Cytochrome b gene sequence and structure of Pyrenophora teres and P. tritici-repentis and implications for QoI resistance

Baseline Sensitivity of Botryosphaeria spp. Isolated from Apples to Pyraclostrobin in Korea

The genus Botryosphaeria cause white rot disease on apple trees, and control of this pathogens were primary relied on the fungicide applications. To investigate the pyraclostrobin sensitivity of Botryosphaeria spp. in Korea, 329 isolates were collected from eight regions between 2005 and 2023. Phylogenetic analysis based on the concatenated sequences of internal transcribed spacer, tef1, and tub2 revealed B. sinensis (287 out of 329 isolates) and B. kuwatsukai (42 out of 329 isolates). EC50 values of isolates ranged from 0.01 to 34.16 μg/ml (average, 3.03 μg/ml). Mean EC50 values and frequency distributions were similar among isolate groups, indicating no significant differences in sensitivity. Twenty less-sensitive and 20 sensitive isolates were selected and their cytochrome b (cyt b) genes analyzed, revealing no mutations in codons 129, 137, and 143. Whole gene sequencing revealed three distinct cyt b gene structures among Botryosphaeria spp., and all strains, including those with different EC50 values and species, showed consistent amino acid sequences. Furthermore, control efficacy on pyraclostrobin-treated apple fruits indicated no significant differences between the five least sensitive and five most sensitive isolates. These results provide the baseline sensitivity of Botryosphaeria spp. to pyraclostrobin and highlight the structural characteristics of their cyt b gene. In conclusion, the assessment of Botryosphaeria isolates from various regions in Korea revealed no evidence of resistance to pyraclostrobin so far. However, the risk of resistance of Botryosphaeria populations still exists so it is assumed that continuous monitoring of risk assessment is necessary for Botryosphaeria in Korea.

Molecular Monitoring of Fungicide Resistance in Crop Phytopathogens

The fight against crop pathogens relies mainly on host genetics and chemistry; however, both areas are compromised by the evolution of resistance in the pathogen population. Fungicide resistance is an ongoing challenge to global food security, as it threatens these important crop protection chemistries. One critical component of resistance management is an effective detection and monitoring program, which needs to be agile, scalable, sensitive, accurate, and cost effective. A rapidly evolving suite of molecular tools are being developed for the detection of fungicide resistance mutations in phytopathogen populations, including high-throughput PCR-based quantitative assays and cutting-edge third-generation DNA sequencing. A single "silver bullet" detection technology that will satisfy all study objectives does not exist; thus, every tool has a niche in an integrated detection and monitoring program. This review presents an overview of the rapidly changing landscape of fungicide resistance detection, illustrates how molecular techniques are being exploited to combat fungicide resistance in cereal crop phytopathogens, and highlights challenges and future research directions to aid in the design of effective monitoring systems that aim to apply fungicides strategically and minimize the cost of resistance. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Colletotrichum Species Causing Glomerella Leaf Spot and Apple Bitter Rot in the Southeastern United States Exhibit Disparities in Relative Frequency, Morphological Phenotype, and Quinone Outside Inhibitor Sensitivity

Glomerella leaf spot (GLS), Glomerella fruit rot (GFR), and apple bitter rot (ABR), caused by Colletotrichum spp., are among the most devastating apple diseases in the southeastern United States. Although several species have been identified as causal pathogens of GLS, GFR, and ABR, their relative frequency and fungicide sensitivity status in the southeastern United States is unknown. In total, 381 Colletotrichum isolates were obtained from symptomatic leaves and fruit from 18 conventionally managed apple orchards and two baseline populations in western North Carolina and Georgia in 2016 and 2017. Multilocus DNA sequence analysis revealed that C. chrysophilum was the predominant cause of GLS and GFR and C. fioriniae was the causal agent of ABR. Baseline and commercial populations of Colletotrichum spp. were evaluated for sensitivity to pyraclostrobin and trifloxystrobin, and no statistical differences in sensitivity between the two species were observed for conidial germination. However, the effective concentration that inhibited growth by 50% values were significantly lower for C. fioriniae compared with C. chrysophilum for both fungicides regarding mycelial inhibition. Isolates recovered from commercial orchards revealed that five populations of C. chrysophilum and one population of C. fioriniae had reduced sensitivity to trifloxystrobin, and one C. fioriniae population had reduced sensitivity to pyraclostrobin via conidial germination assays. The cytb gene for 27 isolates of C. fioriniae, C. chrysophilum, and C. fructicola with different quinone outside inhibitor (QoI) sensitivities revealed the G143A mutation in a single isolate of C. chrysophilum with insensitivity to both fungicides. The results of these studies suggest that two Colletotrichum spp. predominantly cause GLS and ABR in the southeastern United States and that a reduction in sensitivity to some QoI fungicides may be responsible for control failures. This study also provides a basis for monitoring shifts in QoI sensitivity in Colletotrichum spp. causing disease on apple in the southeastern United States.

Fungicide Sensitivity and Nontarget Site Resistance in Rhizoctonia zeae Isolates Collected from Corn and Soybean Fields in Nebraska

Rhizoctonia zeae was recently identified as the major Rhizoctonia species in corn and soybean fields in Nebraska and was shown to be pathogenic on corn and soybean seedlings. Fungicide seed treatments commonly used to manage seedling diseases include prothioconazole (demethylation inhibitor), fludioxonil (phenylpyrrole), sedaxane (succinate dehydrogenase inhibitor), and azoxystrobin (quinone outside inhibitor [QoI]). To establish the sensitivity of R. zeae to these fungicides, we isolated this pathogen from corn and soybean fields in Nebraska during 2015 to 2017 and estimated the relative effective concentration for 50% inhibition (EC50) of a total of 91 R. zeae isolates from Nebraska and Illinois. Average EC50 for prothioconazole, fludioxonil, sedaxane, and azoxystrobin was 0.219, 0.099, 0.078, and >100 µg ml-1, respectively. In planta assays showed that azoxystrobin did not significantly reduce the disease severity on soybean (P > 0.05). The cytochrome b gene of R. zeae did not harbor any mutation known to confer QoI resistance and had a type I intron directly after codon 143, suggesting that a G143A mutation is unlikely to evolve in this pathogen. For prothioconazole, fludioxonil, and sedaxane, the EC50 of the isolates did not differ significantly among the years of collection (P > 0.05), and their single discriminatory concentrations were identified as 0.1 µg ml-1. This is the first study to establish nontarget site resistance of R. zeae to azoxystrobin and the sensitivity of R. zeae to commonly used seed treatment fungicides in Nebraska. This information will help to guide strategies for chemical control of R. zeae and monitor sensitivity shifts in the future.

Sensitivity Analysis of Pyrenophora tritici-repentis to Quinone-Outside Inhibitor and 14α-Demethylase Inhibitor Fungicides in Latvia

Tan spot caused by Pyrenophora tritici-repentis is a severe threat to wheat production in all major wheat-growing regions. Sustainable tan spot control can be achieved by an integrated approach, including responsible management of fungicide sprays. The data about the sensitivity of P. tritici-repentis to various fungicides in the Baltic Sea region are rare. In this study, we described the variation of P. tritici-repentis sensitivity to four fungicide active ingredients to detect the formation of resistance to the most commonly used quinone-outside inhibitor (QoI) and 14α-demethylase inhibitor (DMI) fungicides in the pathogen's population in Latvia. The effect of prothioconazole, mefentrifluconazole, pyraclostrobin, and azoxystrobin on 93 P. tritici-repentis strains from various hosts was tested in vitro by assessing mycelium linear growth inhibition at three different active ingredient concentrations (0 0.01, 0.1 and 0.5 mg L-1). Pathogen sensitivity significantly (p < 0.001) varied between the fungicide active ingredients and strains. The prothioconazole (concentration 0.5 mg L-1) had the most significant effect, with a median mycelial growth inhibition of 70.34%, followed by pyraclostrobin (47.02%), azoxystrobin (24.24%), and mefentrifluconazole (11.11%). Mutation G143A was detected in cytb gene sequences and confirmed the resistance formation in Latvia's P. tritici-repentis population, while F129L and G137R mutations were absent. This study provided insight into P. tritici-repentis population's sensitivity to active ingredients of DMI and OoI fungicide groups, helping to fill the knowledge gap about the pathogen fungicide sensitivity in this region.

Different Infection Structures and Point Mutation of Diaporthe citri Showing Resistant against Systemic Fungicides

Infection behaviors of some susceptible and resistant Diaporthe citri isolates against two fungicides such as benomyl and kresoxim-methyl were observed on citrus leaves. On the chemically unsprayed leaves, there were no differences in not only the conidial germination rate but also hyphal growth between the resistant and susceptible isolates. However, on the benomyl or kresoximmethyl-pretreated leaves, both conidial germination rate and hyphal growth of the resistant isolates were not decreased, which was different with those of the susceptible isolates. These unchanging germination rate and hyphal growth of the resistant isolates, resulting in the lack of chemical efficacy, coincided with the previous studies in which strong infection was observed by the resistant isolates after pre-treatment with each chemical. On the other hand, a point mutation occurred at 198th amino acid of β-tubulin gene in the resistant isolate NEL21-2 which may cause the resistant against benomyl. However, no mutation was found in cytochrome b in the resistant isolates indicating other genomic changes may be responsible for the resistant against kresoxim-methyl.

Comparative Fitness of Monilinia fructicola Isolates with Multiple Fungicide-Resistant Phenotypes

This study characterized 52 isolates of Monilinia fructicola from peach and nectarine orchards for their multiresistance patterns to thiophanate-methyl (TF), tebuconazole (TEB), and azoxystrobin (AZO) using in vitro sensitivity assays and molecular analysis. The radial growth of M. fructicola isolates was measured on media amended with a single discriminatory dose of 1 μg/ml for TF and AZO and 0.3 μg/ml for TEB. Cyt b, CYP51, and β-tubulin were tested for point mutations that confer resistance to quinone outside inhibitors (QoIs), demethylation inhibitors (DMIs), and methyl benzimidazole carbamates (MBCs), respectively. Eight phenotypes were identified, including isolates with single, double, and triple in vitro resistance to QoI, MBC, and DMI fungicides. All resistant phenotypes to TF and TEB presented the H6Y mutation in β-tubulin and the G641S mutation in CYP51. None of the point mutations typically linked to QoI resistance were present in the Monilinia isolates examined. Moreover, fitness of the M. fructicola phenotypes was examined in vitro and in detached fruit assays. Phenotypes with single resistance displayed equal fitness in vitro and in fruit assays compared with the wild type. In contrast, the dual- and triple-resistance phenotypes suffered fitness penalties based on osmotic sensitivity and aggressiveness on peach fruit. In this study, multiple resistance to MBC, DMI, and QoI fungicide groups was confirmed in M. fructicola. Results suggest that Monilinia populations with multiple resistance phenotypes are likely to be less competitive in the field than those with single resistance, thereby impeding their establishment over time and facilitating disease management.

Antimalarial mechanism of action of the natural product 9-methoxystrobilurin G

The natural product 9-methoxystrobilurin G (9MG) from Favolaschia spp basidiomycetes is a potent and selective antimalarial. The mechanism of action of 9MG is unknown. We induced 9MG resistance in Plasmodium falciparum 3D7 and Dd2 strains and identified mutations associated with resistance by genome sequencing. All 9MG-resistant clones possessed missense mutations in the cytochrome b (CYTB) gene, a key component of mitochondrial complex III. The mutations map to the quinol oxidation site of CYTB, which is also the target of antimalarials such as atovaquone. In a complementary approach to identify protein targets of 9MG, a photoactivatable derivative of 9MG was synthesized and applied in chemoproteomic-based target profiling. Three components of mitochondrial complex III (QCR7, QCR9, and COX15) were specifically enriched consistent with 9MG targeting CYTB and complex III function in P. falciparum. Inhibition of complex III activity by 9MG was confirmed by ubiquinone cytochrome c reductase assay using P. falciparum extract. The findings from this study may be useful for developing novel antimalarials targeting CYTB.

Workflows for detecting fungicide resistance in net form and spot form net blotch pathogens

BACKGROUND

Fungicide resistance in Pyrenophora teres f. maculata and P. teres f. teres has become an important disease management issue. Control of the associated barley foliar diseases, spot form and net form net blotch, respectively, relies on three major groups of fungicides, demethylation inhibitors (DMIs), succinate dehydrogenase inhibitors (SDHIs) and quinone outside inhibitors (QoIs). However, resistance has been reported for the DMI and SDHI fungicides in Australia. To enhance detection of different resistance levels, phenotyping and genotyping workflows were designed.

RESULTS

The phenotyping workflow generated cultures directly from lesions and compared growth on discriminatory doses of tebuconazole (DMI) and fluxapyroxad (SDHI). Genotyping real-time polymerase chain reaction (PCR) assays were based on alleles associated with sensitivity or resistance to the DMI and SDHI fungicides. These workflows were applied to spot form and net form net blotch collections from 2019 consisting predominantly of P. teres f. teres from South Australia and P. teres f. maculata from Western Australia. For South Australia the Cyp51A L489-3 and SdhC-R134 alleles, associated with resistance to tebuconazole and fluxapyroxad, respectively, were the most prevalent. These alleles were frequently found in single isolates with dual resistance. This study also reports the first detection of a 134 base pair insertion located at position-66 (PtTi-6) in the Cyp51A promoter of P. teres f. maculata from South Australia. For Western Australia, the PtTi-1 insertion was the most common allele associated with resistance to tebuconazole.

CONCLUSION

The workflow and PCR assays designed in this study have been demonstrated to efficiently screen P. teres collections for both phenotypic and genetic resistance to DMI and SDHI fungicides. The distribution of reduced sensitivity and resistance to DMI and SDHI fungicides varied between regions in south-western Australia, suggesting the emergence of resistance was impacted by both local pathogen populations and disease management programmes. The knowledge of fungicide resistance in regional P. teres collections will be important for informing appropriate management strategies. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Fungicide Sensitivity Profile of Pyrenophora teres f. teres in Field Population

Pyrenophora teres f. teres (Ptt) is a severe pathogen to spring barley in Northern Europe. Ptt with relevant mutations in fungicide target proteins, sterol 14α-demethylase (CYP51A), cytochrome b (Cyt b), and succinate dehydrogenase (SDH) would put efficient disease control at risk. In the growing seasons of 2021 and 2022, 193 Ptt isolates from Estonia were analysed. In this study, mutation detection and in vitro fungicide sensitivity assays of single-spore isolates were carried out. Reduced sensitivity phenotype to mefentrifluconazole was evident in Ptt isolates with a F489L mutation in CYP51A or with 129 bp insert in the Cyp51A gene-promoter region. However, sensitivity to a prothioconazole-desthio remained high regardless of these molecular changes. The Ptt population was mostly sensitive to bixafen, fluxapyroxad, pyraclostrobin, and azoxystrobin. The sensitivity of fluxapyroxad and bixafen has been affected by two mutations, C-S135R and D-H134R, found in SDH subunits. The F129L mutation in Cyt b influenced azoxystrobin but not pyraclostrobin sensitivity. In total, 30 isolates from five fields had relevant mutations in three target protein genes simultaneously. Most of these isolates had a reduced sensitivity phenotype to mefentrifluconazole, fluxapyroxad, and azoxystrobin, while sensitivity to other tested fungicides remained high. Furthermore, possible sexual reproduction may enhance the pathogen's fitness and help it adapt to fungicides.

Resistance Risk and Molecular Mechanism of Tomato Wilt Pathogen Fusarium oxysporum f. sp. lycopersici to Pyraclostrobin

Tomato wilt disease caused by Fusarium oxysporum f. sp. lycopersici (Fol) results in a decrease in tomato yield and quality. Pyraclostrobin, a typical quinone outside inhibitor (QoI), inhibits the cytochrome bc1 complex to block energy transfer. However, there is currently limited research on the effectiveness of pyraclostrobin against Fol. In this study, we determined the activity of pyraclostrobin against Fol and found the EC50 values for pyraclostrobin against 100 Fol strains (which have never been exposed to QoIs before). The average EC50 value is 0.3739 ± 0.2413 μg/mL, indicating a strong antifungal activity of pyraclostrobin against Fol, as shown by unimodal curves of the EC50 values. Furthermore, we generated five resistant mutants through chemical taming and identified four mutants with high-level resistance due to the Cytb-G143S mutation and one mutant with medium-level resistance due to the Cytb-G137R mutation. The molecular docking results indicate that the Cytb-G143S or Cytb-G137R mutations of Fol lead to a change in the binding mode of Cytb to pyraclostrobin, resulting in a decrease in affinity. The resistant mutants exhibit reduced fitness in terms of mycelial growth (25 and 30 °C), virulence, and sporulation. Moreover, the mutants carrying the Cytb-G143S mutation suffer a more severe fitness penalty compared to those carrying the Cytb-G137R mutation. There is a positive correlation observed among azoxystrobin, picoxystrobin, fluoxastrobin, and pyraclostrobin for resistant mutants; however, no cross-resistance was detected between pyraclostrobin and pydiflumetofen, prochloraz, or cyazofamid. Thus, we conclude that the potential risk of resistance development in Fol toward pyraclostrobin can be categorized as ranging from low to moderate.

Attributes of Cyazofamid-Resistant Phytophthora litchii Mutants and Its Impact on Quality of Litchi Fruits

In this study, we determined the sensitivity of 148 Phytophthora litchii isolates to cyazofamid, yielding a mean EC50 value of 0.0091 ± 0.0028 μg/mL. Through fungicide adaptation, resistant mutants (RMs) carrying the F220L substitution in PlCyt b were derived from wild-type isolates. Notably, these RMs exhibited a lower fitness compared with the parental isolates. Molecular docking analysis further revealed that the F220L change contributed to a decrease in the binding energy between cyazofamid and PlCyt b. The total phenol and flavonoid contents in the litchi pericarp treated with cyazofamid on day 5 were significantly higher than in other treatments. Overall, the laboratory assessment indicated a moderate risk of cyazofamid resistance in P. litchii, but the emergence of the F220L change could lead to a high level of resistance. Thus, cyazofamid represents a promising agrochemical for controlling postharvest litchi downy blight and extending the shelf life of litchi fruits.

Isolates of Colletotrichum truncatum with Resistance to Multiple Fungicides from Soybean in Northern Thailand

In Thailand, four systemic fungicides-carbendazim (Car), azoxystrobin (Azo), difenoconazole (Dif), and penthiopyrad (Pen)-are commonly used to control soybean anthracnose caused by Colletotrichum truncatum; however, the pathogen has developed resistance. From 2019 to 2020, fungicide resistance in C. truncatum from fields in Chiang Rai and Chiang Mai was monitored. In tests of 85 C. truncatum isolates for resistance to multiple fungicides, 15.3% were CarRAzoR, 34.1% were triple resistant (CarRAzoRDifR or CarRAzoRPenR), and 50.6% were CarRAzoRDifRPenR. Surprisingly, all isolates tested had lost their sensitivity to one or more of the fungicides tested. The carbendazim-resistant isolates carried a point mutation in the β-tubulin gene at codon 198 (E198A) or 200 (F200Y), and all azoxystrobin-resistant isolates had a mutation in the cytochrome b gene at codon 143 (G143A) or 129 (F129L). Moreover, a novel mutation at codon 208 (S208Y) in the gene encoding succinate dehydrogenase subunit B was detected in all of the isolates highly resistant to penthiopyrad. No mutation linked with difenoconazole resistance was detected in the genes encoding cytochrome P450 sterol 14α-demethylase. To the best of our knowledge, this is the first report of C. truncatum isolates resistant to multiple fungicides and serves as a warning to take measures to prevent the occurrence and distribution of these multiple-fungicide-resistant populations in soybean fields.

Screening for Fungicide Efficacy in Controlling Blackleg Disease in Wasabi (Eutrema japonicum)

Blackleg disease is devastating for wasabi (Eutrema japonicum) production, occurring at any time and everywhere within the main production area of the Sichuan Province, China. There have been very few studies on the chemical control of this disease. In this study, we isolated and identified a local popular strain of the pathogen Plenodomus wasabiae. The isolated fungus strain caused typical disease spots on the leaves and rhizomes upon inoculation back to wasabi seedlings. The symptoms of blackleg disease developed very quickly, becaming visible on the second day after exposure to P. wasabiae and leading to death within one week. We then evaluated the efficacy of ten widely used fungicides to screen out effective fungicides. The efficacy of the tested fungicides was determined through mycelial growth inhibition on medium plates. As a result, tebuconazole and pyraclostrobin were able to inhibit the mycelial growth of P. wasabiae, and the most widely used dimethomorph in local production areas produced the lowest inhibition activity (13.8%). Nevertheless, the highest control efficacy of tebuconazole and pyraclostrobin on wasabi seedlings was only 47.48% and 39.03%, respectively. Generally, the control efficacy of spraying the fungicide before inoculation was better than that after inoculation. An increase in the application concentration of the two fungicides did not proportionately result in improved performance. We cloned the full-length sequence of sterol 14-demethylase (CYP51) and cytochrome B (CYTB) of which the mutations may contribute to the possible antifungalresistance. These two genes of the isolated fungus do not possess any reported mutations that lead to fungicide resistance. Previous studies indicate that there is a significant difference between fungicides in terms of the effectiveness of controlling blackleg disease; however, the control efficacy of fungicides is limited in blackleg control. Therefore, field management to prevent wound infection and unfavorable environmental conditions are more important than pesticide management.

Ascochyta blight in North Dakota field pea: the pathogen complex and its fungicide sensitivity

Worldwide, Ascochyta blight is caused by a complex of host-specific fungal pathogens, including Ascochyta pisi, Didymella pinodes, and Didymella pinodella. The application of foliar fungicides is often necessary for disease management, but a better understanding of pathogen prevalence, aggressiveness, and fungicide sensitivity is needed to optimize control. Leaf and stem samples were obtained from 56 field pea production fields in 14 counties in North Dakota from 2017 to 2020 and isolates were collected from lesions characteristic of Ascochyta blight. Based on fungal characteristics and sequencing the ITS1-5.8S-ITS2 region, 73% of isolates were confirmed to be D. pinodes (n = 177) and 27% were A. pisi (n = 65). Across pathogens, aggressiveness was similar among some isolates in greenhouse assays. The in vitro pyraclostrobin sensitivity of all D. pinodes isolates collected from 2017 to 2020 was lower than that of the three baseline isolates. Sensitivity of 91% of A. pisi isolates collected in 2019 and 2020 was lower than the sensitivity of two known sensitive isolates. Resistance factors (Rf) from mean EC50 values of pyraclostrobin baseline/known sensitive isolates to isolates collected from 2017 to 2020 ranged from 2 to 1,429 for D. pinodes and 1 to 209 for A. pisi. In vitro prothioconazole sensitivity of 91% of D. pinodes isolates collected from 2017 to 2020 was lower than the sensitivity of the baseline isolates and 98% of A. pisi isolates collected from 2019 to 2020 was lower than the sensitivity of the known sensitive isolates. Prothioconazole Rf ranged from 1 to 338 for D. pinodes and 1 to 127 for A. pisi. Based on in vitro results, 92% of D. pinodes and 98% of A. pisi isolates collected displayed reduced-sensitivity/resistance to both fungicides when compared to baseline/known sensitive isolates. Disease control under greenhouse conditions of both pathogens provided by both fungicides was significantly lower in isolates determined to be reduced-sensitive or resistant in in vitro assays when compared to sensitive. Results reported here reinforce growers desperate need of alternative fungicides and/or management tools to fight Ascochyta blight in North Dakota and neighboring regions.

Defining Fungicide Resistance Mechanisms in the Corynespora cassiicola Population from Mississippi Soybean

Target spot, caused by Corynespora cassiicola, is a common lower canopy soybean disease in the southern United States. Recently, target spot has resurged in importance especially following the identification of resistance to the quinone outside inhibitor (QoI) fungicides. As a result, a survey of C. cassiicola from soybean throughout Mississippi began in 2018. A total of 819 C. cassiicola monoconidial isolates were obtained from 228 fields in 75 counties. The molecular mechanism of QoI resistance was determined, which resulted from an amino acid substitution from glycine (G) to alanine (A) at position 143 using a PCR-RFLP method and comparing nucleotide sequences of the cytochrome b gene. Five previously defined geographic regions were used to present the distribution of the G143A substitution and included the Capital, Coast, Delta, Hills, and Pines. The Capital had the greatest proportion of G143A-containing isolates (95.0%), followed by the Coast (92.9%), Delta (89.8%), Pines (78.8%), and Hills (69.4%). In all, 85.8% of the C. cassiicola isolates carried the G143A substitution. In addition, the effective fungicide concentration (EC50) of randomly selected C. cassiicola isolates to azoxystrobin was used to characterize isolates as resistant (n = 14) (based on the presence of the G143A substitution and EC50 values >52 μg/ml) or sensitive (n = 11) (based on the absence of the G143A substitution and EC50 values <46 μg/ml). The EC50 values varied among isolates (P < 0.0001), with QoI-sensitive isolates exhibiting lower EC50 values than QoI-resistant isolates. The current study revealed that a reduction in sensitivity to QoI fungicides has likely resulted based on the percentage of C. cassiicola isolates containing the G143A substitution identified in Mississippi.

Fungicide Sensitivity of Sclerotinia sclerotiorum from U.S. Soybean and Dry Bean, Compared to Different Regions and Climates

Fungicide use is integral to reduce yield loss from Sclerotinia sclerotiorum on dry bean and soybean. Increasing fungicide use against this fungus may lead to resistance to the most common fungicides. Resistance has been reported in Brazil (Glycine max) and China (Brassica napus subsp. napus), however, few studies have investigated fungicide sensitivity of S. sclerotiorum in the United States. This work was conducted to determine if there was a difference in fungicide sensitivity of S. sclerotiorum isolates in the United States from: (i) dry bean versus soybean and (ii) fields with different frequencies of fungicide application. We further hypothesized that isolates with fungicide applications of a single active ingredient from tropical Brazil and subtropical Mexico were less sensitive than temperate U.S. isolates due to different management practices and climates. The EC50(D) fungicide sensitivity of 512 S. sclerotiorum isolates from the United States (443), Brazil (36), and Mexico (33) was determined using a discriminatory concentration (DC) previously identified for tetraconazole (2.0 ppm; EC50(D) range of 0.197 to 2.27 ppm), boscalid (0.2; 0.042 to 0.222), picoxystrobin (0.01; 0.006 to 0.027), and thiophanate-methyl, which had a qualitative DC of 10 ppm. Among the 10 least sensitive isolates to boscalid and picoxystrobin, 2 presented mutations known to confer resistance in the SdhB (qualitative) and SdhC (quantitative) genes; however, no strong resistance was found. This study established novel DCs that can be used for further resistance monitoring and baseline sensitivity of S. sclerotiorum to tetraconazole worldwide plus baseline sensitivity to boscalid in the United States.

Frequency of Alternaria Genotypes Resistant to SDHI Fungicides in California Pistachio Orchards Determined by Real-Time PCR

Real-time PCR methods were developed to quantify the frequency of SDHC-H134R and SDHB-H277Y mutants associated with succinate dehydrogenase inhibitors (SDHI) resistance in Alternaria populations from pistachio. The linearity of the standard curves demonstrated the applicability in the quantification of the assays. The accuracy and reliability of the qPCR protocols to determine the frequency of mutants in real samples were corroborated. Orchards visibly affected by Alternaria late blight were sampled. The frequency of mutants was determined using the qPCR assays, while the frequency of resistant phenotypes was determined using a single discriminatory dose. The statistical analysis showed that the frequencies of the mutation SDHC-H134R determined with the qPCR assay were highly correlated with those estimated with the conventional method. The survey also evidenced that resistance to boscalid is still widespread in California. Results also indicated the possible contribution of other mutations to SDHI resistance. Our results confirmed the prevalence of SDHC-H134R mutants and the occurrence of mutation SDHB-H277Y at low frequencies. The real-time PCR methods developed in this study were able to detect differences in the frequencies of resistant mutants caused by the use of chemical fungicides. Finally, the effects of two fungicide programs on the frequency of mutants resistant to SDHI and quinone outside inhibitors fungicides were studied using qPCR assays. The experiments demonstrated that the use of anilinopyrimidine and demethylation inhibitors fungicides in the same program reduced the frequency of these mutations in Alternaria populations. The qPCR methods developed and used in this study can be used to track resistance levels in the pistachio orchards on a large scale.

Detection of Cytb Point Mutation (G143A) that Confers High-Level Resistance to Pyraclostrobin in Glomerella cingulata Using LAMP Method

Glomerella leaf spot (GLS) caused by Glomerella cingulata is a newly emerging disease that results in severe defoliation and fruit spots in apples. In China, the compound of pyraclostrobin and tebuconazole was registered to control GLS in 2018 and has achieved excellent control efficiency. In this study, we showed that the high-level resistant isolates of G. cingulata to pyraclostrobin, caused by the point mutation at codon 143 (GGT→GCT, G143A) in the cytochrome b gene, has appeared in apple orchards in Shandong Province in 2020, and the resistance frequency was 4.8%. Based on the genotype of the resistant isolates, we developed a loop-mediated isothermal amplification (LAMP) assay for detection of the pyraclostrobin resistance. The LAMP assay was demonstrated to have good specificity, sensitivity, and repeatability, and it exhibited high accuracy in detecting pyraclostrobin resistance in the field. This study reported the resistance status of GLS to pyraclostrobin in Shandong Province and developed a molecular tool for the detection of pyraclostrobin resistance, which is of practical significance for the scientific control of GLS.

Molecular and Biochemical Characterization of Field Resistant Isolates of Glomerella cingulata to Pyraclostrobin in China

Glomerella leaf spot (GLS) caused by Glomerella cingulata is a destructive disease that results in severe defoliation and fruit spots in apples worldwide. The compound of pyraclostrobin and tebuconazole was registered in 2018 in China to control GLS. In 2020, the high-level resistance of G. cingulata to pyraclostrobin was found in the field in Shandong Province, with a resistance frequency of 4.8%. Except for a significant decrease in virulence, there was no fitness penalty in mycelial growth, sporulation, and stress tolerance of G. cingulata associated with the resistance to pyraclostrobin. No cross-resistance was detected between pyraclostrobin and tebuconazole or bromothalonil. The point mutation GGT (G) → GCT (A) at codon 143 in the Cytochrome b (Cytb) gene was identified in the pyraclostrobin-resistant isolates. Molecular docking analysis suggested that G143A significantly alters the affinity of pyraclostrobin to the Cytb protein. Based on the point mutation (G143A) in the Cytb gene, a cleaved amplified polymorphic sequences method was developed to detect pyraclostrobin resistance in G. cingulata populations. Results of this study will provide valuable information for the scientific management of GLS.

Identification of Quinone Outside Inhibitor Fungicide-Resistant Isolates of Parastagonospora nodorum from Illinois and Kentucky

Stagonospora leaf and glume blotch, caused by Parastagonospora nodorum, is a major disease of winter wheat (Triticum aestivum) in the United States capable of significantly reducing grain yield and quality. Pathogens such as P. nodorum that overwinter in crop residue are often an increased concern in cropping systems that utilize no-till farming. In addition, the lack of wheat cultivars with complete resistance to P. nodorum has led to the reliance on foliar fungicides for disease management. Quinone outside inhibitor (QoI) fungicides (Fungicide Resistance Action Committee group 11) are one of the major classes used to manage foliar diseases in wheat. Use of the QoI class of fungicides tends to select isolates of fungal pathogens with resistance due to mutations in the fungal cytochrome b gene. Isolates of P. nodorum were collected from Illinois in 2014 and Kentucky in 2018, 2019, and 2020. Amplification and sequencing of a segment of the cytochrome b gene from these isolates revealed a mutation at codon 143 that confers a change from glycine to alanine in the amino acid sequence (known as the G143A mutation). In vitro plate assays and greenhouse trials were used to confirm and characterize the QoI resistance caused by the G143A mutation. The frequency of the tested isolates with the G143A mutation was 46% (57 of 123 isolates) and 5% (3 of 60 isolates) for Kentucky and Illinois, respectively. This research is the first to identify the G143A mutation in P. nodorum isolates with resistance to QoI fungicides in Illinois and Kentucky.

Comprehensive Overview of β-Methoxyacrylate Derivatives as Cytochrome bc1 Inhibitors for Novel Pesticide Discovery

β-Methoxyacrylate derivatives represent a new class of pesticides, which have attracted increasing attention owing to their unique structure, broad biological activity, and unique mechanisms of action. They inhibit mitochondrial respiration via preventing electron transfer at the Qo site of the cytochrome bc₁ complex and thus are identified as cyt bc₁ inhibitors. A variety of β-methoxyacrylate derivatives have been reported by many research groups for discovery of novel pesticides with improved expected activities. This review focuses on development of β-methoxyacrylate derivatives with great significance as pesticides such as fungicides, acaricides, insecticides, herbicides, and antiviral agents. In addition, the structure-activity relationships (SARs) of β-methoxyacrylate derivatives are summarized. Moreover, the cause of resistance to β-methoxyacrylate fungicides and some solutions are also introduced. Finally, the development trend of β-methoxyacrylate derivatives as pesticides is explored. We hope the review will give a guide to develop novel β-methoxyacrylate pesticides in the future.

Cytochrome b Gene-Based Assay for Monitoring the Resistance of Colletotrichum spp. to Pyraclostrobin

Resistance to pyraclostrobin due to a single nucleotide polymorphism at 143rd amino acid position on the cytochrome b gene has been a major source of concern in red pepper field infected by anthracnose in Korea. Therefore, this study investigated the response of 24 isolates of C. acutatum and C. gloeosporioides isolated from anthracnose infected red pepper fruits using agar dilution method and other molecular techniques such as cytochrome b gene sequencing, polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), and allele-specific polymerase chain reaction (PCR). The result showed that four isolates were resistant to pyraclostrobin on agar dilution method and possessed GCT (alanine) codon at 143rd amino acid position, whereas the sensitive isolates possessed GGT (glycine). Furthermore, this study illustrated the difference in the cytochrome b gene structure of C. acutatum and C. gloeosporioides. The use of cDNA in this study suggested that the primer Cacytb-P2 can amplify the cytochrome b gene of both C. acutatum and C. gloeosporioides despite the presence of various introns in the cytochrome b gene structure of C. gloeosporioides. The use of allele-specific PCR and PCR-RFLP provided clear difference between the resistant and sensitive isolates. The application of molecular technique in the evaluation of the resistance status of anthracnose pathogen in red pepper provided rapid, reliable, and accurate results that can be helpful in the early adoption of fungicide-resistant management strategies for the strobilurins in the field.

The G143A/S substitution of mitochondrially encoded cytochrome b (Cytb) in Magnaporthe oryzae confers resistance to quinone outside inhibitors

BACKGROUND

Rice blast, caused by Magnaporthe oryzae, is a destructive disease threatening the production of staple foods worldwide. Quinone outside inhibitors (QoIs) are a group of chemicals exhibiting excellent activity against a majority of plant pathogens, with the disadvantage that pathogens can easily develop resistance to QoIs.

RESULTS

Here, we investigated the activity of picoxystrobin against M. oryzae, which showed a great inhibitory effect on 100 strains of M. oryzae with half-maximal effective concentrations (EC₅₀ ) ranging from 0.0251 to 0.1337 μg ml^-1 . The EC₅₀ values showed a continuous unimodal distribution that was identical to the normal distribution, suggesting the potency of our study to represent baseline sensitivity. In addition, nine resistant mutants were obtained by exposing M. oryzae to a high dosage of picoxystrobin in the laboratory; all of them showed cross-resistance to the other five QoI fungicides. Although some mutants showed a decreased resistance factor after ten successive cultures on fungicide-free medium, the resistance to picoxystrobin was still inheritable. Amino acid substitution of G143S was detected in eight of nine picoxystrobin-resistant mutants, and G143A was detected in only one of nine mutants. A fitness penalty was found in the mutants carrying G143S rather than G143A.

CONCLUSION

Our findings suggested that M. oryzae had a mid to high risk of resistance to picoxystrobin. Considering this, we should be vigilant to the resistance risk and apply picoxystrobin sensibly in the field. © 2022 Society of Chemical Industry.

Analysis of resistance risk and resistance-related point mutations in Cyt b of QioI fungicide ametoctradin in Phytophthora litchii

BACKGROUND

Litchi downy blight, caused by Phytophthora litchii, is one of the most important diseases of litchi. Ametoctradin, as the only QioI (quinone inside and outside inhibitor) fungicide, has been registered in China in 2019. However, the ametoctradin-resistance risk and molecular basis in Phytophthora litchii have not been reported.

RESULTS

In this study, the sensitivity profile of 144 Phytophthora litchii strains to ametoctradin was determined, with a mean median effective concentration (EC₅₀ ) value of 0.1706 ± 0.091 μg mL^-1 . Nine stable resistant Phytophthora litchii mutants [resistance factor (RF) > 400] were derived from sensitive isolates using fungicide adaption. The compound fitness index of three resistant-mutants (HN10-1-1, HN10-1-2 and HN10-2-1) was similar or higher than that of their parental isolates in vitro. All these ametoctradin-resistant mutants were sensitive to metalaxyl, dimethomorph, oxathiapiprolin and cyazofamid. Two point mutations, leading to the S33L and D228N changes in PlCyt b (cytochrome b) were found in ametoctradin-resistant mutants. Eight ametoctradin-resistant mutants containing S33L showed increased sensitivity to azoxystrobin and amisulbrom, and one mutant containing D228N exhibited increased sensitivity to cyazofamid. In vitro enzyme activity test showed that ametoctradin could not inhibit the activity of cytochrome bc1 complex with S33L and D228N point mutation. AS-PCR primers were designed based on the S33L change to detect the ametoctradin-resistant strains in the future.

CONCLUSION

These results suggest that Phytophthora litchii has a medium to high resistance risk to ametoctradin in the laboratory. Two changes, S33L and D228N, in PlCyt b are likely to be associated with the observed ametoctradin resistance. © 2022 Society of Chemical Industry.

Detection and Characterization of Quinone Outside Inhibitor-Resistant Phytophthora cactorum and P. nicotianae Causing Leather Rot in Florida Strawberry

Phytophthora cactorum and P. nicotianae cause leather rot (LR) of fruit and Phytophthora crown rot (PhCR) in strawberry. LR occurs sporadically but can cause up to 70% fruit loss when weather is conducive. In Florida's annual strawberry winter production system, PhCR can be severe, resulting in plant stunting, mortality, and severe yield loss. Azoxystrobin is labeled for control of LR but not for PhCR. The aims of this research were to determine the sensitivity of P. cactorum and P. nicotianae isolates from strawberry to azoxystrobin and to investigate mechanisms of quinone-outside-inhibitor resistance present in P. cactorum and P. nicotianae based on the known point mutations within the cytochrome b (cytb) gene. Isolates of both Phytophthora spp. causing LR and PhCR were collected from multiple strawberry fields in Florida between 1997 and 2020. Isolates were tested for sensitivity to azoxystrobin at 0, 0.01, 0.1, 1.0, 10, and 50 μg/ml on potato dextrose agar amended with salicylhydroxamic acid (100 μg/ml). Isolates were separated into two groups - sensitive isolates with the 50% effective concentration (EC₅₀) values <1.0 μg/ml, and resistant isolates having EC₅₀ values >50 μg/ml. P. cactorum and P. nicotianae resistance to azoxystrobin was found for isolates collected after 2010. The first 450 nucleotides of the mitochondrial cytb gene were sequenced from a selection of resistant and sensitive isolates of both species. The G143A mutation reported to confer resistance to azoxystrobin was found in all resistant P. cactorum isolates. However, in P. nicotianae, qualitative resistance was observed, but the isolates lacked all the known mutations in the cytb gene. This is the first report of resistance to azoxystrobin in P. cactorum and P. nicotianae.

Management of Pyrenophora teres f. teres, the Causal Agent of Net Form Net Blotch of Barley, in A Two-Year Field Experiment in Central Italy

Pyrenophora teres is the causal agent of barley net blotch (NB), a disease that can be found in two different forms: net form (NFNB), caused by P. teres f. teres, and spot form (SFNB), caused by P. teres f. maculata. A two-year field experiment was carried out to evaluate the response to NB of six different barley cultivars for malt or feed/food production. In addition, the efficacy of several recently developed foliar fungicides with different modes of action (SDHI, DMI, and QoI) towards the disease was examined. After NB leaf symptom evaluation, the identification of P. teres forms was performed. Grain yield was determined, and pathogen biomass was quantified in the grain by qPCR. In the two experimental years characterized by different climatic conditions, only P. teres f. teres was detected. The tested cultivars showed different levels of NFNB susceptibility. In particular, the two-row cultivars for malt production showed the highest disease incidence. All applied fungicides exhibited a high efficacy in reducing disease symptoms on leaves and pathogen accumulation in grains. In fact, high levels of fungal biomass were detected only in the grain of the untreated malting barley cultivars. For some cultivars, grain yield was positively influenced by the application of fungicides.

Sensitivity of the U.S. Wheat Powdery Mildew Population to Quinone Outside Inhibitor Fungicides and Determination of the Complete Blumeria graminis f. sp. tritici Cytochrome b Gene

Wheat powdery mildew, caused by Blumeria graminis f. sp. tritici, is managed primarily with cultivar resistance and foliar fungicides. Quinone outside inhibitors (QoIs), which target the mitochondrial cytochrome b (cytb) gene, are one of the two main fungicide classes used on wheat. While European populations of B. graminis f. sp. tritici are widely insensitive to QoIs, largely because of the cytb mutation G143A, the QoI sensitivity of the U.S. B. graminis f. sp. tritici population had never been evaluated despite years of QoI use on U.S. wheat. A total of 381 B. graminis f. sp. tritici isolates from 15 central and eastern U.S. states were screened for sensitivity to QoI fungicides pyraclostrobin and picoxystrobin. A modest range of sensitivities was observed, with maximum resistance factors of 11.2 for pyraclostrobin and 5.3 for picoxystrobin. The F129L, G137R, and G143A cytb mutations were not detected in the U.S. B. graminis f. sp. tritici population, nor were mutations identified in the PEWY loop, a key part of the Qo site. Thus, no genetic basis for the observed quantitative variation in QoI sensitivity of U.S. B. graminis f. sp. tritici was identified. Isolate sporulation was weakly negatively associated with reduced QoI sensitivity, suggesting a fitness cost. In the course of the study, the complete B. graminis f. sp. tritici cytb gene sequence was determined for the first time in the isolate 96224 v. 3.16 reference genome. Contrary to previous reports, the gene has an intron that appears to belong to intron group II, which is unusual in fungi. The study was the first QoI sensitivity screening of a large, geographically diverse set of U.S. B. graminis f. sp. tritici isolates, and while the population as a whole remains relatively sensitive, some quantitative loss of efficacy was observed.

Development of a LAMP method for detecting F129L mutant in azoxystrobin-resistant Pyricularia oryzae

Azoxystrobin has been widely used since 1996 to control rice blast caused by Pyricularia oryzae. Azoxystrobin resistance related to mutations at the P. oryzae target protein (F129L of Cytb) has been reported worldwide. To quickly identify and detect resistant strains in the field, this research established a rapid loop-mediated isothermal amplification (LAMP) detection system for the F129L mutation. The system could detect the P. oryzae F129L (TTC-TTA) mutation at 62 °C within 60 min, with a detection limit of 100 fg/μL, which is 10 times higher than for conventional PCR. The method had high specificity and repeatability and could detect the F129L (TTC-TTA) mutation in plant tissues within 3 h. The LAMP method established in this study will be useful to detect azoxystrobin-resistant P. oryzae F129L mutant strains and generate significant data for the management of resistant P. oryzae isolates.

Molecular Mechanisms Underlying Fungicide Resistance in Citrus Postharvest Green Mold

The necrotrophic fungus Penicillium digitatum (Pd) is responsible for the green mold disease that occurs during postharvest of citrus and causes enormous economic losses around the world. Fungicides remain the main method used to control postharvest green mold in citrus fruit storage despite numerous occurrences of resistance to them. Hence, it is necessary to find new and more effective strategies to control this type of disease. This involves delving into the molecular mechanisms underlying the appearance of resistance to fungicides during the plant–pathogen interaction. Although mechanisms involved in resistance to fungicides have been studied for many years, there have now been great advances in the molecular aspects that drive fungicide resistance, which facilitates the design of new means to control green mold. A wide review allows the mechanisms underlying fungicide resistance in Pd to be unveiled, taking into account not only the chemical nature of the compounds and their target of action but also the general mechanism that could contribute to resistance to others compounds to generate what we call multidrug resistance (MDR) phenotypes. In this context, fungal transporters seem to play a relevant role, and their mode of action may be controlled along with other processes of interest, such as oxidative stress and fungal pathogenicity. Thus, the mechanisms for acquisition of resistance to fungicides seem to be part of a complex framework involving aspects of response to stress and processes of fungal virulence.

No Evidence of Resistance to Trifloxystrobin, Triflumizole, and Boscalid in Podosphaera leucotricha Isolates From U.S. Commercial Apple Orchards

Apple powdery mildew, caused by Podosphaera leucotricha, continues to be a challenge in commercial apple orchards in the U.S. Pacific Northwest and worldwide. In this study, P. leucotricha isolates were collected in 2018 and 2019 from two organic (baseline) and eight conventional (exposed) apple orchards in Washington, New York, and Virginia, and assessed for their sensitivity to trifloxystrobin (TRI, n = 232), triflumizole (TFZ, n = 217), and boscalid (BOS, n = 240) using a detached leaf assay. Effective concentrations inhibiting 50% growth (EC₅₀) were not significantly different between baseline and exposed isolates, and ranged from 0.001 to 0.105, 0.09 to 6.31, and 0.05 to 2.18 µg/ml, for TRI, TFZ, and BOS, respectively. Reduction in sensitivity by factors of 105, 63, and 22 to TRI, TFZ, and BOS, respectively, were observed in some isolates, but all isolates were controlled by the commercial label rates of the three fungicides on detached leaves. Sequencing of the cytochrome b (cytb), cytochrome P450 sterol 14α-demethylase (CYP51), and the iron-sulfur protein subunit (SdhB) genes in isolates with high EC₅₀ revealed no mutation previously reported to confer resistance to these fungicides in other fungi, and presence of a group I intron after codon 143 in the cytb gene. Significant (P < 0.001) moderate positive correlations (r = 0.38) observed between sensitivity to TRI and TFZ warrant continuous rotations of fungicides with different modes of action in conventional orchards. The established baseline sensitivities and the molecular markers will help in selecting discriminatory doses and bypassing the challenging in vivo testing for future sensitivity monitoring in P. leucotricha.

Multiresistance to Nonazole Fungicides in Aspergillus fumigatus TR34/L98H Azole-Resistant Isolates

Drug resistance is a worldwide problem affecting all pathogens. The human fungal pathogen Aspergillus fumigatus coexists in the environment with other fungi targeted by crop protection compounds, being unintentionally exposed to the selective pressure of multiple antifungal classes and leading to the selection of resistant strains. A. fumigatus azole-resistant isolates are emerging in both clinical and environmental settings. Since their approval, azole drugs have dominated clinical treatment for aspergillosis infections and the agriculture fungicide market. However, other antifungal classes are used for crop protection, including benzimidazoles (methyl benzimidazole carbamates [MBCs]), strobilurins (quinolone oxidation inhibitors [QoIs]), and succinate dehydrogenase inhibitors (SDHIs). Mutations responsible for resistance to these fungicides have been widely researched in plant pathogens, but resistance has not been explored in A. fumigatus. In this work, the genetic basis underlying resistance to MBCs, QoIs, and SDHIs was studied in azole-susceptible and -resistant A. fumigatus strains. E198A/Q and F200Y mutations in β-tubulin conferred resistance to MBCs, G143A and F129L substitutions in cytochrome b conferred resistance to QoIs, and H270R/Y mutations in SdhB conferred resistance to SDHIs. Characterization of susceptibility to azoles showed a correlation between strains resistant to these fungicides and the ones with tandem-repeat (TR)-based azole resistance mechanisms. Whole-genome sequencing analysis showed a genetic relationship among fungicide multiresistant strains, which grouped into subclusters that included only strains carrying the TR-based azole resistance mechanisms, indicating a common ancestor/evolution pattern and confirming the environmental origin of this type of azole-resistant A. fumigatus.

Resistance to Azoxystrobin and Thiophanate-Methyl Is Widespread in Colletotrichum spp. Isolates From the Mid-Atlantic Strawberry Fields

Multiple Colletotrichum species have been found to be responsible for strawberry anthracnose, and prevalence of each species seems to vary by regions and/or host tissues. In this study, a total of 200 Colletotrichum isolates were obtained from different strawberry cultivars displaying anthracnose symptoms in the mid-Atlantic fields. Analysis of g3pdh, tub2, and/or internal transcribed spacer sequences revealed four Colletotrichum species, including C. nymphaeae, C. fioriniae, C. siamense, and C. lineola. C. nymphaeae was the predominant species, representing 90% of all isolates collected. This species was found from all strawberry organs/tissues examined, whereas C. siamense and C. fioriniae were limited to the crown and fruit, respectively. Further, all Colletotrichum isolates were screened for resistance to azoxystrobin in vitro, and all C. siamense isolates were additionally screened for resistance to thiophanate-methyl. The overall frequency of resistance to azoxystrobin and thiophanate-methyl was 48 and 67%, respectively. G143A in the cytochrome b gene was found in all C. nymphaeae and C. siamense isolates with high level of resistance, with EC₅₀ >100 µg/ml, while F129L was found in two of the five C. nymphaeae isolates with moderate resistance, with EC₅₀ values ranging from 2.6 to 7.8 µg/ml. All C. fioriniae isolates tested were found to be less sensitive to azoxystrobin, with EC₅₀ values ranging from 9.7 to 14.4 µg/ml, despite no mutations detected in the cytochrome b gene. Moreover, E198A in tub2 was linked with C. siamense isolates resistant to thiophanate-methyl (EC₅₀ >100 µg/ml). These results revealed that resistance in Colletotrichum spp. to primary fungicides is widespread in the mid-Atlantic strawberry fields.

Resistance mechanisms and fitness of pyraclostrobin-resistant isolates of Lasiodiplodia theobromae from mango orchards

Background

Stem-end rot, caused by Lasiodiplodia theobromae (Pat.) Griffon & Maubl is a serious postharvest disease in mango. In China, a high prevalence of the QoI fungicides resistance has been reported in the last decade. The study aimed to discuss factors determining rapid development of pyraclostrobin-resistance and its resistance mechanisms.

Methods

To determine the resistance stability and fitness of pyraclostrobin resistance in L. theobromae, three phenotypes of pyraclostrobin resistance were compared and analyzed for the EC₅₀ values, mycelial growth, virulence and temperature sensitivity and osmotic stress sensitivity. The relative conductivity and enzyme activities of different phenotypes were compared under fungicide stress to explore possible biochemical mechanisms of pyraclostrobin resistance in L. theobromae. The Cytb gene sequences of different phenotypes were analysed.

Results

All isolates retained their original resistance phenotypes during the 10 subcultures on a fungicide-free PDA, factor of sensitivity change (FSC) was approximately equal to 1. The resistance-pyraclostrobin of the field isolates should be relatively stable. Two pyraclostrobin-resistant phenotypes shared similar mycelial growth, virulence and temperature sensitivity with pyraclostrobin-sensitive phenotype. After treated by pyraclostrobin, the relative conductivity of the sensitive phenotype was significantly increased. The time of Pyr-R and Pyr-HR reached the most conductivity was about 8–10 times than that of Pyr-S, the time for the maximum value appearance showed significant differences between sensitive and resistant phenotypes. The activities of Glutathione S-transferase (GST), catalase (CAT) and peroxidase (POD) of Pyr-HR were 1.78, 5.45 and 1.65 times respectively, significantly higher than that of Pyr-S after treated by 200 mg/l pyraclostrobin.

Conclusion

The results showed that the pyraclostrobin-resistant phenotypes displayed high fitness and high-risk. The nucleotide sequences were identical among all pyraclostrobin-resistant and -sensitive isolates. The pyraclostrobin resistance was not attributable to Cytb gene alterations, there may be some of other resistance mechanisms. Differential response of enzyme activity and cell membrane permeability were observed in resistant- and sensitive-isolates suggesting a mechanism of metabolic resistance.

Occurrence of Quinone Outside Inhibitor Resistance in Virginia Populations of Parastagonospora nodorum Infecting Wheat

Stagonospora nodorum blotch (SNB) of wheat, caused by Parastagonospora nodorum, is managed using cultural practices, resistant varieties, and foliar fungicides. Frequent fungicide use can select for fungicide resistance, making certain chemistries less effective; this may in part explain the increasing severity of SNB in the mid-Atlantic United States. Quinone outside inhibitor (QoI) resistance has been documented for a diversity of fungi, but it has not been reported for P. nodorum in the United States. The objectives of this study were (i) to evaluate QoI sensitivity of P. nodorum from Virginia wheat fields, (ii) to screen P. nodorum for QoI target site mutations in the cytochrome b gene, and (iii) to develop a molecular assay to detect target site mutations associated with QoI resistance. Sensitivity of 16 isolates to pyraclostrobin and azoxystrobin was evaluated with radial growth assays, and the cytochrome b gene was sequenced. One isolate was insensitive to both fungicides and had the G143A mutation in the cytochrome b gene. For azoxystrobin, 10 isolates without target site mutations had reduced sensitivity. Additional isolates (n = 58) were sequenced. A total of seven isolates had the G143A mutation and also had reduced sensitivity to pyraclostrobin and azoxystrobin compared with a sensitive control isolate without the mutation. A pyrosequencing assay targeting G143A was developed as a rapid method to screen P. nodorum for the QoI resistance-conferring mutation. To our knowledge, this is the first report of QoI-resistant P. nodorum in the United States. Overall resistance frequency was low, but resistance management practices are needed to maintain the efficacy of fungicides for SNB control.

Molecular Identification of Mutations Conferring Resistance to Azoxystrobin in Cercospora nicotianae

Cercospora nicotianae, the causal agent of frogeye leaf spot (FLS) of tobacco, has been exposed to quinone outside inhibitor (QoI) fungicides for more than a decade through azoxystrobin applications targeting other major foliar diseases. From 2016 to 2018, a total of 124 isolates were collected from tobacco fields throughout Kentucky. Sensitivity of these isolates to azoxystrobin was previously characterized by determining the effective concentration to inhibit 50% conidial germination (EC₅₀). Based on azoxystrobin EC₅₀, isolates were categorized into three discrete groups: high sensitivity (<0.08 µg/ml), moderate sensitivity (0.14 to 0.64 µg/ml), and low sensitivity (>1.18 µg/ml). Variability in sensitivity in a limited number of C. nicotianae isolates was previously shown to be a result of resistance mutations in the fungicide target gene. To improve understanding of C. nicotianae cytochrome b (cytb) structure, the gene was cloned from three isolates representing each EC₅₀ group, and sequences were compared. Our analysis showed that cytb gene in C. nicotianae consists of 1,161 nucleotides encoding 386 amino acids. The cytb sequence among the cloned isolates was identical with the exception of the F129L and G143A point mutations. To more rapidly determine the resistance status of C. nicotianae isolates to azoxystrobin, a polymerase chain reaction (PCR) assay was developed to screen for mutations. According to this assay, 80% (n = 99) of tested C. nicotianae isolates carried an F129L mutation and were moderately resistant to azoxystrobin, and 7% (n = 9) carried the G143A mutation and were highly resistant. A receiver operating characteristic curve analysis suggested the PCR assay was a robust diagnostic tool to identify C. nicotianae isolates with different sensitivity to azoxystrobin in Kentucky tobacco production. The prevalence of both the F129L and G143A mutations in C. nicotianae from Kentucky differs from that of other pathosystems where resistance to QoI fungicides has been identified, in which the majority of sampled isolates of the pathogen species have a broadly occurring cytb mutation.

Pyrenophora teres: Taxonomy, Morphology, Interaction With Barley, and Mode of Control

Net blotch, induced by the ascomycete Pyrenophora teres, has become among the most important disease of barley (Hordeum vulgare L.). Easily recognizable by brown reticulated stripes on the sensitive barley leaves, net blotch reduces the yield by up to 40% and decreases seed quality. The life cycle, the mode of dispersion and the development of the pathogen, allow a quick contamination of the host. Crop residues, seeds, and wild grass species are the inoculum sources to spread the disease. The interaction between the barley plant and the fungus is complex and involves physiological changes with the emergence of symptoms on barley and genetic changes including the modulation of different genes involved in the defense pathways. The genes of net blotch resistance have been identified and their localizations are distributed on seven barley chromosomes. Considering the importance of this disease, several management approaches have been performed to control net blotch. One of them is the use of beneficial bacteria colonizing the rhizosphere, collectively referred to as Plant Growth Promoting Rhizobacteria. Several studies have reported the protective role of these bacteria and their metabolites against potential pathogens. Based on the available data, we expose a comprehensive review of Pyrenophora teres including its morphology, interaction with the host plant and means of control.

Contrasting levels of genetic predictability in the evolution of resistance to major classes of fungicides

The evolution of resistance has been seen across all major classes of xenobiotics, including antimicrobial drugs and agricultural pesticides. This repeated emergence of resistance is a case of phenotypic parallel evolution, but often the parallelism extends to the molecular level too, with multiple species gaining the same mutation in response to the same chemical treatment. We review the degree of repeatability in target-site resistance mutations affecting different classes of site-specific agricultural fungicides used in crop protection, comparing the extent to which resistance in different pathogen species has evolved via the same or different mutations. For all major fungicide target sites, substantial levels of molecular parallel evolution can be seen, with at least one mutation recurring in over 50% of species. Target-site mutations appear to be most repeatable in cytochrome b, target site of quinone-outside inhibitor fungicides, and least predictable for CYP51, target site of the azoles. Intermediate levels of repeatability are seen for the MBC target site β-tubulin, and the SDHI target site succinate dehydrogenase. Repeatability may be lower where there are selective trade-offs between resistance and pleiotropic fitness penalties, or differing levels of cross-resistance across members of a fungicide class; or where single mutations confer only partial resistance, and epistatic interactions between multiple mutations result in a rugged fitness landscape. This affects the predictive power of in vitro mutation studies, and has practical implications for resistance monitoring strategies and diagnostic methods.

Fungicide Resistance in Venturia effusa, Cause of Pecan Scab: Current Status and Practical Implications

Pecan scab, caused by Venturia effusa, is the most economically damaging disease of pecan in the southeastern United States, and annual epidemics are most effectively managed through multiple fungicide applications. The fungicide applications can be the single greatest operating cost for commercial growers and the return on that investment is impacted by fungicide resistance. V. effusa produces multiple generations of conidia per season, exhibits substantial genetic diversity, overwinters as stromata in the tree, and is under immense selection from the applied fungicides, all of which lead to a high risk for developing fungicide resistance. Since the mid-1970s, resistance or reduced sensitivity has been observed in isolates of V. effusa to the methyl benzimidazole carbamates, demethylation inhibitors, quinone outside inhibitors, organotin compounds, and the guanidines. Over the last 10 years, several studies have been conducted that have improved both scab management and fungicide resistance management in V. effusa. The aim of this review is to summarize recent developments in our understanding of fungicide resistance in V. effusa in the context of scab management in southeastern pecan orchards. The history, modes of action, general use of the labeled fungicides, and mechanisms and stability of fungicide resistance in V. effusa are discussed; conclusions and future research priorities are also presented.

Fungicide Resistance Evolution and Detection in Plant Pathogens: Plasmopara viticola as a Case Study

The use of single-site fungicides to control plant pathogens in the agroecosystem can be associated with an increased selection of resistance. The evolution of resistance represents one of the biggest challenges in disease control. In vineyards, frequent applications of fungicides are carried out every season for multiple years. The agronomic risk of developing fungicide resistance is, therefore, high. Plasmopara viticola, the causal agent of grapevine downy mildew, is a high risk pathogen associated with the development of fungicide resistance. P. viticola has developed resistance to most of the fungicide classes used and constitutes one of the most important threats for grapevine production. The goals of this review are to describe fungicide resistance evolution in P. viticola populations and how to conduct proper monitoring activities. Different methods have been developed for phenotyping and genotyping P. viticola for fungicide resistance and the different phases of resistance evolution and life cycles of the pathogen are discussed, to provide a full monitoring toolkit to limit the spread of resistance. A detailed revision of the available tools will help in shaping and harmonizing the monitoring activities between countries and organizations.

Allele-Specific Detection Methods for QoI Fungicide-Resistant Erysiphe necator in Vineyards

Grapevine powdery mildew (GPM), caused by the fungus Erysiphe necator, is a constant threat to worldwide production of grape berries, requiring repeated use of fungicides for management. The frequent fungicide applications have resulted in resistance to commonly used quinone outside inhibitor (QoI) fungicides and the resistance is associated with single-nucleotide polymorphisms (SNPs) in the mitochondrial cytochrome b gene (cytb). In this study, we attempted to detect the most common SNP causing a glycine to alanine substitution at amino acid position 143 (i.e., G143A) in the cytb protein, to track this resistance using allele-specific TaqMan probe and digital-droplet PCR-based assays. Specificity and sensitivity of these assays showed that these two assays could discriminate SNPs and were effective on mixed samples. These diagnostic assays were implemented to survey E. necator samples collected from leaf and air samples from California and Oregon grape-growing regions. Sequencing of PCR amplicons and phenotyping of isolates also revealed that these assays accurately detected each allele (100% agreement), and there was an absolute agreement between the presence or absence of the G143A mutation and resistance to QoIs in the E. necator sampled. These results indicate that the developed diagnostic tools will help growers make informed decisions about fungicide selections and applications which, in turn, will facilitate GPM disease management and improve grape production systems.

Three point-mutations in cytochrome b confer resistance to trifloxystrobin in Magnaporthe oryzae

BACKGROUND

Rice blast, caused by Magnaporthe oryzae, is the most devastating disease in rice. Recently, trifloxystrobin was registered for the control of M. oryzae in China. The resistance profile and mechanism of M. oryzae to trifloxystrobin were investigated in the present study, providing important data for the recommended use of trifloxystrobin.

RESULTS

The baseline sensitivity was established at a half maximal effective concentration (EC₅₀ ) of 0.024 μg mL^-1 . Nine stable trifloxystrobin-resistant mutants were generated with EC₅₀ values ranging from 12.75 to 171.49 μg mL^-1 . The mutants exhibited strong adaptive traits in sporulation, conidial germination, and pathogenicity. Positive cross-resistance was only observed between trifloxystrobin and azoxystrobin, but not between trifloxystrobin and carbendazim, isoprothiolane, prochloraz, or chlorothalonil. The point mutation G143S in cytochrome b (cyt b) protein was found in eight high-resistance mutants with resistant factor ranging from 2295.16 to 13 200.00; and the double mutation G137R/M296V only occurred in Mg117-1 with resistance factor ≈ 900. The G143S mutation weakened hydrogen bond interactions, and G137R/M296V changed the conformation of trifloxystrobin in the cyt b binding pocket. A molecular detection method was established for the rapid detection of G143S mutants in M. oryzae.

CONCLUSION

The resistance risk of M. oryzae to trifloxystrobin could be moderate to high. Two genotypes with three point-mutations G143S, G137R, and M296V conferred resistance to trifloxystrobin in M. oryzae. © 2020 Society of Chemical Industry.

The cytochrome bc1 complex as an antipathogenic target

The cytochrome bc₁ complex is a key component of the mitochondrial respiratory chains of many eukaryotic microorganisms that are pathogenic for plants or humans, such as fungi responsible for crop diseases and Plasmodium falciparum, which causes human malaria. Cytochrome bc₁ is an enzyme that contains two (ubi)quinone/quinol-binding sites, which can be exploited for the development of fungicidal and chemotherapeutic agents. Here, we review recent progress in determination of the structure and mechanism of action of cytochrome bc₁ , and the associated development of antimicrobial agents (and associated resistance mechanisms) targeting its activity.

Decreased Sensitivity of Leptosphaeria maculans to Pyraclostrobin in Alberta, Canada

Leptosphaeria maculans, the causal agent of blackleg of canola (Brassica napus), can be managed with pyraclostrobin and other strobilurin fungicides. Their frequent application, however, poses a risk for the development of insensitivity in fungal populations. A collection of L. maculans single-spore isolates recovered from infected canola stubble in Alberta, Canada, in 2016 was evaluated for its pyraclostrobin sensitivity. In conventional growth plate assays, the concentration of pyraclostrobin required to inhibit fungal growth by 50% (EC₅₀) was determined to be 0.28 mg/liter in a subset of 38 isolates. This EC₅₀ was four times greater than the mean EC₅₀ (0.07 mg/liter) of baseline isolates collected in 2011. Two hundred sixty-three isolates were screened further with two discriminatory doses of 0.28 and 3.5 mg/liter of pyraclostrobin, resulting in growth inhibition values ranging from 16 to 82% and 41 to 100%, respectively. In microtiter plate assays with the same isolates, the mean EC₅₀ was determined to be 0.0049 mg/liter, almost 3.3 times greater than the mean EC₅₀ (0.0015 mg/liter) of the baseline isolates. The sensitivity of the isolates was also evaluated in microtiter plate assays with discriminatory doses of 0.006 and 0.075 mg/liter of pyraclostrobin, resulting in inhibition values ranging from 20 to 88% and 49 to 100%, respectively. This is the first report of isolates of L. maculans with increased insensitivity to pyraclostrobin in Canada, suggesting the need for improved fungicide stewardship.

Sensitivity of the Pyrenophora teres Population in Algeria to Quinone outside Inhibitors, Succinate Dehydrogenase Inhibitors and Demethylation Inhibitors

Net blotch of barley caused by Pyrenophora teres (Died.) Drechsler, is one of the most destructive diseases on barley in Algeria. It occurs in two forms: P. teres f. teres and P. teres f. maculata. A total of 212 isolates, obtained from 58 fields sampled in several barley growing areas, were assessed for fungicide sensitivity by target gene analysis. F129L and G137R mitochondrial cytochrome b substitution associated with quinone outside inhibitors (QoIs) resistance, and succinate dehydrogenase inhibitors (SDHIs) related mutations (B-H277, C-N75S, C-G79R, C-H134R, and C-S135R), were analyzed by pyrosequencing. In vitro sensitivity of 45 isolates, towards six fungicides belonging to three chemical groups (QoI, demethylase inhibitor, and SDHI) was tested by microtiter technique. Additionally, sensitivity towards three fungicides (azoxystrobin, fluxapyroxad, and epoxiconazole) was assessed in planta under glasshouse conditions. All tested isolates were QoI-sensitive and SDHI-sensitive, no mutation that confers resistance was identified. EC50 values showed that pyraclostrobin and azoxystrobin are the most efficient fungicides in vitro, whereas fluxapyroxad displayed the best disease inhibition in planta (81% inhibition at 1/9 of the full dose). The EC₅₀ values recorded for each form of net blotch showed no significant difference in efficiency of QoI treatments and propiconazole on each form. However, in the case of fluxapyroxad, epoxiconazole and tebuconazole treatments, analysis showed significant differences in their efficiency. To our knowledge, this study is the first investigation related to mutations associated to QoI and SDHI fungicide resistance in Algerian P. teres population, as well as it is the first evaluation of the sensitivity of P. teres population towards these six fungicides.

Cytochrome b Mutations F129L and G143A Confer Resistance to Azoxystrobin in Cercospora nicotianae, the Frogeye Leaf Spot Pathogen of Tobacco

Azoxystrobin is the only synthetic, systemic fungicide labeled in the United States for management of frogeye leaf spot (FLS) of tobacco (Nicotiana tabacum L.), caused by Cercospora nicotianae. Though traditionally considered a minor disease in the United States, FLS has recently become yield and quality limiting. In 2016 and 2017, 100 C. nicotianae isolates were collected from symptomatic tobacco from eight counties in Kentucky, United States. Prior to azoxystrobin sensitivity testing, some C. nicotianae isolates were found to utilize the alternative oxidase pathway and, after assay comparisons, conidial germination was utilized to evaluate sensitivity in C. nicotianae as opposed to mycelial growth. Azoxystrobin sensitivity was determined by establishing the effective concentration to inhibit 50% conidial germination (EC50) for 47 (in 2016) and 53 (in 2017) C. nicotianae isolates. Distributions of C. nicotianae EC50 values indicated three qualitative levels of sensitivity to azoxystrobin. Partial cytochrome b sequence, encompassing the F129L and G143A mutation sites, indicated single-nucleotide polymorphisms (SNPs) conferring the F129L mutation in C. nicotianae of moderate resistance (azoxystrobin at 0.177 ≤ EC50 ≤ 0.535 µg/ml) and the G143A mutation in isolates with an azoxystrobin-resistant phenotype (azoxystrobin EC50 > 1.15 µg/ml). Higher frequencies of resistant isolates were identified from greenhouse transplant (4 of 17) and conventionally produced (58 of 62) tobacco samples, as compared with field-grown tobacco (<4 weeks prior to harvest; 4 of 62) or organically produced samples (1 of 7), respectively. Together, these results suggest that resistance to azoxystrobin in C. nicotianae occurs broadly in Kentucky, and generate new hypotheses about selection pressure affecting resistance mutation frequencies.

Antifungal activity of metyltetraprole against the existing QoI-resistant isolates of various plant pathogenic fungi: Metyltetraprole against QoI-R isolates

BACKGROUND

Metyltetraprole is a novel quinol oxidation site of Complex III inhibitor (QoI) fungicide that inhibits mitochondrial electron transport at the Qo site of the cytochrome bc1 complex. Previous reports have demonstrated that it is also active against the QoI-resistant (QoI-R) isolates of Zymoseptoria tritici and Pyrenophora teres with the mutations G143A and F129L in their cytochrome b gene, respectively. Further studies on cross-resistance between metyltetraprole and existing QoIs were performed using an increased number of isolates of Z. tritici, P. teres, Ramularia collo-cygni, Pyrenophora tritici-repentis, and several other plant pathogenic fungi.

RESULTS

Differences in the EC₅₀ values between the wild-type and QoI-R isolates with the mutations G143A or F129L were always smaller for metyltetraprole compared to those for the existing QoIs, and they were never greater than five in terms of resistance factor. The 2-year field experiments showed that the metyltetraprole treatment did not increase the percentage of QoI-R isolates likely to harbor the G143A mutation in a Z. tritici population.

CONCLUSION

The unique behavior of metyltetraprole against the existing QoI-R isolates was confirmed for all tested pathogen species. Our results provide important information to establish a fungicide resistance management strategy using metyltetraprole in combination or alternation with other fungicides. © 2019 Society of Chemical Industry.

Fungicide Sensitivity Shifting of Zymoseptoria tritici in the Finnish-Baltic Region and a Novel Insertion in the MFS1 Promoter

Septoria tritici blotch (STB) is caused by the ascomycete Zymoseptoria tritici and one of the predominating diseases in wheat (Triticum aestivum) in Europe. The control of STB is highly reliant on frequent fungicide applications. The primary objective of this study was to assess sensitivity levels of Z. tritici to different fungicide groups. The fungicides included in this study were epoxiconazole, prothioconazole-desthio, tebuconazole, and fluxapyroxad. A panel of 63 isolates from Estonia, Latvia, and Lithuania, and 10 isolates from Finland were tested. Fungicide sensitivity testing was carried out as a bioassay analyzing single pycnidium isolates on different fungicide concentrations. The average EC₅₀ value in Baltic countries and Finland to epoxiconazole was high ranging from 1.04 to 2.19 ppm. For prothioconazole-desthio and tebuconazole, EC₅₀ varied from 0.01 to 0.24 ppm, and 1.25 to 18.23 ppm, respectively. The average EC₅₀ value for fluxapyroxad varied from 0.07 to 0.33 ppm. To explain the range of sensitivity, the samples were analyzed for CYP51 and Sdh mutations, as well as cytb G143A, CYP51 overexpression, and multidrug resistance (MDR). Frequencies of ZtCYP51 mutations D134G, V136A/C, A379G, I381V, and S524T in the Finnish-Baltic region were lower than in other European countries, but have increased compared to previous years. The frequency of cytb G143A conferring strobilurin resistance also augmented to 50-70% in the Z. tritici populations from Estonia, Finland, Latvia, and Lithuania. No Sdh mutations were found in this study, and neither strains of MDR phenotypes. However, we found a strain harboring a previously unknown transposon insertion in the promoter of the MFS1 gene, involved in drug efflux and multi-drug resistance. This new insert, however, does not confer an MDR phenotype to the strain.

Widespread QoI Fungicide Resistance Revealed Among Corynespora cassiicola Tomato Isolates in Florida

Target spot of tomato caused by Corynespora cassiicola is one of the most economically destructive diseases of tomato in Florida. A collection of 123 isolates from eight counties in Florida were evaluated for sensitivity to azoxystrobin and fenamidone based on mycelial growth inhibition (MGI), spore germination (SG), detached leaflet assays (DLAs), and sequence-based analysis of the cytochrome b gene (cytb). Cleavage of cytb by restriction enzyme (Fnu4HI) revealed the presence of a mutation conferring a glycine (G) to alanine (A) mutation at amino acid position 143 (G143A) in approximately 90% of the population, correlating with quinone outside inhibitor (QoI) resistance based on MGI (<40% at 5 μg/ml), SG (<50% at 1 and 10 μg/ml), and DLA (<10% severity reduction). The mutation conferring a phenylalanine (F) to leucine (L) substitution at position 129 (F129L) was confirmed in moderately resistant isolates (#9, #19, and #74) based on MGI (40 to 50% at 5 μg/ml), SG (<50% at 1 μg/ml and >50% at 10 μg/ml), and DLA (>10% and <43% severity reduction) for both QoI fungicides, whereas sensitive isolates (#1, #4, #7, #28, #29, #46, #61, #74, #75, #76, #91, #95, and #118) based on MGI (>50% at 5 μg/ml), SG (>50% at 1 μg/ml and 10 μg/ml), and DLA (>50% severity reduction) correlated to non-mutation-containing isolates or those with a silent mutation. This study indicates that QoI resistance among C. cassiicola isolates from tomato is widespread in Florida and validates rapid screening methods using MGI or molecular assays to identify resistant isolates in future studies.