Mechanisms influencing the evolution of resistance to Qo inhibitor fungicides

Flexibility and Hydration of the Qo Site Determine Multiple Pathways for Proton Transfer in Cytochrome bc1

The detailed catalytic activity of cytochrome bc1 (or respiratory complex III) and the molecular mechanism of the Q cycle remain elusive. At the Qo site, the cycle begins with oxidation of the coenzyme-Q substrate (quinol form) in a bifurcated two-electron transfer to the iron-sulfur (FeS) cluster and the heme bL center. The release of two protons during quinol oxidation and their transfer is less understood, with one proton likely delivered to the histidine side chain attached to the FeS cluster. Here, we present extensive molecular dynamics simulations with enhanced sampling of side-chain torsions at the Qo site and analyze available sequences and structures of several bc1 homologs to probe the interactions of quinol with potential proton acceptors and identify viable pathways for proton transfer. Our findings reveal that side chains at the Qo site are highly flexible and can adopt multiple conformations. Consequently, the quinol head is also flexible, adopting three distinct binding modes. Two of these modes are proximal to the heme bL and represent reactive conformations capable of electron and proton transfer, while the third, more distal mode likely, represents a prereactive state, consistent with recent cryo-EM structures of bc1 with bound coenzyme-Q. The Qo site is highly hydrated, with several water molecules bridging interactions between the quinol head and the conserved side chains Tyr147, Glu295, and Tyr297 in cytochrome b (numbering according to Rhodobacter sphaeroides), facilitating proton transfer. A hydrogen bond network and at least five distinct proton wires are established and possibly transport protons via a Grotthuss mechanism. Asp278 and propionate-A of heme bL in cytochrome b are in direct contact with external water and are proposed as the final proton acceptors. The intervening water molecules in these proton wires exhibit low mobility, and some have been resolved in recent experimental structures. These results help to elucidate the intricate molecular mechanism of the Q-cycle and pave the way to a detailed understanding of chemical proton transport in several bioenergetic enzymes that catalyze coenzyme-Q redox reactions.

Unveiling the potential: exploring the efficacy of complex III inhibitors in fungal disease control

Phytopathogenic fungi are a key challenge to maximizing crop yield and quality for a growing global population. In this review, we give an overview of representative compounds that inhibit complex III, also known as bc1 complex, covering quinone inside inhibitors, quinone outside inhibitors, and quinone inside and outside inhibitors via the stigmatellin binding mode. Novel solutions to the escalating problem of resistance are still required, therefore compounds with alternative scaffolds, alternative docking modes, different mechanisms of action and improved efficacy against complex III necessitate ongoing research. © 2024 Society of Chemical Industry.

Prevalence of Mutations Associated with QoIs, QiIs, QioSIs, and CAA Fungicide Resistance Within Plasmopara viticola in North America and a Tool to Detect CAA-Resistant Isolates

Grape downy mildew, caused by Plasmopara viticola, poses a significant threat to grape cultivation globally. Early detection of fungicide resistance is critical for effective management. This study aimed to assess the prevalence and distribution of mutations associated with resistance to quinone outside inhibitor (FRAC 11), quinone inside inhibitor (FRAC 21), carboxylic acid amide (CAA, FRAC 40), and quinone inside and outside inhibitor, stigmatellin binding mode (FRAC 45) fungicides in P. viticola populations in the eastern United States and Canada and to evaluate whether these mutations are linked to fungicide resistance correlated with specific P. viticola clades. A total of 658 P. viticola samples were collected from commercial vineyards across different states and years in the eastern United States and Canada and sequenced for the PvCesA3 and cytb genes and the internal transcribed spacer (ITS)1 region. The results showed that P. viticola clades aestivalis, vinifera, and riparia were prevalent in the eastern United States and Canada. Quinone outside inhibitor resistance was widespread, and the A-143 resistant genotype was prevalent in P. viticola clades aestivalis and vinifera. The G143A mutation did not show specificity based on clade differentiation. CAA resistance, associated with the G1105S mutation, was mainly identified in P. viticola clade aestivalis from Georgia, New York, and Ontario. G1105-S1105 mixed-genotype samples were observed in P. viticola clades vinifera and riparia from Wisconsin, Michigan, and New York. However, mutations associated with quinone inside and outside inhibitor and quinone inside inhibitor fungicides were not detected. A TaqMan probe-based assay was developed to detect the G1105S mutation in P. viticola conferring CAA fungicide resistance. The TaqMan assay demonstrated sensitivity at low DNA concentrations and specificity in distinguishing between sensitive and resistant genotypes. The assay accurately distinguished the G1105S mutation in leaf and air samples. This study provides insight into the geographic distribution of fungicide resistance in P. viticola populations and presents a reliable method for detecting CAA resistance in P. viticola. These findings can be utilized to implement effective fungicide resistance management strategies in viticulture.

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.

Genomic Surveillance and Molecular Evolution of Fungicide Resistance in European Populations of Wheat Powdery Mildew

Fungicides are used in agriculture to manage fungal infections and maintain crop yield and quality. In Europe, their application on cereals increased drastically starting from the mid 1970s, contributing to a significant improvement in yields. However, extensive usage has led to the rapid evolution of resistant pathogen populations within just a few years of fungicide deployment. Here we focus on wheat powdery mildew, a disease caused by the ascomycete fungus Blumeria graminis forma specialis tritici (Bgt). Previous research on Bgt documented the emergence of resistance to different fungicides and identified various resistance mechanisms. Yet, the frequency, distribution and evolutionary dynamics of fungicide resistance in Bgt populations remain largely unexplored. In this study, we leveraged extensive sampling and whole-genome sequencing of Bgt populations in Europe and the Mediterranean to investigate the population genetics and molecular epidemiology of fungicide resistance towards five major fungicide classes. We analysed gene sequences and copy number variation of eight known fungicide target genes in 415 Bgt isolates sampled between 1980 and 2023. We observed that mutations conferring resistance to various fungicides increased in frequency over time and had distinct geographic distributions, probably due to diverse deployment of fungicides across different regions. For demethylation inhibitor fungicides, we identified multiple independent events of resistance emergence with distinct mutational profiles, and we tracked their rapid spread in the last decades. Overall, we revealed the evolutionary and epidemiological dynamics of fungicide resistance mutations in European Bgt populations. These results underscore the potential of genomic surveillance and population genetics to enhance our understanding of fungicide resistance.

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

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

Chemical Management Strategies for Halo Blight of Hop and In Vitro Sensitivity of Diaporthe humulicola Populations to Various Fungicide Classes

Halo blight of hop, caused by Diaporthe humulicola, has increased in eastern North America since 2018. When left untreated, the disease can cause yield loss ranging from 17 to 56%. Currently, there are no fungicides registered for use on halo blight of hop. From 2020 to 2022, field trials were conducted using 10 fungicides registered for use on powdery and downy mildew of hop to determine their efficacy against halo blight. To validate field results, the effective concentration of fungicide required for 50% growth inhibition (EC50) value was determined for each active ingredient including flutriafol, tebuconazole + fluopyram, cyflufenamid, and trifloxystrobin + salicylhydroxamic acid (SHAM). Each fungicide tested had an EC50 value less than 50 ppm. A discriminatory dose was used to test the sensitivity of 206 D. humulicola isolates collected from the eastern United States and Canada in a poison agar assay. Results showed that tebuconazole + fluopyram decreased the incidence and severity of halo blight in the field. Also, this fungicide combination had EC50 values of 2.26 × 10-1 ppm and significantly reduced the growth of most of the isolates tested. Trifloxystrobin + SHAM decreased the presence of halo blight in the field trial, but some isolates were less sensitive in discriminatory dose testing. Our results show that fungicides in FRAC groups 3, 7, and 11 were the most effective to control halo blight. Analyses of field trials showed a positive correlation between the severity of early-season downy mildew infections and late-season halo blight infections.

In Vitro and in Planta Fungicide Testing for Management of Wheat Rusts

The application of fungicides is a measure complementary to host genetic resistance to control the occurrence and severity of rust diseases that has been estimated to cost over $17.25 per acre annually in wheat fields on the Canadian Prairies. The most often used fungicides include the class of demethylation inhibitors (DMIs), acting on fungal sterol biosynthesis, and the class of strobilurins (quinone outside [mitochondrial respiration] inhibitor [QoI]) acting on fungal mitochondrial respiration. Fungicides are designed to target fungal pathogens but also have been reported to trigger some effects on the host plants. Therefore, an improved diagnostic protocol is developed in this chapter for evaluating the effects and efficacy of commercial fungicides: DMI and QoI on in vitro germination of rust fungus urediniospores and rust disease development of infected, detached wheat leaves as well as whole plants. The purpose is to optimize fungicide application to better control rust fungus diseases of wheat without impacting crop growth, and while mitigating fungicide applications to minimize environmental and financial costs associated with fungicide overapplication.

Leveraging Natural Product-Inspired Antifungals to Investigate the Mechanism of Action of Peniciaculin A

Ubiquinone mimics known as quinone outside inhibitors (QoIs) are one of the most prominent fungicides used to protect crops in the agricultural industry. Due to chemotype similarities with known QoIs, peniciaculin A, a triaryl natural product, was proposed to exhibit similar broad spectrum antifungal activity against phytopathogens. Instability of the tertiary alcohol and phenol motif, however, prompted exploration of the antifungal properties of simplified analogues to probe possible overlap in mechanism of action between the natural product and QoIs. Peniciaculin A inspired analogues mimicking known QoI scaffolds displayed broad spectrum antifungal activity while those containing scaffolds dissimilar to QoIs possessed negligible bioactivity. These activity profiles suggest peniciaculin A is likely acting as a QoI.

Cryo-EM Structures Reveal the Unique Binding Modes of Metyltetraprole in Yeast and Porcine Cytochrome bc1 Complex Enabling Rational Design of Inhibitors

Cytochrome bc1 (complex III) represents a significant target for the discovery of both drugs and fungicides. Metyltetraprole (MET) is commonly classified as a quinone site inhibitor (QoI) that combats the G143A mutated isolate, which confers high resistance to strobilurin fungicides such as pyraclostrobin (PYR). The binding mode and antiresistance mechanism of MET remain unclear. Here, we determined the high-resolution structures of inhibitor-bound S. cerevisiae complex III (MET, 2.52 Å; PYR, 2.42 Å) and inhibitor-bound porcine complex III (MET, 2.53 Å; PYR, 2,37 Å) by cryo-electron microscopy. The distinct binding modes of MET and PYR were observed for the first time. Notably, the MET exhibited different binding modes in the two species. In S. cerevisiae, the binding site of MET was the same as PYR, serving as a Pm-type inhibitor of the Qo site. However, in porcine, MET acted as a dual-target inhibitor of both Qo and Qi. Based on the structural insights, a novel inhibitor (YF23694) was discovered and demonstrated excellent fungicidal activity against downy mildew and powdery mildew fungi. This work provides a new starting point for the design of the next generation of inhibitors to overcome the resistance.

Triazole Sulfonamide Derivates: Inhibitors of the bc1 Complex to Control Cucumber Downy Mildew

Cucumber downy mildew (CDM), caused by Pseudoperonospora cubensis, is a destructive disease that affects greenhouse cucumbers and causes significant losses for growers. Amisulbrom, a triazole sulfonamide fungicide targeting the Qi site in the bc1 complex, has shown potential in effectively combating CDM. However, its detailed binding mode with the target is unclear. In this study, a three-dimensional (3D) structure of the bc1 complex from P. cubensis was built, and its interaction with amisulbrom was investigated by integrating molecular docking, molecular dynamics, and molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) methods. Based on the binding mode of amisulbrom with the Pc-bc1 complex, a scaffold hopping strategy was performed, and compounds 11a-o and 12a-v were designed. Among them, compound 12g showed excellent fungicidal properties against CDM in field trials. The present work indicated that the oxime ether moiety could be further optimized for better results. Furthermore, compound 12g has the potential to serve as a lead compound in the search for new Qi-site inhibitors of the bc1 complex.

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

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

The G143S mutation in cytochrome b confers high resistance to pyraclostrobin in Fusarium pseudograminearum

BACKGROUND

Wheat crown rot (WCR), primarily caused by Fusarium pseudograminearum has become more and more prevalent in winter wheat areas in China. However, limited fungicides have been registered for the control of WCR in China so far. Pyraclostrobin is a representative quinone outside inhibitor (QoI) with excellent activity against Fusarium spp. There is currently limited research on the resistance risk and resistance mechanism of F. pseudograminearum to pyraclostrobin.

RESULTS

Here, we determined the activity of pyraclostrobin against F. pseudograminearum. The EC50 values ranged from 0.022 to 0.172 μg mL-1 with an average EC50 value of 0.071 ± 0.030 μg mL-1. Four highly pyraclostrobin-resistant mutants were obtained from two sensitive strains by ultraviolet (UV) mutagenesis in the laboratory. The mutants showed decreased mycelial growth rate and virulence as compared with the corresponding wild-type strains, indicating that pyraclostrobin resistance suffered a fitness penalty in F. pseudograminearum. It was found that the high resistance of four mutants was caused by the G143S mutation in Cytb. Molecular docking analysis also further confirms that the G143S mutation in Cytb decreased the binding affinity between pyraclostrobin and Cytb.

CONCLUSION

The resistance risk of F. pseudograminearum to pyraclostrobin could be low to medium. Although a mutation at the G143S position of Cytb could potentially occur, this mutation decreases the fitness of the mutant, which may reduce its survival in the environment. Therefore, the negative consequences of a possible mutation are lower. This makes pyraclostrobin a good candidate for controlling crown rot in wheat. © 2024 Society of Chemical Industry.

The occurrence and mechanism of field resistance to boscalid and pyraclostrobin in Stemphylium solani, the causal agent of tomato gray leaf spot in China

The destructive disease gray leaf spot, caused by Stemphylium solani, is prevalent in tomato plants in China. A variety of fungicides have been extensively used for controlling the disease, with a particular focus on succinate dehydrogenase inhibitors (SDHIs) and quinone outside inhibitors (QoIs). However, there was a lack of information regarding the resistance of S. solani to boscalid (SDHI) and pyraclostrobin (QoI) in China. In this study, the sensitivity of S. solani to boscalid and pyraclostrobin was monitored. The EC50 values for boscalid ranged from 0.02 to 3.0 μg∙mL-1, with an average value of 0.62 μg∙mL-1, while the EC50 values for pyraclostrobin ranged from 0.21 to 14.71 μg∙mL-1, with an average value of 6.03 μg∙mL-1. Based on these findings, the frequencies of observed resistance were as follows: 36.7% for boscalid and 50% for pyraclostrobin; while the resistance frequency to both boscalid and pyraclostrobin in S. solani was 19.4%. The mutation associated with boscalid resistance in S. solani within tomato fields was identified as SdhB-H277Y, while the mutation related to pyraclostrobin resistance was found in cytochrome b, specifically Cytb-G143A. The resistant mutants displayed diminished fitness in terms of mycelial growth, yet their pathogenicity exhibited no significant disparities. To delay the development of resistance, it is advisable to employ a rotation strategy using alternative fungicides with different modes of action or mix with fungicides with multi-site-contact activity for disease management.

Deciphering fungicide resistance in Phytophthora: mechanisms, prevalence, and sustainable management approaches

The genus Phytophthora contains more than 100 plant pathogenic species that parasitize a wide range of plants, including economically important fruits, vegetables, cereals, and forest trees, causing significant losses. Global agriculture is seriously threatened by fungicide resistance in Phytophthora species, which makes it imperative to fully comprehend the mechanisms, frequency, and non-chemical management techniques related to resistance mutations. The mechanisms behind fungicide resistance, such as target-site mutations, efflux pump overexpression, overexpression of target genes and metabolic detoxification routes for fungicides routinely used against Phytophthora species, are thoroughly examined in this review. Additionally, it assesses the frequency of resistance mutations in various Phytophthora species and geographical areas, emphasizing the rise of strains that are resistant to multiple drugs. The effectiveness of non-chemical management techniques, including biological control, host resistance, integrated pest management plans, and cultural practices, in reducing fungicide resistance is also thoroughly evaluated. The study provides important insights for future research and the development of sustainable disease management strategies to counter fungicide resistance in Phytophthora species by synthesizing current information and identifying knowledge gaps.

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.

Development of a Greenhouse Assay to Screen Soybean Varieties for Resistance to Aerial Blight Caused by Rhizoctonia solani Anastomosis Group 1-IA

Aerial blight, caused by the fungus Rhizoctonia solani anastomosis group (AG) 1-IA, is an economically important soybean disease in the mid-Southern United States. Management has relied on fungicide applications during the season, but there is an increasing prevalence of resistance to commonly used strobilurin fungicides and an urgent need to identify soybean varieties resistant to aerial blight. Because the patchy distribution of the pathogen complicates field variety screening, the present study aimed to develop a greenhouse screening protocol to identify soybean varieties resistant to aerial blight. For this, 88 pathogen isolates were collected from commercial fields and research farms across five Louisiana parishes, and 77% were confirmed to be R. solani AG1-IA. Three polymorphic codominant microsatellite markers were used to explore the genetic diversity of 43 R. solani AG1-IA isolates, which showed high genetic diversity, with 35 haplotypes in total and only two haplotypes common to two other locations. Six genetically diverse isolates were chosen and characterized for their virulence and fungicide sensitivity. The isolate AC2 was identified as the most virulent and was resistant to both active ingredients, azoxystrobin and pyraclostrobin, tested. The six isolates were used in greenhouse variety screening trials using a millet inoculation protocol. Of the 31 varieties screened, only Armor 48-D25 was classified as moderately resistant, and plant height to the first node influenced final disease severity. The study provides short-term solutions for growers to choose less susceptible varieties for planting and lays the foundation to characterize host resistance against this important soybean pathogen.

The fungicide pyraclostrobin affects gene expression by altering the DNA methylation pattern in Magnaporthe oryzae

Introduction

Rice blast disease caused by Magnaporthe oryzae has long been the main cause of rice (Oryza sativa L.) yield reduction worldwide. The quinone external inhibitor pyraclostrobin is widely used as a fungicide to effectively control the spread of pathogenic fungi, including M. oryzae. However, M. oryzae can develop resistance through multiple levels of mutation, such as target protein cytb mutation G143A/S, leading to a decrease in the effectiveness of the biocide after a period of application. Therefore, uncovering the possible mutational mechanisms from multiple perspectives will further provide feasible targets for drug development.

Methods

In this work, we determined the gene expression changes in M. oryzae in response to pyraclostrobin stress and their relationship with DNA methylation by transcriptome and methylome.

Results

The results showed that under pyraclostrobin treatment, endoplasmic reticulum (ER)-associated and ubiquitin-mediated proteolysis were enhanced, suggesting that more aberrant proteins may be generated that need to be cleared. DNA replication and repair processes were inhibited. Glutathione metabolism was enhanced, while lipid metabolism was impaired. The number of alternative splicing events increased. These changes may be related to the elevated methylation levels of cytosine and adenine in gene bodies. Both hypermethylation and hypomethylation of differentially methylated genes (DMGs) mainly occurred in exons and promoters. Some DMGs and differentially expressed genes (DEGs) were annotated to the same pathways by GO and KEGG, including protein processing in the ER, ubiquitin-mediated proteolysis, RNA transport and glutathione metabolism, suggesting that pyraclostrobin may affect gene expression by altering the methylation patterns of cytosine and adenine.

Discussion

Our results revealed that 5mC and 6mA in the gene body are associated with gene expression and contribute to adversity adaptation in M. oryzae. This enriched the understanding for potential mechanism of quinone inhibitor resistance, which will facilitate the development of feasible strategies for maintaining the high efficacy of this kind of fungicide.

Border cell population size and oxidative stress in the root apex of Triticum aestivum seedlings exposed to fungicides

Fungicides reduce the risk of mycopathologies and reduce the content of mycotoxins in commercial grain. The effect of fungicides on the structural and functional status of the root system of grain crops has not been studied enough. In this regard, we studied the phytocytotoxic effects tebuconazole (TEB) and epoxiconazole (EPO) and azoxystrobin (AZO) in the roots of Triticum aestivum seedlings in hydroponic culture. In the presence of EPO and AZO (but not TEB) inhibition of the root growth was accompanied by a dose-dependent increase in the content of malondialdehyde, carbonylated proteins, and proline in roots. TEB was characterized by a dose-dependent decrease in the total amount of border cells (BCs) and the protein content in root extracellular trap (RET). For EPO and AZO, the dose curves of changes in the total number of BCs were bell-shaped. AZO did not affect the protein content in RET. The protein content in RET significantly decreased by 3 times for an EPO concentration of 1 µg/mL. The obtained results reveal that the BC-RET system is one of the functional targets of fungicides in the root system of wheat seedlings. Studied fungicides induce oxidative stress and structural and functional alterations in the BC-RET system that can affect their toxicity to the root system of crops.

Mitochondrial Cytochrome bc1 Complex as Validated Drug Target: A Structural Perspective

Mitochondrial respiratory chain Complex III, also known as cytochrome bc1 complex or cyt bc1, is a validated target not only for antibiotics but also for pesticides and anti-parasitic drugs. Although significant progress has been made in understanding the mechanisms of cyt bc1 function and inhibition by using various natural and synthetic compounds, important issues remain in overcoming drug resistance in agriculture and in evading cytotoxicity in medicine. In this review, we look at these issues from a structural perspective. After a brief description of the essential and common structural features, we point out the differences among various cyt bc1 complexes of different organisms, whose structures have been determined to atomic resolution. We use a few examples of cyt bc1 structures determined via bound inhibitors to illustrate both conformational changes observed and implications to the Q-cycle mechanism of cyt bc1 function. These structures not only offer views of atomic interactions between cyt bc1 complexes and inhibitors, but they also provide explanations for drug resistance when structural details are coupled to sequence changes. Examples are provided for exploiting structural differences in evolutionarily conserved enzymes to develop antifungal drugs for selectivity enhancement, which offer a unique perspective on differential interactions that can be exploited to overcome cytotoxicity in treating human infections.

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

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

The mechanisms of target and non-target resistance to QoIs in Corynespora Cassiicola

Corynespora leaf spot, caused by Corynespora cassiicola, is a foliar disease in cucumber. While the application of quinone outside inhibitors (QoIs) is an effective measure for disease control, it carries the risk of resistance development. In our monitoring of trifloxystrobin resistance from 2008 to 2020, C. cassiicola isolates were categorized into three populations: sensitive isolates (S, 0.01 < EC50 < 0.83 μg/mL), moderately resistant isolates (MR, 1.18 < EC50 < 55.67 μg/mL), and highly resistant isolates (HR, EC50 > 56.98 μg/mL). The resistance frequency reached up to 90% during this period, with an increasing trend observed in the annual average EC50 values of all the isolates. Analysis of the CcCytb gene revealed that both MR and HR populations carried the G143A mutation. Additionally, we identified mitochondrial heterogeneity, with three isolates carrying both G143 and A143 in MR and HR populations. Interestingly, isolates with the G143A mutation (G143A-MR and G143A-HR) displayed differential sensitivity to QoIs. Further experiments involving gene knockout and complementation demonstrated that the major facilitator superfamily (MFS) transporter (CcMfs1) may contribute to the disparity in sensitivity to QoIs between the G143A-MR and G143A-HR populations. However, the difference in sensitivity caused by the CcMfs1 transporter is significantly lower than the differences observed between the two populations. This suggests additional mechanisms contributing to the variation in resistance levels among C. cassiicola isolates. Our study highlights the alarming level of trifloxystrobin resistance in C. cassiicola in China, emphasizing the need for strict prohibition of QoIs use. Furthermore, our findings shed light on the occurrence of both target and non-target resistance mechanisms associated with QoIs in C. cassiicola.

Characterization of QoI-Fungicide Resistance in Cercospora Isolates Associated with Cercospora Leaf Blight of Soybean from the Southern United States

Cercospora leaf blight (CLB) of soybean, caused by Cercospora cf. flagellaris, C. kikuchii, and C. cf. sigesbeckiae, is an economically important disease in the southern United States. Cultivar resistance to CLB is inconsistent; therefore, fungicides in the quinone outside inhibitor (QoI) class have been relied on to manage the disease. Approximately 620 isolates from plants exhibiting CLB were collected between 2018 and 2021 from 19 locations in eight southern states. A novel polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay based on two genes, calmodulin and histone h3, was developed to differentiate between the dominant species of Cercospora, C. cf. flagellaris, and C. cf. sigesbeckiae. A multilocus phylogenetic analysis of actin, calmodulin, histone h3, ITS rDNA, and transcription elongation factor 1-α was used to confirm PCR-RFLP results and identify remaining isolates. Approximately 80% of the isolates collected were identified as C. cf. flagellaris, while 15% classified as C. cf. sigesbeckiae, 2% as C. kikuchii, and 3% as previously unreported Cercospora species associated with CLB in the United States. PCR-RFLP of cytochrome b (cytb) identified QoI-resistance conferred by the G143A substitution. Approximately 64 to 83% of isolates were determined to be QoI-resistant, and all contained the G143A substitution. Results of discriminatory dose assays using azoxystrobin (1 ppm) were 100% consistent with PCR-RFLP results. To our knowledge, this constitutes the first report of QoI resistance in CLB pathogen populations from Alabama, Arkansas, Kentucky, Mississippi, Missouri, Tennessee, and Texas. In areas where high frequencies of resistance have been identified, QoI fungicides should be avoided, and fungicide products with alternative modes-of-action should be utilized in the absence of CLB-resistant soybean cultivars.

Transcriptome Analysis Reveals the Involvement of Mitophagy and Peroxisome in the Resistance to QoIs in Corynespora cassiicola

Quinone outside inhibitor fungicides (QoIs) are crucial fungicides for controlling plant diseases, but resistance, mainly caused by G143A, has been widely reported with the high and widespread use of QoIs. However, two phenotypes of Corynespora casiicola (RI and RII) with the same G143A showed significantly different resistance to QoIs in our previous study, which did not match the reported mechanisms. Therefore, transcriptome analysis of RI and RII strains after trifloxystrobin treatment was used to explore the new resistance mechanism in this study. The results show that 332 differentially expressed genes (DEGs) were significantly up-regulated and 448 DEGs were significantly down-regulated. The results of GO and KEGG enrichment showed that DEGs were most enriched in ribosomes, while also having enrichment in peroxide, endocytosis, the lysosome, autophagy, and mitophagy. In particular, mitophagy and peroxisome have been reported in medicine as the main mechanisms of reactive oxygen species (ROS) scavenging, while the lysosome and endocytosis are an important organelle and physiological process, respectively, that assist mitophagy. The oxidative stress experiments showed that the oxidative stress resistance of the RII strains was significantly higher than that of the RI strains: specifically, it was more than 1.8-fold higher at a concentration of 0.12% H2O2. This indicates that there is indeed a significant difference in the scavenging capacity of ROS between the two phenotypic strains. Therefore, we suggest that QoIs' action caused a high production of ROS, and that scavenging mechanisms such as mitophagy and peroxisomes functioned in RII strains to prevent oxidative stress, whereas RI strains were less capable of resisting oxidative stress, resulting in different resistance to QoIs. In this study, it was first revealed that mitophagy and peroxisome mechanisms available for ROS scavenging are involved in the resistance of pathogens to fungicides.

TaqMan-MGB PCR Method for Rapid Detection of QoI Fungicide Resistance in Chinese Populations of Plasmopara viticola

Grape downy mildew caused by Plasmopara viticola is one of the most devastating diseases of grapevine worldwide. Quinone outside inhibitor (QoI) fungicides are commonly used for the control of the pathogen in grape fields across China. However, their recurrent use could lead to the emergence of resistance against these compounds. Based on the most common mutation in resistant isolates, a glycine to alanine substitution at amino acid position 143 (G143A) in the cytochrome b protein, a TaqMan-MGB PCR was developed for the rapid detection of resistance to the QoI fungicide azoxystrobin in P. viticola. Specificity and sensitivity of this method showed it could specifically detect the point mutations linked with QoI resistance in P. viticola, and the detection limit was 0.2 pg. It could also quantify the resistance allele even in isolate mixtures containing as little as 5% QoI-resistant P. viticola strains. With this method, a large P. viticola population (n = 2,373) was screened, and QoI-resistant isolates were identified for the first time in China. The average frequencies of the resistant genotype from eight major-grapevine regions were up to 66%. Taken together, the results not only provide a novel tool for the rapid distinction and quantification of the QoI-resistant allele in P. viticola but also provide important references for fungicide selection and application, which will facilitate resistance management of grape downy mildew and improve grape production systems in Chinese vineyards.

ABCC Transporter Gene MoABC-R1 Is Associated with Pyraclostrobin Tolerance in Magnaporthe oryzae

Rice blast is a worldwide fungal disease that poses a threat to food security. Fungicide treatment is one of the most effective methods to control rice blast disease. However, the emergence of fungicide tolerance hampers the control efforts against rice blast. ATP-binding cassette (ABC) transporters have been found to be crucial in multidrug tolerance in various phytopathogenic fungi. This study investigated the association between polymorphisms in 50 ABC transporters and pyraclostrobin sensitivity in 90 strains of rice blast fungus. As a result, we identified MoABC-R1, a gene associated with fungicide tolerance. MoABC-R1 belongs to the ABCC-type transporter families. Deletion mutants of MoABC-R1, abc-r1, exhibited high sensitivity to pyraclostrobin at the concentration of 0.01 μg/mL. Furthermore, the pathogenicity of abc-r1 was significantly diminished. These findings indicate that MoABC-R1 not only plays a pivotal role in fungicide tolerance but also regulates the pathogenicity of rice blast. Interestingly, the combination of MoABC-R1 deletion with fungicide treatment resulted in a three-fold increase in control efficiency against rice blast. This discovery highlights MoABC-R1 as a potential target gene for the management of rice blast.

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

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

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

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

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

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

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

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

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

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

Structure of complex III with bound antimalarial agent CK-2-68 provides insights into selective inhibition of Plasmodium cytochrome bc1 complexes

Among the various components of the protozoan Plasmodium mitochondrial respiratory chain, only Complex III is a validated cellular target for antimalarial drugs. The compound CK-2-68 was developed to specifically target the alternate NADH dehydrogenase of the malaria parasite respiratory chain, but the true target for its antimalarial activity has been controversial. Here, we report the cryo-EM structure of mammalian mitochondrial Complex III bound with CK-2-68 and examine the structure-function relationships of the inhibitor's selective action on Plasmodium. We show that CK-2-68 binds specifically to the quinol oxidation site of Complex III, arresting the motion of the iron-sulfur protein subunit, which suggests an inhibition mechanism similar to that of Pf-type Complex III inhibitors such as atovaquone, stigmatellin, and UHDBT. Our results shed light on the mechanisms of observed resistance conferred by mutations, elucidate the molecular basis of the wide therapeutic window of CK-2-68 for selective action of Plasmodium vs. host cytochrome bc1, and provide guidance for future development of antimalarials targeting Complex III.

Appressoria Formation in Phytopathogenic Fungi Suppressed by Antimicrobial Peptides and Hybrid Peptides from Black Soldier Flies

Antimicrobial peptides (AMPs) from black solider flies (Hermetia illucens, BSF) exhibiting broad-spectrum antimicrobial activity are the most promising green substitutes for preventing the infection of phytopathogenic fungi; therefore, AMPs have been a focal topic of research. Recently, many studies have focused on the antibacterial activities of BSF AMPs against animal pathogens; however, currently, their antifungal activities against phytopathogenic fungi remain unclear. In this study, 7 AMPs selected from 34 predicted AMPs based on BSF metagenomics were artificially synthesized. When conidia from the hemibiotrophic phytopathogenic fungi Magnaporthe oryzae and Colletotrichum acutatum were treated with the selected AMPs, three selected AMPs-CAD1, CAD5, and CAD7-showed high appressorium formation inhibited by lengthened germ tubes. Additionally, the MIC₅₀ concentrations of the inhibited appressorium formations were 40 μM, 43 μM, and 43 μM for M. oryzae, while 51 μM, 49 μM, and 44 μM were observed for C. acutatum, respectively. A tandem hybrid AMP named CAD-Con comprising CAD1, CAD5, and CAD7 significantly enhanced antifungal activities, and the MIC₅₀ concentrations against M. oryzae and C. acutatum were 15 μM and 22 μM, respectively. In comparison with the wild type, they were both significantly reduced in terms of virulence when infection assays were performed using the treated conidia of M. oryzae or C. acutatum by CAD1, CAD5, CAD7, or CAD-Con. Meanwhile, their expression levels of CAD1, CAD5, and CAD7 could also be activated and significantly increased after the BSF larvae were treated with the conidia of M. oryzae or C. acutatum, respectively. To our knowledge, the antifungal activities of BSF AMPs against plant pathogenic fungi, which help us to seek potential AMPs with antifungal activities, provide proof of the effectiveness of green control strategies for crop production.

Antifungal Activity of Guiera senegalensis: From the Chemical Composition to the Mitochondrial Toxic Effects and Tyrosinase Inhibition

Pest resistance against fungicides is a widespread and increasing problem, with impact on crop production and public health, making the development of new fungicides an urgent need. Chemical analyses of a crude methanol extract (CME) of Guiera senegalensis leaves revealed the presence of sugars, phospholipids, phytosterols, guieranone A, porphyrin-containing compounds, and phenolics. To connect chemical composition with biological effects, solid-phase extraction was used to discard water-soluble compounds with low affinity for the C18 matrix and obtain an ethyl acetate fraction (EAF) that concentrates guieranone A and chlorophylls, and a methanol fraction (MF) dominated by phenolics. While the CME and MF exhibited poor antifungal activity against Aspergillus fumigatus, Fusarium oxysporum and Colletotrichum gloeosporioides, the EAF demonstrated antifungal activity against these filamentous fungi, particularly against C. gloeosporioides. Studies with yeasts revealed that the EAF has strong effectiveness against Saccharomyces cerevisiae, Cryptococcus neoformans and Candida krusei with MICs of 8, 8 and 16 μg/mL, respectively. A combination of in vivo and in vitro studies shows that the EAF can function as a mitochondrial toxin, compromising complexes I and II activities, and as a strong inhibitor of fungal tyrosinase (Ki = 14.40 ± 4.49 µg/mL). Thus, EAF appears to be a promising candidate for the development of new multi-target fungicides.

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.

Comparative Study of Three Biological Control Agents and Two Conventional Fungicides against Coriander Damping-off and Root Rot Caused by Rhizoctonia solani

The in vitro and in vivo efficacy of three biocontrol agents, Trichoderma viride, Pseudomonas fluorescence, and Bacillus subtilis, were tested against Rhizoctonia solani (AG-4) infection compared to two conventional fungicides (Rizolex-T 50%wettable powder and Amistar 25%). Antifungal enzyme activity was assayed in the culture filtrate of the biocontrol agents. The impact of the tested biocontrol agents on the induction of the coriander immune system was investigated against R. solani by assessing the resistance-related enzymes and compounds in biocontrol agent-treated plants compared with the control. The obtained results revealed that all tested biocontrol agents significantly reduced the linear growth of R. solani, and T. viride recorded the highest inhibition percentage. This could be linked to the ability of T. viride to produce higher activities of antimicrobial enzymes, i.e., cellulase, chitinase, and protease, compared to P. fluorescence and B. subtilis. Applying the tested biocontrol agents significantly alleviated pre- and post-emergence damping-off and root rot/wilt diseases of infected coriander compared with untreated plants. The tested biocontrol agents exhibited significantly higher germination percentage and vigor index of the coriander than the tested fungicides. The tested biocontrol agents significantly minimized the reduction of photosynthetic pigments induced by R. solani. In addition, the results showed a significant increase in enzymes/molecules (i.e., phenylalanine, catalase, peroxidase, catalase, superoxide dismutase, phenylalanine ammonia-lyase, phenolics, ascorbic acids, and salicylic acid) involved directly and indirectly in coriander resistance to R. solani. The principal component analysis of the recorded data recommended the role of the high accumulation of oxidative parameters (hydrogen peroxide and lipid peroxidation) and the inhibition of phenolic compounds in the downregulation of coriander resistance against R. solani. The heatmap analysis results revealed that biocontrol agents, especially Trichoderma, enhanced the resistance against R. solani via the stimulation of salicylic acid, phenolics, and antioxidant enzymes. Overall, the data recommended the efficacy of biocontrol agents, especially T. viride, against R. solani infecting coriander plants, which could be an efficient and a safer alternative to conventional fungicides.

Determining the Distribution of QoI Fungicide-Resistant Cercospora sojina on Soybean from Indiana

Frogeye leaf spot (FLS) is a foliar disease of soybean (Glycine max) caused by Cercospora sojina. Application of fungicide products that contain quinone outside inhibitor (QoI) active ingredients has been one of the major tools used in the management of this disease, but, since 2010, QoI-resistant C. sojina isolates have been confirmed in over 20 states in the United States, including Indiana. In summer 2019 and 2020, 406 isolates of C. sojina were collected from 32 counties across Indiana and screened for QoI resistance using a PCR-restriction fragment length polymorphism (RFLP) method. An in vitro fungicide sensitivity test was also performed on a subset of isolates to evaluate their sensitivity to three QoI fungicides: azoxystrobin, pyraclostrobin, and picoxystrobin. A discriminatory dose of picoxystrobin was established as 1 µg/ml by testing five concentrations (0.001, 0.01, 0.1, 1, and 10 µg/ml). QoI-resistant isolates were found in 29 counties, and 251 of the 406 isolates (61.8%) were confirmed to be resistant to QoI fungicides based on PCR-RFLP results. Partial nucleotide sequences of the cytochrome b gene from four resistant and four sensitive isolates corroborated the presence and absence, respectively, of the G143A mutation. Results from the sensitivity assays with discriminatory doses of azoxystrobin (1 µg/ml) and pyraclostrobin (0.1 µg/ml) also supported the findings from the PCR-RFLP assay, because all QoI-resistant isolates were inhibited less than 50% relative to a no-fungicide control when exposed to these doses. Resistant isolates harboring the G143A mutation also exhibited resistance to picoxystrobin. The effective concentrations to inhibit mycelial growth by 50% relative to the nonamended control (EC₅₀) in QoI-sensitive isolates ranged from 0.087 to 0.243 µg/ml, with an overall mean of 0.152 µg/ml, while EC₅₀ values in QoI-resistant isolates were established as >10 µg/ml for picoxystrobin. Results from this study indicated that QoI-resistant C. sojina isolates are spread throughout Indiana and exhibit cross-resistance to QoI fungicides.

Bioinformatics toolbox for exploring target mutation-induced drug resistance

Drug resistance is increasingly among the main issues affecting human health and threatening agriculture and food security. In particular, developing approaches to overcome target mutation-induced drug resistance has long been an essential part of biological research. During the past decade, many bioinformatics tools have been developed to explore this type of drug resistance, and they have become popular for elucidating drug resistance mechanisms in a low cost, fast and effective way. However, these resources are scattered and underutilized, and their strengths and limitations have not been systematically analyzed and compared. Here, we systematically surveyed 59 freely available bioinformatics tools for exploring target mutation-induced drug resistance. We analyzed and summarized these resources based on their functionality, data volume, data source, operating principle, performance, etc. And we concisely discussed the strengths, limitations and application examples of these tools. Specifically, we tested some predictive tools and offered some thoughts from the clinician's perspective. Hopefully, this work will provide a useful toolbox for researchers working in the biomedical, pesticide, bioinformatics and pharmaceutical engineering fields, and a good platform for non-specialists to quickly understand drug resistance prediction.

Transcriptomic Profiling of Fusarium pseudograminearum in Response to Carbendazim, Pyraclostrobin, Tebuconazole, and Phenamacril

Fusarium pseudograminearum has been identified as a significant pathogen. It causes Fusarium crown rot (FCR), which occurs in several major wheat-producing areas in China. Chemical control is the primary measure with which to control this disease. In this study, transcriptome sequencing (RNA-Seq) was used to determine the different mechanisms of action of four frequently used fungicides including carbendazim, pyraclostrobin, tebuconazole, and phenamacril on F. pseudograminearum. In brief, 381, 1896, 842, and 814 differentially expressed genes (DEGs) were identified under the carbendazim, pyraclostrobin, tebuconazole, and phenamacril treatments, respectively. After the joint analysis, 67 common DEGs were obtained, and further functional analysis showed that the ABC transported pathway was significantly enriched. Moreover, FPSE_04130 (FER6) and FPSE_11895 (MDR1), two important ABC multidrug transporter genes whose expression levels simultaneously increased, were mined under the different treatments, which unambiguously demonstrated the common effects. In addition, Mfuzz clustering analysis and WGCNA analysis revealed that the core DEGs are involved in several critical pathways in each of the four treatment groups. Taken together, these genes may play a crucial function in the mechanisms of F. pseudograminearum's response to the fungicides stress.

Resistance of Black Aspergilli Species from Grape Vineyards to SDHI, QoI, DMI, and Phenylpyrrole Fungicides

Fungicide applications constitute a management practice that reduces the size of fungal populations and by acting as a genetic drift factor, may affect pathogen evolution. In a previous study, we showed that the farming system influenced the population structure of the Aspergillus section Nigri species in Greek vineyards. The current study aimed to test the hypothesis that the differences in the population structure may be associated with the selection of fungicide-resistant strains within the black aspergilli populations. To achieve this, we determined the sensitivity of 102, 151, 19, and 22 for the A. uvarum, A. tubingensis, A. niger, and A. carbonarious isolates, respectively, originating either from conventionally-treated or organic vineyards to the fungicides fluxapyroxad-SDHIs, pyraclostrobin-QoIs, tebuconazole-DMIs, and fludioxonil-phenylpyrroles. The results showed widespread resistance to all four fungicides tested in the A. uvarum isolates originating mostly from conventional vineyards. In contrast, all the A. tubingensis isolates tested were sensitive to pyraclostrobin, while moderate frequencies of only lowly resistant isolates were identified for tebuconazole, fludioxonil, and fluxapyroxad. Sequencing analysis of the corresponding fungicide target encoding genes revealed the presence of H270Y, H65Q/S66P, and G143A mutations in the sdhB, sdhD, and cytb genes of A. uvarum resistant isolates, respectively. No mutations in the Cyp51A and Cyp51B genes were detected in either the A. uvarum or A. tubingensis isolates exhibiting high or low resistance levels to DMIs, suggesting that other resistance mechanisms are responsible for the observed phenotype. Our results support the initial hypothesis for the contribution of fungicide resistance in the black aspergilli population structure in conventional and organic vineyards, while this is the first report of A. uvarum resistance to SDHIs and the first documentation of H270Y or H65Q/S66P mutations in sdhB, sdhD, and of the G143A mutation in the cytb gene of this fungal species.

Carboxylic Acid Amide but Not Quinone Outside Inhibitor Fungicide Resistance Mutations Show Clade-Specific Occurrence in Pseudoperonospora cubensis Causing Downy Mildew in Commercial and Wild Cucurbits

Since its reemergence in 2004, Pseudoperonospora cubensis, the causal agent of cucurbit downy mildew (CDM), has experienced significant changes in fungicide sensitivity. Presently, frequent fungicide applications are required to control the disease in cucumber due to the loss of host resistance. Carboxylic acid amides (CAA) and quinone outside inhibitors (QoI) are two fungicide groups used to control foliar diseases in cucurbits, including CDM. Resistance to these fungicides is associated with single nucleotide polymorphism (SNP) mutations. In this study, we used population analyses to determine the occurrence of fungicide resistance mutations to CAA and QoI fungicides in host-adapted clade 1 and clade 2 P. cubensis isolates. Our results revealed that CAA-resistant genotypes occurred more prominently in clade 2 isolates, with more sensitive genotypes observed in clade 1 isolates, while QoI resistance was widespread across isolates from both clades. We also determined that wild cucurbits can serve as reservoirs for P. cubensis isolates containing fungicide resistance alleles. Finally, we report that the G1105W substitution associated with CAA resistance was more prominent within clade 2 P. cubensis isolates while the G1105V resistance substitution and sensitivity genotypes were more prominent in clade 1 isolates. Our findings of clade-specific occurrence of fungicide resistance mutations highlight the importance of understanding the population dynamics of P. cubensis clades by crop and region to design effective fungicide programs and establish accurate baseline sensitivity to active ingredients in P. cubensis populations.

New insights from short and long reads sequencing to explore cytochrome b variants in Plasmopara viticola populations collected from vineyards and related to resistance to complex III inhibitors

Downy mildew is caused by Plasmopara viticola, an obligate oomycete plant pathogen, a devasting disease of grapevine. To protect plants from the disease, complex III inhibitors are among the fungicides widely used. They specifically target the mitochondrial cytochrome b (cytb) of the pathogen to block cellular respiration mechanisms. In the French vineyard, P. viticola has developed resistance against a first group of these fungicides, the Quinone outside Inhibitors (QoI), with a single amino acid substitution G143A in its cytb mitochondrial sequence. The use of QoI was limited and another type of fungicide, the Quinone inside Inhibitors, targeting the same gene and highly effective against oomycetes, was used instead. Recently however, less sensitive P. viticola populations were detected after treatments with some inhibitors, in particular ametoctradin and cyazofamid. By isolating single-sporangia P. viticola strains resistant to these fungicides, we characterized new variants in the cytb sequences associated with cyazofamid resistance: a point mutation (L201S) and more strikingly, two insertions (E203-DE-V204, E203-VE-V204). In parallel with the classical tools, pyrosequencing and qPCR, we then benchmarked short and long-reads NGS technologies (Ion Torrent, Illumina, Oxford Nanopore Technologies) to sequence the complete cytb with a view to detecting and assessing the proportion of resistant variants of P. viticola at the scale of a field population. Eighteen populations collected from French vineyard fields in 2020 were analysed: 12 showed a variable proportion of G143A, 11 of E203-DE-V204 and 7 populations of the S34L variant that confers resistance to ametoctradin. Interestingly, the long reads were able to identify variants, including SNPs, with confidence and to detect a small proportion of P. viticola with multiple variants along the same cytb sequence. Overall, NGS appears to be a promising method for assessing fungicide resistance of pathogens linked to cytb modifications at the field population level. This approach could rapidly become a robust decision support tool for resistance management in the future.

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

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

Aggressive strains of the late wilt fungus of corn exist in Israel in mixed populations and can specialize in disrupting growth or plant health

Maize late wilt disease caused by the fungus Magnaporthiopsis maydis significantly damages crops in Israel and in other countries. Resistant maize cultivars are the preferred method for disease restraining. However, the pathogen populations of Spain and Egypt have varying aggressiveness, and virulent strains can overcome host resistance. In 2001 and from 2016 to -2019, 17 M. maydis strains were isolated from infected maize fields in Israel. The isolates' effects on seed germination, plant development, and disease symptoms severity were evaluated. The isolates from Israel display a diverse degree of aggressiveness that is not linked to their geographic distribution. The virulent strains are found in mixed populations, whereas less virulent M. maydis isolates exist. Aggressive strains harmed the development of plants and ears and caused severe wilting and death. In contrast, plants inoculated with less virulent strains exhibited only mild dehydration signs, and crop yield was similar to that of the non-infected control. Interestingly, different host cultivars can evoke specific virulence of M. maydis strains. Moreover, some pathogen strains significantly repress plant development, while the impact of other strains was evidenced by wilting symptoms. The current research further increases our understanding of the pathogen and our ability to control it.

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.

Resistance characterization of the natural population and resistance mechanism to pyraclostrobin in Lasiodiplodia theobromae

Lasiodiplodia theobromae is the main pathogen of mango stem-end rot disease, causing mango fruit decay and major economic loss. QoI resistance has been found in field populations of L. theobromae. The characterization and resistance mechanism of pyraclostrobin-resistant L. theobromae was investigated by using a combination of bioassays and biochemical and molecular methods. The pyraclostrobin resistance among the L. theobromae population samples from Hainan was 93.41%. The resistant isolates were stable after successive subculturing for 10 times on PDA. Cross-resistance was observed only between the Qols pyraclostrobin and azoxystrobin. The alternative oxidase (AOX) inhibitor SHAM notably decreased the EC₅₀ values of pyraclostrobin for all tested L. theobromae isolates. Induction of AOX by pyraclostrobin was observed in mycelia cells of L. theobromae. After treatment with pyraclostrobin, the final ATP and AOX contents of all sensitive isolates were significantly lower than those of resistant isolates. The relevant mutation and high expression of the cytochrome b gene were not detected in resistant isolates. However, there were 4 mutations in the AOX gene, which were only observed in highly resistant isolates. Pretreatment with pyraclostrobin resulted in a significant upregulation of AOX gene expression, and the average expression level of the highly resistant isolates was 33-fold that of the control group. These results suggested that the AOX pathway is responsible for resistance to pyraclostrobin, and that the AOX-related resistance mechanism is common in field populations of L. theobromae in Hainan mango orchards.

In Vitro Determination of Sensitivity of Fusarium fujikuroi to Fungicide Azoxystrobin and Investigation of Resistance Mechanism

Rice bakanae disease (RBD) caused by Fusarium fujikuroi is a widespread and destructive disease of rice. It is urgent to introduce a new class of fungicide to manage the fungicidal resistance problem and effectively control the disease. Azoxystrobin (AZO) is an active fungicide with a broad antifungal spectrum, while its activity against F. fujikuroi is not well investigated. In this study, the baseline sensitivity of F. fujikuroi to AZO was established by testing the sensitivity of 100 isolates, collected from Anhui Province of China. The mechanism of resistance to AZO was also investigated. AZO exhibited a strong activity against the 100 F. fujikuroi isolates with EC₅₀ values of 0.822 ± 0.285 and 0.762 ± 0.283 μg/mL for mycelial growth and conidial germination, respectively, and both of the baseline sensitivity curves were validated as unimodal curves. To investigate the resistance mechanism, six mutants with resistance factor (RF) values >50 were generated from wild-type sensitive strains through UV mutagenesis, and sequence analysis showed that mutation G143A in cyt b conferred the resistance to AZO. Mycelial growth, conidia production, pathogenicity, and ATP production were decreased in all six resistant mutants as compared to the parental strains, indicating the fitness penalties in this phenotype of resistance mutation. In addition, the cross-resistance assay showed that there was no cross-resistance between AZO and carbendazim, prochloraz, phenamacril, or pydiflumetofen. AZO can be an efficient candidate to control RBD in China with moderate to low fungal resistance risk, but continuous resistance monitoring should be performed during the application of this fungicide.

Sensitivity of Colletotrichum acutatum Species Complex from Strawberry to Fungicide Alternatives to Quinone-Outside Inhibitors

Colletotrichum acutatum is a species complex that causes anthracnose fruit rot and root necrosis on strawberry. The major and minor species within the complex that affect strawberry production are C. nymphaeae and C. fioriniae, respectively. The disease can significantly reduce yield under conducive weather, and its management has greatly relied on quinone-outside inhibitor fungicides (QoI). However, due to the emergence of resistant isolates, such products are no longer effective. Therefore, alternative fungicides were investigated. C. nymphaeae and C. fioriniae isolates were collected from multiple strawberry fields in the United States from 1995 to 2017. The sensitivity of benzovindiflupyr, penthiopyrad, pydiflumetofen, fluazinam, fludioxonil, and cyprodinil was assessed by in vitro and in vivo assays. Both Colletotrichum species were sensitive to benzovindiflupyr, penthiopyrad, fluazinam, and fludioxonil based on mycelial growth assays. Interestingly, of these products, only penthiopyrad did not inhibit conidial germination at 100 µg/ml. For cyprodinil, C. nymphaeae was sensitive based on the mycelial growth, whereas C. fioriniae was not inhibited. Neither species was inhibited by pydiflumetofen in mycelial growth, conidial germination, nor detached fruit assays. The prepackaged mixtures fludioxonil + cyprodinil and fludioxonil + pydiflumetofen were effective in a field trial; however, their use should be carefully considered because of the lack of efficacy of one of the compounds in the mixture. This study sheds light on the potential registration of products alternative to QoIs, such as benzovindiflupyr and fluazinam, which could improve the management of strawberry anthracnose.