Project code: PRR21-020
Project Leads:
Martin Laforest - Agriculture and Agri-Food Canada
Marie-Josée Simard - Agriculture and Agri-Food Canada
Robert Nurse - Agriculture and Agri-Food Canada
Objective
To continue developing and making available to growers rapid genetic tools for early identification and mitigation of herbicide-resistant weeds in agricultural crops
Background
Weeds are an important challenge for viable crop production that contribute significantly to yield losses. Typical weed management in vegetable crops relies on regular application of herbicides. However, because only few herbicides are available to growers for certain weeds, and same active ingredients are used repeatedly, development of weed types resistant to herbicides has become a major risk. The rapid proliferation and spread of herbicide-resistance in weeds poses an increasing threat to the sustainability of crop production. Field surveys reveal constant appearance of new resistant weeds.
To effectively curb resistance development, it is essential that it is detected quickly and early, crops are monitored regularly, and weeds are properly controlled using appropriate products as part of an integrated management system. Traditional resistance detection methods, such as dose response assays using living plants grown in the greenhouse, can take up to a year to get results back to growers. Making appropriate in-season management decisions requires growers to have access to tools which deliver much quicker turn-around time for results on presence of resistant weeds in their crops. Technological innovations for such tools was necessary to support the growers overcome this challenge.
Two previous projects led by Agriculture and Agri-Food Canada (AAFC) researchers and supported through the Pest Management Centre (PMC) in 2016-2019 (Early detection, monitoring and management of herbicide resistant weeds in field vegetables and in 2019-2021 have successfully delivered 17 quick genetic tests for various weed species. The protocols for these molecular-based herbicide-resistance diagnostic tests developed by AAFC scientists have been shared with appropriate provincial labs offering sample testing services for local growers. These tests can generate results quickly, allowing to communicate findings back to growers in less than a week.
Following successful outcomes from these earlier projects, a similar new project was initiated with PMC’s support to meet growing demands of the sector to address newly identified resistant weeds. Similar to the work in the past, this project aimed to develop new genetic tests and protocols for: i) Canada fleabane (Conyza canadensis) conferring resistance to group 2 herbicides; ii) green pigweed (Amaranthus viridis) conferring resistance to group 5 and 7 herbicides; and iii) abutilon (Abutilon theophrasti) conferring resistance to group 2 herbicides.
Approaches
The project was conducted at AAFC’s Saint-Jean-sur-Richelieu Research and Development Centre (Quebec). Suspected herbicide-resistant weeds of the species targeted in this project were sampled in commercial farms in Ontario and Quebec, by Ontario Ministry of Agriculture, Food and Rural Affair and Quebec Ministry of Agriculture, Fisheries and Food specialists. Sampled foliar materials were submitted for analyses to the AAFC’s lab. Molecular markers were developed as rapid diagnostic tools for each suspected weed and herbicide combination. This was achieved by extracting DNA from leaf samples of resistant plants and comparing it to the DNA of susceptible (non-resistant) populations in order to identify mutations that confer herbicide resistance. The RNASeq technique was used to identify mutation in abutilon. With the information generated, techniques like TaqMan assays were used to develop the markers needed to build the genetic test protocols and enable provincial service labs to detect these mutations in future weed samples to be submitted by growers.
The samples used in this project were taken form weed types which were already confirmed as resistant to respective herbicides through traditional diagnostic methods.
Result
As result of this project, three new rapid genetic tests were successfully developed for the targeted weed species: one for fleabane and 2 for green pigweed. For abutilon, sequencing RNASeq procedures confirmed that there was no genetic mutation occurring in the gene encoding for the protein targeted by the herbicide, suggesting that a more complex mechanism might be involved for this weed to confer resistance to group 2 herbicides. This mechanism remains to be investigated.
Based on a standing agreement, protocols for the three additional genetic tests developed through this project have been transferred to the designated labs: Quebec’s Ministry of Agriculture, Fisheries and Food Pest Diagnostic Lab and Harvest Genomics Lab in Ontario). These labs have already adopted these new protocols in summer 2022, along with past protocols as part of their regular services to growers to support their informed decision making process. With such rapid tests generating results in less than a week, growers are able to quickly test weed samples from their fields and detect resistance presence early, thus enabling them to make appropriate in-season decisions about suitable herbicide choices to use for best efficacy outcomes.
This work brings to 20 the total number of rapid genetic test protocols developed and made commercially available todate. Below is the list of weed types for which test protocols are available for detection of herbicide resistance:
| Nr. | Weed with confirmed herbicide resistance | Resistant to herbicide group (number) | Provinces involved in sampling and coordinating testing operations to serve grower needs | The year that the tests were made available commercially (transferred to which provincial labs) |
|---|---|---|---|---|
| 1 | Large crabgrass | Group 1 herbicides | ON & QC | 2019 (ON & QC) |
| 2 | Eastern black nightshade | Group 2 herbicides | ON & QC | 2019 (ON & QC) |
| 3 | Giant foxtail | Group 2 herbicides | ON & QC | 2019 (ON & QC) |
| 4 | Redroot pigweed* | Group 2 herbicides | ON & QC | 2019 (ON & QC) |
| 5 | Waterhemp* | Group 2 herbicides | ON & QC | 2019 (ON & QC) |
| 6 | Common chickweed (2 tests) |
Group 2 herbicides | ON & QC | 2019 (ON & QC) |
| 7 | Common ragweed | Group 2 herbicides | ON & QC | 2019 (ON & QC) |
| 8 | Canada fleabane | Group 2 herbicides | ON & QC | 2022 (ON & QC) |
| 9 | Tumble pigweed* | Group 5 herbicides | ON & QC | 2019 (ON & QC) |
| 10 | Hair fescue | Group 5 herbicides | PEI & NB | 2020 (PEI and NB) |
| 11 | Lamb’s quarter | Group 5 herbicides | ON, PEI, NB & QC | 2019 (ON & QC) |
| 12 | Common ragweed | Group 5/7 herbicides | ON & QC | 2019 (ON & QC) |
| 13 | Green pigweed (2 tests)* | Group 5/7 herbicides | ON & QC | 2022 (ON & QC) |
| 14 | Canada fleabane | Group 9 herbicides | ON & QC | 2019 (ON & QC) |
| 15 | Brassica spp. | Group 9 herbicides | ON & QC | 2019 (ON & QC) |
| 16 | Waterhemp (2 tests)** | Group 9 herbicides | ON & QC | 2019 (ON & QC) |
| 17 | Waterhemp* | Group 14 herbicides | ON & QC | 2019 (ON & QC) |
* Tests developed for one amaranth sp. usually work well with other amaranth spp., being genetically close.
** One for target-site resistance and the other for metabolic or non-target-site resistance.
Rapid diagnosis can lower the use of ineffective herbicides in the field where the resistant population is found and can help to maintain the effectiveness of current tools. Proper management of resistant population can reduce its spread. Improved understanding of weed resistance dynamics and early detection of resistant weeds enables growers to make better choices for effective weed management and reduce the use of unnecessary herbicide applications, thus preventing resistance proliferation.
An added benefit resulting from this and past similar projects is that they have strengthened cross-provincial collaboration among AAFC scientists, provincial specialists and growers. The provincial experts in particular have been instrumental in coordinating sample collections from their respective regions, matching grower needs with access to lab tests as these become available, and facilitating communication with growers to convey results and provide management advice on a timely basis.