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The rise of fungicide resistance

How (in)sensitive to fungicides have Prairie pathogens become?


May 4, 2021
By Jennifer Bogdan

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For years, Ascochyta blight in chickpea has served as the textbook example of “fungicide insensitivity.” But recently, the Prairie pathogen world has become more inclusive, with fungicide resistant populations being detected in other crops, such as lentils, barley and peas.

Randy Kutcher, professor in the plant sciences department at the University of Saskatchewan, identifies a number of factors contributing to the rising risk and incidence of fungicide insensitivity. “A number of years with above-average precipitation resulted in high disease severity that impacted growers, and fungicides were very effective in those years. One of the greatest factors favouring fungicide use, and therefore increased risk of insensitivity, is the intensification of cropping systems, including two-year rotations such as canola-wheat or lentil-durum, large field sizes, and high yield expectations. These factors allow pathogen inoculum to build up quickly and spread easily. In wheat, the arrival of Fusarium head blight has greatly increased the amount of fungicide used in this crop,” he says.

 The most recent pathogen to make the fungicide insensitive list is Colletotrichum lentis, the cause of anthracnose in lentils.  In 2019, Group 11 insensitive C. lentis was confirmed in multiple lentil fields in Saskatchewan. According to Sherrilyn Phelps, agronomy manager with Saskatchewan Pulse Growers, this discovery was somewhat surprising to growers and industry representatives.  

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“We were all caught off guard with the level of insensitivity identified in these fields, but in some ways, it was not surprising as the fields were sampled very late in the season after fungicide applications had attempted to control the disease. However, it was likely a matter of time before this insensitivity happened, as there has been heavy use of G11 fungicides in lentil-producing areas for many years. Since G11s are very widely used in fungicide formulations and are often combined with other active ingredients in products, the management of these insensitive populations is now much more of a challenge,” she says.

With the increased fungicide use on the Prairies, researchers have recognized the need to evaluate where our pathogen populations are at, and have established a sensitivity “baseline” in some key pathogens.

“Understanding baseline sensitivity is important so that researchers and industry know the typical level of variation among isolates of a particular pathogen for a particular active ingredient. Then, if growers suspect that the fungicides they are using are not as effective as in the past, or in situations where they believe there has been a rapid change, such as from one year to the next, it will be possible to test isolates from those fields and compare them to what we have found to be ‘normal’ variation in these baseline studies,” Kutcher says.

Fungicide sensitivity research has recently wrapped up in Kutcher’s lab, with favourable results. Three graduate students have provided valuable baseline sensitivity research on pathogens causing common diseases targeted by fungicide applications in Western Canada:  Fusarium head blight in wheat (by Gursahib Singh), tan spot in wheat (by Dustin MacLean), and pasmo in flax (by Tonima Islam). The good news? No insensitivity was detected in any of these pathogens for the fungicides tested.

But not all baseline sensitivity tests have had such a happy ending. In his PhD research, Alireza Akhavan, now the provincial plant disease specialist for the Saskatchewan Ministry of Agriculture, discovered fungicide insensitive isolates of Pyrenophora teres, the cause of net blotch in barley. Insensitivity to propiconazole (G3) was detected in two isolates of the pathogen that causes the net form of net blotch, and pyraclostrobin (G11) insensitivity was found in one spot form net blotch isolate.

“The net blotch pathogen population is genetically diverse, producing both the sexual and asexual stages, and is frequently exposed to these site-specific fungicides which pose a high risk for the selection of insensitivity. If the pathogen develops increased insensitivity, then with many asexual cycles during the following growing season, the insensitive individuals may multiply and form a significant portion of a new emerging population,” Akhavan explains.

According to Kelly Turkington, research scientist at Agriculture and Agri-Food Canada in Lacombe, net blotch insensitivity has not yet been observed in the field, which typically occurs after significant shifts in sensitivity of the pathogen population. However, the identification of these particular insensitive isolates is certainly something to take note of.  

“The G3 and G11 insensitive net blotch isolates highlights the importance for farmers and industry to adopt integrated disease management strategies to avoid fungicide failure. Moreover, it emphasizes the critical need to continually monitor barley leaf disease pathogens for shifts in fungicide sensitivity and to encourage responsible stewardship of fungicides by farmers as well as the agrochemical and farm supply industries,” he says.

Turkington also advises caution to the practice of using single active fungicides at herbicide timing, which could play a key role in selecting for insensitive populations. “We completed fungicide timing research on barley leaf spots in the late 1990s and more recently from 2010-2012. Our findings clearly showed fungicides applied at the herbicide time were of limited benefit in terms of disease control, and as a consequence, producers would have to go in later at the flag leaf to anthesis stages to apply fungicide again to protect the key upper canopy leaves.  This meant that barley fungicides were being used twice during the growing season, often with a single active ingredient, thereby increasing the selection pressure on the pathogen population,” he explains.

Fungicide insensitivity is influenced by the fungicide itself (i.e. the mode of action), the pathogen and its biology, as well as the agronomic factors imposed on the crop, including the environment. While a grower can’t control the weather, one can choose agronomic practices that best help manage disease development, and minimize the selection of fungicide insensitive isolates in the natural population.

Turkington suggests looking at the fungicide use history on the farm and taking note of the particular active ingredients that were used, much like one does when evaluating herbicide mode of action use for managing weed resistance. If the fungicide groups have stayed the same for a number of years and the products used are single actives, it’s time to switch to fungicides with more than one mode of action.  

Phelps adds that it is best to have more than one effective active ingredient targeting the specific pathogen to reduce the risk of developing insensitivity, and to rotate between different modes of action to reduce development of multiple resistance. She also advocates learning which pathogen each active ingredient controls. “Just because there are two or more active ingredients in a product, it doesn’t mean they all provide control of the same disease(s),” she explains.

One additional issue that Turkington mentions is the potential role of volunteer plants, whereby fungicides used in previous crops may share the same active ingredients used in subsequent crops. Here, pathogens infecting volunteer plants (e.g. cereals) can be exposed to similar fungicide actives being used in non-host crops (e.g. canola). Thus, good volunteer control will help to reduce selection pressure for more insensitive members of a particular pathogen population. 

Fungicides should also not be relied on as the only method of controlling plant diseases.  “Look at your crop rotation and the varieties being grown, as tight rotations and susceptible varieties will mean increased dependence on fungicides as the sole management tool. Limit your fungicide use to situations where there is economic benefit. If weather conditions are not conducive to disease, and/or adequate rotations and less susceptible varieties are being used, then a fungicide application will be of limited to no benefit,” Turkington advises. 

Crop Disease & Pathogen Pathogen Sensitivity Details and References
Wheat Fusarium head blight

Fusarium graminearum

No insensitivity to tebuconazole (G3), metconazole (G3), or prothioconazole (G3) detected. Baseline test of 253 isolates collected from AB, SK, and MB in 2014 – 2017 (Singh et al., unpublished)
Tan spot

Pyrenophora tritici-repentis

No insensitivity to propiconazole (G3) or pyraclostrobin (G11) detected. Baseline test of 88 isolates collected from AB and SK in 2010 – 2014 (MacLean et al. 2017)
Barley Net blotch (net form)

Pyrenophora teres f. teres

Insensitivity to propiconazole (G3) detected in 2 isolates. No insensitivity to pyraclostrobin (G11) detected. Evaluation of 39 isolates collected from AB, SK, and MB in 2009 – 2012 (Akhavan et al. 2017)
Net blotch (spot form)

Pyrenophora teres f. maculata

No insensitivity to propiconazole (G3) detected. Insensitivity to pyraclostrobin (G11) detected in 1 isolate. Evaluation of 27 isolates collected from AB, SK, and MB in 2009 – 2012 (Akhavan et al. 2017)
Canola Sclerotinia stem rot

Sclerotinia sclerotiorum

Insensitivity to benomyl (G1) detected in 2 isolates from 2 canola fields where reduced efficacy was suspected. Testing of 15 isolates collected from 12 alfalfa and 3 canola fields in southern AB in 2000 (Gossen et al. 2001)
Blackleg

Leptosphaeria maculans

No insensitivity to pyraclostrobin (G11) detected. 117 isolates collected from AB in 2011 (Fraser et al. 2017)
Peas Mycosphaerella blight

Mycosphaerella pinodes

Insensitivity to pyraclostrobin (G11) detected. 324 isolates collected from AB, SK, ND, and WA in 2010 – 2011 (Bowness et al. 2016)
Lentils Anthracnose

Colletotrichum lentis

Strobilurin (G11) insensitivity detected in fields in SK. BASF conducted a targeted field survey of heavily diseased lentils in SK in 2019.  A widespread field survey led by AAFC was conducted in SK in 2020 to determine baseline levels (results expected in 2021).
Chickpeas Ascochyta blight

Ascochyta rabiei

Strobilurin (G11) insensitivity is wide-spread in fields.  A 2019 survey in SK found G11 insensitivity in 100% of fields (33 fields surveyed).

Chlorothalonil (GM5), mancozeb (GM3), and pyraclostrobin (G11) insensitivity detected in lab.  Group M insensitivity has not been reported in the field.

Baseline test of 106 isolates (88 from SK) first detected one G11 insensitive isolate from SK in 2003 (Gossen and Anderson. 2004).  BASF confirmed field insensitivity in SK in 2006.

66 isolates collected from AB in 2003 – 2004 (Chang et al. 2007)

Flax Pasmo

Septoria linicola

No insensitivity to pyraclostrobin or fluxapyroxad detected. Baseline test of 73 isolates collected from 4 locations across AB, SK, and MB in 2014 – 2016 (Islam et al. 2020)