Genetic analysis of fenhexamid-resistant field isolates of the phytopathogenic fungus Botrytis cinerea

Genotypic and phenotypic characterization of resistance to fenhexamid, carboxin, and, prochloraz, in Botrytis cinerea isolates collected from cut roses in Colombia

Gray mold, caused by Botrytis sp., is a significant disease in Colombian rose crops and its control depends primarily on the intensive use of chemically synthesized fungicides. Despite the importance of this pathogen, there is limited information in Colombian floriculture about molecular taxonomy of species, fungicide resistance of populations and their genetic mechanism of resistance. In this study, we analyze 12 isolates of this fungus collected from rose-producing crops in the Department of Cundinamarca and conducted phylogenetic analysis using HSP60, G3PDH, and RPB2 gene sequences. Additionally, we realize phenotypic and genotypic characterization of resistance to the fungicides fenhexamid, carboxin, and prochloraz, evaluating the in vitro EC50 and presence of mutations of target genes of each isolate. All isolates were characterized as Botrytis cinerea in the phylogenetic analysis and presents different levels of resistance to each fungicide. These levels are related to mutations in target genes, with predominancy of L195F and L400F in the ERG27 gene to fenhexamid resistance, H272R/Y in the SDHB gene for carboxin resistance, and Y136F in the CYP51 gene for prochloraz resistance. Finally, these mutations were not related to morphological changes. Collectively, this knowledge, presented for the first time to the Colombian floriculture, contribute to a better understanding of the genetic diversity and population of B. cinerea from rose-producing crops in the department of Cundinamarca, and serve as a valuable tool for making informed decisions regarding disease management, future research, and improving crop management and sustainability in the Colombian floriculture industry.

Fungicide-Resistant Botrytis in Forest Nurseries May Impact Disease Control in Norway Spruce

Gray mold, caused by Botrytis spp., is a serious problem in Norway spruce seedling production in forest nurseries. From 2013 to 2019, 125 isolates of Botrytis were obtained from eight forest nurseries in Norway: 53 from Norway spruce seedlings, 16 from indoor air, 52 from indoor surfaces, and four from weeds growing close to seedlings. The majority of isolates were identified as B. cinerea, and over 60% of these were characterized as Botrytis group S. B. pseudocinerea isolates were obtained along with isolates with DNA sequence similarities to B. prunorum. Fungicide resistance was assessed with a mycelial growth assay, and resistance was found for the following: boscalid (8.8%), fenhexamid (33.6%), fludioxonil (17.6%), pyraclostrobin (36.0%), pyrimethanil (13.6%), and thiophanate-methyl (50.4%). Many isolates (38.4%) were resistant to two to six different fungicides. A selection of isolates was analyzed for the presence of known resistance-conferring mutations in the cytb, erg27, mrr1, sdhB, and tubA genes, and mutations leading to G143A, F412S, ΔL497, H272R, and E198A/F200Y were detected, respectively. Detection of fungicide resistance in Botrytis from Norway spruce and forest nursery facilities reinforces the necessity of employing resistance management strategies to improve control and delay development of fungicide resistance in the gray mold pathogens.[Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Multiple and multidrug resistance in Botrytis cinerea: molecular mechanisms of MLR/MDR strains in Greece and effects of co-existence of different resistance mechanisms on fungicide sensitivity

Botrytis cinerea is a high-risk pathogen for fungicide resistance development. Within the fungal populations, strains have developed multiple mutations in different target genes leading to multiple resistance (MLR) or mutations associated with overexpression of efflux transporters leading to multidrug resistance (MDR). These types of resistance are a major threat, and their successful management is a major challenge. The current study was initiated to a) determine frequencies of MLR/MDR strains in populations originating from several crops, b) identify the types of MDR that occur in Greece, and c) determine interactions between MLR and MDR at the level of sensitivity to botryticides. The frequencies of MLR/MDR phenotypes were determined in 515 isolates subjected to bioassays using discriminatory concentrations of thiophanate-methyl, iprodione, cyprodinil, fenhexamid, boscalid, fluopyram, fludioxonil, pyraclostrobin, and tolnaftate. Interestingly, 7.8% and 31.3% of isolates from strawberry and rootstock seedlings were resistant to every single fungicide class, while MDR phenotypes from strawberries, rootstocks, and tomatoes accounted for 26%, 87%, and 13.4%, respectively. The MLR and MDR isolates were further molecularly analyzed regarding genes erg27, sdhB, Bcpos5, and Mrr1, responsible for resistance to fenhexamid, boscalid and fluopyram, cyprodinil, and MDR, respectively. The different mutations' presence was determined along with a new mutation in Mrr1 leading to MDR. MDR isolates were characterized as MDR1 or MDR1h based on the presence of a 3-bp deletion in Mrr1. MDR1h was predominant in isolates from rootstocks and MDR1 from tomatoes and strawberries, whereas the most frequent target-site mutations were F412S (erg27), H272R (sdhB), and L412F (Bcpos5). To determine whether the accumulation of target-site mutations along with MDR mutations exhibits an additive effect concerning fungicide resistance, the sensitivity of isolates possessing the predominant target-site mutations was calculated in both the presence and the absence of MDR-associated mutations. EC50 in cyprodinil and boscalid increased to about twofold in the presence of MDR mutations, while there was no difference for fenhexamid. In conclusion, MLR/MDR frequencies are notably high in heavily treated crops in Greece, and the combination of MLR and MDR mutations leads to even higher fungicide resistance levels, highlighting the importance of resistance management.

Benzimidazole-Resistant Isolates with E198A/V/K Mutations in the β-Tubulin Gene Possess Different Fitness and Competitive Ability in Botrytis cinerea

Previous studies in Botrytis cinerea showed that resistance to methyl benzimidazole carbamates (MBCs) was mainly related to E198A/V/K and F200Y mutations of the β-tubulin gene, and E198V was the dominant mutation in the resistant subpopulation in Hubei Province of China, indicating that resistant mutations might influence fitness. However, little is known about the effect of each E198A/V/K mutation on fitness. In this study, the fitness and competitive ability of isolates with E198A/V/K mutations were investigated. Results showed that E198A/V/K isolates and wild-type isolates shared similar fitness components in terms of virulence, sporulation, conidial germination, oxidative sensitivity, and sclerotial production and viability. However, slower mycelial growth at 4°C, higher sensitivity to 4% NaCl, and increased sclerotial production percentage at 4°C were observed in the isolates with E198V, E198K, and E198A mutations, respectively. Competitive analysis showed that the wild-type subpopulation became dominant after three disease cycles in the absence of fungicide selection pressure, whereas the resistant subpopulation seized the space of the sensitive subpopulation upon MBC application. Unexpectedly, the frequency of E198V isolates decreased dramatically after the first disease cycle with or without fungicide selection pressure. These results suggest that MBC-resistant isolates suffer little fitness penalty but possess competitive disadvantages in the absence of fungicide selection pressure. Under fungicide selection pressure, E198V isolates could not compete with E198A/K isolates. According to the current results, there is a great possibility that the E198V mutation will lose dominance in the future in China.

Status of Fungicide Resistance and Physiological Characterization of Tebuconazole Resistance in Rhizocotonia solani in Sichuan Province, China

The resistance prevalence of chemical fungicides has caused increasingly serious agro-ecological environmental problems. However, there are few previous reports about resistance to succinate dehydrogenase (SDHI) or sterol demethylation inhibitor (DMI) in Rhizoctonia solani, one of the main agro-diseases. In this study, the fungicide resistance of 122 R. solani isolates in Sichuan Province was monitored by the mycelial growth rate method. Results showed that all isolates were susceptible to hexaconazole and most isolates were susceptible to thifluzamide, except for the field isolate MSRS-2-7 due to a moderate resistance to thifluzamide (16.43-fold resistance ratio, RR), compared to the sensitivity baseline of thifluzamide (0.042 μg/mL EC₅₀ values). On the contrary, many isolates showed moderate or high resistance to tebuconazole (10.59- to 60.78-fold RR), reaching EC₅₀ values of 0.54~3.10 μg/mL, especially for a highly resistant isolate LZHJ-1-8 displaying moderate resistance to epoxiconazole (35.40-fold RR due to a 3.54 μg/mL EC₅₀ value). The fitness determination found that the tebuconazole-resistant isolates showed higher fitness cost with these characteristics, including a lower growth rate, higher relative electric conductivity, an increased ability to tolerate tebuconazole, and high osmotic pressure. Four new mutations of cytochrome P450 sterol 14α-demethylase (CYP51), namely, S94A, N406S, H793R, and L750P, which is the target for DMI fungicides, was found in the tebuconazole-resistant isolates. Furthermore, the lowest binding energy with tebuconazole was also found in the LZHJ-1-8 isolate possessing all the mutations through analyses with Discovery Studio software. Therefore, these new mutation sites of CYP51 may be linked to the resistance against tebuconazole, and its application for controlling R. solani should be restricted in some areas.

Inhibiting C-4 Methyl Sterol Oxidase with Novel Diazaborines to Target Fungal Plant Pathogens

With resistance to current agricultural fungicides rising, a great need has emerged for new antifungals with unexploited targets. In response, we report a novel series of diazaborines with potent activity against representative fungal plant pathogens. To identify their mode of action, we selected for resistant isolates using the model fungus Saccharomyces cerevisiae. Whole-genome sequencing of independent diazaborine-resistant lineages identified a recurring mutation in ERG25, which encodes a C-4 methyl sterol oxidase required for ergosterol biosynthesis in fungi. Haploinsufficiency and allele-swap experiments provided additional genetic evidence for Erg25 as the most biologically relevant target of our diazaborines. Confirming Erg25 as putative target, sterol profiling of compound-treated yeast revealed marked accumulation of the Erg25 substrate, 4,4-dimethylzymosterol and depletion of both its immediate product, zymosterol, as well as ergosterol. Encouraged by these mechanistic insights, the potential utility of targeting Erg25 with a diazaborine was demonstrated in soybean-rust and grape-rot models of fungal plant disease.

Fungicide resistance characterized across seven modes of action in Botrytis cinerea isolated from Australian vineyards

BACKGROUND

Botrytis bunch rot, caused by Botrytis cinerea, is an economically important disease of grapes in Australia and across grape-growing regions worldwide. Control of this disease relies on canopy management and the application of fungicides. Fungicide application can lead to the selection of resistant B. cinerea populations, which has an adverse effect on the management of the disease. Characterizing the distribution and severity of resistant B. cinerea populations is needed to inform resistance management strategies.

RESULTS

In this study, 724 isolates were sampled from 76 Australian vineyards during 2013-2016 and were screened against seven fungicides with different modes of action (MOAs). The resistance frequencies for azoxystrobin, boscalid, fenhexamid, fludioxonil, iprodione, pyrimethanil and tebuconazole were 5%, 2.8%, 2.1%, 6.2%, 11.6%, 7.7% and 2.9%, respectively. Nearly half of the resistant isolates (43.8%) were resistant to more than one of the fungicides tested. The frequency of vineyards with at least one isolate simultaneously resistant to one, two, three, four or five fungicides was 19.7%, 7.9%, 6.6%, 10.5% and 2.6%. Resistance was associated with previously published genotypes in CytB (G143A), SdhB (H272R/Y), Erg27 (F412S), Mrr1 (D354Y), Bos1 (I365S, N373S + Q369P, I365S + D757N) and Pos5 (V273I, P319A, L412F/V). Novel genotypes were also described in Mrr1 (S611N, D616G), Pos5 (V273L) and Cyp51 (P347S). Expression analysis was used to characterize fludioxonil-resistant isolates exhibiting overexpression (6.3-9.6-fold) of the ABC transporter gene AtrB (MDR1 phenotype).

CONCLUSION

Resistance frequencies were lower when compared to most previously published surveys of B. cinerea resistance in grape and other crops. Nevertheless, continued monitoring of critical MOAs used in Australian vineyards is recommended. © 2021 Society of Chemical Industry.

Inhibition of SC4MOL and HSD17B7 shifts cellular sterol composition and promotes oligodendrocyte formation

While the cholesterol biosynthesis pathway has been extensively studied, recent work has forged new links between inhibition of specific sterol pathway enzymes, accumulation of their unique sterol substrates, and biological areas as diverse as cancer, immunology, and neurodegenerative disease. We recently reported that dozens of small molecules enhance formation of oligodendrocytes, a glial cell type lost in multiple sclerosis, by inhibiting CYP51, Sterol 14-reductase, or EBP and inducing cellular accumulation of their 8,9-unsaturated sterol substrates. Several adjacent pathway enzymes also have 8,9-unsaturated sterol substrates but have not yet been evaluated as potential targets for oligodendrocyte formation or in many other biological contexts, in part due to a lack of available small-molecule probes. Here, we show that genetic suppression of SC4MOL or HSD17B7 increases the formation of oligodendrocytes. Additionally, we have identified and optimized multiple potent new series of SC4MOL and HSD17B7 inhibitors and shown that these small molecules enhance oligodendrocyte formation. SC4MOL inhibitor CW4142 induced accumulation of SC4MOL's sterol substrates in mouse brain and represents an in vivo probe of SC4MOL activity. Mechanistically, the cellular accumulation of these 8,9-unsaturated sterols represents a central driver of enhanced oligodendrocyte formation, as exogenous addition of purified SC4MOL and HSD17B7 substrates but not their 8,9-saturated analogs promotes OPC differentiation. Our work validates SC4MOL and HSD17B7 as novel targets for promoting oligodendrocyte formation, underlines a broad role for 8,9-unsaturated sterols as enhancers of oligodendrocyte formation, and establishes the first high-quality small molecules targeting SC4MOL and HSD17B7 as novel tools for probing diverse areas of biology.

Molecular identification and characterization of Botrytis cinerea associated to the endemic flora of semi-desert climate in Chile

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For the first time was detected the presence of B. cinerea on fourteen new host plant.

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We provide evidence for phenotype and genotype diversity in these B. cinerea isolates, where 83.3% of the isolates presented both transposable elements, boty and flipper.

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We found in this study, that some isolates of this fungus lose the ability to produce conidia or sclerotia formation and revealed a great diversity among the isolates concerning both features.

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The 16.6% of the isolates of B. cinerea showed substantially reduced virulence.

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According to fungicide resistance studies the results indicate that resistance to Fenhexamid or Boscalid was observed in the 22.6% of isolates.

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These findings are of great epidemiological importance to several regions, because of the distribution and the possible ecological impact of this disease on native and endemic plants in Chile.

Botrytis cinerea is a phytopathogenic fungus that infects over 200 plant species and can cause significant crop losses in local and worldwide agricultural industries. However, its presence in the endemic flora in the Coquimbo Region and its impact on local flora have not been studied yet. In order to determine whether Botrytis spp is present in the native plant in the Coquimbo Region, fifty-two field-samples were analysed. A total of 30 putative Botrytis spp were isolated and phenotypic and genetically characterized. The internal transcribed spacer (ITS) analysis of these isolates revealed that it corresponded to genus Botrytis. For further confirmation, nuclear protein-coding genes (G3PDH, HSP60, and RPB2) were sequenced and showed 100% identity against B. cinerea. Complementary to this, Botrytis can also be clustered in two different groups, group I (B. pseudocinerea) and group II (B. cinerea), based on DNA polymorphism, the Botrytis isolates were identified as member of group II. On the order hand, we investigated the presence and frequency distribution of the transposable elements boty and flipper in the isolates obtained. The results indicate that 83.3% of the isolates presented both transposable elements, boty and flipper, indicating that the most prevalent genotype was transpose. In addition, 16.6% of the isolates showed substantially reduced virulence in apple fruit in comparison to B05.10 strain. According to fungicide resistance studies, the results indicate that resistance to Fenhexamid or Boscalid was observed in the 22.6% of isolates. The results show for the first time that B. cinerea has not been described before in fourteen new host plants and contributes to our fundamental understanding of the presence of B. cinerea in the native plant in the Coquimbo Region and the possible ecological impact of this disease on native and endemic plants.

Screening of Lactic Acid Bacteria for the Bio-Control of Botrytis cinerea and the Potential of Lactiplantibacillus plantarum for Eco-Friendly Preservation of Fresh-Cut Kiwifruit

Botrytis cinerea, responsible for grey mold, represents the first biological cause of fruit and vegetable spoilage phenomena in post-harvest. Kiwifruit is a climacteric fruit particularly prone to this mold infestation during storage. Lactic acid bacteria (LAB) are food-grade bacteria that can synthesize several metabolites with antimicrobial activity and are, therefore, suggested as promising and eco-friendly resources for the bio-control of molds on fruits and vegetables. In this work, we propose the screening of a collection of 300 LAB previously isolated from traditional sourdoughs for their ability to counteract in vitro the growth of Botrytis cinerea CECT 20973. Only 2% of tested LAB strains belonging to Lactiplantibacillus plantarum species, exerted a strong antagonism against B. cinerea. The cell-free supernatants were partially characterized and results clearly indicated that high levels of lactic acid contributed to the antagonistic activity. PAN01 and UFG 121 cell-free supernatants were investigated as potential bio-control agents in a preliminary in vivo assay using freshly cut kiwifruits as a food model. The application of cell-free supernatants allowed to delay the growth of B. cinerea on artificially contaminated kiwifruits until two weeks. The antagonistic activity was greatly affected by the storage temperature (25 °C and 4 °C) selected for the processed fruits, suggesting the importance to include microbial-based solution in a broader framework of hurdle technologies.

Identification and Characterization of Fungicide Resistance in Botrytis Populations from Small Fruit Fields in the Mid-Atlantic United States

From 2014 to 2019, 249 isolates of Botrytis sp. were collected from blackberry, black raspberry, grape, red raspberry, and strawberry showing gray mold symptoms. All isolates were phylogenetically characterized as Botrytis cinerea. A mycelial growth assay determined the following overall frequencies of resistance to fungicides: 92% to pyraclostrobin, 86% to cyprodinil, 71% to thiophanate-methyl, 48% to fenhexamid, 47% to iprodione, 26% to boscalid, 11% to fludioxonil, 8% to penthiopyrad, 7% to benzovindiflupyr, 4% to pydiflumetofen , and 4% to isofetamid. Isolates collected from blackberry, red raspberry, and strawberry had a higher median chemical class resistance value compared to isolates from black raspberry and grape. Resistance conferring mutations were found in a selection of isolates characterized as resistant to thiophanate-methyl, iprodione, pyraclostrobin, fenhexamid, and boscalid including E198A in β-tubulin; I365N/S, Q369P, and N373S in bos1; G143A in cytb; P238S, N369D, and F412I/S in erg27; and P225F and H272R/Y in sdhB, respectively. Also, multiple drug resistance phenotypes MDR1 and MDR1h were identified by analyzing fludioxonil sensitivity and mrr1 sequences. MDR1 and MDR1h isolates had multiple amino acid variations and two insertions in mrr1 that resembled the group S genotype . A detached grape assay confirmed that the aforementioned mutations in isolates from different small fruit crops resulted in field-relevant resistance. An additional in-vitro assay found that EC50 values of B. cinerea isolates to pydiflumetofen and inpyrfluxam averaged 0.4 and 1.0, 0.8 and 0.7, 149.8 and 23.2, 0.9 and 0.9, and 38.8 and 48.8 µg/ml for the wild-type, H272R, H272Y, N230I, and P225F genotypes, respectively. These results revealed widespread fungicide resistance in B. cinerea from Mid-Atlantic small fruit fields, highlighting the need for resistance management alternatives.

Fungicide Resistance Profiles of Botrytis cinerea Isolates From Michigan Vineyards and Development of a TaqMan Assay for Detection of Fenhexamid Resistance

Botrytis cinerea on grapes causes bunch rot at both pre- and postharvest stages, in which losses can reach up to 100%. Chemical control primarily relies on the prophylactic use of site-specific fungicides. Repeated applications of these products raise the risk of fungicide resistance development in B. cinerea populations, which can result in disease control failures. To determine the extent of resistance, B. cinerea isolates were collected from grape clusters in the northwest and southwest grape growing regions of Michigan in 2014 and 2018 (n = 115 and 125, respectively). These isolates were phenotyped using discriminatory doses of eight fungicides to determine the levels of resistance. Fungicide resistance increased from 2014 to 2018, mostly affecting the active ingredients fenhexamid, fluopyram, and iprodione. B. cinerea isolates resistant to multiple fungicides were detected in 2014 and 2018, with a higher frequency of resistance in 2018. TaqMan real-time PCR has been developed to detect B. cinerea fungicide resistance to fenhexamid and to differentiate the erg27 F412S/I/V alleles. The TaqMan assay was tested for sensitivity, specificity, and reproducibility on purified DNA and infected grape tissue samples. Our data provide essential information to growers about the efficacy for B. cinerea control using the available botryticides. Furthermore, the developed fenhexamid markers will be transferred to diagnostic clinics to assist growers in the management of bunch rot before resistance-related control failures occur.

Sensitivity of Botrytis cinerea to fenpyrazamine in Japan and its disease control efficacy against the low-sensitive isolate

The baseline sensitivity of Botrytis cinerea to fenpyrazamine was evaluated using 323 isolates collected in Japan prior to its launch. In this study, the isolates were classified as "sensitive" and "low-sensitive" according to their mycelial growth on 10 mg/L fenpyrazamine. However, their EC₅₀ values for the germ-tube elongations from conidia were not significantly different between these two classes. In both a pot test and a field trial, diseases caused by the sensitive and low-sensitive isolates were effectively controlled by fenpyrazamine.

CRISPR/Cas with ribonucleoprotein complexes and transiently selected telomere vectors allows highly efficient marker-free and multiple genome editing in Botrytis cinerea

CRISPR/Cas has become the state-of-the-art technology for genetic manipulation in diverse organisms, enabling targeted genetic changes to be performed with unprecedented efficiency. Here we report on the first establishment of robust CRISPR/Cas editing in the important necrotrophic plant pathogen Botrytis cinerea based on the introduction of optimized Cas9-sgRNA ribonucleoprotein complexes (RNPs) into protoplasts. Editing yields were further improved by development of a novel strategy that combines RNP delivery with cotransformation of transiently stable vectors containing telomeres, which allowed temporary selection and convenient screening for marker-free editing events. We demonstrate that this approach provides superior editing rates compared to existing CRISPR/Cas-based methods in filamentous fungi, including the model plant pathogen Magnaporthe oryzae. Genome sequencing of edited strains revealed very few additional mutations and no evidence for RNP-mediated off-targeting. The high performance of telomere vector-mediated editing was demonstrated by random mutagenesis of codon 272 of the sdhB gene, a major determinant of resistance to succinate dehydrogenase inhibitor (SDHI) fungicides by in bulk replacement of the codon 272 with codons encoding all 20 amino acids. All exchanges were found at similar frequencies in the absence of selection but SDHI selection allowed the identification of novel amino acid substitutions which conferred differential resistance levels towards different SDHI fungicides. The increased efficiency and easy handling of RNP-based cotransformation is expected to accelerate molecular research in B. cinerea and other fungi.

In this study, we describe the establishment of the CRISPR/Cas technology for genome editing in the gray mold fungus Botrytis cinerea, one of the economically most important plant pathogens worldwide. We report the development of a strategy which combines the introduction of an optimized nuclear-targeted Cas9-single guide RNA ribonucleoprotein complex (RNP) and a repair template together with unstable telomere vectors for transient selection into fungal protoplasts. A high proportion of the transformants contains the desired genetic changes, and the telomere vector is lost subsequently when selection is stopped. This system allowed introduction of changes into the genome without the requirement of selection markers. It shows superior editing efficiencies compared to existing CRISPR/Cas protocols for filamentous fungi, and leads to a very low number of additional off-target mutations. To demonstrate the performance of our protocol, we conducted for the first time a site-directed, random mutagenesis in a gene encoding an important fungicide target. This approach allows new applications such as in vivo structure-function analysis of proteins and rational fungicide resistance studies. As demonstrated with the rice blast pathogen Magnaporthe oryzae, the RNP-based CRISPR/Cas toolset with telomere vectors can be transferred to other fungi and is expected to boost their genetic manipulation.

Characterization of fungicide sensitivity profiles of Botrytis cinerea populations sampled in Lombardy (Northern Italy) and implications for resistance management

BACKGROUND

Resistance to fungicides is one of the aspects that must be considered when planning treatments to achieve an optimal control of grey mold, caused by Botrytis cinerea, in vineyards. In this study, extensive fungicide resistance monitoring was carried out in Northern Italy (Lombardy region) to evaluate several aspects of fungicide resistance (frequency of resistance, effect of field treatments, mechanism of resistance and fitness) on 720 B. cinerea strains isolated from 36 vineyards.

RESULTS

Of the characterized strains, 12% were resistant to a single fungicide class (3% to the succinate dehydrogenase inhibitor boscalid, 4% to the anilinopirimidine cyprodinil; 5% to the phenylpirrole fludioxonil; 0.1% to the ketoreductase inhibitor fenhexamid) and 0.8% to two fungicide classes contemporaneously. Resistance was associated with mutations reported in the literature for boscalid (H272Y/R) and fenhexamid (P238S or I232M). Two new mutations in sdhC (A187F) and in sdhD (I189L) could be related to boscalid resistance. Strains resistant to fludioxonil did not show any known mutations. No significant differences were found in the fitness of sensitive and resistant strains.

CONCLUSION

Overall, field populations of B. cinerea showed a relatively low frequency of resistance, but the geographical distribution of resistance, genetic mechanisms of resistance and fitness of resistant strains suggest that management of resistance should be implemented, at local and regional levels. Particular attention should be given to the fungicide sprays planned before veraison, since they seem to be associated with a higher frequency of resistant strains in vineyards. © 2020 Society of Chemical Industry.

Population Genetics and Fungicide Resistance of Botrytis cinerea on Vitis and Prunus spp. in California

Botrytis cinerea, the causal agent of gray mold, has high genetic diversity and a broad host range. In Vitis sp. and Prunus spp., B. cinerea causes pre- and postharvest diseases, and fungicides are routinely applied to prevent yield loss. In total, 535 isolates of B. cinerea collected from Vitis sp. and Prunus spp. in 2012, 2016, and 2017 were genotyped using 18 microsatellite markers and the transposable elements (TEs) Boty and Flipper. Only nine of the polymorphic markers and the two TEs were considered informative and retained for the final analyses. Of the 532 isolates, 297 were tested for resistance to seven fungicides representing six Fungicide Resistance Action Committee classes. After clone correction, 295 multilocus genotype groups were retained across the 3 years in 326 individuals, and four genetic subpopulations were detected. High levels of clonality were observed across the dataset. Significant pairwise differentiation was detected among years, locations, and TE composition. However, most of the diversity observed was within a subpopulation and not among subpopulations. No genetic differentiation was detected among resistant and sensitive isolates for individual fungicide classes. When resistance to the total number of fungicides was compared, regardless of the fungicide class, significant differentiation was detected among isolates that are resistant to two fungicide classes and those resistant to three or four fungicide groups. Fungicide resistance frequencies were stable for most chemistries evaluated with the exception of fluopyram, which increased from 2012 to 2016/2017.

Multiple catalytic activities of human 17β-hydroxysteroid dehydrogenase type 7 respond differently to inhibitors

Cholesterol biosynthesis is a multistep process in mammals that includes the aerobic removal of three methyl groups from the intermediate lanosterol, one from position 14 and two from position 4. During the demethylations at position 4, a 3-ketosteroid reductase catalyses the conversion of both 4-methylzymosterone and zymosterone to 4-methylzymosterol and zymosterol, respectively, restoring the alcoholic function of lanosterol, which is also maintained in cholesterol. Unlike other eukaryotes, mammals also use the same enzyme as an estrone reductase that can transform estrone (E1) into estradiol (E2). This enzyme, named 17β-hydroxysteroid dehydrogenase type 7 (HSD17B7), is therefore a multifunctional protein in mammals, and one that belongs to both the HSD17B family, which is involved in steroid-hormone metabolism, and to the family of post-squalene cholesterol biosynthesis enzymes. In the present study, a series of known inhibitors of human HSD17B7's E1-reductase activity have been assayed for potential inhibition against 3-ketosteroid reductase activity. Surprisingly, the assayed compounds lost their inhibition activity when tested in HepG2 cells that were incubated with radiolabelled acetate and against the recombinant overexpressed human enzyme incubated with 4-methylzymosterone (both radiolabelled and not). Preliminary kinetic analyses suggest a mixed or non-competitive inhibition on the E1-reductase activity, which is in agreement with Molecular Dynamics simulations. These results raise questions about the mechanism(s) of action of these possible inhibitors, the enzyme dynamic regulation and the interplay between the two activities.

Status and future of disease protection and grape berry quality alteration by micro-organisms in viticulture

Grapevine is one of the most widely grown fruit crops in the world. At present, however, there is much concern regarding chemical pollution in viticulture due to the application of chemical fungicides and fertilizers. One viticultural practice to resolve this issue is the application of micro-organisms to grapevine as a substitute for chemicals. Some micro-organisms act as an enhancer of grape berry quality as well as a suppresser of disease in grapevine through their antagonistic ability and/or systemic resistance inducing ability. Herein, we review current and prospective applications of micro-organisms in viticulture.

SIGNIFICANCE AND IMPACT OF THE STUDY

In this review, we evaluate the applicability of micro-organisms in viticulture. Micro-organisms can improve grape berry quality through grapevine disease protection and grape berry quality alteration. Because the use of micro-organisms to protect grapevine from plant diseases is safer than the use of chemical fungicides, the use of biofungicides in viticulture is expected to be enhanced by the increasing consumer concern towards chemical fungicides. Micro-organisms also modify plant secondary metabolites for use as flavours, pharmaceuticals and food additives. Studies of micro-organisms that promote polyphenol, anthocyanin and aroma compound biosynthesis are in progress with an eye to improving grape berry quality.

Fludioxonil induced the cancer growth and metastasis via altering epithelial-mesenchymal transition via an estrogen receptor-dependent pathway in cellular and xenografted breast cancer models

Fludioxonil is an antifungal agent used in agricultural applications that is present at measurable amounts in fruits and vegetables. In this study, the effects of fludioxonil on cancer cell viability, epithelial-mesenchymal transition (EMT), and metastasis were examined in MCF-7 clonal variant breast cancer cell (MCF-7 CV cells) with estrogen receptors (ERs). MCF-7 CV cells were cultured with 0.1% DMSO (control), 17β-estradiol (E2; 1 ×10^-9 M, positive control), or fludioxonil (10^-5 -10^-8 M). MTT assay revealed that fludioxonil increased MCF-7 CV cell proliferation 1.2 to 1.5 times compared to the control, while E2 markedly increased the cell proliferation by about 3.5 times. When the samples were co-treated with ICI 182,780 (10^-8 M), an ER antagonist, fludioxonil-induced cell proliferation was reversed to the level of the control. Protein levels of cyclin E1, cyclin D1, Snail, and N-cadherin increased in response to fludioxonil as the reaction to E2, but these increases were not observed when fludioxonil was administered with ICI 182,780. Moreover, the protein level of p21 and E-cadherin decreased in response to treatment with fludioxonil, but remained at the control level when co-treated with ICI 182,780. In xenografted mouse models transplanted with MCF-7 CV cells, fludioxonil significantly increased the tumor mass formation by about 2.5 times as E2 did when compared to vehicle (0.1% DMSO) during the experimental period (80 days). Immunohistochemistry revealed that the protein level of proliferating cell nuclear antigen (PCNA), Snail, and cathepsin D increased in response to fludioxonil as the reaction to E2. These results imply that fludioxonil may have a potential to induce growth or metastatic behaviors of breast cancer by regulation of the expression of cell cycle-, EMT-, and metastasis-related genes via the ER-dependent pathway. © 2016 Wiley Periodicals, Inc. Environ Toxicol 32: 1439-1454, 2017.

A new transformant selection system for the gray mold fungus Botrytis cinerea based on the expression of fenhexamid-insensitive ERG27 variants

The gray mold fungus Botrytis cinerea features a wide host range and causes severe economic losses, making it an important object for molecular research. Thus far, genetic modification of the fungus mainly is relied on two selection systems (nourseothricin and hygromycin), while other selection systems hold significant disadvantages. To broaden the spectrum of available molecular tools, a new selection system based on the cheap and widely used fungicide fenhexamid (hydroxyanilide group) was established. Fenhexamid specifically targets the 3-ketoreductase ERG27 from the ergosterol biosynthesis pathway. We generated a set of expression vectors suitable for deletion or expression of genes of interest (GOIs) in B. cinerea based on fenhexamid-insensitive ERG27 variants. Expression of BcERG27^F412I and Fusarium fujikuroi ERG27 in the sensitive B. cinerea strain B05.10 causes resistance towards fenhexamid (fenR) and allows for the selection of transformants and their genetic purification. A modified split-marker approach facilitates the site-specific integration and expression of GOIs at the bcerg27 locus. No undesired secondary phenotypes regarding virulence, stress responses, the formation of reproductive structures or conidial germination were observed in strains expressing fenhexamid-insensitive ERG27 variants. Thus, the fenR system represents a third reliable selection system for genetic modifications of fenhexamid-sensitive B. cinerea strains.

Fungicide Resistance Profiling in Botrytis cinerea Populations from Blueberry in California and Washington and Their Impact on Control of Gray Mold

Gray mold caused by Botrytis cinerea is a major postharvest disease of blueberry grown in the Central Valley of California and western Washington State. Sensitivities to boscalid, cyprodinil, fenhexamid, fludioxonil, and pyraclostrobin, representing five different fungicide classes, were examined for 249 (California) and 106 (Washington) B. cinerea isolates recovered from decayed blueberry fruit or flowers. In California and Washington, 7 and 17 fungicide-resistant phenotypes, respectively, were detected: 66 and 49% of the isolates were resistant to boscalid, 20 and 29% were moderately resistant to cyprodinil, 29 and 29% were resistant to fenhexamid, and 66 and 55% were resistant to pyraclostrobin. All isolates from California were sensitive to fludioxonil, whereas 70% of the isolates from Washington showed reduced sensitivity to fludioxonil. In California, 26 and 30% of the isolates were resistant to two and three classes of fungicides, respectively. In Washington, 31, 14, 16, and 9% of the isolates were resistant to two, three, four, and five classes of fungicides, respectively. Inherent risk of the development of resistance to quinone outside inhibitor (QoI) fungicides was assessed by detecting the presence of the Bcbi-143/144 intron in gene cytb. The intron was detected in 11.8 and 40% of the isolates in California and Washington, respectively, suggesting that the risk of QoI resistance is higher in California than in Washington. On detached blueberry fruit inoculated with 11 isolates exhibiting different fungicide-resistant phenotypes, most fungicides failed to control gray mold on fruit inoculated with the respective resistant phenotypes but the mixture of cyprodinil and fludioxonil was effective against all fungicide-resistant phenotypes tested. Our findings would be useful in designing and implementing fungicide resistance management spray programs for control of gray mold in blueberry.

Suspension Array for Multiplex Detection of Eight Fungicide-Resistance Related Alleles in Botrytis cinerea

A simple and high-throughput assay to detect fungicide resistance is required for large-scale monitoring of the emergence of resistant strains of Botrytis cinerea. Using suspension array technology performed on a Bio-Plex 200 System, we developed a single-tube allele-specific primer extension assay that can simultaneously detect eight alleles in one reaction. These eight alleles include E198 and 198A of the β-Tubulin gene (BenA), H272 and 272Y of the Succinate dehydrogenase iron–sulfur subunit gene (SdhB), I365 and 365S of the putative osmosensor histidine kinase gene (BcOS1), and F412 and 412S of the 3-ketoreductase gene (erg27). This assay was first established and optimized with eight plasmid templates containing the DNA sequence variants BenA-E198, BenA-198A, SdhB-H272, SdhB-272Y, BcOS1-I365, BcOS1-365S, erg27-F412, and erg27-412S. Results indicated that none of the probes showed cross-reactivity with one another. The minimum limit of detection for these genotypes was one copy per test. Four mutant plasmids were mixed with 10 ng/μL wild-type genomic DNA in different ratios. Detection sensitivity of mutant loci was 0.45% for BenA-E198A, BcOS1-I365S, and erg27-F412S, and was 4.5% for SdhB-H272Y. A minimum quantity of 0.1 ng of genomic DNA was necessary to obtain reliable results. This is the first reported assay that can simultaneously detect mutations in BenA, SdhB, BcOS1, and erg27.

Fitness and Competitive Ability of Botrytis cinerea Isolates with Resistance to Multiple Chemical Classes of Fungicides

Resistance to multiple chemical classes of fungicides in Botrytis cinerea isolates from eastern United States strawberry fields is common and strategies to control them are needed. In this study, we compared fitness and competitive ability of eight sensitive isolates (S), eight isolates resistant to five or six chemical classes of fungicides but not to phenylpyrroles (5CCR), and eight isolates resistant to six or seven chemical classes including phenylpyrroles (6CCR/MDR1h). The latter included the MDR1h phenotype due to overexpression of atrB based on Δ497V/L in mrr1. The 6CCR/MDR1h isolates grew more slowly at 4°C on potato dextrose agar, and both 5CCR and 6CCR/MDR1h isolates were hypersensitive to osmotic stress compared with S isolates. In contrast, no differences were found in oxidative sensitivity, aggressiveness, and spore production in vivo, and sclerotia production and viability in vitro. In competition experiments, the 5CCR and 6CCR/MDR1h isolates were both outcompeted by S isolates and 6CCR/MDR1h isolates were outcompeted by 5CCR isolates in the absence of fungicide pressure. Under selective pressure of a fludioxonil/pyraclostrobin rotation, the 6CCR/MDR1h isolates dominated after coinoculation with 5CCR and S isolates. The competitive disadvantage of 5CCR and especially 6CCR/MDR1h isolates suggest that, in the absence of fungicide selection pressure, S isolates may reduce inoculum potential of multifungicide-resistant isolates under field conditions.

The natural fenhexamid-resistant grey mould populations from strawberry in Zhejiang Province are dominated by Botrytis cinerea group S

BACKGROUND

Recently, a novel clade Botrytis cinerea group S was found to be common in B. cinerea populations from Germany and New Zealand. Fenhexamid, an effective antibotrytis fungicide, has not been registered in China, but our preliminary study detected fenhexamid-resistant (HydR) isolates from strawberry in Zhejiang Province.

RESULTS

Genetic identification of 639 B. cinerea isolates from strawberry found that 331 (62.9%) belonged to B. cinerea group S. The frequency of HydR isolates ranged from 0 to 37.5% among the nine locations. Of the 74 HydR isolates, 71 were B. cinerea group S and moderately resistant to fenhexamid (HydR). Seven new mutations S9G, P57A, P269L, V365A, E368D, E375K and A378T in the target gene erg27 were reported for the first time. Sixty-two (83.8%) HydR isolates simultaneously carried P57A and A378T mutations, and further transformation assays showed that integration of one copy of erg27(P57A) (,) (A378T) into a wild-type strain led to partial resistance. Detached fruit studies showed that fenhexamid at the recommended field rate could control the disease incited by moderately resistant isolates but not by highly resistant isolates.

CONCLUSION

B. cinerea group S isolates are widespread in all strawberry-growing locations in Zhejiang Province. The natural HydR populations from strawberry are dominated by B. cinerea group S. © 2015 Society of Chemical Industry.

Effect of fenhexamid and cyprodinil on the expression of cell cycle- and metastasis-related genes via an estrogen receptor-dependent pathway in cellular and xenografted ovarian cancer models

Fenhexamid and cyprodinil are antifungal agents (pesticides) used for agriculture, and are present at measurable amounts in fruits and vegetables. In the current study, the effects of fenhexamid and cyprodinil on cancer cell proliferation and metastasis were examined. Additionally, the protein expression levels of cyclin D1 and cyclin E as well as cathepsin D were analyzed in BG-1 ovarian cancer cells that express estrogen receptors (ERs). The cells were cultured with 0.1% dimethyl sulfoxide (DMSO; control), 17β-estradiol (E2; 10(-9)M), and fenhexamid or cyprodinil (10(-5)-10(-7)M). Results of a 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay showed that fenhexamid and cyprodinil increased BG-1 cell proliferation about 1.5 to 2 times similar to E2 (5 times) compared to the control. When the cells were co-treated with ICI 182,780 (10(-8)M), an ER antagonist, the proliferation of pesticide-treated BG-1 cells was decreased to the level of the control. A wound healing assay revealed that the pesticides reduced the disrupted area in the BG-1 cell monolayer similar to E2. Protein levels of cyclin D1 and E as well as cathepsin D were increased by fenhexamid and cyprodinil. This effect was reversed by co-treatment with ICI 182,780. In a xenograft mouse model with transplanted BG-1 cells, cyprodinil significantly increased tumor mass formation about 2 times as did E2 (6 times) compared to the vehicle (0.1% DMSO) over an 80-day period. In contrast, fenhexamid did not promote ovarian tumor formation in this mouse model. Cyprodinil also induced cell proliferation along with the expression of proliferating cell nuclear antigen (PCNA) and cathepsin D in tumor tissues similar to E2. Taken together, these results imply that fenhexamid and cyprodinil may have disruptive effects on ER-expressing cancer by altering the cell cycle- and metastasis-related gene expression via an ER-dependent pathway.

A Botrytis cinerea Population from a Single Strawberry Field in Germany has a Complex Fungicide Resistance Pattern

Gray mold, caused by the fungus Botrytis cinerea, is one of the most important diseases of strawberry in Germany. The application of site-specific fungicides remains the main strategy to reduce disease incidence and severity in the field. Isolates (n = 199) were collected from fungicide-treated strawberry fruit at a German research site with a long history of fungicide efficacy trials against gray mold. Sensitivities to the six site-specific botryticides registered in Germany were determined using microtiter assays. Values for the concentration of a fungicide at which fungal development is inhibited by 50% (EC₅₀) ranged from 0.03 to ≥30 ppm for the succinate dehydrogenase inhibitor boscalid, 0.015 to ≥10 ppm for the hydroxyanilide fenhexamid, 0.009 to 0.739 ppm for the phenylpyrrole fludioxonil, 0.55 to 43.45 ppm for the dicarboximide iprodione, 0.021 to ≥3 ppm for the quinone outside inhibitor pyraclostrobin, and 0.106 to ≥30 ppm for the anilinopyrimidine pyrimethanil. Pyrosequencing revealed that amino acid substitutions in the target proteins Bos1 (I365S/N, V368F + Q369H), CytB (G143A), Erg27 (F412S), and SdhB (P225F, N230I, and H272R/Y) were associated with reduced sensitivity levels to the corresponding fungicide classes. In most cases, isolates with a decreased sensitivity to fludioxonil showed a reduced sensitivity to tolnaftate. This reduction is considered to be an indication of multidrug efflux pump activity. The amino acid change I365S, I365N, or V368F + Q369H in Bos1 and H272R in SdhB by itself showed EC₅₀ values of 3.99 to 14.73 ppm, 3.87 to 5.37 ppm, 4.81 to 15.63 ppm, and 2.071 to ≥30 ppm, respectively. When isolates that contained one of these mutations were also multidrug resistant, the ranges of EC₅₀ values shifted to 6.47 to 43.45 ppm for I365S, 7.28 to 29.84 ppm for I365N, 6.89 to 26.67 ppm for V368F + Q369H, and ≥30 ppm for H272R. The reported data suggest that the combination of multidrug resistance and an amino acid change in the target site may result in a lower sensitivity to the fungicides than one resistance mechanism by itself. Although 20% of the population analyzed was sensitive to all six different chemical classes, the majority showed reduced sensitivity to one (6%), two (13%), three (23%), four (17%), five (11%), and six (11%) different fungicides.

Preharvest treatments with chitosan and other alternatives to conventional fungicides to control postharvest decay of strawberry

The effectiveness of the control of postharvest decay of strawberry (Fragaria × ananassa, 'Alba' and 'Romina' cvs.) fruit following field applications of chitosan, laminarin, extracts of Abies spp., Polygonum spp., and Saccharomyces spp., an organic acids and calcium combination, and benzothiadiazole, were compared with a fungicide strategy. These compounds were sprayed every 5 days on the strawberry canopy, from flowering to ripening, in 2012 and 2013. The treatments with alternative compounds provided ∼ 30% reduction in postharvest decay of strawberry compared to the water-treated controls, mainly against gray mold and Rhizopus rot, and without negatively affecting fruit color and firmness. Chitosan and benzothiadiazole were the most effective alternative treatments. Preharvest spraying with these alternative treatments can complement the use of conventional fungicides in the control of postharvest decay of strawberry fruit, especially when disease pressure is low.

Independent Emergence of Resistance to Seven Chemical Classes of Fungicides in Botrytis cinerea

Gray mold, caused by the fungal pathogen Botrytis cinerea, is one of the most destructive diseases of small fruit crops and control is largely dependent on the application of fungicides. As part of a region-wide resistance-monitoring program that investigated 1,890 B. cinerea isolates from 189 fields in 10 states of the United States, we identified seven isolates (0.4%) from five locations in four different states with unprecedented resistance to all seven Fungicide Resistance Action Committee (FRAC) codes with single-site modes of action including FRAC 1, 2, 7, 9, 11, 12, and 17 registered in the United States for gray mold control. Resistance to thiophanate-methyl, iprodione, boscalid, pyraclostrobin, and fenhexamid was based on target gene mutations that conferred E198A and F200Y in β-tubulin, I365N/S in Bos1, H272R/Y in SdhB, G143A in Cytb, and T63I and F412S in Erg27. Isolates were grouped into MDR1 and MDR1h phenotypes based on sensitivity to fludioxonil and variations in transcription factor mrr1. MDR1h isolates had a previously described 3-bp deletion at position 497 in mrr1. Expression of ABC transporter atrB was increased in MDR1 isolates but highest in MDR1h isolates. None of the isolates with seven single resistances (SR) had identical nucleotide variations in target genes, indicating that they emerged independently. Multifungicide resistance phenotypes did not exhibit significant fitness penalties for the parameters used in this study, but MDR1h isolates produced more sclerotia at low temperatures and exhibited increased sensitivity to salt stress. In this study we show that current resistance management strategies have not been able to prevent the geographically independent development of resistance to all seven site-specific fungicides currently registered for gray mold control in the United States and document the presence of MDR1h in North America.

Characterisation of heteroplasmic status at codon 143 of the Botrytis cinerea cytochrome b gene in a semi-quantitative AS-PCR assay

BACKGROUND

An in-depth understanding of quinone outside inhibitor (QoI)-fungicide-resistant Botrytis cinerea isolates in a vineyard is expected to contribute to the development of an optimum disease management programme for the control of grape grey mould.

RESULTS

The resistance and structure of the cytochrome b gene in B. cinerea collected from a Japanese vineyard were characterised. The semi-quantitative allele-specific primer-polymerase chain reaction (AS-PCR) assay developed in the present study was able to distinguish heteroplasmic status from homoplasmic status at codon 143 of the cytochrome b gene in QoI-fungicide-resistant B. cinerea from vineyards in Japan. With this assay it was demonstrated that the repeated introduction of QoI fungicide selection pressure increased the ratio of G143A-mutated cytochrome b genes in B. cinerea isolates.

CONCLUSION

It is proposed that the semi-quantitative AS-PCR assay is a reliable tool for the detection of QoI fungicide resistance and the evaluation of homoplasmic/heteroplasmic status at codon 143 of the cytochrome b gene in B. cinerea isolates.

Population Structure, Fungicide Resistance Profile, and sdhB Mutation Frequency of Botrytis cinerea from Strawberry and Greenhouse-Grown Tomato in Greece

Botrytis cinerea is a pathogen with high genetic variability that has also shown high risk for fungicide resistance development. In total, 1,169 isolates obtained from strawberry (n = 297) and tomato (n = 872) in five geographic regions of Greece were tested for their sensitivity to several botryticides. A high frequency of isolates with multiple resistance to carbendazim, cyprodinil, pyraclostrobin, and boscalid was found in isolates from strawberry. In the isolates from tomato, the predominant phenotype was that of dual resistance to carbendazim and cyprodinil in the Crete island, of single resistance to carbendazim in the region of Preveza, and of sensitive isolates in the region of Kyparissia. None of the tested isolates was found to be fludioxonil resistant. High frequencies of boscalid-resistant phenotypes were observed in the strawberry isolates, while boscalid-resistance frequency in the tomato isolates was lower. H272R was the predominant sdhB mutation, associated with resistance to boscalid, in all the sampled isolates, while other sdhB mutations were found at low frequencies. B. cinerea group S, identified by the presence of a 21-bp insertion in the transcription factor mrr1 gene, was predominant within the tomato isolates obtained from all three sampled regions, with frequencies ranging from 62 to 75% of the isolates; whereas, within strawberry isolates, B. cinerea was predominant, with frequencies of 75 to 95%. Correlations of isolate genotype and fungicide resistance profile showed that B. cinerea sensu stricto isolates were more prone to the development of resistance to boscalid compared with the Botrytis group S isolates, which may explain the observed predominance of B. cinerea sensu stricto in strawberry fields.

Occurrence of fungicide resistance in populations of Botryotinia fuckeliana (Botrytis cinerea) on table grape and strawberry in southern Italy

BACKGROUND

Botryotinia fuckeliana (Botrytis cinerea) is a pathogen with a high risk of development of resistance to fungicides. Fungicide resistance was monitored during 2008-2011 in B. fuckeliana populations from both table-grape vineyards and greenhouse-grown strawberries in southern Italy.

RESULTS

Isolates showing different levels of resistance to anilinopyrimidines (APs) were detected at high frequency (up to 98%) in fields treated intensively with APs (4-7 sprays season(-1) ). A slight decrease in sensitivity to fludioxonil, always combined with AP resistance, was generally found at lower frequencies. The repeated use of fenhexamid on grapevine (3-8 sprays season(-1) ) led to a strong selection of highly resistant isolates (up to 100%). Boscalid-resistant mutants were detected at very variable frequencies (0-73%). Occurrence of resistance to quinone outside inhibitors (QoIs) was also ascertained. Multiple fungicide resistance to 2-6 different modes of action were frequently recovered. Single nucleotide polymorphisms (SNPs) in the target genes Erg27, SdhB and cytb were associated with resistance to fenehexamid, boscalid and QoIs respectively.

CONCLUSION

Resistance to the fungicides commonly used against grey mould on table grape and strawberry is quite common in southern Italy. This is an outcome of the incorrect use of fungicides, often because of the maximum number of detectable residues of plant protection products imposed by big international retailers, and underlines the crucial role of antiresistance strategies in integrated pest management.

The rising threat of fungicide resistance in plant pathogenic fungi: Botrytis as a case study

The introduction of site-specific fungicides almost 50 years ago has revolutionized chemical plant protection, providing highly efficient, low toxicity compounds for control of fungal diseases. However, it was soon discovered that plant pathogenic fungi can adapt to fungicide treatments by mutations leading to resistance and loss of fungicide efficacy. The grey mould fungus Botrytis cinerea, a major cause of pre- and post-harvest losses in fruit and vegetable production, is notorious as a 'high risk' organism for rapid resistance development. In this review, the mechanisms and the history of fungicide resistance in Botrytis are outlined. The introduction of new fungicide classes for grey mould control was always followed by the appearance of resistance in field populations. In addition to target site resistance, B. cinerea has also developed a resistance mechanism based on drug efflux transport. Excessive spraying programmes have resulted in the selection of multiresistant strains in several countries, in particular in strawberry fields. The rapid erosion of fungicide activity against these strains represents a major challenge for the future of fungicides against Botrytis. To maintain adequate protection of intensive cultures against grey mould, strict implementation of resistance management measures are required as well as alternative strategies with non-chemical products.

Diversity in the erg27 Gene of Botrytis cinerea Field Isolates from Strawberry Defines Different Levels of Resistance to the Hydroxyanilide Fenhexamid

The hydroxyanilide (Hyd) fenhexamid has played a major role in gray mold management in Florida strawberry fields since 2000. Recent monitoring of the sensitivity of Botrytis cinerea to fenhexamid indicated that resistance has emerged. In this study, mutations in the target gene erg27 encoding the 3-keto reductase enzyme were investigated and the shift in fenhexamid sensitivity over time was evaluated in 630 isolates collected between 2005 and 2013 from locations sprayed with different spray programs. Overall, 227, 155, 48, and 200 isolates were sensitive (Hyd^S), had reduced sensitivity (HydR2), or were moderately (HydR3^-) and highly (HydR3⁺) resistant, respectively. Analysis of complete sequences of the erg27 gene from 70 isolates revealed seven and five mutations and one deletion in the HydR3^- and HydR3⁺ isolates, respectively, at eight and five different codons, respectively. In addition to the three mutations (F412S, -I, and -V) reported previously at codon 412, two new mutations from glycine to arginine at codon 170 (G170R, two isolates) and from alanine to glycine at codon 210 (A210G, eight isolates) were detected for the first time in HydR3⁺ isolates from Florida. These isolates were not controlled on detached fruit sprayed with the recommended field rate of fenhexamid, whereas all Hyd^S, HydR2, and HydR3^- isolates were controlled on detached fruit. Overall, there was no clear correlation between the spray frequency of fenhexamid and the frequency of resistant phenotypes. This study provides an overview of the current distribution of erg27 genotypes in Florida and will serve as a baseline for future studies on shifts in population diversity and resistance. The frequency of fenhexamid-resistant populations has increased progressively in different strawberry fields but has not reached a plateau yet, indicating that the effective life of fenhexamid could be extended if appropriate rotation and management strategies are implemented. Sensitivity to other sterol biosynthesis inhibitors is discussed.

Spatial distribution of single-nucleotide polymorphisms related to fungicide resistance and implications for sampling

Spatial distribution of single-nucleotide polymorphisms (SNPs) related to fungicide resistance was studied for Botrytis cinerea populations in vineyards and for B. squamosa populations in onion fields. Heterogeneity in this distribution was characterized by performing geostatistical analyses based on semivariograms and through the fitting of discrete probability distributions. Two SNPs known to be responsible for boscalid resistance (H272R and H272Y), both located on the B subunit of the succinate dehydrogenase gene, and one SNP known to be responsible for dicarboximide resistance (I365S) were chosen for B. cinerea in grape. For B. squamosa in onion, one SNP responsible for dicarboximide resistance (I365S homologous) was chosen. One onion field was sampled in 2009 and another one was sampled in 2010 for B. squamosa, and two vineyards were sampled in 2011 for B. cinerea, for a total of four sampled sites. Cluster sampling was carried on a 10-by-10 grid, each of the 100 nodes being the center of a 10-by-10-m quadrat. In each quadrat, 10 samples were collected and analyzed by restriction fragment length polymorphism polymerase chain reaction (PCR) or allele specific PCR. Mean SNP incidence varied from 16 to 68%, with an overall mean incidence of 43%. In the geostatistical analyses, omnidirectional variograms showed spatial autocorrelation characterized by ranges of 21 to 1 m. Various levels of anisotropy were detected, however, with variograms computed in four directions (at 0°, 45°, 90°, and 135° from the within-row direction used as reference), indicating that spatial autocorrelation was prevalent or characterized by a longer range in one direction. For all eight data sets, the β-binomial distribution was found to fit the data better than the binomial distribution. This indicates local aggregation of fungicide resistance among sampling units, as supported by estimates of the parameter θ of the β-binomial distribution of 0.09 to 0.23 (overall median value = 0.20). On the basis of the observed spatial distribution patterns of SNP incidence, sampling curves were computed for different levels of reliability, emphasizing the importance of sample size for the detection of mutation incidence below the risk threshold for control failure.

Fungicide resistance of Botrytis cinerea in tomato greenhouses in the Canary Islands and effectiveness of non-chemical treatments against gray mold

Tomato greenhouses in the Canary Islands, Spain, were surveyed to estimate frequencies of resistance to benzimidazoles, dicarboximides, anilinopyrimidines and N-phenylcarbamates in Botrytis cinerea. Resistance to carbendazim, iprodione, pyrimethanil and diethofencarb was found in 74.2, 86.4, 28.8 and 31.8% of isolates, respectively. Benzimidazole- and anilinopyrimide-resistant isolates were highly resistant, showing EC50 values above 500 µg/ml carbendazim and a mean EC50 value of 28.42 µg/ml pyrimethanil, respectively. By contrast, a low level of resistance was observed among dicarboximide-resistant isolates (mean EC50 value of 1.81 µg/ml iprodione). Phenotypes with double resistance to carbendazim and iprodione, and triple resistance to carbendazim, iprodione and pyrimethanil were the most common, occurring in 36.4 and 28.8% of isolates. The surveyed greenhouses had never been treated with fenhexamid and Signum™ (pre-packed mixture of boscalid and pyraclostrobin), and baseline sensitivities of B. cinerea isolates to these fungicides were determined. The EC50 values were within the range of 0.009-0.795 µg/ml fenhexamid and of 0.014-0.48 µg/ml Signum. In addition, available formulations based on elicitors of plant defense response and biocontrol agents were evaluated against B. cinerea in tomato plants under semi-controlled greenhouse conditions, the yeast Candida sake CPA-1 being able to reduce gray mold significantly when it was applied on petiole wounds and the plants were inoculated 24 h later. Likewise, C. sake was effective against B. cinerea in harvested tomato fruits, yeast-treated tomatoes showed a 70.66 and 30.31% reduction in the diameters of decay lesions compared with controls after 10 days of storage at 20 and 9 °C, respectively.

Selection, Fitness, and Control of Grape Isolates of Botrytis cinerea Variably Sensitive to Fenhexamid

Of 683 Botrytis cinerea isolates collected from a fungicide-trial vineyard, 31 were classified as putatively resistant to fenhexamid (50% effective concentration [EC₅₀] ≥ 0.1 μg/ml). For the resistant isolates that survived and sporulated in culture, colony expansion and conidial germination frequency was significantly reduced relative to the mean of 30 representative baseline isolates (EC₅₀ = 0.03 μg/ml). Grape berries were inoculated with four isolates representing a range of fenhexamid sensitivities and treated preventively or curatively with fenhexamid concentrations (150 to 600 mg/liter) representing 25 to 100% of the recommended rate. All treatments significantly delayed disease onset and progress caused by isolates with EC₅₀ values of 0.03 and 0.15 μg/ml but provided little to no control of isolates with EC₅₀ values of 0.32 and 62.5 μg/ml. The latter isolate exhibited a previously unreported F427V mutation of ERG27, an enzyme of ergosterol biosynthesis. In a duplex quantitative polymerase chain reaction test, the ratio of pathogen/host DNA increased significantly for 14 days after inoculation of untreated berries with a baseline isolate but declined slightly in berries treated with fenhexamid at 600 mg/liter 1 day post inoculation. In the vineyard, disease control was affected by the number and rate of fenhexamid applications but B. cinerea isolates with EC₅₀ ≥ 0.1 μg/ml were not preferentially selected.

Proteomic analysis of mycelium and secretome of different Botrytis cinerea wild-type strains

The necrotrophic fungus Botrytis cinerea is a very damaging phytopathogen of wide host range and environmental persistence. It is difficult to control because of its genetic versatility, expressed in the many phenotypical differences among isolates. The genomes of the B. cinerea B05.10 and T4 strains have been recently sequenced, becoming a model system for necrotrophic pathogens, and thus opening new alternatives for functional genomics analysis. In this work, the mycelium and secreted proteome of six wild-type strains with different host range, and grown in liquid minimal medium, have been analyzed by using complementary gel-based (1-DE and 2-DE) and gel-free/label-free (nUPLC-MS(E)) approaches. We found differences in the protein profiles among strains belonging to both the mycelium and the secretome. A total of 47 and 51 variable proteins were identified in the mycelium and the secretome, respectively. Some of them, such as malate dehydrogenase or peptidyl-prolyl cis-trans isomerase from the mycelium, and endopolygalacturonase, aspartic protease or cerato-platanin protein from the secretome have been reported as virulence factors, which are involved in host-tissue invasion, pathogenicity or fungal development.

BIOLOGICAL SIGNIFICANCE

The necrotrophic fungus Botrytis cinerea is an important phytopathogen of wide host range and environmental persistence, causing substantial economic losses worldwide. In this work, the mycelium and secreted proteome of six B. cinerea wild-type strains with different host range have been analyzed by using complementary gel-based and gel-free/label-free approaches. Fungal genetic versatility was confirmed at the proteome level for both mycelium proteome and secreted proteins. A high number of hypothetical proteins with conserved domains related to toxin compounds or to unknown functions were identified, having qualitative differences among strains. The identification of hypothetical proteins suggests that the B. cinerea strains differ mostly in processes involved in adaptation to a particular environment or a growth condition, rather than in essential metabolic reactions. Proteomics can help in the identification of variable proteins related to the infection and colonization of host plant tissues, as well as of virulence and aggressiveness factors among different B. cinerea wild-type strains. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.

French vineyards provide information that opens ways for effective resistance management of Botrytis cinerea (grey mould)

Resistance to fungicides is an evolutionary process resulting from the selection of advantageous genotypes in naturally diverse populations. Seven fungicide modes of action are authorised to control grey mould caused by Botrytis cinerea on grapevine in France, and five of them have encountered specific resistance, with variable frequencies in populations and possible consequences for field fungicide efficacy. Moreover, multidrug resistance is caused by fungicide efflux and allows a weak resistance towards six unrelated modes of action. Here, a review is given of the fungicide resistance status of B. cinerea in France, particularly in the vineyards of Champagne, which are the most affected. Recently developed resistance and recent findings concerning the associated resistance mechanisms are focused upon in particular. Finally, antiresistance strategies are presented, and examples of managed resistance are discussed in a more general manner with the aim of extending this knowledge to other crops and countries undergoing similar resistance problems.

Phenotypic Characterization of Multifungicide Resistance in Botrytis cinerea Isolates from Strawberry Fields in Florida

Chemical control has always been essential for the management of gray mold, caused by Botrytis cinerea, to ensure sustainable strawberry production. However, lack of knowledge about actual resistance development may have disastrous consequences and lead to severe epidemics such as the one that affected several strawberry fields in 2012 in Florida. In this study, we tested 392 isolates collected from Florida strawberry fields between 2010 and 2012 for their sensitivity to boscalid (Bosc), a succinate dehydrogenase inhibitor (SdhI); pyraclostrobin, a quinone outside inhibitor (QoI); boscalid + pyraclostrobin (Pristine); fenhexamid, a hydroxyanilide (Hyd); pyrimethanil and cyprodinil, anilinopyrimidines; fludioxonil, a phenylpyrrole; and fludioxonil + cyprodinil (Switch). The respective resistance frequencies for boscalid, pyraclostrobin, Pristine, fenhexamid, cyprodinil, and pyrimethanil were 85.4, 86.5, 86.0, 44.4, 52.7, and 59.5%. Overall, 17.8 and 19.8% of isolates showed reduced sensitivity to fludioxonil and Switch, respectively. All fungicides sprayed preventively on detached strawberry fruit failed to control isolates with high levels of resistance to each fungicide except for fludioxonil and Switch. Four phenotypes with multifungicide resistance (MFR) were detected in B. cinerea populations from Florida. Isolates resistant to one fungicide (FR1), two (MFR2), three (MFR3), and four (MFR4) fungicides from different chemical groups represented 5.9, 28.6, 41.8, and 23.7% of the total resistant population, respectively. The MFR3 isolates were predominant and contained two subpopulations, the Bosc-QoI-AP^R isolates (56.5%) and the Bosc-QoI-Hyd^R isolates (40.6%). In addition to reporting on very highly resistant populations to boscalid and QoI fungicides, we show evidence for a widespread multifungicide resistance to B. cinerea that warrants immediate implementation of novel management strategies to impede the development of more resistant populations.

Fenhexamid Resistance in Botrytis cinerea from Strawberry Fields in the Carolinas Is Associated with Four Target Gene Mutations

Botrytis cinerea, the causal agent of gray mold disease, is one of the most important pathogens of strawberry. Its control in commercial strawberry fields is largely dependent on the application of fungicides during bloom and fruit maturation. The hydroxyanilide fenhexamid is one of the most frequently used fungicides in the southeast of the United States for gray mold control. It inhibits the 3-ketoreductase (Erg27) of the ergosterol biosynthesis pathway and, due to this site-specific mode of action, is at risk for resistance development. Single-spore isolates were collected from 11 commercial strawberry fields in North and South Carolina and subjected to a conidial germination assay that distinguished sensitive from resistant phenotypes. Of the 214 isolates collected, 16.8% were resistant to fenhexamid. Resistance was found in three of four locations from North Carolina and in four of seven locations from South Carolina, indicating that resistance was widespread. Mutations in Erg27 (T63I, F412S, F412C, and F412I) were associated with resistance, with F412S the predominant and most widespread mutation. In this study, mutations T63I and F412C in field isolates of B. cinerea are described for the first time. Detached fruit studies showed that field rates of Elevate 50 WDG (fenhexamid) controlled sensitive but not resistant isolates carrying any of the four mutations. Resistant isolates produced the same lesion size and number of sporulating lesions on fruit sprayed with Elevate 50 WDG as on untreated controls, showing the fungicide's loss of efficacy against those isolates. A rapid polymerase chain reaction method was developed to quickly and reliably distinguish isolates sensitive or resistant to fenhexamid in the Carolinas and to determine the mutation associated with resistance. The presence of fenhexamid-resistant strains in B. cinerea from strawberry fields in the Carolinas must be considered in future resistance management practices for sustained gray mold control.

A functional bikaverin biosynthesis gene cluster in rare strains of Botrytis cinerea is positively controlled by VELVET

The gene cluster responsible for the biosynthesis of the red polyketidic pigment bikaverin has only been characterized in Fusarium ssp. so far. Recently, a highly homologous but incomplete and nonfunctional bikaverin cluster has been found in the genome of the unrelated phytopathogenic fungus Botrytis cinerea. In this study, we provided evidence that rare B. cinerea strains such as 1750 have a complete and functional cluster comprising the six genes orthologous to Fusarium fujikuroi ffbik1-ffbik6 and do produce bikaverin. Phylogenetic analysis confirmed that the whole cluster was acquired from Fusarium through a horizontal gene transfer (HGT). In the bikaverin-nonproducing strain B05.10, the genes encoding bikaverin biosynthesis enzymes are nonfunctional due to deleterious mutations (bcbik2-3) or missing (bcbik1) but interestingly, the genes encoding the regulatory proteins BcBIK4 and BcBIK5 do not harbor deleterious mutations which suggests that they may still be functional. Heterologous complementation of the F. fujikuroi Δffbik4 mutant confirmed that bcbik4 of strain B05.10 is indeed fully functional. Deletion of bcvel1 in the pink strain 1750 resulted in loss of bikaverin and overproduction of melanin indicating that the VELVET protein BcVEL1 regulates the biosynthesis of the two pigments in an opposite manner. Although strain 1750 itself expresses a truncated BcVEL1 protein (100 instead of 575 aa) that is nonfunctional with regard to sclerotia formation, virulence and oxalic acid formation, it is sufficient to regulate pigment biosynthesis (bikaverin and melanin) and fenhexamid HydR2 type of resistance. Finally, a genetic cross between strain 1750 and a bikaverin-nonproducing strain sensitive to fenhexamid revealed that the functional bikaverin cluster is genetically linked to the HydR2 locus.

Gray mold populations in german strawberry fields are resistant to multiple fungicides and dominated by a novel clade closely related to Botrytis cinerea

The gray mold fungus Botrytis cinerea is a major threat to fruit and vegetable production. Strawberry fields usually receive several fungicide treatments against Botrytis per season. Gray mold isolates from several German strawberry-growing regions were analyzed to determine their sensitivity against botryticides. Fungicide resistance was commonly observed, with many isolates possessing resistance to multiple (up to six) fungicides. A stronger variant of the previously described multidrug resistance (MDR) phenotype MDR1, called MDR1h, was found to be widely distributed, conferring increased partial resistance to two important botryticides, cyprodinil and fludioxonil. A 3-bp deletion mutation in a transcription factor-encoding gene, mrr1, was found to be correlated with MDR1h. All MDR1h isolates and the majority of isolates with resistance to multiple fungicides were found to be genetically distinct. Multiple-gene sequencing confirmed that they belong to a novel clade, called Botrytis group S, which is closely related to B. cinerea and the host-specific species B. fabae. Isolates of Botrytis group S genotypes were found to be widespread in all German strawberry-growing regions but almost absent from vineyards. Our data indicate a clear subdivision of gray mold populations, which are differentially distributed according to their host preference and adaptation to chemical treatments.

Natural variation in the VELVET gene bcvel1 affects virulence and light-dependent differentiation in Botrytis cinerea

Botrytis cinerea is an aggressive plant pathogen causing gray mold disease on various plant species. In this study, we identified the genetic origin for significantly differing phenotypes of the two sequenced B. cinerea isolates, B05.10 and T4, with regard to light-dependent differentiation, oxalic acid (OA) formation and virulence. By conducting a map-based cloning approach we identified a single nucleotide polymorphism (SNP) in an open reading frame encoding a VELVET gene (bcvel1). The SNP in isolate T4 results in a truncated protein that is predominantly found in the cytosol in contrast to the full-length protein of isolate B05.10 that accumulates in the nuclei. Deletion of the full-length gene in B05.10 resulted in the T4 phenotype, namely light-independent conidiation, loss of sclerotial development and oxalic acid production, and reduced virulence on several host plants. These findings indicate that the identified SNP represents a loss-of-function mutation of bcvel1. In accordance, the expression of the B05.10 copy in T4 rescued the wild-type/B05.10 phenotype. BcVEL1 is crucial for full virulence as deletion mutants are significantly hampered in killing and decomposing plant tissues. However, the production of the two best known secondary metabolites, the phytotoxins botcinic acid and botrydial, are not affected by the deletion of bcvel1 indicating that other factors are responsible for reduced virulence. Genome-wide expression analyses of B05.10- and Δbcvel1-infected plant material revealed a number of genes differentially expressed in the mutant: while several protease- encoding genes are under-expressed in Δbcvel1 compared to the wild type, the group of over-expressed genes is enriched for genes encoding sugar, amino acid and ammonium transporters and glycoside hydrolases reflecting the response of Δbcvel1 mutants to nutrient starvation conditions.

Endocrine disruptors fludioxonil and fenhexamid stimulate miR-21 expression in breast cancer cells

Fenhexamid and fludioxonil are antifungal agents used in agricultural applications, which are present at measurable amounts in fruits and vegetables. Fenhexamid and fludioxonil showed endocrine disruptor activity as antiandrogens in an androgen receptor reporter assay in engineered human breast cancer cells. Little is known about how environmental chemicals regulate microRNA (miRNA) expression. This study examined the effect of fenhexamid and fludioxonil on the expression of the oncomiR miR-21 in MCF-7, T47D, and MDA-MB-231 human breast cancer cells and downstream targets of miR-21 in MCF-7 cells. Fenhexamid and fludioxonil stimulated miR-21 expression in a concentration-dependent manner and reduced the expression of miR-21 target Pdcd4 protein. Antisense to miR-21 blocked the increase in Pdcd4 protein by fenhexamid and fludioxonil. Fenhexamid and fludioxonil reduced miR-125b and miR-181a, demonstrating specificity of miRNA regulation. Induction of miR-21 was inhibited by the estrogen receptor antagonist fulvestrant, by androgen receptor antagonist bicalutamide, by actinomycin D and cycloheximide, and by inhibitors of the mitogen-activated protein kinases and phosphoinositide 3-kinase pathways. Fenhexamid activation was inhibited by the arylhydrocarbon receptor antagonist α-napthoflavone. Fenhexamid and fludioxonil did not affect dihydrotestosterone-induced miR-21 expression. Fludioxonil, but not fenhexamid, inhibited MCF-7 cell viability, and both inhibited estradiol-induced cell proliferation and reduced cell motility. Together these data indicate that fenhexamid and fludioxonil use similar and distinct mechanisms to increase miR-21 expression with downstream antiestrogenic activity.

Strong resistance to the fungicide fenhexamid entails a fitness cost in Botrytis cinerea, as shown by comparisons of isogenic strains

BACKGROUND

Fenhexamid, a sterol biosynthesis inhibitor effective against Botrytis, inhibits the 3-ketoreductase (Erg27) involved in C-4 demethylation. Several fenhexamid-resistant phenotypes have been detected in Botrytis cinerea populations from French vineyards. The field isolates with the highest resistance levels display amino acid changes in Erg27 (F412S, F412I or F412V).

RESULTS

Fenhexamid-resistant mutants were generated by site-directed mutagenesis of the erg27 gene in a sensitive recipient strain to overcome the impact of different genetic backgrounds. The wild-type erg27 allele was replaced by the three mutated alleles (erg27(F412S/I/V)) by homologous recombination. These isogenic strains were shown to be fenhexamid-resistant and were used to quantify the impact of F412 mutations on fungal fitness. Several parameters, including radial growth, the production of sclerotia and conidia, freezing resistance and aggressiveness, were quantified in laboratory conditions. Analysis of variance demonstrated significant differences between the mutant and parental strains for some characters. In particular, the mutants grew more slowly than the wild-type strain and displayed variations in the production of sclerotia and conidia with temperature and susceptibility to freezing.

CONCLUSIONS

The results highlight a moderate but significant impact of F412 mutations on the survival capacity of B. cinerea strains displaying high levels of resistance to fenhexamid in laboratory conditions, potentially limiting their dispersal and persistence, particularly in terms of overwintering, in field conditions.

The allele-specific probe and primer amplification assay, a new real-time PCR method for fine quantification of single-nucleotide polymorphisms in pooled DNA

The evolution of fungicide resistance within populations of plant pathogens must be monitored to develop management strategies. Such monitoring often is based on microbiological tests, such as microtiter plate assays. Molecular monitoring methods can be considered if the mutations responsible for resistance have been identified. Allele-specific real-time PCR approaches, such as amplification refractory mutation system (ARMS) PCR and mismatch amplification mutation assay (MAMA) PCR, are, despite their moderate efficacy, among the most precise methods for refining SNP quantification. We describe here a new real-time PCR method, the allele-specific probe and primer amplification assay (ASPPAA PCR). This method makes use of mixtures of allele-specific minor groove binder (MGB) TaqMan probes and allele-specific primers for the fine quantification of SNPs from a pool of DNA extracted from a mixture of conidia. It was developed for a single-nucleotide polymorphism (SNP) that is responsible for resistance to the sterol biosynthesis inhibitor fungicide fenhexamid, resulting in the replacement of the phenylalanine residue (encoded by the TTC codon) in position 412 of the enzymatic target (3-ketoreductase) by a serine (TCC), valine (GTC), or isoleucine (ATC) residue. The levels of nonspecific amplification with the ASPPAA PCR were reduced at least four times below the level of currently available allele-specific real-time PCR approaches due to strong allele specificity in amplification cycles, including two allele selectors. This new method can be used to quantify a complex quadriallelic SNP in a DNA pool with a false discovery rate of less than 1%.

Botrytis pseudocinerea, a new cryptic species causing gray mold in French vineyards in sympatry with Botrytis cinerea

Botrytis cinerea is a major crop pathogen infesting >220 hosts worldwide. A cryptic species has been identified in some French populations but the new species, B. pseudocinerea, has not been fully delimited and established. The aim of this study was to distinguish between the two species, using phylogenetic, biological, morphological, and ecological criteria. Multiple gene genealogies confirmed that the two species belonged to different, well-supported phylogenetic clades. None of the morphological criteria tested (spore size, germination rate, or mycelial growth) was able to discriminate between these two species. Sexual crosses between individuals from the same species and different species were carried out. Only crosses between individuals from the same species were successful. Moreover, population genetics analysis revealed a high level of diversity within each species and a lack of gene flow between them. Finally, a population survey over time showed that B. cinerea was the predominant species but that B. pseudocinerea was more abundant in spring, on floral debris. This observation could not be explained by temperature adaptation in tests carried out in vitro or by aggressiveness on tomato or bean leaves. This study clearly establishes that B. cinerea and B. pseudocinerea constitute a complex of two cryptic species living in sympatry on several hosts, including grapevine and blackberry. We propose several biological or molecular tools for unambiguous differentiation between the two species. B. pseudocinerea probably makes a negligible contribution to gray mold epidemics on grapevine. This new species has been deposited in the MycoBank international database.

Two promoter rearrangements in a drug efflux transporter gene are responsible for the appearance and spread of multidrug resistance phenotype MDR2 in Botrytis cinerea isolates in French and German vineyards

In French and German vineyards, Botrytis cinerea isolates with multiple fungicide resistance phenotypes have been observed with increasing frequencies. Multidrug resistance (MDR) results from mutations that lead to constitutive overexpression of genes encoding drug efflux transporters. In MDR2 and MDR3 strains, overexpression of the major facilitator superfamily transporter gene mfsM2 has been found to result from a rearrangement in the mfsM2 promoter (type A), caused by insertion of a retroelement (RE)-derived sequence. Here, we report the discovery of another, similar RE-induced rearrangement of the mfsM2 promoter (type B) in a subpopulation of French MDR2 isolates. MDR2 isolates harboring either type A or type B mutations in mfsM2 show the same resistance phenotypes and similar levels of mfsM2 overexpression. RE sequences similar to those in mfsM2 were found in low copy numbers in other but not all B. cinerea strains analyzed, including non-MDR2 strains. Population genetic analyses support the hypothesis that the two rearrangement mutations have only occurred once, and are responsible for the appearance and subsequent spread of all known MDR2 and MDR3 strains in French and German wine-growing regions.