Characterization of laboratory mutants of Venturia inaequalis resistant to the strobilurin-related fungicide kresoxim-methyl

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.

Evolution and maintenance of mtDNA gene content across eukaryotes

Across eukaryotes, most genes required for mitochondrial function have been transferred to, or otherwise acquired by, the nucleus. Encoding genes in the nucleus has many advantages. So why do mitochondria retain any genes at all? Why does the set of mtDNA genes vary so much across different species? And how do species maintain functionality in the mtDNA genes they do retain? In this review, we will discuss some possible answers to these questions, attempting a broad perspective across eukaryotes. We hope to cover some interesting features which may be less familiar from the perspective of particular species, including the ubiquity of recombination outside bilaterian animals, encrypted chainmail-like mtDNA, single genes split over multiple mtDNA chromosomes, triparental inheritance, gene transfer by grafting, gain of mtDNA recombination factors, social networks of mitochondria, and the role of mtDNA dysfunction in feeding the world. We will discuss a unifying picture where organismal ecology and gene-specific features together influence whether organism X retains mtDNA gene Y, and where ecology and development together determine which strategies, importantly including recombination, are used to maintain the mtDNA genes that are retained.

Target and non-target site mechanisms of fungicide resistance and their implications for the management of crop pathogens

Fungicides are indispensable for high-quality crops, but the rapid emergence and evolution of fungicide resistance have become the most important issues in modern agriculture. Hence, the sustainability and profitability of agricultural production have been challenged due to the limited number of fungicide chemical classes. Resistance to site-specific fungicides has principally been linked to target and non-target site mechanisms. These mechanisms change the structure or expression level, affecting fungicide efficacy and resulting in different and varying resistance levels. This review provides background information about fungicide resistance mechanisms and their implications for developing anti-resistance strategies in plant pathogens. Here, our purpose was to review changes at the target and non-target sites of quinone outside inhibitor (QoI) fungicides, methyl-benzimidazole carbamate (MBC) fungicides, demethylation inhibitor (DMI) fungicides, and succinate dehydrogenase inhibitor (SDHI) fungicides and to evaluate if they may also be associated with a fitness cost on crop pathogen populations. The current knowledge suggests that understanding fungicide resistance mechanisms can facilitate resistance monitoring and assist in developing anti-resistance strategies and new fungicide molecules to help solve this issue. © 2023 Society of Chemical Industry.

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

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

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

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

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.

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

BACKGROUND

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

RESULTS

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

CONCLUSION

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

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

BACKGROUND

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

RESULTS

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

CONCLUSION

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

A Genome Resource for Several North American Venturia inaequalis Isolates with Multiple Fungicide Resistance Phenotypes

The apple scab pathogen, Venturia inaequalis, is among the most economically important fungal pathogens that affects apples. Fungicide applications are an essential part of disease management. Implementation of cultural practices and genetic sources of resistance in the host are vital components of scab management. This is the first presentation of multiple, high quality, well-annotated genomes of four North American V. inaequalis isolates having both sensitive and multiple fungicide resistance phenotypes. We envision that these isolates will enable investigations into fungicide resistance mechanisms, exploring fungal virulence factors and delineating phylogenomic relationships among apple scab isolates from around the world.

Identification and characterization of new mutations in mitochondrial cytochrome b that confer resistance to bifenazate and acequinocyl in the spider mite Tetranychus urticae

BACKGROUND

In spider mites, mutations in the mitochondrial cytochrome b Q_o pocket have been reported to confer resistance to the Q_o inhibitors bifenazate and acequinocyl. In this study, we surveyed populations of the two-spotted spider mite Tetranychus urticae for mutations in cytochrome b, linked newly discovered mutations with resistance and assessed potential pleiotropic fitness costs.

RESULTS

We identified two novel mutations in the Q_o site: G132A (equivalent to G143A in fungi resistant to strobilurins) and G126S + A133T (previously reported to cause bifenazate and acequinocyl resistance in Panonychus citri). Two T. urticae strains carrying G132A were highly resistant to bifenazate but not acequinocyl, whereas a strain with G126S + A133T displayed high levels of acequinocyl resistance, but only moderate levels of bifenazate resistance. Bifenazate and acequinocyl resistance were inherited maternally, providing strong evidence for the involvement of these mutations in the resistance phenotype. Near isogenic lines carrying G132A revealed several fitness penalties in T. urticae; a lower net reproductive rate (R₀ ), intrinsic rate of increase (rm) and finite rate of increase (LM); a higher doubling time (DT); and a more male-biased sex ratio.

CONCLUSIONS

Several lines of evidence were provided to support the causal role of newly discovered cytochrome b mutations in bifenazate and acequinocyl resistance. Because of the fitness costs associated with the G132A mutation, resistant T. urticae populations might be less competitive in a bifenazate-free environment, offering opportunities for resistance management. © 2019 Society of Chemical Industry.

Baseline Sensitivity and Control Efficacy of Pyraclostrobin Against Botryosphaeria dothidea Isolates in China

Botryosphaeria dothidea is an important fungal pathogen that causes apple ring rot, which can significantly reduce apple yield. Fungicide applications are the main control measure of apple ring rot worldwide. Pyraclostrobin is a quinone outside inhibitor (QoI) fungicide that has yet to be registered for control of B. dothidea in China. Baseline sensitivity of B. dothidea to pyraclostrobin (EC₅₀ of mycelial growth inhibition) was assessed for 97 isolates collected in Shandong Province. The EC₅₀ values ranged from 0.7010 to 7.1378 μg/ml with the mean value of 3.0870 μg/ml and displayed a unimodal frequency distribution. After cultured on fungicide-free PDA medium or on apples for multiple generations, the B. dothidea-resistant isolates (RS^T) remained resistant to pyraclostrobin, but exhibited similar virulence as the susceptible isolates (S^T). Cross-resistance investigation revealed that pyraclostrobin was not cross-resistant to tebuconazole, flusilazole, carbendazim, and iprodione. Field evolution showed that pyraclostrobin at 200 and 250 g a.i./ha provided greater than 80% control efficacy against apple ring rot disease when applied as a therapeutic or preventive fungicide. The efficacy was similar to fungicides that have been registered for apple.

Cloning of the Cytochrome b Gene From the Tomato Powdery Mildew Fungus Leveillula taurica Reveals High Levels of Allelic Variation and Heteroplasmy for the G143A Mutation

Leveillula taurica is a major pathogen of tomato and several other crops that can cause substantial yield losses in favorable conditions for the fungus. Quinone outside inhibitor fungicides (Q_oIs) are routinely used for the control of the pathogen in tomato fields across California, but their recurrent use could lead to the emergence of resistance against these compounds. Here, we partially cloned the cytochrome b gene from L. taurica (Lt cytb) and searched within populations of the fungus collected from tomato fields across California for mutations that confer resistance to Q_oIs. A total of 21 single nucleotide polymorphisms (SNPs) were identified within a 704 bp fragment of the Lt cytb gene analyzed, of which five were non-synonymous substitutions. Among the most frequent SNPs encountered within field populations of the pathogen was the G143A substitution that confers high levels of resistance against Q_oIs in several fungi. The other four amino acid substitutions were novel mutations, whose effect on Q_oI resistance is currently unknown. Sequencing of the Lt cytb gene from individual single-cell conidia of the fungus further revealed that most SNPs, including the one leading to the G143A substitution, were present in a heteroplasmic state, indicating the co-existence of multiple mitotypes in single cells. Analysis of the field samples showed that the G143A substitution is predominantly heteroplasmic also within field populations of L. taurica in California, suggesting that Q_oI resistance in this fungus is likely to be quantitative rather than qualitative.

The evolutionary origins of pesticide resistance

Durable crop protection is an essential component of current and future food security. However, the effectiveness of pesticides is threatened by the evolution of resistant pathogens, weeds and insect pests. Pesticides are mostly novel synthetic compounds, and yet target species are often able to evolve resistance soon after a new compound is introduced. Therefore, pesticide resistance provides an interesting case of rapid evolution under strong selective pressures, which can be used to address fundamental questions concerning the evolutionary origins of adaptations to novel conditions. We ask: (i) whether this adaptive potential originates mainly from de novo mutations or from standing variation; (ii) which pre-existing traits could form the basis of resistance adaptations; and (iii) whether recurrence of resistance mechanisms among species results from interbreeding and horizontal gene transfer or from independent parallel evolution. We compare and contrast the three major pesticide groups: insecticides, herbicides and fungicides. Whilst resistance to these three agrochemical classes is to some extent united by the common evolutionary forces at play, there are also important differences. Fungicide resistance appears to evolve, in most cases, by de novo point mutations in the target-site encoding genes; herbicide resistance often evolves through selection of polygenic metabolic resistance from standing variation; and insecticide resistance evolves through a combination of standing variation and de novo mutations in the target site or major metabolic resistance genes. This has practical implications for resistance risk assessment and management, and lessons learnt from pesticide resistance should be applied in the deployment of novel, non-chemical pest-control methods.

Fitness Penalties in the Evolution of Fungicide Resistance

The evolution of resistance poses an ongoing threat to crop protection. Fungicide resistance provides a selective advantage under fungicide selection, but resistance-conferring mutations may also result in fitness penalties, resulting in an evolutionary trade-off. These penalties may result from the functional constraints of an evolving target site or from the resource allocation costs of overexpression or active transport. The extent to which such fitness penalties are present has important implications for resistance management strategies, determining whether resistance persists or declines between treatments, and for resistance risk assessments for new modes of action. Experimental results have proven variable, depending on factors such as temperature, nutrient status, osmotic or oxidative stress, and pathogen life-cycle stage. Functional genetics tools allow pathogen genetic background to be controlled, but this in turn raises the question of epistatic interactions. Combining fitness penalties under various conditions into a field-realistic scenario poses an important future challenge.

Heteroplasmy for the Cytochrome b Gene in Podosphaera xanthii and its Role in Resistance to QoI Fungicides in Spain

In Spain, management of the cucurbit powdery mildew pathogen Podosphaera xanthii is strongly dependent on chemicals such as quinone outside inhibitor (QoI) fungicides. In a previous report, widespread resistance to QoI fungicides in populations of P. xanthii in south-central Spain was documented, but the molecular mechanisms of resistance remained unclear. In this work, the role of the Rieske-FeS (risp) and the cytochrome b (cytb) gene mutations in QoI resistance of P. xanthii were examined. No point mutations in the risp gene were found in the three QoI-resistant isolates analyzed. For cytb, sequence analysis revealed the presence of a G143A substitution that occurs in many QoI-resistant fungi. This mutation was always detected in QoI-resistant isolates of P. xanthii; however, it was also detected in sensitive isolates. To better understand the role of heteroplasmy for cytb in QoI resistance of P. xanthii, an allele-specific quantitative PCR was developed to quantify the relative abundance of the G143 (sensitive) and A143 (resistant) alleles. High relative abundance of A143 allele (70%) was associated with isolates resistant to QoI fungicides; however, QoI-sensitive isolates also carried the mutated allele in frequencies ranged from 10 to 60%. Our data suggest that G143A mutation in cytb is the primary factor involved in QoI resistance of P. xanthii but the proportion of G143 and A143 alleles in an isolate may determine its QoI resistance level.

Transmission of the G143A QoI-resistance point mutation through anastomosis in Magnaporthe grisea

BACKGROUND

Soon after the introduction of Qo inhibitor fungicides in 1996, the point mutation leading to the amino acid exchange glycine to alanine at the 143 position of the mitochondrial cytochrome b gene was identified as the main cause of resistance. The present study describes the role of anastomosis in the transmission of the G143A mutation in Magnaporthe grisea.

RESULTS

Two M. grisea mutants were co-cultivated on oatmeal agar and also co-inoculated on barley leaves. The mutants differed by the presence of the G143A mutation in one isolate and a disrupted AOX gene by insertion of a hygromycin gene in the other (M-145). Specific resistant (r) or sensitive (s) phenotypes of 409 monosporic cultures were determined on media amended with either hygromycin (H) or azoxystrobin (S) plus SHAM. The phenotypes identified reflected not only the phenotypes of mutants M-145 and G143A but also the wild-type parent phenotype HsSs and a new HrSr isolate.

CONCLUSION

Identification of the M. grisea phenotypes HrSr and HsSs suggests that anastomosis occurred during co-cultivation and co-inoculation of the mutants M-145 and G143A, allowing the transfer of the G143A point mutation from the QoI-resistant isolate to the susceptible isolate.

Fitness of Erysiphe necator with G143A-Based Resistance to Quinone Outside Inhibitors

Management of grape powdery mildew (Erysiphe necator) using quinone outside inhibitors (QoIs) has eroded in an increasing number of regions due to resistance development. To determine persistence of resistance when QoIs are withdrawn, competition assays were conducted on unsprayed grape plants (Vitis vinifera 'Chardonnay') by cycling mixtures of resistant and sensitive isolates characterized as genetically diverse based on microsatellite analyses. Under laboratory conditions, %G143A, quantified by quantitative polymerase chain reaction (qPCR), increased significantly, indicating competitiveness of the resistant fraction. To confirm competitiveness in the field, trials using potted plants were conducted. Percent G143A tended to decrease in one growing season, probably due to spore migration and mixing of populations with natural background inoculum. In a second season, QoI resistance persisted at high frequency for 4 weeks. Resistant populations were also found to persist in one vineyard without QoI application for four consecutive years. The frequency was still about 25% in the fourth year, with higher frequency (36%) in a hotspot section. QoI-resistant populations with >5% G143A also harbored Y136F in the cyp51 gene that confers some resistance to sterol demethylation inhibitors, another fungicide class for powdery mildew control. Double resistance could have been partly responsible for persistence of QoI resistance at this location.

QoI-Resistance Stability in Relation to Pathogenic and Saprophytic Fitness Components of Alternaria alternata from Citrus

The phenotypic stability, fitness components, and ability to cause disease of isolates of the Alternaria alternata tangerine pathotype resistant to quinone-outside inhibitors (QoIs) were studied. Stability of resistance to azoxystrobin (AZ) and pyraclostrobin (PYR) was determined after consecutive transfers on potato dextrose agar (PDA). The sensitivity to QoIs did not change significantly after 10 transfers on PDA compared with the initial sensitivity of all isolates tested. Fitness components evaluated in vitro were mycelial growth, conidial germination, and conidial production. Incubation period, number of lesions per leaf area, and virulence were determined with detached leaf assays using four cultivars: Dancy, Minneola, Murcott, and Sunburst. Variability in fitness components was observed among isolates within the same sensitivity group. As a group, no significant differences in the mean values of these fitness components were observed between resistant and sensitive phenotypes, except for virulence. Resistant isolates were significantly (P < 0.05) more virulent than the sensitive isolates on Dancy, Minneola, and Sunburst but not on Murcott (P = 0.3506). There was no significant correlation between individual fitness components and the level of sensitivity to AZ and PYR. Preventive applications of Abound (commercial formulation of AZ) at full field rates failed to control disease caused by QoI-resistant isolates under greenhouse conditions. Our results suggest that QoI resistance in A. alternata tangerine pathotype is stable in the absence of QoI selection pressure and that resistance development did not affect the fitness of resistant isolates.

Heteroplasmy of the cytochrome b gene in Venturia inaequalis and its involvement in quantitative and practical resistance to trifloxystrobin

Quantitative (partial) and qualitative (complete) resistance responses to quinone outside inhibitor (QoI) fungicides have been documented for the apple scab pathogen Venturia inaequalis. Resistance monitoring efforts have traditionally focused on the detection of qualitative resistance based on a single point mutation, G143A, within the cytochrome b (cyt b) gene. In order to better understand the role of heteroplasmy of the cyt b gene in the QoI resistance response for isolates and populations of V. inaequalis, an allele-specific quantitative polymerase chain reaction was developed to quantify the relative abundance of the A143 (resistant) allele in 45 isolates of V. inaequalis with differing in vitro resistance responses to the QoI fungicide trifloxystrobin. Although a high relative abundance of the A143 allele (>62%) was associated with isolates with high resistance responses (50 to 100% relative growth on trifloxystrobin-amended medium), heteroplasmy of the cyt b gene was not the primary factor involved in isolates with moderate resistance responses (29 to 49% relative growth). The relative abundance of the A143 allele in isolates with moderate resistance to trifloxystrobin rarely exceeded 8%, suggesting that other resistance mechanisms are involved in moderate resistance and, therefore, that the Qol resistance response is polygenic. In research orchards where QoI fungicides failed to control apple scab (practical resistance), field trials were conducted to demonstrate the link between practical resistance and the abundance of the A143 allele. Relative abundance of the A143 allele in these orchard populations exceeded 20% in 2011 and 2012. Similarly, of the eight additional commercial orchards screened in 2011, the relative abundance of the A143 allele always exceeded 20% in those with QoI practical resistance. Although heteroplasmy of the cyt b gene did not entirely explain the response of isolates with moderate resistance to QoIs, the relative abundance of A143 in orchard populations of V. inaequalis helps to explain the point of emergence for practical resistance to trifloxystrobin across several orchard populations with differing production histories.

Prevalence and Stability of Qualitative QoI Resistance in Populations of Venturia inaequalis in the Northeastern United States

Quinone-outside-inhibitor (QoI) fungicides are a safe and effective means of managing apple scab caused by Venturia inaequalis. To determine the prevalence of both quantitative (partial) and qualitative (complete) QoI resistance in V. inaequalis in the northeastern United States, we sampled single-lesion conidial isolates (n = 4,481) from 120 commercial and research orchards from 2004 to 2011 with a range of exposure to QoI fungicides from none to several applications a year. In all, 67% of these orchard populations of V. inaequalis were sensitive to QoI fungicides, 28% exhibited QoI practical resistance, and 5% were not sensitive QoI fungicides but had not become practically resistant. Isolates with qualitative QoI resistance, conferred by the G143A cytochrome b gene mutation, were found in 13 of the 34 QoI-resistant orchard populations. To evaluate the stability of the G143A mutation, 27 isolates were selected from different orchard populations to represent the scope of regional populations. These isolates were subcultured continuously in the presence or absence of the QoI fungicide trifloxystrobin. All isolates that initially possessed qualitative resistance maintained the resistant genotype (G143A) for six transfers over 6 months in both the absence and presence of trifloxystrobin. Given the observed QoI resistance in orchard populations of V. inaequalis and the stability of the G143A mutation in individual isolates, apple scab management paradigms must encompass strategies to limit selection of QoI resistance in the sensitive orchard populations remaining in the region.

Genetic analysis and molecular characterisation of laboratory and field mutants of Botryotinia fuckeliana (Botrytis cinerea) resistant to QoI fungicides

BACKGROUND

QoI fungicides, inhibitors of mitochondrial respiration, are considered to be at high risk of resistance development. In several phytopathogenic fungi, resistance is caused by mutations (most frequently G143A) in the mitochondrial cytochrome b (cytb) gene. The genetic and molecular basis of QoI resistance were investigated in laboratory and field mutants of Botryotinia fuckeliana (de Bary) Whetz. exhibiting in vitro reduced sensitivity to trifloxystrobin.

RESULTS

B. fuckeliana mutants highly resistant to trifloxystrobin were obtained in the laboratory by spontaneous mutations in wild-type strains, or from naturally infected plants on a medium amended with 1-3 mg L(-1) trifloxystrobin and 2 mM salicylhydroxamic acid, an inhibitor of alternative oxidase. No point mutations were detected, either in the complete nucleotide sequences of the cytb gene or in those of the aox and Rieske protein genes of laboratory mutants, whereas all field mutants carried the G143A mutation in the mitochondrial cytb gene. QoI resistance was always maternally inherited in ascospore progeny of sexual crosses of field mutants with sensitive reference strains.

CONCLUSIONS

The G143A mutation in cytb gene is confirmed to be responsible for field resistance to QoIs in B. fuckeliana. Maternal inheritance of resistance to QoIs in progeny of sexual crosses confirmed that it is caused by extranuclear genetic determinants. In laboratory mutants the heteroplasmic state of mutated mitochondria could likely hamper the G143A detection, otherwise other gene(s) underlying different mechanisms of resistance could be involved.

Cytological evaluation of the effect of azoxystrobin and alternative oxidase inhibitors in Botrytis cinerea

Azoxystrobin (AZ), a strobilurin-derived fungicide, is known to inhibit mitochondrial respiration in fungi by blocking the electron transport chain in the inner mitochondrial membrane. Germination was strongly inhibited when Botrytis cinerea spore suspension was treated with AZ and the alternative oxidase (AOX) inhibitors, salicylhydroxamic acid (SHAM) and n-propyl gallate. However, chemical death indicators trypan blue and propidium iodide showed that those spores were still alive. When the spore suspension in the AZ and SHAM solution was replaced with distilled water, the germination rate almost recovered, at least during the first 2 days of incubation with AZ and SHAM solution. No morphological alteration was detected in the cells treated with AZ and SHAM, especially in mitochondria, using transmission electron microscopy. Therefore, simultaneous application of AZ and AOX inhibitors has a fungistatic, rather than a fungicidal, action.

Stability and fitness of pyraclostrobin- and boscalid-resistant phenotypes in field isolates of Botrytis cinerea from apple

Phenotype stability, fitness, and competitive ability of pyraclostrobin- and boscalid-resistant isolates of Botrytis cinerea from apple were investigated. Stability of resistance was determined after consecutive transfers on potato dextrose agar (PDA) or being cycled on apple fruit. In vitro fitness components mycelial growth, osmotic sensitivity, conidial germination, and sporulation were evaluated on agar media. Pathogenicity, virulence and sporulation on apple fruit were evaluated at both 20 and 0°C. Competition between fungicide-resistant and -sensitive isolates on apple fruit also was evaluated. Resistance to the two fungicides was retained at levels similar to that of the initial generation after 20 and 10 transfers on PDA and five and three disease cycles on apple fruit at 20 and 0°C, respectively. Great variability in individual fitness components tested was observed among isolates within the same phenotype groups either sensitive or resistant to the fungicides but, when compared as phenotype groups, there were no significant differences in the mean values of these fitness components between resistant and sensitive phenotypes except that the phenotype resistant only to boscalid produced fewer conidia in vitro than sensitive isolates. Resistant isolates were as pathogenic and virulent on apple fruit as sensitive isolates. There was no significant correlation between the values of individual fitness components tested and the level of resistance to pyraclostrobin or boscalid, except that virulence at 20°C positively correlated with the level of resistance to the two fungicides. The final frequency of pyraclostrobin-resistant individuals in the populations was significantly decreased compared with the initial generation and no boscalid-resistant individuals were detected after four disease cycles on apple fruit inoculated with a pair mixture of a dual-sensitive isolate and one isolate each of the three phenotypes resistant to pyraclostrobin, boscalid, or both. The results suggest that resistance of B. cinerea to pyraclostrobin and boscalid was stable in the absence of the fungicides and that resistance to the two fungicides did not significantly impair individual fitness components tested. However, both pyraclostrobin- and boscalid-resistant isolates exhibited competitive disadvantage over the dual-sensitive isolate on apple fruit.

Evaluation of the incidence of the G143A mutation and cytb intron presence in the cytochrome bc-1 gene conferring QoI resistance in Botrytis cinerea populations from several hosts

BACKGROUND

Previous studies have shown that resistance of Botrytis cinerea to QoI fungicides has been attributed to the G143A mutation in the cytochrome b (cytb) gene, while, in a part of the fungal population, an intron has been detected at codon 143 of the gene, preventing QoI resistance. During 2005-2009, 304 grey mould isolates were collected from strawberry, tomato, grape, kiwifruit, cucumber and apple in Greece and screened for resistance to pyraclostrobin and for the presence of the cytb intron, using a novel real-time TaqMan PCR assay developed in the present study.

RESULTS

QoI-resistant phenotypes existed only within the population collected from strawberries. All resistant isolates possessed the G143A mutation. Differences were observed in the genotypic structure of cytb. Individuals possessing the intron were found at high incidence in apple fruit and greenhouse-grown tomato and cucumber populations, whereas in the strawberry population the intron frequency was lower. Cultivation of QoI-resistant and QoI-sensitive isolates for ten culture cycles on artificial nutrient medium in the presence or absence of fungicide selection showed that QoI resistance was stable.

CONCLUSIONS

The results of the study suggest that a high risk for selection of QoI-resistant strains exists in crops heavily treated with QoIs, in spite of the widespread occurrence of the cytb intron in B. cinerea populations. The developed real-time TaqMan PCR constitutes a powerful tool to streamline detection of the mutation by reducing pre- and post-amplification manipulations, and can be used for rapid screening and quantification of QoI resistance.

Occurrence of QoI Resistance and Detection of the G143A Mutation in Michigan Populations of Venturia inaequalis

Control strategies for Venturia inaequalis rely heavily on chemical fungicides. Single-site fungicides such as the quinone-outside inhibitors (QoI) have been used in Michigan apple orchards for more than 11 years. In 2008, we sampled eight commercial orchards in the Fruit Ridge growing region of Michigan in which apple scab control failures were observed on 'McIntosh' apple following applications of kresoxim-methyl or trifloxystrobin. QoI resistance was assessed in 210 total isolates (a total of 17 orchards) using a spore germination assay and in 319 isolates using a polymerase chain reaction (PCR) assay to detect the G143A mutation located within the V. inaequalis cytochrome b gene (CYTB). The G143A mutation is known to confer high-level QoI resistance in plant-pathogenic fungi. QoI resistance was confirmed in 50 and 64% of the isolates tested with the spore germination and PCR assays, respectively, and there was a 97% concordance observed between the assays. In 2009, we sampled and examined an additional 1,201 V. inaequalis isolates from 64 orchards in Michigan and 86 isolates from four baseline sites in Ohio. All of these isolates were assayed for the G143A mutation and it was detected within 67 and 0% of the Michigan and Ohio isolates, respectively. Our results indicate the widespread occurrence of QoI resistance in Michigan commercial orchard populations of V. inaequalis. Loss of QoI fungicides further limits the arsenal of fungicides available to commercial apple growers for successful scab management.

Venturia inaequalis: the causal agent of apple scab

The fungus Venturia inaequalis infects members of the Maloideae, and causes the disease apple scab, the most important disease of apple worldwide. The early elucidation of the gene-for-gene relationship between V. inaequalis and its host Malus has intrigued plant pathologists ever since, with the identification of 17 resistance (R)-avirulence (Avr) gene pairings. The Avr gene products are presumably a subset of the total effector arsenal of V. inaequalis (predominantly proteins secreted in planta assumed to facilitate infection). The supposition that effectors from V. inaequalis act as suppressors of plant defence is supported by the ability of the pathogen to penetrate the cuticle and differentiate into large pseudoparenchymatous structures, termed stromata, in the subcuticular space, without the initiation of an effective plant defence response. If effectors can be identified that are essential for pathogenicity, the corresponding R genes will be durable and would add significant value to breeding programmes. An R gene cluster in Malus has been cloned, but no V. inaequalis effectors have been characterized at the molecular level. However, the identification of effectors is likely to be facilitated by the resolution of the whole genome sequence of V. inaequalis.

TAXONOMY

Teleomorph: Venturia inaequalis Cooke (Wint.); Kingdom Fungi; Phylum Ascomycota; Subphylum Euascomycota; Class Dothideomycetes; Family Venturiaceae; genus Venturia; species inaequalis. Anamorph: Fusicladium pomi (Fr.) Lind or Spilocaea pomi (Fr.). LIFE CYCLE: V. inaequalis is a hemibiotroph and overwinters as pseudothecia (sexual fruiting bodies) following a phase of saprobic growth in fallen leaf tissues. The primary inoculum consists of ascospores, which germinate and penetrate the cuticle. Stromata are formed above the epidermal cells but do not penetrate them. Cell wall-degrading enzymes are only produced late in the infection cycle, raising the as yet unanswered question as to how V. inaequalis gains nutrients from the host. Conidia (secondary inoculum) arise from the upper surface of the stromata, and are produced throughout the growing season, initiating multiple rounds of infection. VENTURIA INAEQUALIS AS A MODEL PATHOGEN OF A WOODY HOST: V. inaequalis can be cultured and is amenable to crossing in vitro, enabling map-based cloning strategies. It can be transformed readily, and functional analyses can be conducted by gene silencing. Expressed sequence tag collections are available to aid in gene identification. These will be complemented by the whole genome sequence, which, in turn, will contribute to the comparative analysis of different races of V. inaequalis and plant pathogens within the Dothideomycetes.

Site-directed mutagenesis of the cytochrome b gene and development of diagnostic methods for identifying QoI resistance of rice blast fungus

BACKGROUND

It is possible that a single nucleotide polymorphism (SNP) (G143A mutation) in the cytochrome b gene could confer resistance to quinone outside inhibiting (QoI) fungicides (strobilurins) in rice blast fungus because this mutation caused a high level of resistance to fungicides such as azoxystrobin in Pyricularia grisea Sacc. and other fungal plant pathogens. The aim of this study was to survey Magnaporthe oryzae B Couch sp. nov. isolates in Japan for resistance to QoIs, and to try to develop molecular detection methods for QoI resistance.

RESULTS

A survey on the QoI resistance among M. oryzae isolates from rice was conducted in Japan. A total of 813 single-spore isolates of M. oryzae were tested for their sensitivity to azoxystrobin using a mycelial growth test on PDA. QoI fungicide resistance was not found among these isolates. The introduction of G143A mutation into a plasmid containing the cytochrome b gene sequence of rice blast fungus was achieved by site-directed mutagenesis. Molecular diagnostic methods were developed for identifying QoI resistance in rice blast fungus using the plasmid construct.

CONCLUSION

As the management of rice blast disease is often dependent on chemicals, the rational design of control programmes requires a proper understanding of the fungicide resistance phenomenon in field populations of the pathogen. Mutation of the cytochrome b gene of rice blast fungus would be specifically detected from diseased leaves and seeds using the molecular methods developed in this study.

Fitness and Competitive Ability of an Azoxystrobin-Resistant G143A Mutant of Magnaporthe oryzae from Perennial Ryegrass

Development of azoxystrobin resistance in Magnaporthe oryzae from perennial ryegrass has been reported in certain locations in the United States, and possible development of resistance in additional areas is a major concern in the golf course industry. The study was undertaken to evaluate the relative fitness and competitive ability of a field-collected azoxystrobin-resistant G143A mutant by comparing it with a wild-type strain using detached perennial ryegrass blades. A fitness comparison experiment indicated that the disease severity of the wild-type strain was significantly higher than that of the mutant; however, the mutant produced greater secondary inoculum. When inoculated with three mixed populations of resistant and wild-type strains at different ratios, the production of conidia by the wild-type strain increased and that of the mutant decreased after infection occurred in all three populations tested. In an experiment on the effect of various fungicides on the population initially containing 5% of the mutant, preventive application of azoxystrobin allowed 5% of the mutant to dominate the population after the infection. However, other non-quinone outside inhibitor fungicides and mixtures of azoxystrobin with contact fungicides eliminated the entire mutant. This study demonstrates that the wild-type strain of M. oryzae has a competitive advantage over the mutant within the environment tested. Mixtures and alternations of fungicides with different modes of actions may prevent rapid build-up of resistance in the gray leaf spot pathosystem.

Characterisation of QoI-resistant field isolates of Botrytis cinerea from citrus and strawberry

BACKGROUND

In 2004, field isolates of Botrytis cinerea Pers. ex Fr., resistant to strobilurin fungicides (QoIs), were first found in commercial citrus orchards in Wakayama Prefecture, Japan. Subsequently, QoI-resistant isolates of this fungus were also detected in plastic strawberry greenhouses in Saga, Ibaraki and Chiba prefectures, Japan. Biological and molecular characterisation of resistant isolates was conducted in this study.

RESULTS

QoI-resistant isolates of B. cinerea grew well on PDA plates containing kresoxim-methyl or azoxystrobin at 1 mg L(-1), supplemented with 1 mM of n-propyl gallate, an inhibitor of alternative oxidase, whereas the growth of sensitive isolates was strongly suppressed. Results from this in vitro test were in good agreement with those of fungus inoculation tests in vivo. In resistant isolates, the mutation at amino acid position 143 of the cytochrome b gene, known to be the cause of high QoI resistance in various fungal pathogens, was found, but only occasionally. The heteroplasmy of cytochrome b gene was confirmed, and the wild-type sequence often present in the majority of resistant isolates, indicating that the proportion of mutated cytochrome b gene was very low.

CONCLUSION

The conventional RFLP and sequence analyses of PCR-amplified cytochrome b gene are insufficient for molecular identification of QoI resistance in B. cinerea.

A molecular mechanism of azoxystrobin resistance in Penicillium digitatum UV mutants and a PCR-based assay for detection of azoxystrobin-resistant strains in packing- or store-house isolates

Sixty-five isolates of Pencillium digitatum (Pers.:Fr) Sacc., a causative agent of green mold of postharvest citrus, were collected from various locations in Zhejiang province in 2000, 2005 and 2006, and assayed for their sensitivity to the quinone outside inhibitor (QoI) fungicide azoxystrobin. The results showed that azoxystrobin is highly effective against P. digitatum, in vitro, and that the effective concentrations resulting in reduction of conidial germination and mycelial growth by 50% (EC(50)) averaged 0.0426 microg/ml and 0.0250 microg/ml, respectively. Twenty-eight azoxystrobin-resistant mutants were obtained by UV mutagenesis and subsequent selection on medium amended with azoxystrobin (12 microg/ml) and salicylhydroxamic acid. All obtained mutants were highly resistant to azoxystrobin and their resistance was genetically stable. Analysis of the cytochrome b gene structure of P. digitatum (Pdcyt b) showed the absence of type I intron in the first hot spot region of mutation. These results indicate that P. digitatum is likely to evolve high levels of resistance to azoxystrobin after its application. Analysis of partial sequences of Pdcyt b from both the azoxystrobin-sensitive parental isolate and the 28 azoxystrobin-resistant mutants revealed that a point mutation, which leads to the substitution at code 143 of alanine for glycine (G143A), is responsible for the observed azoxystrobin resistance in the laboratory mutants. Based on this point mutation, two allele-specific PCR primers were designed and optimized for allele-specific PCR detection of azoxystrobin-resistant isolates of P. digitatum.

Monitoring of Venturia inaequalis harbouring the QoI resistance G143A mutation in French orchards as revealed by PCR assays

BACKGROUND

Genetic resistance to QoI fungicides may account for recent failures to control Venturia inaequalis (Cooke) Winter in French orchards. Two PCR-based assays were developed to detect the G143A point mutation in the fungal mitochondrial cytochrome b gene. The mutation is known to confer a high level of resistance to QoI fungicides. Occurrence of the G143A mutation in French field isolates collected from 2004 to 2007 was monitored.

RESULTS

The QoI-resistant cytochrome b allele was specifically detected either following the cleavage of the amplified marker by a restriction endonuclease (CAPS assay) or its amplification using an allele-specific PCR primer. Using either method, the G143A mutation was found in 42% of the 291 field samples originating from French orchards in which apple scab proved difficult to be controlled. Monitoring of the G143A mutation in orchards located in 15 French administrative regions indicated that the mutation was detected at least once in nine of the regions, and its presence ranged from 33% to 64% of the orchards analysed in 2004 and in 2007 respectively.

CONCLUSION

The PCR-based methods developed in this study efficiently reveal the presence of the G143A mutation in French V. inaequalis field populations.

Adaptation to fungicides in Monilinia fructicola isolates with different fungicide resistance phenotypes

The ability to develop fungicide resistance was assessed in Monilinia fructicola isolates with different fungicide sensitivity phenotypes by adapting mycelium and conidia to increasing concentrations of selective fungicides and UV mutagenesis. Results showed that adaptation to Quinone outside inhibitor (QoI) fungicide azoxystrobin and sterol demethylation inhibitor (DMI) fungicide propiconazole was more effective in conidial-transfer experiments compared to mycelial-transfer experiments. DMI-resistant (DMI-R) isolates adapted to significantly higher doses of azoxystrobin in both, mycelial- and conidial-transfer experiments compared to benzimidazole-resistant (BZI-R) and sensitive (S) isolates. Adaptation to propiconazole in conidial-transfer experiments was accelerated in BZI-R isolates when a stable, nonlethal dose of 50 microg/ml thiophanate-methyl was added to the selection medium. One of two azoxystrobin-resistant mutants from DMI-R isolates did not show any fitness penalties; the other isolate expired before further tests could be carried out. The viable mutant caused larger lesions on detached peach fruit sprayed with azoxystrobin compared to the parental isolate. The azoxystrobin sensitivity of the viable mutant returned to baseline levels after the mutant was transferred to unamended medium. However, azoxystrobin resistance recovered quicker in the mutant compared to the corresponding parental isolate after renewed subculturing on medium amended with 0.2 and 1 microg/ml azoxystrobin; only the mutant but not the parental isolate was able to adapt to 5 microg/ml azoxystrobin. In UV mutagenesis experiments, the DMI-R isolates produced significantly more mutants compared to S isolates. All of the UV-induced mutants showed stable fungicide resistance with little fitness penalty. This study indicates the potential for QoI fungicide resistance development in M. fructicola in the absence of a mutagen and provides evidence for increased mutability and predisposition to accelerated adaptation to azoxystrobin in M. fructicola isolates resistant to DMI fungicides.

Molecular Characterization and Diagnosis of QoI Resistance in Cucumber and Eggplant Fungal Pathogens

ABSTRACT The molecular mechanism of QoI fungicide resistance was studied using isolates of cucumber Corynespora leaf spot fungus (Corynespora cassiicola) and the eggplant leaf mold (Mycovellosiella nattrassii). In both pathogens, a mutation at position 143 from glycine to alanine (G143A) was detected in the cytochrome b gene that encodes for the fungicide-targeted protein. Moreover, the nucleotide sequence at amino acid position 143 was converted from GGT or GGA in sensitive (wild-type) to GCT or GCA in resistant (mutant-type) isolates. The methods of polymerase chain reaction restriction fragment length polymorphism commonly used for QoI resistance monitoring were employed successfully, leading to the amplified gene fragment from resistant isolates being cut with the restriction enzyme ItaI. However, heteroplasmy (the coexistence of wild-type and mutated alleles) was found when the resistant isolates of C. cassiicola, M. nattrassii, and Colletotrichum gloeosporioides (strawberry anthracnose fungus) were subcultured in the presence or absence of QoI fungicides. QoI resistance of cucumber powdery and downy mildew isolates persisted for a few years following the removal of the selection pressure imposed by the fungicide under both laboratory and commercial greenhouse conditions. The proportion of mutated sequences in cytochrome b gene decreased over time in the pathogen population. The protective efficacy of the full dose of azoxystrobin decreased when the populations of powdery and downy mildews contained resistant isolates at 10%. Using FMBIO, a fluorescence bio-imaging analyzer, the mutant allele from the QoI-resistant isolates could be detected at the level of 1%, whereas the detection sensitivity of ethidium-bromide-stained gels was approximately 10 times lower.

Dynamics of QoI Sensitivity in Mycosphaerella fijiensis in Costa Rica During 2000 to 2003

ABSTRACT From 1997 onward, the strobilurin fungicide azoxystrobin was widely used in the main banana-production zone in Costa Rica against Mycosphaerella fijiensis var. difformis causing black Sigatoka of banana. By 2000, isolates of M. fijiensis with resistance to the quinolene oxidase inhibitor fungicides were common on some farms in the area. The cause was a single point mutation from glycine to alanine in the fungal target protein, cytochrome b gene. An amplification refractory mutation system Scorpion quantitative polymerase chain reaction assay was developed and used to determine the frequency of G143A allele in samples of M. fijiensis. Two hierarchical surveys of spatial variability, in 2001 and 2002, found no significant variation in frequency on spatial scales <10 m. This allowed the frequency of G143A alleles on a farm to be estimated efficiently by averaging single samples taken at two fixed locations. The frequency of G143A allele in bulk samples from 11 farms throughout Costa Rica was determined at 2-month intervals. There was no direct relationship between the number of spray applications and the frequency of G143A on individual farms. Instead, the frequency converged toward regional averages, presumably due to the large-scale mixing of ascospores dispersed by wind. Using trap plants in an area remote from the main producing area, immigration of resistant ascospores was detected as far as 6 km away both with and against the prevailing wind.

Enhanced activity of strobilurin and fludioxonil by using berberine and phenolic compounds to target fungal antioxidative stress response

AIMS

Identify natural products that effectively target antioxidative signal transduction/stress response systems [i.e., mitogen-activated protein kinase (MAPK) pathway, mitochondrial superoxide dismutase (Mn-SOD)] of fungi. Enhance activity of strobilurin or fludioxonil with discovered compounds.

METHODS AND RESULTS

Enhancement of antifungal activity of strobilurins, inhibitors of complex III of the mitochondrial respiratory chain, was tested using berberine hemisulfate and different phenolic compounds. The Saccharomyces cerevisiae sod2Delta, a deletion mutant lacking Mn-SOD gene, was highly sensitive to berberine and veratraldehyde. Functional complementation analysis verified these compounds target Mn-SOD. Activity of strobilurin (25-50 micromol l(-1)) was elevated on most aspergilli and Penicillium expansum by co-application with berberine or veratraldehyde (2-4 mmol l(-1)). These compounds also prevented Aspergillus fumigatus MAPK mutants (sakADelta and mpkCDelta) from escaping toxicity of fludioxonil (a phenylpyrrole fungicide potentiated by the MAPK pathway), a typical phenotype of fungal MAPK mutants.

CONCLUSIONS

Strobilurin activity or prevention of fungal escape from fludioxonil toxicity can be enhanced by co-application of certain alkaloids or phenolics.

SIGNIFICANCE AND IMPACT OF THE STUDY

Natural products can be used to target cellular stress response systems in fungal pathogens and serve as alternatives/additives to commercial antifungal agents.

Incidence of Myclobutanil- and Kresoxim-Methyl-Insensitive Isolates of Venturia inaequalis in Quebec Orchards

Sensitivity of baseline and exposed populations of Venturia inaequalis to myclobutanil and to kresoxim-methyl were evaluated in vitro. For myclobutanil, the population was constructed with 238 monoconidial isolates of V. inaequalis collected from 48 orchards. For kresoxim-methyl, the population was constructed with 251 monoconidial isolates collected from 49 orchards. Baseline populations were constructed with 34 and 29 monoconidial isolates collected from apple trees that had never been treated for myclobutanil and kresoxim-methyl, respectively. Sensitivity to fungicides was evaluated based on 50% effective dose (ED₅₀) values. The V. inaequalis population that was not exposed to myclobutanil had a baseline sensitivity (mean ED₅₀) of 0.064 μg/ml and showed a lognormal distribution. The V. inaequalis population constructed with isolates from commercial orchards had a mean ED₅₀ of 2.600 μg/ml, which was significantly higher than the baseline sensitivity. The distribution of ED₅₀ values did not follow a lognormal distribution. In response to declining levels of scab control with myclobutanil and other sterol demethylation inhibitor fungicides (DMIs), three orchards were more deeply investigated. The mean ED₅₀ values were 1.618 (n = 23), 3.079 (n = 29), and 1.500 μg/ml (n = 20) in orchards one, two, and three, respectively. Resistant isolates, according to criteria set by other studies, accounted for 39, 76, and 85% of the isolates tested. The V. inaequalis population that had never been exposed to kresoxim-methyl had a baseline sensitivity (mean ED₅₀) of 0.092 μg/ml and showed a lognormal distribution. The V. inaequalis population constructed with isolates from commercial orchards had a mean ED₅₀ of 6.093 μg/ml, which was significantly higher than the baseline sensitivity. The distribution of ED₅₀ values followed a lognormal distribution. However, when a subsample of isolates was retested for their sensitivity to kresoxim-methyl with the addition of salicylhydroxamic acid (an inhibitor of alternative oxidase) at 100 μg/ml to the growth medium, more than 98% inhibition was observed for all isolates. The results from in vitro tests showed a high level of resistance to myclobutanil and a low level of resistance to kresoxim-methyl, suggesting that the use of myclobutanil and DMIs should be discontinued or significantly reduced before practical resistance is reached.

Controlling food-contaminating fungi by targeting their antioxidative stress-response system with natural phenolic compounds

The antioxidative stress-response system is essential to fungi for tolerating exposure to phenolic compounds. We show how this system can be targeted to improve fungal control by using compounds that inhibit the fungal mitochondrial respiratory chain. Targeting mitochondrial superoxide dismutase with selected phenolic acid derivatives (e.g., vanillyl acetone) resulted in a 100- to 1,000-fold greater sensitivity to strobilurin or carboxin fungicides. This synergism is significantly greater with strobilurin than with carboxin, suggesting that complex III of the mitochondrial respiratory chain is a better target than complex II for fungal control, using phenolics. These results show certain natural compounds are effective synergists to commercial fungicides and can be used for improving control of food-contaminating pathogens. These results suggest that the use of such compounds for fungal control can reduce environmental and health risks associated with commercial fungicides, lower cost for control, and the probability for development of resistance.

Identification of phenolics for control of Aspergillus flavus using Saccharomyces cerevisiae in a model target-gene bioassay

The yeast Saccharomyces cerevisiae was used in a high-throughput bioassay to identify phenolic agents for control of the aflatoxigenic fungus Aspergillus flavus. Veratraldehyde, 1, cinnamic acid, 5, and the respective benzoic acid derivatives vanillin, 2, vanillic acid, 3, and vanillylacetone, 4, and cinnamic acid derivatives o-coumaric acid, 6, m-coumaric acid, 7, and p-coumaric acid, 8, showed significant antifungal activities (from highest to lowest, 2, 5 > 1 > 6, 7 > 4 > 3, 8) in the yeast system, with caffeic acid, 9, having little to no effect. Antifungal activity levels against A. flavus were similar. This similarity in antifungal activity demonstrated the usefulness of the S. cerevisiae bioassay for screening antifungal compounds. Assays using deletion mutants of yeast identified signal transduction and antioxidative stress response genes important to fungal tolerance. Targeting the antioxidative stress response system with certain compounds (e.g., 4) in combination with strobilurin fungicides had a synergistic effect against both fungi.

A Two-Phase Resistance Response of Venturia inaequalis Populations to the QoI Fungicides Kresoxim-Methyl and Trifloxystrobin

The class of fungicides acting as respiration inhibitors by binding to the Qo center of cyto-chrome b (QoIs) are in wide use for the management of apple scab caused by Venturia inaequalis. In order to assess responses of V. inaequalis populations to treatments with QoIs, sensitivities of isolates were determined for germinating conidia or for mycelial colonies developing from germinating conidia. Under both test conditions, inhibitory potencies of kresoxim-methyl and trifloxystrobin were largely equivalent. V. inaequalis populations treated with QoIs in a commercial and an experimental orchard both responded with significant shifts toward declining QoI sensitivities. However, the population responses were quantitative in nature, and highly resistant isolates indicative of a cytochrome b target site mutation were not detected. V. inaequalis populations from both orchards investigated also were fully resistant to sterol de-methylation-inhibiting fungicides (DMIs) such as fenarimol and myclobutanil, but isolate sensitivities to QoIs and DMIs were largely unrelated. Performance tests with kresoxim-methyl and trifloxystrobin at the experimental orchard diagnosed as DMI-resistant revealed that the quantitative shift toward declining QoI sensitivities did not constitute the status of practical QoI resistance. In contrast to these quantitative responses, emergence of qualitative QoI resistance was documented for V. inaequalis in an orchard in North Germany, which had been treated intensively with a total of 25 QoI applications over four consecutive seasons. Isolates retrieved from the orchard were highly resistant to both kresoxim-methyl and trifloxystrobin and were characterized as G143A cytochrome b mutants. The results indicated that the paths of QoI resistance can be both quantitative and qualitative in nature. A similar phenomenon has not been described before. Circumstantial evidence suggests that the quantitative phase of V. inaequalis population responses to QoIs might be succeeded by a quantitative selection of highly resistant G143A target-site mutants.

Characterization of Colletotrichum graminicola Isolates Resistant to Strobilurin-Related QoI Fungicides

Isolates of Colletotrichum graminicola were collected from annual bluegrass or bent grass turf in Japan and the United States, and their sensitivities to QoI fungicides (QoIs) as well as their cytochrome b sequences were characterized. Five isolates sampled from turf treated repeatedly with azoxystrobin were highly QoI resistant under both in vivo and in vitro test conditions. The nucleotide sequences of a large cytochrome b gene segment involving the binding site of QoIs were fully homologous for all resistant isolates and contained the G143A target site mutation known to confer QoI resistance in other pathogens. QoI-sensitive isolates collected prior to treatments with QoIs were more diverse with regard to their cytochrome b gene sequences and their phenotype responses to QoIs. All wild-type isolates retained a glycine in position 143 of cytochrome b. Three of the four QoI-sensitive isolates were, in addition, distinguished by leucines in positions 95, 130, and 141, which were exchanged to threonine in all resistant but also in one of the sensitive isolates. In addition to a more pronounced divergence of cytochrome b sequences, the sensitive wild-type isolates also were diverse with regard to the induction of alternative respiration in response to QoI action, as indicated by comparisons of QoI sensitivities displayed in the absence or presence of the alternative oxidase inhibitor salicylhydroxamic acid. These different phenotype responses expressed under in vitro test conditions had no or only a slight impact on anthracnose control in protective applications of azoxystrobin. Isolate responses in vitro were very similar for trifloxystrobin, indicating cross-resistance among the class of QoIs. Our results imply that C. graminicola falls into the class of pathogens with a potential for rapid selection of highly QoI-resistant phenotypes. Frequent monitoring of population sensitivities will be required to determine the status of population responses toward practical QoI resistance.

Field Resistance to Strobilurin (Q(o)I) Fungicides in Pyricularia grisea Caused by Mutations in the Mitochondrial Cytochrome b Gene

ABSTRACT Gray leaf spot caused by Pyricularia grisea is a highly destructive disease of perennial ryegrass turf. Control of gray leaf spot is dependent on the use of preventative fungicide treatments. Strobilurin-based (Q(o)I) fungicides, which inhibit the cytochrome bc(1) respiratory complex, have proven to be very effective against gray leaf spot. However, in August 2000, disease was diagnosed in Q(o)I-treated perennial ryegrass turf on golf courses in Lexington, KY, Champaign, IL, and Bloomington, IL. To determine if resistance was due to a mutation in the fungicide target, the cytochrome b gene (CYTB) was amplified from baseline and resistant isolates. Nucleotide sequence analysis revealed an intronless coding region of 1,179 bp. Isolates that were resistant to Q(o)I fungicides possessed one of two different mutant alleles, each of which carried a single point mutation. The first mutant allele had a guanine-to-cytosine transition at nucleotide position +428, resulting in a replacement of glycine 143 by alanine (G143A). Mutant allele two exhibited a cytosine-to-adenine transversion at position +387, causing a phenylalanine-to-leucine change (F129L). Cleavable amplified polymorphic sequence analysis revealed that neither mutation was present in a collection of baseline isolates collected before Q(o)I fungicide use and indicated that suspected Q(o)I- resistant isolates found in 2001 in Indiana and Maryland possessed the F129L mutation. The Pyricularia grisea isolates possessing the G143A substitution were significantly more resistant to azoxystrobin and trifloxystrobin, in vitro, than those having F129L. DNA fingerprinting of resistant isolates revealed that the mutations occurred in just five genetic backgrounds, suggesting that field resistance to the Q(o)I fungicides in Pyricularia grisea is due to a small number of ancestral mutations.

A critical evaluation of the role of alternative oxidase in the performance of strobilurin and related fungicides acting at the Qo site of complex III

Mitochondrial respiration conserves energy by linking NADH oxidation and electron-coupled proton translocation with ATP synthesis, through a core pathway involving three large protein complexes. Strobilurin fungicides block electron flow through one of these complexes (III), and disrupt energy supply. Despite an essential need for ATP throughout fungal disease development, strobilurins are largely preventative; indeed some diseases are not controlled at all, and several pathogens have quickly developed resistance. Target-site variation is not the only cause of these performance difficulties. Alternative oxidase (AOX) is a strobilurin-insensitive terminal oxidase that allows electrons from ubiquinol to bypass Complex III. Its synthesis is constitutive in some fungi but in many others is induced by inhibition of the main pathway. AOX provides a strobilurin-insensitive pathway for oxidation of NADH. Protons are pumped as electrons flow through Complex I, but energy conservation is less efficient than for the full respiratory chain. Salicylhydroxamic acid (SHAM) is a characteristic inhibitor of AOX, and several studies have explored the potentiation of strobilurin activity by SHAM. We present a kinetic-based model which relates changes in the extent of potentiation during different phases of disease development to a changing importance of energy efficiency. The model provides a framework for understanding the varying efficacy of strobilurin fungicides. In many cases, AOX can limit strobilurin effectiveness once an infection is established, but is unable to interfere significantly with strobilurin action during germination. A less stringent demand for energy efficiency during early disease development could lead to insensitivity towards this class of fungicides. This is discussed in relation to Botrytis cinerea, which is often poorly controlled by strobilurins. Mutations with a similar effect may explain evidence implicating AOX in resistance development in normally well-controlled plant pathogens, such as Venturia inaequalis.

Impact of alternative respiration and target-site mutations on responses of germinating conidia of Magnaporthe grisea to Qo-inhibiting fungicides

Qo-inhibiting fungicides act as respiration inhibitors by binding to the Qo center of cytochrome b. Sensitivities of fungi to Qo inhibitors can be influenced by the induction of alternative respiration or by mutational changes of the cytochrome b target site. Previous studies on both mechanisms in Magnaporthe grisea (Hebert) Barr were focused on the mycelial stage of the pathogen. The present study describes the expression and impact of both resistance mechanisms during the stage of conidia germination. In the absence of a host, alternative respiration provided a >500-fold rescue from azoxystrobin during the germination of conidia derived from four wild-type isolates of M. grisea. This rescue potential during conidia gemination was substantially more pronounced than for mycelial growth. However, the pronounced effectiveness of alternative respiration during conidia germination was not apparent when barley leaves were protected with azoxystrobin prior to inoculation with conidia. In a comparison of a wild-type strain and an alternative respiration-deficient mutant, azoxystrobin efficacies in suppressing symptom development differed by a factor of two, with full disease control achieved for both genotypes at 1 microg ml(-1) azoxystrobin. In contrast, conidia derived from two QoI-resistant target site mutants were highly resistant to azoxystrobin and trifloxystrobin and fully capable of infecting leaf surfaces protected with 10 microg ml(-1) of azoxystrobin. Both target-site mutants had emerged spontaneously in the presence of high azoxystrobin doses when residual mycelial growth was supported by alternative respiration. The effective silencing of alternative respiration in protective applications of Qo-inhibiting fungicides might constitute a strategy of slowing the emergence of highly resistant target site mutants.

Characterization of spontaneous mutants of Magnaporthe grisea expressing stable resistance to the Qo-inhibiting fungicide azoxystrobin

The class of Qo-inhibiting fungicides (QoIs) act as respiration inhibitors by binding to the Qo center of cytochrome b. The longevity of these fungicides has been challenged by the selection of fungal sub-populations resisting high doses of QoI fungicides, with a G143A amino acid exchange in the cytochrome b target site identified as the most common cause of resistance. In contrast, the mechanism of alternative respiration, as another mechanism of fungal QoI resistance, has thus far not been affiliated with practical resistance. In the present study, azoxystrobin-resistant mutants of Magnaporthe grisea were generated and characterized. Emergence of these spontaneous mutants was facilitated when resting melanized mycelia were allowed to escape full inhibition by azoxystrobin. This escape was related to the intactness of alternative respiration, indicating that residual expression of this rescue mechanism was involved in the spontaneous emergence of target-site mutants. The two mutants characterized resisted high doses of the QoI, azoxystrobin, with resistance factors exceeding 1,000. Two different mutations of the cytochrome b gene were identified as exchanges of guanine, leading to a G143A or a G143S amino acid exchange. Resistance of both target-site mutants remained stable during four consecutive disease cycles in the absence of azoxystrobin. Several parameters tested to measure fitness penalties inherent to the mutational changes revealed that the G143A mutant was not compromised. In contrast, the conidia production of the G143S mutant was significantly lower under both saprophytic and pathogenic conditions of reproduction.

A non-Mendelian inheritance of resistance to strobilurin fungicides in Ustilago maydis

Mutants of Ustilago maydis (DC) Corda with high resistance to azoxystrobin (RF 164 to 4714, based on EC50 values), an inhibitor of mitochondrial electron transport at the cytochrome bc1 complex, were isolated in a mutation frequency of 2.3 x 10(-7) after nitrosoguanidine mutagenesis and selection on media containing 1 microgram ml-1 azoxystrobin in addition to 0.5 mM salicylhydroxamate (SHAM), a specific inhibitor of cyanide-resistant (alternative) respiration. Oxygen uptake in whole cells was strongly inhibited in the wild-type strains by azoxystrobin (1.5 micrograms ml-1) in addition to SHAM (1 mM), but not in the mutant isolates. Genetic analysis with nine such mutant isolates resulted in progeny phenotypes which did not follow Mendelian segregation, but satisfied the criteria of non-Mendelian (cytoplasmic) heredity. In crosses between three mutant isolates with the compatible wild-type strains, the sensitivity was inherited by progeny maternally from the wild-type parent strain (criterion of uniparental inheritance). In crosses between wild-type strains and remaining mutant isolates, a continuous distribution of sensitivity in the progeny was found (criterion of vegetative segregation). The third criterion of cytoplasmic resistance (criterion of intracellular selection) was fulfilled by experiments on the stability of resistance phenotypes. With two exceptions, a reduction of resistance was observed in the mutant strains when they were grown on inhibitor-free medium. Recovery of the high resistance level was observed after they were returned to the selection medium. Cross-resistance studies with other fungicides, which also inhibit electron transport through complex III of respiratory chain, showed that mutations for resistance to azoxystrobin were also responsible for reduced sensitivity to kresoxim-methyl (RF 18 to 1199) and to antimycin-A (RF 20 to 305), which act at the Qo and Qi sites of the cytochrome bc1 complex, respectively. Studies of the fitness of azoxystrobin-resistant isolates showed that these mutations appeared to be pleiotropic, having significant adverse effects on growth in liquid culture and pathogenicity on young corn plants.

Sensitivity to Azoxystrobin Among Isolates of Uncinula necator: Baseline Distribution and Relationship to Myclobutanil Sensitivity

Two hundred fifty-six single-conidial chain isolates of Uncinula necator were assayed for their sensitivity to azoxystrobin and myclobutanil. These isolates were collected from two sites in New York in 1999: an "organic" vineyard where no synthetic fungicides have been used (baseline population) and a commercial vineyard having a history of compromised powdery mildew control with myclobutanil (demethylation inhibitor [DMI]-resistant population). Mean coefficients of variance for a leaf disk assay used to test fungicide sensitivities were 31% for azoxystrobin and 41% for myclobutanil. Baseline ED₅₀ values ranged from 0.0037 to 0.028 μg/ml (mean 0.0097μg/ml) for azoxystrobin and from 0.0049 to 0.69 μg/ml (mean 0.075 μg/ml) for myclobutanil. A shift in the mean ED50 value for azoxystrobin to 0.018 μg/ml was observed in the DMI-resistant population; with the strongest shift observed for isolates collected from vines treated exclusively with myclobutanil (0.024 μg/ml). For the 256 tested isolates, there was a moderate, but statistically significant, correlation between azoxystrobin and myclobutanil sensitivities (R² = 0.36, P < 0.001). Tests with three other strobilurin fungicides (kresoxim-methyl, pyraclostrobin, and trifloxystrobin) indicate clear differences in the intrinsic activity of these compounds against U. necator, and the applicability of the methods developed with azoxystrobin for assays with pyraclostrobin and trifloxystrobin. Isolates from the high and low ends of the azoxystrobin sensitivity distribution (15× difference in mean ED₅₀ values) were equally controlled in planta by protectant or postinfection treatment with azoxystrobin at 250 μg a.i./ml, but postinfection application at lower rates (2.5 and 25 μg a.i./ml) resulted in a 41 and 44% decrease, respectively, in the control of the low-sensitivity isolates versus high-sensitivity isolates. The results of this study document the baseline sensitivity distribution of U. necator to azoxystrobin, provide evidence of partial cross-sensitivity between azoxystrobin and myclobutanil, and illustrate the potential selection for individuals with reduced sensitivity (quantitative range) to azoxystrobin by postinfection application and reduced rates of this fungicide.

Resistance to QoI (Strobilurin-like) Fungicides in Isolates of Pyricularia grisea from Perennial Ryegrass

In August 2000, azoxystrobin was ineffective in controlling gray leaf spot of perennial ryegrass at a golf course in Lexington, KY and at two golf courses in Illinois. Isolates suspected of being fungicide-resistant ("suspect isolates") were compared to "baseline" isolates obtained from sites with no known use of quinol-oxidizing inhibitor (Q_oI) fungicides. Conidial germination of Pyricularia grisea was tested in vitro with 100 μg of salicylhydroxamic acid per ml. For baseline isolates, 50% effective concentration (EC₅₀) values for azoxystrobin and trifloxystrobin were 0.015 to 0.064 and 0.013 to 0.078 μg/ml, respectively; EC₅₀ values for suspect isolates were 2.39 to 44.8 and 0.31 to 111, respectively. All suspect isolates exhibited significantly (P = 0.05) lower sensitivity to Q_oI fungicides than all baseline isolates. The mean EC₅₀ values for suspect isolates for azoxystrobin and trifloxystrobin were 690 and 827 times higher, respectively, than the means for baseline isolates. In the laboratory, azoxystrobin and trifloxystrobin provided essentially complete control of disease induced by nine baseline isolates in vivo. Azoxystrobin and trifloxystrobin provided poor to no control of disease induced by six of eight suspect isolates; control of disease induced by the remaining two isolates was partial for azoxystrobin and complete for trifloxystrobin. We conclude that one or more biotypes of perennial ryegrass-infecting strains of P. grisea with resistance to Q_oI fungicides have emerged. This is the first report of resistance to Q_oI fungicides in P. grisea. Furthermore, this is one of two Q_oIresistant fungal pathogens collected in the United States during the 2000 growing season, the first instances reported for North America.

Occurrence and molecular characterization of strobilurin resistance in cucumber powdery mildew and downy mildew

ABSTRACT Between 1998 and 1999, control failure of powdery mildew (Podosphaera fusca) and downy mildew (Pseudoperonospora cubensis) by the strobilurin fungicides azoxystrobin and kresoxim-methyl was observed in cucumber-growing areas of Japan. Results from inoculation tests carried out on intact cucumber plants and leaf disks clearly showed the distribution of pathogen isolates highly resistant to azoxystrobin and kresoximmethyl. Fragments of the fungicide-targeted mitochondrial cytochrome b gene were polymerase chain reaction amplified from total pathogen DNA and their sequences analyzed to elucidate the molecular mechanism of resistance. A single point mutation (GGT to GCT) in the cytochrome b gene, resulting in substitution of glycine by alanine at position 143, was found in resistant isolates of downy mildew. This substitution in cytochrome b seemed to result in high resistance to strobilurins in this pathogen. The same mutation was found in some but not all resistant isolates of powdery mildew. This study suggests that a mutation at position 143 in the target-encoding gene, resulting in an amino acid substitution, was probably a major cause of the rapid development of high strobilurin resistance in these two pathogens.

Sensitivity of mitochondrial respiration to different inhibitors in Venturia inaequalis

The sensitivity of Venturia inaequalis field isolates to inhibitors of the cytochrome bc1 complex at the Qo site (QoIs) was characterised at the molecular, biochemical and physiological level, and compared to other respiration inhibitors. Comparison of a sensitive and a QoI-resistant isolate revealed very high resistance factors both in mycelium growth and spore germination assays. Cross-resistance was observed among QoIs such as trifloxystrobin, azoxystrobin, famoxadone, strobilurin B and myxothiazol. In the mycelium growth assay, antimycin A, an inhibitor of the cytochrome bc1 complex at the Qi site, was less active against the QoI-resistant than against the sensitive isolate. The mixture of QoIs with salicylhydroxamic acid (SHAM), an inhibitor of the alternative oxidase, exerted synergistic effects in the spore germination but not in the mycelium growth assay. Thus, the cytochrome and the alternative respiration pathways are assumed to play different roles, depending on the developmental stage of the fungus. Induction of alternative oxidase (AOX) by trifloxystrobin was observed in mycelium cells at the molecular level for the sensitive but not the resistant isolate. Following QoI treatment, respiration parameters such as oxygen consumption, ATP level, membrane potential and succinate dehydrogenase activity were only slightly reduced in Qo-resistant mycelium cells, and remained at much higher levels than in sensitive cells. In contrast, no difference was observed between sensitive and resistant isolates when NADH consumption was measured. Comparison of the cytochrome b (cyt b) gene of the sensitive and resistant isolates did not reveal any point mutations as is known to occur in resistant isolates of other plant pathogens. It is assumed that QoI resistance in V inaequalis may be based on a compensation of the energy deficiency following QoI application upstream of the NADH dehydrogenase of the respiratory chain.