Development and implementation of a novel CAPS assay reveals high prevalence of a boscalid resistance marker and its co-occurrence with an azole resistance marker in Erysiphe necator

Succinate dehydrogenase inhibitors (SDHIs), are frequently used against powdery mildew (PM) fungi, such as Erysiphe necator, the causal agent of grapevine PM. Fungicide resistance, however, hinders effective control. DNA-based monitoring facilitates the recognition of resistance. We aimed (i) to adapt an effective method to detect a widespread genetic marker of resistance to boscalid, a commonly used SDHI, and (ii) to study the co-occurrence of the marker with a marker of resistance to demethylase inhibitor (DMI) fungicides. Sequencing of the sdhB gene identified a non-synonymous substitution, denoted as sdhB-A794G, leading to an amino acid change (H242R) in the sdhB protein. In vitro fungicide resistance tests showed that E. necator isolates carrying sdhB-A794G were resistant to boscalid. We adopted a cleaved amplified polymorphic sequence-based method and screened more than 500 field samples collected from five Hungarian wine regions in two consecutive years. The sdhB-A794G marker was detected in all wine regions and in both years, altogether in 61.7% of samples, including 20.5% in which both sdhB-A794G and the wild-type were present. The frequency of sdhB-A794G was higher in SDHI-treated vineyards than in vineyards without any SDHI application. A significant difference in the presence of the marker was detected among wine regions; its prevalence ranged from none to 100%. We identified significant co-occurrence of sdhB-A794G with the CYP51-A495T (Y136F) mutation of the CYP51 gene, a known marker of resistance to DMIs. The monitoring of fungicide resistance is fundamental for the successful control of E. necator. Our rapid, cost-effective diagnostic method will support decision-making and fungicide resistance monitoring and management.

Do Growers Using Solo Fungicides Affect the Durability of Disease Control of Growers Using Mixtures and Alternations? The Case of Spot-Form Net Blotch in Western Australia

Growers often use alternations or mixtures of fungicides to slow down the development of resistance to fungicides. However, within a landscape, some growers will implement such resistance management methods, whereas others do not, and may even apply solo components of the resistance management program. We investigated whether growers using solo components of resistant management programs affect the durability of disease control in fields of those who implement fungicide resistance management. We developed a spatially implicit semidiscrete epidemiological model for the development of fungicide resistance. The model simulates the development of epidemics of spot-form net blotch disease, caused by the pathogen Pyrenophora teres f. maculata. The landscape comprises three types of fields, grouped according to their treatment program, with spore dispersal between fields early in the cropping season. In one field type, a fungicide resistance management method is implemented, whereas in the two others, it is not, with one of these field types using a component of the fungicide resistance management program. The output of the model suggests that the use of component fungicides does affect the durability of disease control for growers using resistance management programs. The magnitude of the effect depends on the characteristics of the pathosystem, the degree of inoculum mixing between fields, and the resistance management program being used. Additionally, although increasing the amount of the solo component in the landscape generally decreases the lifespan within which the resistance management program provides effective control, situations exist where the lifespan may be minimized at intermediate levels of the solo component fungicide. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

FgSdhC Paralog Confers Natural Resistance toward SDHI Fungicides in Fusarium graminearum

Fusarium graminearum exhibited natural resistance to a majority of succinate dehydrogenase inhibitor fungicides (SDHIs) and the molecular mechanisms responsible for the natural resistance were still unknown. Succinate dehydrogenase subunit C (SdhC) is an essential gene for maintaining succinate-ubiquinone oxidoreductase (SQR) function in fungi. In F. graminearum, a paralog of FgSdhC named as FgSdhC1 was identified. Based on RNA-Seq and qRT-PCR assay, we found that the expression level of FgSdhC1 was very low but upregulated by SDHIs treatment. Based on reverse genetics, we demonstrated that FgSdhC1 was an inessential gene in normal growth but was sufficient for maintaining SQR function and conferred natural resistance or reduced sensitivity toward SDHIs. Additionally, we found that the standard F. graminearum isolate PH-1 had high sensitivity to a majority of SDHIs. A single nucleotide variation (C to T) in the FgSdhC1 of isolate PH-1, resulting in a premature termination codon (TAA) replacing the fourth amino acid glutamine (Q), led to the failure of FgSdhC1 to perform functions of conferring nature resistance. These results established that a dispensable paralogous gene determined SDHIs resistance in natural populations of F. graminearum.

Discovery of Highly Efficient Novel Antifungal Lead Compounds Targeting Succinate Dehydrogenase: Pyrazole-4-carboxamide Derivatives with an N-Phenyl Substituted Amide Fragment

Developing environmentally friendly fungicides is crucial to tackle the issue of rising pesticide resistance. In this study, a series of novel pyrazole-4-carboxamide derivatives containing N-phenyl substituted amide fragments were designed and synthesized. The structures of target compounds were confirmed by 1H NMR, 13C NMR, and HRMS, and the crystal structure of the most active compound N-(1-(4-(4-(tert-butyl)benzamido)phenyl)propan-2-yl)-3-(difluoromethyl)-N-methoxy-1-methyl-1H-pyrazole-4-carboxamide (U22) was further determined by X-ray single-crystal diffraction. The bioassay results indicated that the 26 target compounds possessed good in vitro antifungal activity against Sclerotinia sclerotiorum with EC50 values for compounds U12, U13, U15, U16, U18, U22, and U23 being 4.17 ± 0.46, 8.04 ± 0.71, 7.01 ± 0.71, 12.77 ± 1.00, 8.11 ± 0.70, 0.94 ± 0.11, and 9.48 ± 0.83 μg·mL-1, respectively, which were the similar to controls bixafen (6.70 ± 0.47 μg·mL-1), fluxapyroxad (0.71 ± 0.14 μg·mL-1), and pydiflumetofen (0.06 ± 0.01 μg·mL-1). Furthermore, in vivo antifungal activity results against S. sclerotiorum indicated that compounds U12 (80.6%) and U22 (89.9%) possessed excellent preventative efficacy at 200 μg·mL-1, which was the same as the control pydiflumetofen (82.4%). Scanning electron microscopy and transmission electron microscopy studies found that the compound U22 could destroy the hyphal morphology and damage mitochondria, cell membranes, and vacuoles. The results of molecular docking of compound U22 and pydiflumetofen with succinate dehydrogenase (SDH) indicated they interact well with the active site of SDH. This study validated our approach and design strategy to produce compounds with an enhanced biological activity as compared to the parent structure.

Impact of Exposure to Pyraclostrobin and to a Pyraclostrobin/Boscalid Mixture on the Mitochondrial Function of Human Hepatocytes

Fungicides are widely used in agriculture for crop protection. Succinate dehydrogenase inhibitors (SDHIs) and strobilurins inhibit mitochondria electron transport chain (ETC) in fungi, by blocking complex II and complex III, respectively. Questions regarding their selectivity of action for fungi have been raised in the literature, and we previously showed that boscalid and bixafen (SDHIs) alter the mitochondrial function of human hepatocytes. Here, we analyzed the impact of the exposure of human hepatocytes to pyraclostrobin, a fungicide belonging to the class of strobilurins. Using electron paramagnetic resonance (EPR), we observed a decrease in oxygen consumption rate (OCR) and an increase in mitochondrial superoxide levels after 24 h exposure to 0.5 µM concentration. As a consequence, the content in ATP amount in the cells was reduced, the ratio reduced/oxidized glutathione was decreased, and a decrease in cell viability was observed using three different assays (PrestoBlue, crystal violet, and annexin V assays). In addition, as SDHIs and strobilurins are commonly associated in commercial preparations, we evaluated a potential "cocktail" toxic effect. We selected low concentrations of boscalid (0.5 µM) and pyraclostrobin (0.25 µM) that did not induce a mitochondrial dysfunction in liver cells when used separately. In sharp contrast, when both compounds were used in combination at the same concentration, we observed a decrease in OCR, an increase in mitochondrial superoxide production, a decrease in the ratio reduced/oxidized glutathione, and a decrease in cell viability in three different assays.

Resistance Profiles of Botrytis cinerea to Fluxapyroxad from Strawberry Fields in Shanghai, China

Fluxapyroxad, a type of succinate dehydrogenase inhibitor fungicide, has been used to control the growth of gray mold on strawberry for more than 5 years in China. Selection for resistance to the causal agent Botrytis cinerea became a threat to the efficacy of fluxapyroxad. In total, 160 B. cinerea isolates collected from Shanghai during 2020 and 2021 were tested for their resistance to fluxapyroxad using mycelial growth inhibition. The results indicated that the curve of baseline sensitivity was unimodal, with an approximately normal distribution and a mean effective concentration of the fungicide that inhibited growth by 50% (EC50) of 0.18 ± 0.01 μg/ml. In total, 27.78 and 48.57% of isolates were resistant to fluxapyroxad in 2020 and 2021, respectively, where the lowest EC50 value of mycelial growth inhibition was 0.03 μg/ml and the highest value was 51.3 μg/ml. Resistance mechanism analysis showed that the succinate dehydrogenase subunit B (SdhB) N230I mutation could lead to resistance and P225F mutation could lead to higher resistance. These data suggest that the resistance frequency of B. cinerea isolates to fluxapyroxad increased in 2021 compared with 2020, which requires appropriate fungicide rotation strategies to be implemented in order to control gray mold on strawberry in the future.

Design, Synthesis, and Evaluation of Antifungal Bioactivity of Novel Pyrazole Carboxamide Thiazole Derivatives as SDH Inhibitors

Agricultural production is seriously threatened by plant pathogens. The development of new fungicides with high efficacy and low toxicity is urgently needed. In this study, a series of pyrazole carboxamide thiazole derivatives were designed, synthesized, and evaluated for their antifungal activities against nine plant pathogens in vitro. Bioassay results showed that most compounds (3i, 5i, 6i, 7i, 9i, 12i, 16i, 19i, and 23i) exhibited good antifungal activities against Valsa mali. In particular, compounds 6i and 19i exhibited better antifungal activities against Valsa mali with EC₅₀ values of 1.77 and 1.97 mg/L, respectively, than the control drug boscalid (EC₅₀ = 9.19 mg/L). Additionally, compound 23i exhibited excellent inhibitory activity against Rhizoctonia solani, with an EC₅₀ value of 3.79 mg/L. Compound 6i at 40 mg/L showed a satisfactory in vivo protective effect against Valsa mali. Scanning electron microscopy analyses revealed that compound 6i could significantly damage the surface morphology to interfere with the growth of Valsa mali. In molecular docking, the results showed that compound 6i interacts with TRP O: 173, SER P: 39, TYR Q: 58, and ARG P: 43 of succinate dehydrogenase (SDH) through hydrogen bonding and σ-π interaction, and its binding mode is similar to that of boscalid and SDH. The enzyme activity experiment also further verified its action mode. Our studies suggested that pyrazole carboxamide thiazole derivative 6i provided a valuable reference for the further development of succinate dehydrogenase inhibitors.

Risk Evaluation of Benzovindiflupyr Resistance of Verticillium dahliae Population in Maine

Verticillium dahliae causes Verticillium wilt, resulting in significant losses to potato production. Benzovindiflupyr, a succinate dehydrogenase inhibitor, effectively controls V. dahliae. However, frequent applications of the chemical may expedite the development of fungicide resistance in the pathogen population. To evaluate the risk of benzovindiflupyr resistance, 38 V. dahliae strains were obtained from diseased potatoes in Maine. The sensitivity of the field population was determined based on effective concentration for 50% inhibition (EC₅₀), which ranged from 0.07 to 11.28 μg ml^-1 with a median of 1.08. Segregated clusters of EC₅₀ values indicated that Maine V. dahliae populations have developed benzovindiflupyr resistance. By exposing conidia of V. dahliae to a high concentration of benzovindiflupyr, 18 benzovindiflupyr-resistant mutants were obtained. To examine their fitness, the mutants were continuously subculture-transferred for up to 10 generations. Mycelial growth, conidial production, competitiveness, pathogenicity, and cross resistance of the 10th generation mutants were examined. Results showed that 50% of the resistant mutants retained an adaptive level in mycelial growth, and 60% maintained conidial production similar to their parents. Pathogenicity did not change for any of the mutants. No cross resistance was detected between benzovindiflupyr and either azoxystrobin, boscalid, fluopyram, or pyrimethanil. Thus, the resistance risk in V. dahliae to benzovindiflupyr should be considered in Maine potato production.

Fungicide sensitivity levels in the Lithuanian Zymoseptoria tritici population in 2021

Zymoseptoria tritici causes the disease known as septoria leaf blotch in winter wheat and is a major factor in yield loss worldwide. Farmers are inclined to use fungicides to protect their crops; however, the efficacy of these measures is rapidly decreasing due to the natural mechanisms of mutation emergence in pathogen populations. Increasing fungicide resistance is being recorded worldwide, therefore, screening of the current situation in Lithuania is essential to determine the subsequent steps of crop protection strategies. In this study, in vitro fungicide sensitivity tests, mutation detection, and field experiments were carried out. The mean EC₅₀ values for prothioconazole-desthio and mefentrifluconazole were 0.14 and 0.28 mg/l, respectively. Increased frequency of the mutation S524T, linked to DMIs resistance, was observed. Results revealed that the dominant point mutation in the gene CYP51 was I381V, and the most frequent CYP51 haplotype was D13 (V136C, I381V, Y461H, S524T). The mutation G143A, linked to QoI resistance, was detected in ¾ of the population. Mutations conferring resistance to SDHIs were not detected in single pycnidium isolates. Two-year field experiments likewise showed no decline in field efficacy of SDHI fungicide in Lithuania. Moreover, the baseline sensitivity of the Lithuanian Z. tritici population to QiI fungicide fenpicoxamid was established. The findings of this study provide an update on the current status of fungicide resistance in the Lithuanian Z. tritici population.

Chronic toxic effects of isoflucypram on reproduction and intestinal energy metabolism in zebrafish (Danio rerio)

The intestine is a vital organ involved in chemical and nutrient uptake and biotransformation. Intestinal dysfunction can impair energy and material supply for reproduction. Isoflucypram, a new succinate dehydrogenase inhibitor fungicide, is highly toxic to aquatic systems. However, the chronic toxic effects of isoflucypram on intestinal differentiation in aquatic organisms remain unknown. In this study, zebrafish (F0, 4-month-old) were exposed to 0, 0.008, or 0.08 μM isoflucypram for 120 days. After 90 days of exposure, F0 generations of adult zebrafish were paired, and the corresponding F1 generation embryos were obtained and observed. After 120 days of exposure, the gut of F0 generation zebrafish was collected, and intestinal histopathology and mitochondrial morphology were analyzed. Exposure to 0.08 μM isoflucypram resulted in significant death, hatching delay, and malformation (blood clot clustering, pericardial edema, and microphthalmia) of F1 embryos and larvae. Exposure to isoflucypram caused irregular and swollen villi in the zebrafish gut, accompanied by alterations in the intestinal mitochondrial ultrastructure. In addition, the differentially expressed genes involved in mitochondrial energy metabolism were significantly enriched. Overall, our data suggest that chronic exposure to isoflucypram is associated with reproductive and intestinal dysfunction in adult zebrafish.

Functional characterization of MoSdhB in conferring resistance to pydiflumetofen in blast fungus Magnaporthe oryzae

BACKGROUND

Rice (Oryza sativa) is an important cereal crop around the world, and has constantly been threaten by the most destructive fungus Magnaporthe oryzae. Pydiflumetofen, a novel succinate dehydrogenase inhibitor (SDHI), is currently being used for controlling various fungal diseases. However, the potential resistance risk of M. oryzae to pydiflumetofen has remained unclear to date, and finding the resistance mechanism is critical for the usage of this fungicide.

RESULTS

The M. oryzae strain Guy11 is sensitive to pydiflumetofen, with EC₅₀ value of 1.24 μg mL^-1 . 58 pydiflumetofen-resistant (PR) mutants were obtained through pydiflumetofen-induced spontaneous mutation, with a mean EC₅₀ value >500 μg mL ^-1 , and the resistance factor (RF) >400. The PR mutants displayed positive cross-resistance to carboxin, but were more sensitive to fluopyram. Sequencing analysis showed that all PR mutants presented a cytosine-to-thymine transition at nucleotide position +1218, resulting in a replacement of histidine 245 by tyrosine (H245Y) on MoSdhB. The mutation of MoSdhB exhibited strong resistant phenotype, but no detectable growth deficits in fungal development, including vegetative growth and pathogenicity of M. oryzae. An allele-specific PCR for rapid detection of the H245Y mutants was established in M. oryzae.

CONCLUSION

The M. oryzae is sensitive to pydiflumetofen, and shows a medium to high resistance risk to pydiflumetofen. A point mutation of MoSdhB (H245Y) is responsible for the fungal resistance to pydiflumetofen in M. oryzae. © 2022 Society of Chemical Industry.

Succinate dehydrogenase inhibitor seed treatments positively affect the physiological condition of maize under drought stress

Improvements in agricultural production are needed, as the growing human population demands more resources and exerts stronger effects on climate. Water scarcity is one of the main factors limiting the yield of maize in many regions of the world. One possible method to mitigate the negative effects of drought is seed mortars; its use improves plant development from the early stages onwards. In this study, we tested 12 various seed treatments with and without succinate dehydrogenase inhibitors (SDHI; sedaxane) on maize "SY Fanatic." Physiological parameters of germinating seeds, of young maize seedlings under drought, and of seedlings recuperated from drought were assessed and compared across 12 seed treatments and with non-stressed plants. The seed treatments varied greatly in their influence on the germination and the physiological state of seedlings under drought and after regeneration. Seeds under treatments No. 6, 11, and 12 showed the highest germination energy (97.3%). The use of SDHI-containing seed treatments significantly improved the development of the maize root system. The longest roots, ~13 cm in length, were recorded for treatments No. 6 and 12, both containing sedaxane. These treatments also boosted the functioning of plants growing under optimal soil moisture conditions and under drought stress, influencing the photosynthesis process, increasing the absorption of CO₂, and improving the parameters of chlorophyll fluorescence in relation to non-treated controls. Our data indicated that using substances from the SDHI group can possibly reduce the drought-related stress reactions in maize, helping this important crop to face the progressing climate change.

Aggressiveness of Small-Spored Alternaria spp. and Their Sensitivity to Succinate Dehydrogenase Inhibitor Fungicides

Brown leaf spot of potato is caused by a number of small-spored Alternaria spp. Alternaria alternata sensu stricto, A. arborescens, and A. tenuissima have been reported with increasing frequency in commercial potato fields. Potato cultivars with resistance to small-spored Alternaria spp. have yet to be developed; therefore, the application of foliar fungicides is a primary management strategy. Greenhouse inoculation assays demonstrated that isolates of these three small-spored Alternaria spp. were pathogenic. Significant differences in aggressiveness were observed across isolates; however, there was no trend in aggressiveness based on species. Significant fungicide by isolate interactions in in vitro fungicide sensitivity and significant differences between baseline and nonbaseline isolates were observed in all three small-spored Alternaria spp. The ranges of in vitro sensitivity of A. alternata baseline isolates to boscalid (EC₅₀ <0.010 to 0.89 µg/ml), fluopyram (<0.010 to 1.14 µg/ml) and solatenol (<0.010 to 1.14 µg/ml) were relatively wide when compared with adepidyn (<0.010 to 0.023 µg/ml). The baseline sensitivities of A. arborescens and A. tenuissima isolates to all four fungicides were <0.065 µg/ml. Between 10 and 21% of nonbaseline A. alternata isolates fell outside the baseline range established for the four succinate dehydrogenase inhibitor (SDHI) fungicides evaluated. In A. arborescens, 10 to 80% of nonbaseline isolates had higher sensitivities than the baseline. A. tenuissima isolates fell outside the baseline for boscalid (55%), fluopyram (14%), and solatenol (14%), but none fell outside the baseline range for adepidyn. Evaluations of in vivo fungicide efficacy demonstrated that most isolates were equally controlled by the four SDHI fungicides. However, reduced boscalid efficacy was observed for four isolates (two each of A. arborescens and A. tenuissima) and reduced fluopyram control was observed in one A. alternata isolate. Results of these studies demonstrate that isolates of all three species could be contributing to the brown leaf spot pathogen complex and that monitoring both species diversity and fungicide sensitivity could be advantageous for the management of brown leaf spot in potatoes with SDHI fungicides.

Retinal toxicity of isoflucypram to zebrafish (Danio rerio)

Isoflucypram is an active succinate dehydrogenase inhibitor (SDHI) fungicide. Recent studies have demonstrated that isoflucypram is toxic to non-target aquatic organisms such as zebrafish, Danio rerio. However, current knowledge of the potential risks presented by the SDHI to non-target aquatic organism remains limited. To investigate the teratogenic effects of isoflucypram on retinogenesis, zebrafish embryos were exposed to isoflucypram (0.025, 0.25, and 2.5 μM) from the blastula stage (3 h post-fertilization, hpf) to the larval stage (96 hpf). Prolonged exposure to isoflucypram induced abnormalities in retinal development in zebrafish larvae, resulted in the expression of a microphthalmic phenotype, disrupted retinal lamination, and altered the expression levels of retinal markers (opn1sw1, opn1sw2, opn1mw1, opn1lw1, rho, atoh7, vsx1, prox1a, and sox2). Retinal cell apoptosis was also significantly higher in the isoflucypram-exposed larvae than in the control larvae. Catalase activity decreased significantly and malondialdehyde content increased markedly after exposure to isoflucypram. Thus, isoflucypram should be regarded as having retinal neurotoxicity in zebrafish.

Sensitivity of Rhizoctonia solani Anastomosis Group 2-2 Isolates from Soybean and Sugar Beet to Selected SDHI and QoI Fungicides

Rhizoctonia solani causes root and stem diseases on soybean and sugar beet, and fungicides are commonly used to manage these diseases. Quinone outside inhibitor (QoI) fungicides (pyraclostrobin and azoxystrobin) have been used for in-furrow and postemergence application since 2000. Succinate dehydrogenase inhibitor (SDHI) fungicides (sedaxane, penthiopyrad, and fluxapyroxad) became popular seed treatments after their registration in Minnesota and North Dakota between 2012 and 2016. Periodic monitoring of sensitivity to these fungicides in R. solani anastomosis group (AG) 2-2 is important to detect potential shifts in sensitivity over time. R. solani AG 2-2 isolates (n = 35) collected from soybean and sugar beet in Minnesota and North Dakota were evaluated in vitro for sensitivity. Isolates were considered as baseline or nonbaseline for the above-mentioned fungicides based on previous potential exposure. The effective concentration (EC50) required to suppress radial fungal growth by 50% was determined. The mean EC50 values for sedaxane, penthiopyrad, fluxapyroxad, and pyraclostrobin were 0.1, 0.15, 0.16, and 0.25 (µg ml-1), respectively. The mean EC50 value for azoxystrobin for 22 isolates was 0.76 to 1.56 µg ml-1; and EC50 could not be determined for 13 isolates because of <50% inhibition at the highest concentrations used. The EC50 values for the QoI fungicides did not differ significantly between baseline and nonbaseline isolates. EC50 values for SDHI fungicides were significantly higher for isolates collected from soybean than from sugar beet, and isolates collected from both crops had similar EC50 values for pyraclostrobin. All SDHI fungicides and pyraclostrobin effectively suppressed R. solani isolates from soybean and sugar beet at low concentrations in vitro.

Sensitivity assessment and SDHC-I86F mutation frequency of Phakopsora pachyrhizi populations to benzovindiflupyr and fluxapyroxad fungicides from 2015 to 2019 in Brazil

BACKGROUND

Fungicides of the succinate dehydrogenase inhibitors (SDHIs) group have been used in soybean to control Asian soybean rust (ASR) caused by Phakopsora pachyrhizi. Fungal populations with less sensitivity to SDHI fungicides have been reported since 2015.

RESULTS

In this study, fungal sensitivity to benzovindiflupyr (BZV) and fluxapyroxad (FXD) was assessed using a total of 770 P. pachyrhizi populations sampled over four soybean growing seasons. Cross-resistance, intrinsic activity, and frequency of SDHC-I86F mutation were also analyzed. The average effective concentration to inhibit 50% (EC₅₀ ) and SDHC-I86F frequency increased over the 2015/2016, 2016/2017, 2017/2018 and 2018/2019 soybean-seasons. Fourteen P. pachyrhizi populations had the EC₅₀ value above 10 mg L^-1 for both carboxamides. No difference was found in intrinsic active to BZV and FXD fungicides for sensitive P. pachyrhizi populations. For P. pachyrhizi classified as less sensitive BZV showed the highest fungitoxicity effect. High frequency of the C-I86F mutation was observed in samples collected in volunteer soybean plants. The maximum frequency of SDHC-I86F mutation in the population was 50% and resulting in ASR populations with low sensitivity to SDHIs. A low correlation between bioassay and SDHC-I86F mutation was observed possible due to the dikaryotic nature of rust fungi or other mutations in the other succinate dehydrogenase subunits.

CONCLUSION

The present work provides an overview of a large sampling size of P. pachyrhizi populations and their performance over the four crop seasons. The high frequency of SDHC-I86F mutation and low sensitivity to SDHIs are widely distributed in the main soybean growing regions in Brazil and present in volunteer plants in the soybean-free period. Further detailed studies are needed to identify novel point mutations affecting the effectiveness of SDHIs. © 2021 Society of Chemical Industry.

The Short-Term Exposure to SDHI Fungicides Boscalid and Bixafen Induces a Mitochondrial Dysfunction in Selective Human Cell Lines

Fungicides are used to suppress the growth of fungi for crop protection. The most widely used fungicides are succinate dehydrogenase inhibitors (SDHIs) that act by blocking succinate dehydrogenase, the complex II of the mitochondrial electron transport chain. As recent reports suggested that SDHI-fungicides could not be selective for their fungi targets, we tested the mitochondrial function of human cells (Peripheral Blood Mononuclear Cells or PBMCs, HepG2 liver cells, and BJ-fibroblasts) after exposure for a short time to Boscalid and Bixafen, the two most used SDHIs. Electron Paramagnetic Resonance (EPR) spectroscopy was used to assess the oxygen consumption rate (OCR) and the level of mitochondrial superoxide radical. The OCR was significantly decreased in the three cell lines after exposure to both SDHIs. The level of mitochondrial superoxide increased in HepG2 after Boscalid and Bixafen exposure. In BJ-fibroblasts, mitochondrial superoxide was increased after Bixafen exposure, but not after Boscalid. No significant increase in mitochondrial superoxide was observed in PBMCs. Flow cytometry revealed an increase in the number of early apoptotic cells in HepG2 exposed to both SDHIs, but not in PBMCs and BJ-fibroblasts, results consistent with the high level of mitochondrial superoxide found in HepG2 cells after exposure. In conclusion, short-term exposure to Boscalid and Bixafen induces a mitochondrial dysfunction in human cells.

Isoflucypram cardiovascular toxicity in zebrafish (Danio rerio)

Isoflucypram belongs to the new generation of succinate dehydrogenase inhibitor (SDHI) fungicides that are commonly used in crop fungal disease control. Evidence indicates that isoflucypram poses a potential risk to aquatic organisms. However, the effects of isoflucypram during early embryogenesis are not fully understood. In the present study, zebrafish embryos were exposed to 0.025, 0.25, or 2.5 μM isoflucypram for three days. Isoflucypram caused severe developmental abnormalities (yolk sac edema, pericardial edema, and blood clotting clustering), hatching delay, and decreased heart rates in zebrafish. The expression levels of cardiac-specific genes (nkx2.5, myh7, myl7, and myh6) and erythropoiesis-related genes (gata1a, hbbe1, hbbe2, and alas2) were disrupted after isoflucypram exposure. Furthermore, enrichment analysis indicated that most of the differentially expressed genes (DEGs) were enriched in heart development or hemopoiesis processes. Overall, these findings suggest that exposure to isoflucypram is associated with developmental and cardiovascular toxicity in zebrafish.

Fungicide Resistance Evolving in Ramularia collo-cygni Population in Estonia

Ramularia leaf spot caused by the fungus Ramularia collo-cygni, has recently become widespread in Estonian barley fields. Currently, disease control in barley fields relies on SDHI and DMI fungicides, which might be threatened by R. collo-cygni isolates that are well-adapted to fungicide pressure. In a two-year study, 353 R. collo-cygni isolates were collected from spring barley fields in Estonia. A total of 153 R. collo-cygni isolates were examined for sensitivity to azoles (DMIs; prothioconazole-desthio, epoxiconazole, mefentrifluconazole) and succinate dehydrogenase inhibitors (SDHIs; boscalid, fluxapyroxad). Epoxiconazole was the least effective and a new fungicide mefentrifluconazole was the most effective DMI. Among SDHIs, fluxapyroxad was more effective than boscalid. Also, single R. collo-cygni isolates with high resistance to tested fungicides occurred, which could affect fungicide control of the pathogen. The entire collection of R. collo-cygni was analysed for mutations in fungicide target proteins. Six mutations were identified in CYP51 gene, the most dominant being I381T, I384T, and S459C. Also, numerous point mutations in the SdhC gene were present. The mutation G143A in strobilurin target protein CytB dominates in over 80% of the R. collo-cygni population, confirming the low efficacy of strobilurin fungicides in barley disease control.

High frequency of fungicide resistance-associated mutations in the wheat yellow rust pathogen Puccinia striiformis f. sp. tritici

BACKGROUND

Reliance on fungicides to manage disease creates selection pressure for the evolution of resistance in fungal and oomycete pathogens. Rust fungi (Pucciniales) are major pathogens of cereals and other crops and have been classified as low-risk for developing resistance to fungicides; no case of field failure of fungicides in a cereal rust disease has yet been recorded. Recently, the Asian soybean rust pathogen, Phakopsora pachyrhizi evolved resistance to several fungicide classes, prompting us to screen a large sample of the globally widespread wheat yellow rust pathogen, Puccinia striiformis f. sp. tritici (Pst), for mutations associated with fungicide resistance.

RESULTS

We evaluated 363 Pst isolates from Europe, the USA, Ethiopia, Chile, China and New Zealand for mutations in the target genes of demethylase inhibitor (DMI; Cyp51) and succinate dehydrogenase inhibitor (SDHI; SdhB, SdhC and SdhD) fungicides. A high proportion of Pst isolates carrying a Y134F DMI resistance-associated substitution in the Cyp51 gene was found among those from China and New Zealand. A set of geographically diverse Pst isolates was also found to display a substitution in SdhC (I85V) that is homologous to that reported recently in P. pachyrhizi and linked to SDHI resistance.

CONCLUSION

The identification of resistance-associated alleles confirms that cereal rusts are not immune to fungicide resistance and that selection for resistance evolution is operating at high levels in certain locations. It highlights the need to adopt fungicide resistance management practices and to monitor cereal rust species for development of resistance. © 2021 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Development of a PacBio Long-Read Sequencing Assay for High Throughput Detection of Fungicide Resistance in Zymoseptoria tritici

Fungicide resistance has become a challenging problem in management of Septoria tritici blotch (STB), caused by Zymoseptoria tritici, the most destructive disease of winter wheat throughout western and northern Europe. To ensure the continued effectiveness of those fungicides currently used, it is essential to monitor the development and spread of such resistance in field populations of the pathogen. Since resistance to the key families of fungicides used for STB control (demethyalation inhibitors or azoles, succinate dehydrogenase inhibitors or SDHIs and Quinone outside Inhibitors or QoIs) is conferred through target-site mutations, the potential exists to monitor resistance through the molecular detection of alterations in the target site genes. As more efficient fungicides were developed and applied, the pathogen has continuously adapted through accumulating multiple target-site alterations. In order to accurately monitor these changes in field populations, it is therefore becoming increasingly important to completely sequence the targeted genes. Here we report the development of a PacBio assay that facilitates the multiplex amplification and long-read sequencing of the target gene(s) for the azole (CYP51), SDHI (Sdh B, C, and D), and QoI (cytochrome b) fungicides. The assay was developed and optimised using three Irish Z. tritici collections established in spring 2017, which capture the range of fungicide resistance present in modern European populations of Z. tritici. The sequences obtained through the PacBio assay were validated using traditional Sanger sequencing and in vitro sensitivity screenings. To further exploit the long-read and high throughput potential of PacBio sequencing, an additional nine housekeeping genes (act, BTUB, cal, cyp, EF1, GAPDH, hsp80-1, PKC, TFC1) were sequenced and used to provide comprehensive Z. tritici strain genotyping.

Field Assessment of Six Point-Mutations in SDH Subunit Genes Conferring Varying Resistance Levels to SDHIs in Clarireedia spp

Dollar spot, caused by Clarireedia spp. (formerly Sclerotinia homoeocarpa F.T. Bennett), is the most economically important turfgrass disease causing considerable damage on golf courses. While cultural practices are available for reducing dollar spot infection, chemical fungicide use is often necessary for maintaining optimal turf quality. Since the release of boscalid in 2003, the succinate dehydrogenase inhibitor (SDHI) class has become an invaluable tool for managing dollar spot. However, resistance to this class has recently been reported in Clarireedia spp. and many other plant pathogenic fungi. After SDHI field failure on four golf courses and one university research plot, a total of six unique SDH mutations conferring differential in vitro sensitivities to SDHIs have been identified in Clarireedia spp. In 2018 and 2019, turf research plots were inoculated with sensitive, non-mutated isolates of Clarireedia spp., as well as resistant isolates harboring each unique identified mutation. Fungicide efficacy trials were conducted on inoculated plots to assess differential sensitivity to five SDHI active ingredients (boscalid, fluxapyroxad, isofetamid, fluopyram, and pydiflumetofen) across mutations under field conditions. Results indicate unique mutations are associated with distinct SDHI field efficacy profiles as shown in in-vitro sensitivity assays. Isolate populations with B subunit mutations (H267Y/R) were more sensitive to fluopyram, whereas isolate populations with C subunit mutations (C-G91R, C-G150R) showed resistance to all SDHIs tested. Mutation-associated differential sensitivity observed under field conditions indicates a need for a nation-wide survey and frequent monitoring of SDHI sensitivity of dollar spot populations on golf courses in the USA. Further, the information gained from this study will be useful in providing sustainable management recommendations for controlling site-specific resistant populations of Clarireedia spp.

Succinate dehydrogenase inhibitors: in silico flux analysis and in vivo metabolomics investigations show no severe metabolic consequences for rats and humans

Succinate dehydrogenase complex II inhibitors (SDHIs) are widely used fungicides since the 1960s. Recently, based on published in vitro cell viability data, potential health effects via disruption of the mitochondrial respiratory chain and tricarboxylic acid cycle have been postulated in mammalian species. As primary metabolic impact of SDH inhibition, an increase in succinate, and compensatory ATP production via glycolysis resulting in excess lactate levels was hypothesized. To investigate these hypotheses, genome-scale metabolic models of Rattus norvegicus and Homo sapiens were used for an in silico analysis of mammalian metabolism. Moreover, plasma samples from 28-day studies with the SDHIs boscalid and fluxapyroxad were subjected to metabolome analyses, to assess in vivo metabolite changes induced by SDHIs. The outcome of in silico analyses indicated that mammalian metabolic networks are robust and able to compensate different types of metabolic perturbation, e.g., partial or complete SDH inhibition. Additionally, the in silico comparison of rat and human responses suggested no noticeable differences between both species, evidencing that the rat is an appropriate testing organism for toxicity of SDHIs. Since no succinate or lactate accumulation were found in rats, such an accumulation is also not expected in humans as a result of SDHI exposure.

Baseline and Temporal Changes in Sensitivity of Zymoseptoria tritici Isolates to Benzovindiflupyr in Oregon, U.S.A., and Cross-Sensitivity to Other SDHI Fungicides

Zymoseptoria tritici is the causal agent of Septoria tritici blotch (STB), a disease of wheat (Triticum aestivum) that results in significant yield loss worldwide. Z. tritici's life cycle, reproductive system, effective population size, and gene flow put it at high likelihood of developing fungicide resistance. Succinate dehydrogenase inhibitor (SDHI) fungicides (FRAC code 7) were not widely used to control STB in the Willamette Valley until 2016. Field isolates of Z. tritici collected in the Willamette Valley at dates spanning the introduction of SDHI (2015 to 2017) were screened for sensitivity to four SDHI active ingredients: benzovindiflupyr, penthiopyrad, fluxapyroxad, and fluindapyr. Fungicide sensitivity changes were determined by the fungicide concentration at which fungal growth is decreased by 50% (EC₅₀) values. The benzovindiflupyr EC₅₀ values increased significantly, indicating a reduction in sensitivity, following the adoption of SDHI fungicides in Oregon (P < 0.0001). Additionally, significant reduction in cross-sensitivity among SDHI active ingredients was also observed with a moderate and significant relationship between penthiopyrad and benzovindiflupyr (P = 0.0002) and a weak relationship between penthiopyrad and fluxapyroxad (P = 0.0482). No change in cross-sensitivity was observed with fluindapyr, which has not yet been labeled in the region. The results document a decrease in SDHI sensitivity in Z. tritici isolates following the introduction of the active ingredients to the Willamette Valley. The reduction in cross-sensitivity observed between SDHI active ingredients highlights the notion that careful consideration is required to manage fungicide resistance and suggests that within-group rotation is insufficient for resistance management.

Isoflucypram, the first representative of a new succinate dehydrogenase inhibitor fungicide subclass: Its chemical discovery and unusual binding mode

Succinate dehydrogenase inhibitors (SDHIs) have played a crucial role in disease control to protect cereals as well as fruit and vegetables for more than a decade. Isoflucypram, the first representative of a newly installed subclass of SDHIs inside the Fungicide Resistance Action Committee (FRAC) family of complex II inhibitors, offers unparalleled long-lasting efficacy against major foliar diseases in cereals. Herein we report the chemical optimization from early discovery towards isoflucypram and the first hypothesis of its altered binding mode in the ubiquinone binding site of succinate dehydrogenase. © 2020 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Development of a novel fungicide, pyraziflumid

Pyraziflumid is a novel succinate dehydrogenase inhibitor (SDHI) fungicide discovered and developed by Nihon Nohyaku Co., Ltd. It exhibits excellent fungicidal activities against a broad range of plant diseases and has a favorable safety profile for the Integrated Pest Management (IPM) program. This compound was found by researching the unique chemical derivatives, 3-(trifluoromethyl)pyrazine-2-carboxamides, and has good biological properties, such as preventive, residual and curative activity, and rain-fastness. Pyraziflumid was registered and launched in Japan in 2018. It was registered in South Korea in 2018 and is now under development in other countries. This paper describes the discovery, synthesis, biological activity, safety profile and mode of action of pyraziflumid.

A revised model of fungicide translaminar activity

Translaminar redistribution is valuable for fungicide activity but difficult to measure and predict. The translaminar activity of 38 fungicides active against cucumber powdery mildew was measured experimentally and used to develop a QSAR (Quantitative structure-activity relationship) model of translaminar movement from calculated parameters. Over 300 physiochemical parameters generated from energy-minimized 3D structures were considered and one-parameter, two-parameter, and five-parameter models were developed. The one-parameter lipophilicity model explained 39% of variability in translaminar activity in the full dataset but none of the variability in the small succinate dehydrogenase inhibitor (SDHI) set. Adding a polar surface area parameter to the lipophilicity parameter improved predictability to 52% and explained over 70% of the variability in the SDHI class. The expanded model with five physiochemical parameters explained more than 80% of the variability in overall translaminar redistribution. The three additional parameters were correlated with molecular size and reactivity. The models were validated with a Leave-One-Out method that showed excellent robustness (r²adj = 0.83, q² = 0.79, p < .0001) for the five-parameter model. Because the models require only calculated parameters from a 3D chemical structure, they could enable the design or selection of compounds likely to be translaminar.

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.

In vitro toxicity of fungicides with different modes of action to alfalfa anthracnose fungus, Colletotrichum destructivum

Sensitivity of 24 isolates of Colletotrichum destructivum O'Gara, collected from alfalfa plants in Serbia, to eight selected fungicides, was investigated in this study. Molecular identification and pathogenicity test of isolates tested were also performed. Fungicide sensitivity was evaluated in vitro, using mycelial growth assay method. All isolates exhibited significant pathogenicity, causing necrosis at the alfalfa seedling root tips two days after inoculation. Using the primer pair GSF1-SR1 and by comparing the amplified fragments of the tested isolates with the marker (M), the presence of the amplicon of the expected size of about 900 bp was determined for all isolates. The isolates tested in this study showed different sensitivity towards fungicides in vitro. Mycelial growth was highly inhibited by QoI (quinone outside inhibitors) fungicide pyraclostrobin (mean EC₅₀=0.39 µg mL^-1) and by DMI (demethylation-inhibiting) fungicide tebuconazole (mean EC₅₀=0.61 µg mL^-1), followed by azoxystrobin (mean EC₅₀=2.83 µg mL^-1) and flutriafol (mean EC₅₀=2.11 µg mL^-1). Multi-site fungicide chlorothalonil and MBC (methyl benzimidazole carbamate) fungicide thiophanate-methyl evinced moderate inhibition with mean EC₅₀=35.31 and 62.83 µg mL^-1, respectively. Thirteen isolates were sensitive to SDHI (succinate dehydrogenase inhibitors) fungicide boscalid and fluxapyroxad, (mean EC₅₀=0.49 and 0.19 µg mL^-1, respectively), while the rest of isolates were highly resistant.

Synthesis and biological activity of a novel fungicide, pyraziflumid

Pyraziflumid was discovered as a novel SDHI fungicide chemically characterized by the 3-(trifluoromethyl)pyrazine-2-carboxamide group. This chemical series showed particularly high fungicidal activities against a broad spectrum of plant diseases in the case of N-(biphenyl-2-yl) as well as N-(1,1,3-trimethylindan-4-yl)carboxamides. Various N-(biphenyl-2-yl)pyrazine-2-carboxamides were synthesized, and their structure-activity relationships were studied. The optimization of the fungicidal performance of the series finally led to the identification of pyraziflumid, which could control a wide range of plant diseases. In this report, details of the structure-activity relationships from the lead compound to pyraziflumid are described.

Proposal for a unified nomenclature for target-site mutations associated with resistance to fungicides

Evolved resistance to fungicides is a major problem limiting our ability to control agricultural, medical and veterinary pathogens and is frequently associated with substitutions in the amino acid sequence of the target protein. The convention for describing amino acid substitutions is to cite the wild-type amino acid, the codon number and the new amino acid, using the one-letter amino acid code. It has frequently been observed that orthologous amino acid mutations have been selected in different species by fungicides from the same mode of action class, but the amino acids have different numbers. These differences in numbering arise from the different lengths of the proteins in each species. The purpose of the present paper is to propose a system for unifying the labelling of amino acids in fungicide target proteins. To do this we have produced alignments between fungicide target proteins of relevant species fitted to a well-studied 'archetype' species. Orthologous amino acids in all species are then assigned numerical 'labels' based on the position of the amino acid in the archetype protein. © 2016 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

A pyrosequencing-based method to quantify genetic substitutions associated with resistance to succinate dehydrogenase inhibitor fungicides in Botrytis spp. populations

BACKGROUND

The genetic underlying resistance mechanisms in the population of the phytopathogenic fungus Botrytis cinerea are well documented. Specifically, several genetic substitutions associated with succinate dehydrogenase inhibitor (SDHI)-based fungicide resistance have been identified in the succinate dehydrogenase gene. The objective of the present work was to develop a molecular tool for accurate quantification of these genetic substitutions within Botrytis populations. A test using the PyroMark Q24 instrument was designed to detect and quantify five genetic substitutions associated with SDHI resistance.

RESULTS

The technique is based on sequencing by synthesis, and it generated quantitative and accurate data with a limit of quantification of a minimum of 500 spores. There was a linear relationship between the known and estimated percentages of spores with the targeted genetic substitutions and wild-type strains at ratios of 0-100%, with a 20% increment.

CONCLUSION

With the pyrosequencing assay developed in this study, a large number of Botrytis spp. individuals can be characterised in a timely fashion with greater accuracy than by commonly used methods. Hence, pyrosequencing-based methods will be useful for improving our understanding of fungicide resistance, detecting the arrival of new genetic substitutions, monitoring shifts in fungal populations and assessing the effectiveness of antiresistance strategies, and for routine monitoring of fungicide resistance.

A pleiotropic drug resistance transporter is involved in reduced sensitivity to multiple fungicide classes in Sclerotinia homoeocarpa (F.T. Bennett)

Dollar spot, caused by Sclerotinia homoeocarpa, is a prevalent turfgrass disease, and the fungus exhibits widespread fungicide resistance in North America. In a previous study, an ABC-G transporter, ShatrD, was associated with practical field resistance to demethylation inhibitor (DMI) fungicides. Mining of ABC-G transporters, also known as pleiotropic drug resistance (PDR) transporters, from RNA-Seq data gave an assortment of transcripts, several with high sequence similarity to functionally characterized transporters from Botrytis cinerea, and others with closest blastx hits from Aspergillus and Monilinia. In addition to ShatrD, another PDR transporter showed significant over-expression in replicated RNA-Seq data, and in a collection of field-resistant isolates, as measured by quantitative polymerase chain reaction. These isolates also showed reduced sensitivity to unrelated fungicide classes. Using a yeast complementation system, we sought to test the hypothesis that this PDR transporter effluxes DMI as well as chemically unrelated fungicides. The transporter (ShPDR1) was cloned into the Gal1 expression vector and transformed into a yeast PDR transporter deletion mutant, AD12345678. Complementation assays indicated that ShPDR1 complemented the mutant in the presence of propiconazole (DMI), iprodione (dicarboximide) and boscalid (SDHI, succinate dehydrogenase inhibitor). Our results indicate that the over-expression of ShPDR1 is correlated with practical field resistance to DMI fungicides and reduced sensitivity to dicarboximide and SDHI fungicides. These findings highlight the potential for the eventual development of a multidrug resistance phenotype in this pathogen. In addition, this study presents a pipeline for the discovery and validation of fungicide resistance genes using de novo next-generation sequencing and molecular biology techniques in an unsequenced plant pathogenic fungus.

A reassessment of the risk of rust fungi developing resistance to fungicides

Rust fungi are major pathogens of many annual and perennial crops. Crop protection is largely based on genetic and chemical control. Fungicide resistance is a significant issue that has affected many crop pathogens. Some pathogens have rapidly developed resistance and hence are regarded as high-risk species. Rust fungi have been classified as being low risk, in spite of sharing many relevant features with high-risk pathogens. An examination of the evidence suggests that rust fungi may be wrongly classified as low risk. Of the nine classes of fungicide to which resistance has developed, six are inactive against rusts. The three remaining classes are quinone outside inhibitors (QoIs), demethylation inhibitors (DMIs) and succinate dehydrogenase inhibitors (SDHIs). QoIs have been protected by a recently discovered intron that renders resistant mutants unviable. Low levels of resistance have developed to DMIs, but with limited field significance. Older SDHI fungicides were inactive against rusts. Some of the SDHIs introduced since 2003 are active against rusts, so it may be that insufficient time has elapsed for resistance to develop, especially as SDHIs are generally sold in mixtures with other actives. It would therefore seem prudent to increase the level of vigilance for possible cases of resistance to established and new fungicides in rusts.