.
One of these tools is DNA metabarcoding, which relies on DNA barcodes to identify multiple species in parallel. There are characteristic differences in certain short gene sequences unique to each plant species. These DNA barcodes are similar to barcodes at the grocery store, both acting as fingerprints.
We are conducting preliminary research to explore the potential applications of this technology using jointed goatgrass, a Class 1 Prohibited Noxious Weed that infests wheat fields. We have found that 2 DNA barcodes are needed to distinguish jointed goatgrass from 9 closely related species and wheat. By increasingly diluting 1 jointed goatgrass seed in large samples of wheat seeds, we are able to test this method’s sensitivity and accuracy.
A second approach our lab is piloting to improve weed identification is DNA macro-barcoding. Usually, multiple DNA barcodes are required since there is no singular universal plant barcode. It can be time consuming to discover all the DNA barcodes needed to distinguish target plant species and then process them in the lab. Macro-barcodes work on the same principle as standard DNA barcodes, but they can be 10 times larger. This size allows them to capture more genetic information, enabling species distinction without extensive optimization, while still only using modest amounts of starting material.
At present, we are testing this tool with pigweed species, whose seeds can contaminate canola exports. One of the macro-barcodes we have designed can distinguish 11 pigweed species, including tall water-hemp, Powell’s amaranth, and redroot pigweed. Ultimately, we aim to expand these tools to test for the presence of other agriculturally relevant weeds species like false cleavers, wild oat, and wild mustard.
Study limitations and next steps
Our research at MIRL is meant to support other tools for weed seed identification, with an aim to eventually enhance our regulatory testing toolkit. But we still have work to do! Further research can help address limitations and determine if and how DNA metabarcoding and DNA macro-barcoding could be applied for regulatory or certification purposes.
In our research, we used destructive testing methods that ground up samples to extract DNA. This type of test would not be practical if we needed to preserve the individual seeds or sample integrity for further testing, sale or trade. We are currently working on methods where we can perform DNA extraction with no or minimal effects on seed integrity.
Additionally, non-seed DNA sources found in samples, including other plant tissues like root pieces, can complicate testing. This is because a detection could be triggered without the presence of an actual seed, which is what matters for regulatory and trade decisions.
While we have initially designed DNA barcodes and macro-barcodes for a select number of species, we are working to expand this list. The aim is to be able to test seed lots being assessed for certification for multiple weeds.
Overall, DNA-based tools are very powerful and complement traditional seed identification methods by improving accuracy in species determination. This is particularly helpful for near-identical or closely related species that are very difficult for experts to distinguish based on their physical traits. Molecular techniques can also help to reduce pressure on human expertise when testing demands are high.
In the future, these DNA-based technologies will become an important addition to weed seed detection methods, enhancing confidence and supporting regulatory enforcement.
More information
Want to learn more about my research or discuss other innovations in weed science? Connect with me on LinkedIn or reach out to me at saanchi.singh@inspection.gc.ca.