Investigation of the sensitivity of Plasmopara viticola to amisulbrom and ametoctradin in French vineyards using bioassays and molecular tools

The role of selection pressure in shaping zoxamide resistance in Plasmopara viticola populations

BACKGROUND

Zoxamide, a β-tubulin inhibitor, is widely used in vineyards to control downy mildew caused by the high-risk pathogen Plasmopara viticola. This study aimed to investigate the selection of zoxamide resistance and its characterization, providing practical insights for resistance management, through a twofold approach: a quantitative assessment of selection pressure effects on oospore populations and the molecular characterization of resistance-associated mutations in P. viticola strains.

RESULTS

A total of 126 populations sampled from 57 vineyards mainly located in North-eastern Italy, were analyzed over a 6-year period (2017-2022). Based on toxicological parameters, 90% of the samples were fully sensitive to zoxamide (EC50 < 0.2 mg/L; EC95 and MIC<10 mg/L). Resistant individuals, able to germinate at 100 mg/L zoxamide, were detected in low frequency (<12%) within 13 samples. Only two samples showed a high frequency of resistant individuals (24-33%). Resistance was primarily found in vineyards treated more than four times per season with zoxamide. Partial sequencing of β-tubulin gene revealed different polymorphisms at codon 239 associated with resistant isolates: the known C239S/G mutations, with the SG genotype being predominant, and a potential novel C239T mutation, not previously reported.

CONCLUSION

This study highlighted a low risk of resistance under moderate fungicide application frequencies, indicating the importance of limiting fungicide applications to preserve sensitivity. The genetic diversity of resistance mechanisms, reflected in the various mutations in the β-tubulin gene, underscores the need for a deeper investigation into the fitness of the different genotypes to evaluate resistance spread in P. viticola populations. © 2025 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Verification of Resistance Mechanism of Mitochondrial Electron Transport Chain Complex III Inhibitors in Phytophthora sojae through Ectopic Overexpression

While Cytb point mutations are recognized as a contributing factor to the resistance of plant pathogens against mitochondrial electron transport chain (mETC) complex III inhibitors, there remains a notable absence of direct genetic transformation data. In this study, we verified that 24 point mutations increase the resistance of Phytophthora sojae to different types of mETC complex III inhibitors through ectopic expression of the PsCytb gene. Notably, S33L, F220L, and M124I mutations confer resistance to certain inhibitors, while simultaneously increasing sensitivity to other types of mETC complex III inhibitors. Molecular docking results demonstrated that variations in binding energy between PsCytb harboring different point mutations and various mETC complex III inhibitors constitute the primary mechanism underlying these negative cross-resistances. Our research findings offer strategic guidance for managing fungicide resistance and designing novel fungicides targeting mETC complex III.

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.

Sensitivity to Boscalid and Trifloxystrobin and Fitness of Corynespora cassiicola Associated with CcSdh & CcCytb in Cucumber

The extensive use of succinate dehydrogenase inhibitors (SDHIs) and quinone outside inhibitors (QoIs) has led to the development of resistance in Corynespora cassiicola, which causes corynespora leaf spot (CLS) in cucumber. In this study, the sensitivity and the resistance phenotypes to SDHIs and QoIs were monitored, and the fitness of C. cassiicola carrying CcSdh & CcCytb mutations was measured. The average 50% effective suppressive concentration (EC50) values of C. cassiicola to boscalid from 2019 to 2021 ranged from 6.65 to 24.16 μg/mL, while the average EC50 values of C. cassiicola to trifloxystrobin from 2007 to 2021 ranged from 105.11 to 462.02 μg/mL. Ten fungicide resistance phenotypes and 19 resistance genotypes were found. The D-D95E&Cytb-G143A and B-H278L&Cytb-G143A mutants presented increased fitness, while the B-H278Y&Cytb-G143A mutant showed significant fitness costs, and the other mutants presented no or slight fitness costs. These findings provide a basis for the formulation of resistance management strategies of CLS.

Resistance Risk and Novel Resistance-Related Point Mutations in Target Protein Cyt b of Florylpicoxamid in Colletotrichum truncatum

Anthracnose, caused by Colletotrichum truncatum, is an economically important disease in soybean plants. Florylpicoxamid, a novel quinone inside inhibitor (QiI) fungicide, exhibits broad spectrum activity against pathogenic ascomycete fungi. However, little is known about the development of resistance risk to florylpicoxamid and the underlying mechanisms in C. truncatum. In the current study, the sensitivities of C. truncatum isolates to florylpicoxamid were characterized, with an average EC50 value of 0.1540 ± 0.1642 μg/mL. Eleven florylpicoxamid-resistant mutants were obtained, which exhibited fitness comparable to that of the parental isolates. Florylpicoxamid treatment had a lesser impact on ATP production and the activity of the cytochrome bc1 complex in the mutants compared to the parental isolates. Overall, C. truncatum has a medium resistance risk to florylpicoxamid. Additionally, cross-resistance was not observed between florylpicoxamid and the other fungicides tested herein. Three types of point mutations in the Cyt b protein, N31S/A37V, A37V, and S207P, were found to confer varying levels of resistance to florylpicoxamid in C. truncatum, as further proved by molecular docking.

Resistance risk assessment of Rhizoctonia solani to four fungicides

BACKGROUND

Hexaconazole, thifluzamide, difenoconazole and azoxystrobin are widely used fungicides for the control of Rhizoctonia solani in China. However, few studies have assessed the sensitivity and resistance risk of R. solani to these four fungicides.

RESULTS

The sensitivities of 126 R. solani isolates to hexaconazole, thifluzamide, difenoconazole and azoxystrobin were determined, with average half maximal effective concentration (EC50) values of 0.0386, 0.0659, 0.663 and 1.508 μg mL-1, respectively. Field resistance monitoring of the four fungicides showed that the three isolates had moderate resistance to difenoconazole. Resistant mutants to the four fungicides were obtained by fungicide adaptation, and resistance could be stably inherited by most mutants. Compared with those of the parent isolates, the biological characteristics of hexaconazole-resistant mutants exhibited enhanced or similar compound fitness index (CFI), whereas most of the other mutants displayed reduced or comparable CFI. There was evidence of positive cross-resistance between hexaconazole and difenoconazole. In the presence of fungicides, the expression of the CYP51 genes in hexaconazole- and difenoconazole-resistant mutants significantly increased, the expression of SDH genes in thifluzamide-resistant mutants significantly decreased, and the expression of the Cyt b gene in azoxystrobin-resistant mutants did not significantly change.

CONCLUSION

Based on these data, we speculated that R. solani had a low-to-medium resistance risk to four fungicides. The change of target gene expression may be one of the reasons for fungicide resistance in R. solani. This study provides a theoretical basis for monitoring resistance emergence and developing resistance management strategies to control R. solani. © 2024 Society of Chemical Industry.

Droplet Digital PCR: A New Molecular Method to Detect G1105S/V Mutations in Plasmopara viticola CesA3 Gene

Plasmopara viticola is the causal agent of Grapevine Downy Mildew (GDM), which is a devastating disease of grapevines in humid temperate regions. The most employed method for protecting grapevines against GDM is the application of chemical fungicides. In Spain, Carboxylic Acid Amides (CAAs) are a fungicide group currently utilized in GDM control. In P. viticola, resistance to CAAs is conferred by G1105S and G1105V mutations in the CesA3 gene. Droplet digital polymerase chain reaction (ddPCR) is an innovative technique that combines PCR and droplet microfluidics to disperse the sample into thousands of water-in-oil droplets in which an amplification reaction is individually performed. In this study, we set up a ddPCR protocol to quantify S1105 and V1105 mutations conferring resistance to CAAs in P. viticola. The optimal PCR conditions were established, and the sensitivity and precision of the protocol were assessed. Four P. viticola populations coming from commercial vineyards in northern Spain were analyzed, and different allele frequencies were found in the analyzed samples corresponding to the different fungicide management strategies, ranging from 7.72% to 100%. Knowing the level of mutated alleles allows for designing resistance management strategies suited for each location. This suggests that similar ddPCR assays could be developed for studying mutations implicated in fungicide resistance in other fungicide groups and plant pathogens.

Advances in viticulture via smart phenotyping: current progress and future directions in tackling soil copper accumulation

Modern viticulture faces significant challenges including climate change and increasing crop diseases, necessitating sustainable solutions to reduce fungicide use and mitigate soil health risks, particularly from copper accumulation. Advances in plant phenomics are essential for evaluating and tracking phenotypic traits under environmental stress, aiding in selecting resilient vine varieties. However, current methods are limited, hindering effective integration with genomic data for breeding purposes. Remote sensing technologies provide efficient, non-destructive methods for measuring biophysical and biochemical traits of plants, offering detailed insights into their physiological and nutritional state, surpassing traditional methods. Smart phenotyping is essential for selecting crop varieties with desired traits, such as pathogen-resilient vine varieties, tolerant to altered soil fertility including copper toxicity. Identifying plants with typical copper toxicity symptoms under high soil copper levels is straightforward, but it becomes complex with supra-optimal, already toxic, copper levels common in vineyard soils. This can induce multiple stress responses and interferes with nutrient acquisition, leading to ambiguous visual symptoms. Characterizing resilience to copper toxicity in vine plants via smart phenotyping is feasible by relating smart data with physiological assessments, supported by trained professionals who can identify primary stressors. However, complexities increase with more data sources and uncertainties in symptom interpretations. This suggests that artificial intelligence could be valuable in enhancing decision support in viticulture. While smart technologies, powered by artificial intelligence, provide significant benefits in evaluating traits and response times, the uncertainties in interpreting complex symptoms (e.g., copper toxicity) still highlight the need for human oversight in making final decisions.

Sensitivity of Plasmopara viticola to selected fungicide groups and the occurrence of the G143A mutant in Australian grapevine isolates

BACKGROUND

Grapevine downy mildew, caused by Plasmopara viticola, is an economically important disease in Australia and worldwide. The application of fungicides is the main tool to control this disease. Frequent fungicide applications can lead to the selection of resistant P. viticola populations, which has negative impacts on the management of the disease. Identification of resistance and its prevalence is necessary to inform resistance management strategies.

RESULTS

A total of 86 P. viticola isolates were collected between 2017 and 2022 from vineyards in 15 growing regions across Australia for four fungicide groups; phenylamide (PA, group 4), carboxylic acid amide (CAA, group 40), quinone outside inhibitor (QoI, group 11) and quinone outside inhibitor stigmatellin binding type (QoSI, group 45). Decreased phenotypic sensitivity was detected for all four groups, and resistance to metalaxyl-M (PA) and pyraclostrobin (QoI), was detected. Genetic analysis to detect the G143A (QoI) and G1105S (CAA) mutations using amplicon-based sequencing was performed for 239 and 65 isolates collected in 2014-2017 and 2017-2022, respectively. G143A was detected in 8% and 52% of isolates, respectively, with strong association to phenotypic resistance. However, G1105S was not detected in any isolates.

CONCLUSION

Plasmopara viticola isolates in Australia with resistance to at least two fungicide groups have been detected, therefore it is necessary to adopt resistance management strategies where resistance has been detected. Vineyards should continue to be monitored to improve management strategies for downy mildew. © 2024 Society of Chemical Industry.

Ametoctradin resistance risk and its resistance-related point mutation in PsCytb of Phytophthora sojae confirmed using ectopic overexpression

Ametoctradin is mainly used to treat plant oomycetes diseases, but the mechanism and resistance risk of ametoctradin in Phytophthora sojae remain unknown. This study determined the ametoctradin sensitivity of 106 P. sojae isolates and found that the frequency distribution of the median effective concentration (EC50) of ametoctradin was unimodal with a mean value of 0.1743 ± 0.0901 μg/mL. Furthermore, ametoctradin-resistant mutants had a substantially lower fitness index compared with that of wild-type isolates. Although ametoctradin did not show cross-resistance to other fungicides, negative cross-resistance to amisulbrom was found. In comparison to sensitive isolates, the control efficacy of ametoctradin to resistant mutants was lower, implying a low to moderate ametoctradin resistance risk in P. sojae. All ametoctradin-resistant mutants contained a S33L point mutation in PsCytb. A system with overexpression of PsCytb in the nucleus was established. When we ectopically overexpressed S33L-harboring PsCytb, P. sojae developed ametoctradin resistance. We hypothesized that the observed negative resistance between ametoctradin and amisulbrom could be attributed to conformational changes in the binding cavity of PsCytb at residues 33 and 220.

Evaluation of Amisulbrom Products for the Management of Clubroot of Canola (Brassica napus)

Clubroot, caused by Plasmodiophora brassicae, is an important disease of canola (Brassica napus). Amisulbrom, a quinone inside inhibitor (QiI), was evaluated for its effectiveness in clubroot management in Alberta, Canada. Resting spores of P. brassicae were treated in vitro with 0, 0.01, 0.1, 1, and 10% (w/v) amisulbrom to determine its effect on spore germination and viability. Amisulbrom inhibited resting spore germination by up to 79% and reduced viable spores by 31% relative to the control. Applications of a liquid solution (AL1000, 1000 g active ingredient (ai) ha-1) and granular formulations (AF700, 700 g ai ha-1; AF1000, 1000 g ai ha-1; AF1500, 1500 g ai ha-1) of amisulbrom were tested on the canola cultivars '45H31' (clubroot-susceptible) and 'CS2000' (moderately resistant) under greenhouse conditions and in field experiments in 2019 and 2020. In the greenhouse, the treatments were evaluated at inoculum concentrations of 1 × 105 or 1 × 107 resting spores g-1 soil. A trend of decreasing clubroot severity with an increasing amisulbrom rate was observed. At the lower spore concentration, treatment with AF1500 resulted in a clubroot disease severity index (DSI) <20% for both cultivars, while the lowest DSI under both low and high spore concentrations was obtained with AL1000. The field results indicated a significant reduction in DSI, with varied effects of rates and liquid vs. granular formulations. The greatest reductions (up to 58.3%) in DSI were obtained with AF1500 and AL1000 in 2020. These findings suggest that amisulbrom holds promise as part of an integrated clubroot management approach.

Only One of Three Bcs1 Homologs in Aspergillus fumigatus Confers Respiratory Growth

The mitochondrial translocase Bcs1 is required for the correct assembly of complex III of the mitochondrial respiratory chain. Because of its importance, Bcs1 was recently proposed as a target for antifungal agents. The function of this AAA (ATPase Associated with diverse cellular Activities) protein has been extensively characterized in Saccharomyces cerevisiae. This yeast as well as previously studied mammals each encode only one homolog. In contrast, the pathogenic mold Aspergillus fumigatus encodes three putative Bcs1 homologs, none of which have been characterized to date. To study the role of these three homologs in A. fumigatus, conditional and deletion mutants of the respective genes AFUA_3G13000 (bcs1A), AFUA_4G01260 (bcs1B), and AFUA_2G14760 (bcs1C) were generated. A deletion or downregulation of bcs1A resulted in drastically reduced growth and sporulation rates and in a significantly altered susceptibility to azole antifungals. In contrast, mutants lacking Bcs1B or Bcs1C did not show any phenotypes differing from the wild type. Salicylhydroxamic acid-an inhibitor of the alternative oxidase that allows the respiratory chain to bypass complex III in some species-caused a complete growth arrest of the bcs1A deletion mutant. In a Galleria mellonella infection model, the deletion of bcs1A resulted in significantly decreased virulence. Only Bcs1A was able to partially complement a deletion of BCS1 in S. cerevisiae. The subcellular localization of Bcs1B and Bcs1C outside of mitochondria suggests that these Bcs1 homologs exert cellular functions different from that of Bcs1. Our data demonstrate that Bcs1A is the sole Bcs1 ortholog in A. fumigatus.

Resistance risk and resistance-related point mutations in cytochrome b of florylpicoxamid in Colletotrichum scovillei

Anthracnose caused by Colletotrichum scovillei is one of the most destructive diseases of chili worldwide. Florylpicoxamid is a new quinone inside inhibitor (QiI) fungicide, which shows intensively inhibitory activity against C. scovillei. Currently, florylpicoxamid is in the registration process to control chili anthracnose in China. This study investigated the risk of resistance and resistance genetic mechanism of C. scovillei to florylpicoxamid. Baseline sensitivity of 141C. scovillei isolates to florylpicoxamid was established with an average EC50 value of 0.2328 ± 0.0876 μg/mL. A total of seven stable florylpicoxamid-resistant mutants were obtained with resistance factors ranging from 41 to 276. The mutants showed similar or weaker traits in mycelial growth, sporulation, conidial germination and pathogenicity than their parental isolates. Generally, the resistance risk of C. scovillei to florylpicoxamid would be moderate. In addition, there was no cross-resistance between florylpicoxamid and the commercially available fungicides tested. A37V and S207L mutations in the cytochrome b protein were detected in four high-resistance and three moderate-resistance mutants, respectively, of which, S207L is a new mutation. Molecular docking showed that the two mutations conferred different resistance levels to florylpicoxamid. These results provide a new perspective for QiI fungicide-resistance mechanism and may help in the reasonable use of florylpicoxamid against chili anthracnose in the future.

Resistance Risk and Resistance-Related Point Mutations in Target Protein Cyt b of the Quinone Inside Inhibitor Amisulbrom in Phytophthora litchii

Amisulbrom is a novel quinone inside inhibitor, which exhibits excellent inhibitory activity against phytopathogenic oomycetes. However, the resistance risk and mechanism of amisulbrom in Phytophthora litchii are rarely reported. In this study, the sensitivity of 147 P. litchii isolates to amisulbrom was determined, with an average EC₅₀ of 0.24 ± 0.11 μg/mL. The fitness of resistant mutants, obtained by fungicide adaption, was significantly lower than that of the parental isolates in vitro. Cross-resistance was detected between amisulbrom and cyazofamid. Amisulbrom could not inhibit the cytochrome bc1 complex activity with H15Y and G30E + F220L point mutations in cytochrome b (Cyt b) in vitro. Molecular docking indicated that the H15Y or G30E point mutation can decrease the binding energy between amisulbrom and P. litchii Cyt b. In conclusion, P. litchii might have a medium resistance risk to amisulbrom, and a novel point mutation H15Y or G30E in Cyt b could cause high amisulbrom resistance in P. litchii.

Baseline sensitivity and control efficacy of a new QiI fungicide, florylpicoxamid, against Botrytis cinerea

BACKGROUND

Gray mold caused by Botrytis cinerea is an airborne plant pathogen with a necrotrophic lifestyle that infects more than 200 crops worldwide. Florylpicoxamid is a second-generation picolinamide fungicide inspired by a natural product. Florylpicoxamid targets the Qi site of the mitochondrial cytochrome bc1 complex and is currently being registered in China for the control of gray mold in a variety of crops. Although a broad spectrum of activity and attributes have been reported for florylpicoxamid, little is known about its effectiveness against gray mold or its protective and curative properties.

RESULTS

Florylpicoxamid exhibited substantial inhibitory activity against 12 tested species of plant-pathogenic fungi, with effective concentration for 50% growth inhibition (EC₅₀ ) values ranging from 0.017 to 2.096 μg ml^-1 . A total of 129 isolates of B. cinerea from ten regions were tested for their sensitivity to florylpicoxamid, and the mean EC₅₀ value was 0.04 ± 0.017 μg ml^-1 . Furthermore, florylpicoxamid was observed to substantially inhibit all developmental stages of B. cinerea, with mycelial development, sclerotium germination, germ tube elongation and conidial germination being restrained with an EC₅₀ value of 0.051 ± 0.0072, 0.012 ± 0.0069, 0.019 ± 0.0041 and 0.0062 ± 0.0007 μg ml^-1 , respectively. No cross-resistance was observed between florylpicoxamid and quinone outside inhibitor (QoI), methyl benzimidazole carbamates or succinate dehydrogenase inhibitor. Florylpicoxamid also exhibited protective and curative activity against the development of B. cinerea infection in tests on tomato fruits. At application rates of 90, 112.5 and 135 g a.i. ha^-1 , florylpicoxamid was also observed to provide more-effective control than boscalid (300 g a.i. ha^-1 ).

CONCLUSION

This study demonstrated that the novel fungicide florylpicoxamid exhibits strong inhibitory activity against B. cinerea, regardless of the resistance profiles of those isolates to tested fungicides with different modes of action. This makes florylpicoxamid a powerful new solution to optimize gray mold control and manage fungicide resistance. © 2022 Society of Chemical Industry.

Baseline sensitivity of European Zymoseptoria tritici populations to the complex III respiration inhibitor fenpicoxamid

BACKGROUND

Fenpicoxamid is a recently developed fungicide belonging to the quinone inside inhibitor (QiI) group. This is the first fungicide within this group to be active against the Zymoseptoria tritici, which causes Septoria tritici blotch on wheat. The occurrence of pre-existing resistance mechanisms was monitored, using sensitivity assays and Illumina sequencing, in Z. tritici populations sampled in multiple European countries before the introduction of fenpicoxamid.

RESULTS

Although differences in sensitivity to all three fungicides tested (fenpicoxamid, fentin chloride and pyraclostrobin) existed between the isolate collections, no alterations associated with QiI resistance were detected. Among the isolates, a range in sensitivity to fenpicoxamid was observed (ratio between most sensitive/least sensitive = 53.1), with differences between the most extreme isolates when tested in planta following limited fenpicoxamid treatment. Sensitivity assays using fentin chloride suggest some of the observed differences in fenpicoxamid sensitivity are associated with multi-drug resistance. Detailed monitoring of the wider European population using Illumina-based partial sequencing of the Z. tritici also only detected the presence of G143A, with differences in frequencies of this alteration observed across the region.

CONCLUSIONS

This study provides a baseline sensitivity for European Z. tritici populations to fenpicoxamid. Target-site resistance appears to be limited or non-existing in European Z. tritici populations prior to the introduction of fenpicoxamid. Non-target site resistance mechanisms exist, but their impact in the field is predicted to be limited. © 2022 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of 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.

Interaction of picolinamide fungicide primary metabolites UK-2A and CAS-649 with the cytochrome bc1 complex Qi site: mutation effects and modelling in Saccharomyces cerevisiae

BACKGROUND

Fenpicoxamid and florylpicoxamid are picolinamide fungicides targeting the Qi site of the cytochrome bc₁ complex, via their primary metabolites UK-2A and CAS-649, respectively. We explore binding interactions and resistance mechanisms for picolinamides, antimycin A and ilicicolin H in yeast by testing effects of cytochrome b amino acid changes on fungicide sensitivity and interpreting results using molecular docking.

RESULTS

Effects of amino acid changes on sensitivity to UK-2A and CAS-649 were similar, with highest resistance associated with exchanges involving G37 and substitutions N31K and L198F. These changes, as well as K228M, also affected antimycin A, while ilicicolin H was affected by changes at G37 and L198, as well as Q22E. N31 substitution patterns suggest that a lysine at position 31 introduces an electrostatic interaction with neighbouring D229, causing disruption of a key salt-bridge interaction with picolinamides. Changes involving G37 and L198 imply resistance primarily through steric interference. G37 changes also showed differences between CAS-649 and UK-2A or antimycin A with respect to branched versus unbranched amino acids. N31K and substitution of G37 by large amino acids reduced growth rate substantially while L198 substitutions showed little effect on growth.

CONCLUSION

Binding of UK-2A and CAS-649 at the Qi site involves similar interactions such that general cross-resistance between fenpicoxamid and florylpicoxamid is anticipated in target pathogens. Some resistance mutations reduced growth rate and could carry a fitness penalty in pathogens. However, certain changes involving G37 and L198 carry little or no growth penalty and may pose the greatest risk for resistance development in the field. © 2022 Society of Chemical Industry.

Florylpicoxamid, a new picolinamide fungicide with broad spectrum activity

BACKGROUND

Following the introduction of fenpicoxamid, a natural product-based fungicide targeting the Qi site of mitochondrial cytochrome bc1 complex, a second generation fully synthetic picolinamide, florylpicoxamid, was discovered and its biological activity and attributes were characterized.

RESULTS

In vitro fungal growth inhibition assays and in planta glasshouse biological activity evaluations showed florylpicoxamid was active against 21 different plant pathogenic fungi within the phyla Ascomycota and Basidiomycota. Among the pathogens evaluated, florylpicoxamid was most potent against Zymoseptoria tritici, the causal organism of wheat leaf blotch, providing 80% growth inhibition in vitro at 0.0046 mg L^-1 and 80% disease control in planta at 0.03 mg L^-1 when applied as a preventative treatment. Florylpicoxamid was more efficacious than epoxiconazole, fluxapyroxad, and benzovindiflupyr versus a Z. tritici wild-type isolate when applied as curative and preventative treatments, with superior 10-day curative reachback activity. Analytical studies and in planta tests demonstrated that florylpicoxamid partitioned into plants quickly and showed good systemicity and translaminar activity on both monocot and dicot plants. No cross-resistance was observed between florylpicoxamid and strobilurin or azole fungicides. Florylpicoxamid exerts its preventative effect by preventing spore germination on the leaf surface and curative activity by arresting mycelial growth and pycnidia development in leaf tissue.

CONCLUSIONS

With strong broad spectrum fungicidal activity, florylpicoxamid delivers an innovative solution for growers to sustain high productivity and quality of many crops, and also provides a new option for developing effective strategies for fungicide resistance management. © 2021 Society of Chemical Industry.

Directed evolution predicts cytochrome b G37V target site modification as probable adaptive mechanism towards the QiI fungicide fenpicoxamid in Zymoseptoria tritici

Acquired resistance is a threat to antifungal efficacy in medicine and agriculture. The diversity of possible resistance mechanisms and highly adaptive traits of pathogens make it difficult to predict evolutionary outcomes of treatments. We used directed evolution as an approach to assess the resistance risk to the new fungicide fenpicoxamid in the wheat pathogenic fungus Zymoseptoria tritici. Fenpicoxamid inhibits complex III of the respiratory chain at the ubiquinone reduction site (Qi site) of the mitochondrially encoded cytochrome b, a different site than the widely used strobilurins which inhibit the same complex at the ubiquinol oxidation site (Q_o site). We identified the G37V change within the cytochrome b Q_i site as the most likely resistance mechanism to be selected in Z. tritici. This change triggered high fenpicoxamid resistance and halved the enzymatic activity of cytochrome b, despite no significant penalty for in vitro growth. We identified negative cross-resistance between isolates harbouring G37V or G143A, a Q_o site change previously selected by strobilurins. Double mutants were less resistant to both QiIs and quinone outside inhibitors compared to single mutants. This work is a proof of concept that experimental evolution can be used to predict adaptation to fungicides and provides new perspectives for the management of QiIs.

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.

Non-Target Site Mechanisms of Fungicide Resistance in Crop Pathogens: A Review

The rapid emergence of resistance in plant pathogens to the limited number of chemical classes of fungicides challenges sustainability and profitability of crop production worldwide. Understanding mechanisms underlying fungicide resistance facilitates monitoring of resistant populations at large-scale, and can guide and accelerate the development of novel fungicides. A majority of modern fungicides act to disrupt a biochemical function via binding a specific target protein in the pathway. While target-site based mechanisms such as alternation and overexpression of target genes have been commonly found to confer resistance across many fungal species, it is not uncommon to encounter resistant phenotypes without altered or overexpressed target sites. However, such non-target site mechanisms are relatively understudied, due in part to the complexity of the fungal genome network. This type of resistance can oftentimes be transient and noninheritable, further hindering research efforts. In this review, we focused on crop pathogens and summarized reported mechanisms of resistance that are otherwise related to target-sites, including increased activity of efflux pumps, metabolic circumvention, detoxification, standing genetic variations, regulation of stress response pathways, and single nucleotide polymorphisms (SNPs) or mutations. In addition, novel mechanisms of drug resistance recently characterized in human pathogens are reviewed in the context of nontarget-directed resistance.

Fantastic Downy Mildew Pathogens and How to Find Them: Advances in Detection and Diagnostics

Downy mildews affect important crops and cause severe losses in production worldwide. Accurate identification and monitoring of these plant pathogens, especially at early stages of the disease, is fundamental in achieving effective disease control. The rapid development of molecular methods for diagnosis has provided more specific, fast, reliable, sensitive, and portable alternatives for plant pathogen detection and quantification than traditional approaches. In this review, we provide information on the use of molecular markers, serological techniques, and nucleic acid amplification technologies for downy mildew diagnosis, highlighting the benefits and disadvantages of the technologies and target selection. We emphasize the importance of incorporating information on pathogen variability in virulence and fungicide resistance for disease management and how the development and application of diagnostic assays based on standard and promising technologies, including high-throughput sequencing and genomics, are revolutionizing the development of species-specific assays suitable for in-field diagnosis. Our review provides an overview of molecular detection technologies and a practical guide for selecting the best approaches for diagnosis.

Catalytic Reactions and Energy Conservation in the Cytochrome bc1 and b6f Complexes of Energy-Transducing Membranes

This review focuses on key components of respiratory and photosynthetic energy-transduction systems: the cytochrome bc1 and b6f (Cytbc1/b6f) membranous multisubunit homodimeric complexes. These remarkable molecular machines catalyze electron transfer from membranous quinones to water-soluble electron carriers (such as cytochromes c or plastocyanin), coupling electron flow to proton translocation across the energy-transducing membrane and contributing to the generation of a transmembrane electrochemical potential gradient, which powers cellular metabolism in the majority of living organisms. Cytsbc1/b6f share many similarities but also have significant differences. While decades of research have provided extensive knowledge on these enzymes, several important aspects of their molecular mechanisms remain to be elucidated. We summarize a broad range of structural, mechanistic, and physiological aspects required for function of Cytbc1/b6f, combining textbook fundamentals with new intriguing concepts that have emerged from more recent studies. The discussion covers but is not limited to (i) mechanisms of energy-conserving bifurcation of electron pathway and energy-wasting superoxide generation at the quinol oxidation site, (ii) the mechanism by which semiquinone is stabilized at the quinone reduction site, (iii) interactions with substrates and specific inhibitors, (iv) intermonomer electron transfer and the role of a dimeric complex, and (v) higher levels of organization and regulation that involve Cytsbc1/b6f. In addressing these topics, we point out existing uncertainties and controversies, which, as suggested, will drive further research in this field.

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.

Plasmopara viticola infection affects mineral elements allocation and distribution in Vitis vinifera leaves

Plasmopara viticola is one of the most important pathogens infecting Vitis vinifera plants. The interactions among P. viticola and both susceptible and resistant grapevine plants have been extensively characterised, at transcriptomic, proteomic and metabolomic levels. However, the involvement of plants ionome in the response against the pathogen has been completely neglected so far. Therefore, this study was aimed at investigating the possible role of leaf ionomic modulation during compatible and incompatible interactions between P. viticola and grapevine plants. In susceptible cultivars, a dramatic redistribution of mineral elements has been observed, thus uncovering a possible role for mineral nutrients in the response against pathogens. On the contrary, the resistant cultivars did not present substantial rearrangement of mineral elements at leaf level, except for manganese (Mn) and iron (Fe). This might demonstrate that, resistant cultivars, albeit expressing the resistance gene, still exploit a pathogen response mechanism based on the local increase in the concentration of microelements, which are involved in the synthesis of secondary metabolites and reactive oxygen species. Moreover, these data also highlight the link between the mineral nutrition and plants' response to pathogens, further stressing that appropriate fertilization strategies can be fundamental for the expression of response mechanisms against pathogens.

The Climate-Driven Genetic Diversity Has a Higher Impact on the Population Structure of Plasmopara viticola Than the Production System or QoI Fungicide Sensitivity in Subtropical Brazil

Downy mildew, caused by Plasmopara viticola, is the main disease affecting vineyards in subtropical Brazil. Here, we collected 94 P. viticola isolates from four organic and conventional vineyards in the two main grape-growing states of Brazil to evaluate the sensitivity to the quinone outside inhibitor (QoI) azoxystrobin by pheno- and genotyping assays. The impact of location, production system and sensitivity to QoI fungicides on the population genetics and structure of P. viticola was determined using 10 microsatellite markers. Cytochrome b sequencing revealed that 28 and 100% of the isolates from vineyards under organic and conventional management carried the G143A mutation, respectively. The G143A mutation was associated with high levels of azoxystrobin resistance. Three out of the 94 isolates analyzed carried the M125I alteration, not previously described in P. viticola, which was associated with a five-fold reduction in azoxystrobin sensitivity compared to wild-type isolates. Haplotype network analysis based on cytochrome b gene sequences suggested that the Brazilian populations are more closely related to the European than the North American population. A total of six haplotypes were identified, with two of them carrying the G143A mutation. Microsatellite analysis revealed high allelic and genotypic variation among the four populations. Population differentiation analyses indicated that state of origin directly influences the population biology of P. viticola, while production system and QoI sensitivity have little effect. Great genetic diversity, sexual reproduction and high levels of admixture were observed in Rio Grande do Sul State. In contrast, populations in São Paulo State were dominated by a few clonal genotypes, and no admixed genotype was detected between the two genetic pools identified in the state. This study raises the hypothesis that winter weather conditions influence the overwinter survival strategy with profound effects in the population biology of P. viticola.