Simultaneous Detection of Multiple Benzimidazole-Resistant β-Tubulin Variants of Botrytis cinerea using Loop-Mediated Isothermal Amplification

Monitoring Corynespora cassiicola Resistance to Boscalid, Trifloxystrobin, and Carbendazim in China

Cucumber leaf spot (CLS), caused by Corynespora cassiicola, is a serious disease of greenhouse cucumbers. With frequent use of existing fungicides, C. cassiicola has developed resistance to some of them, with serious implications for the control of CLS in the field. With a lack of new fungicides, it is necessary to use existing fungicides for effective control. Therefore, this study monitored the resistance of C. cassiicola to three commonly used and effective fungicides, boscalid, trifloxystrobin, and carbendazim, from 2017 to 2021. The frequency of resistance to boscalid showed an increasing trend, and the highest frequency was 85.85% in 2020. The frequency of resistance to trifloxystrobin was greater than 85%, and resistance to carbendazim was maintained at 100%. Among these fungicides, strains with multiple resistance to boscalid, trifloxystrobin, and carbendazim were found, accounting for 32.00, 25.25, 33.33, 43.06, and 37.24%, respectively. Of the strains that were resistant to boscalid, 87% had CcSdh mutations, including seven genotypes: B-H278L/Y, B-I280V, C-N75S, C-S73P, D-D95E, and D-G109V. Also, six mutation patterns of the Ccβ-tubulin gene were detected: E198A, F167Y, E198A&M163I, E198A&F167Y, M163I&F167Y, and E198A&F200C. Detection of mutations of the CcCytb gene in resistant strains showed that 98.8% were found to have only the G143A mutation. A total of 27 mutation combinations were found and divided into 14 groups for analysis. The resistance levels differed according to genotype. The development of genotypes showed a complex trend, increasing from 4 in 2017 to 13 in 2021 and varying by region. Multiple fungicide resistance is gradually increasing. Therefore, it is necessary to understand the types of mutations and the trend of resistance to guide the use of fungicides to achieve disease control.

A growing threat: Investigating the high incidence of benzimidazole fungicides resistance in Iranian Botrytis cinerea isolates

Effective management of fungicide application programs requires monitoring the profile of resistant populations of Botrytis cinerea, given its high-risk nature. This research aimed to examine the sensitivity of 200 B. cinerea isolates collected from different plant species and regions across Iran towards thiophanate-methyl and carbendazim fungicides. To distinguish between susceptible and resistant isolates, the discriminatory dose assay was employed, followed by the selection of representative isolates from each group for EC50 analysis. To identify potential modifications in codon 198 of the β-tubulin gene in B. cinerea resistant isolates, the researchers employed the PCR-RFLP diagnostic method. More than two-thirds of the isolates exhibited a varying degree of resistance to MBC fungicides, even in farms where the application of these fungicides had not taken place in recent years. After treatment with the BsaI enzyme, the PCR product of sensitive isolates displayed two bands measuring 98 and 371 bp, while only one band of 469 bp was identified in resistant isolates. The study also evaluated whether resistance to fungicides could affect the pathogenicity and mycelial growth of the isolates. The findings showed no significant difference between the resistant and sensitive groups in terms of these factors, indicating that resistance does not come at a cost to the pathogen's fitness. Considering the high incidence of resistance and the absence of negative consequences on fitness, it is recommended to exercise caution in the employment of benzimidazole fungicides as part of B. cinerea management strategies.

Dynamics of Carbendazim-Resistance Frequency of Pathogens Associated with the Epidemic of Fusarium Head Blight

Carbendazim resistance was detected using 4,701 Fusarium graminearum species complex isolates collected from major wheat-producing regions in China from 2018 to 2020. A total of 348 carbendazim-resistant isolates were identified. The majority of carbendazim-resistant isolates were detected in Jiangsu and Anhui Provinces. In total, 227 and 88 isolates were obtained from each of the Jiangsu and Anhui Provinces, with a high resistance frequency of 41.12 and 20.56%, respectively. The predominant resistant isolates harboring point mutations were F167Y (79.31%), followed by E198Q (16.38%) and F200Y (4.31%). Compared with F. graminearum, F. asiaticum isolates were more likely to produce carbendazim resistance. In this study, we first detected carbendazim-resistant isolates in Hebei, Shaanxi, Sichuan, and Hunan Provinces. In Jiangsu, Anhui, and Zhejiang, the frequency of carbendazim-resistant isolates maintained a high level, resulting in stable carbendazim-resistant populations. We also found the dynamic of carbendazim-resistance frequency in most provinces showed similar trends to the epidemic of Fusarium Head Blight (FHB). Our results facilitate the understanding of the current situation of carbendazim resistance of FHB pathogens and will be helpful for fungicides selection in different wheat-producing areas in China.

A multiplex fluorescence-based loop-mediated isothermal amplification assay for identifying chicken parvovirus, chicken infectious anaemia virus, and fowl aviadenovirus serotype 4

Chicken parvovirus (ChPV), chicken infectious anaemia virus (CIAV) and fowl adenovirus serotype 4 (FAdV-4) are avian viruses that have emerged in recent years and have endangered the global poultry industry, causing great economic loss. In this study, a multiplex fluorescence-based loop-mediated isothermal amplification (mLAMP) assay for detecting ChPV, CIAV and FAdV-4 was developed to simultaneously diagnose single and mixed infections in chickens. Three primer sets and composite probes were designed according to the conserved regions of the NS gene of ChPV, VP1 gene of CIAV and hexon gene of FAdV-4. Each composite probe was labelled with a different fluorophore, which was detached to release the fluorescence signal after amplification. The target viruses were distinguished based on the colour of the mLAMP products. The mLAMP assay was shown to be sensitive, with detection limits of 307 copies of recombinant plasmids containing the ChPV target genes, 749 copies of CIAV and 648 copies of FAdV-4. The assay exhibited good specificity and no cross-reactivity with other symptomatically related avian viruses. When used on field materials, the results of the mLAMP assay were in 100% agreement with those of the previously published PCR assay. The mLAMP assay is rapid, economical, sensitive and specific, and the results of amplification are directly observable by eye. Therefore, the mLAMP assay is a useful tool for the clinical detection of ChPV, CIAV and FAdV-4 and can be applied in rural areas.

Development of a visual multiplex fluorescent LAMP assay for the detection of foot-and-mouth disease, vesicular stomatitis and bluetongue viruses

Loop-mediated isothermal amplification (LAMP) is a nucleic acid amplification technique that can be used to amplify target genes at a constant temperature, and it has several advantages, including convenience, specificity and sensitivity. However, due to the special interpretation methods of this technology for reaction results, all the previously reported LAMP detection methods have been restricted to identifying a single target, which limits the application of this technology. In this study, we modified conventional LAMP to include a quencher-fluorophore composite probe complementary to the F1c segment of the inner primer FIP; upon strand separation, a gain in the visible fluorescent signal was observed. The probes could be labeled with different fluorophores, showing different colors at the corresponding wavelengths. Therefore, this multiplex LAMP (mLAMP) assay can simultaneously detect 1-3 target sequences in a single LAMP reaction tube, and the results are more accurate and intuitive. In this study, we comprehensively demonstrated a single-reaction mLAMP assay for the robust detection of three cattle viruses without nonspecific amplification of other related pathogenic cattle viruses. The detection limit of this mLAMP assay was as low as 526-2477 copies/reaction for the recombinant plasmids. It is expected that this mLAMP assay can be widely used in clinical diagnosis.

Rapid visual detection of benzimidazole resistance in Botrytis cinerea by recombinase polymerase amplification combined with a lateral flow dipstick

BACKGROUND

Benzimidazole resistance in Botrytis cinerea is related to point mutations in the target β-tubulin gene (TUB2). Three mutations (E198A, E198K, E198V) at codon 198 account for most of the resistant strains. A rapid on-site diagnostic assay would be useful to detect the presence and monitor further spread of this resistance mechanism.

RESULTS

A recombinase polymerase amplification combined with lateral flow detection (RPA-LFD) method was established for the rapid detection of methyl benzimidazole carbamate (MBC) resistance in B. cinerea. Based on the three mutations at TUB2 codon 198, three sets of RPA-LFD primers were designed, and each of these primer sets was able to specifically amplify the DNA containing its corresponding mutation; no amplification was detected with other mutated or wild-type DNA. The assay was optimized for specificity and sensitivity and was shown to detect the presence of 2 × 10² copies μl^-1 of target DNA per reaction within 10 min. DNA from eight other common fungal species of small fruit did not yield a signal. The system worked well over a wide range of temperatures from 25 to 45°C. Crude DNA obtained from boiled mycelium and conidia of symptomatic fruit could be used as templates, which simplified the assay process.

CONCLUSION

This study developed a novel assay based on RPA-LFD for the rapid and equipment-free detection of MBC-resistant isolates. In combination with a simple DNA extraction method, the assay could detect B. cinerea MBC-resistant isolates even without specialized equipment within 30 min. Considering its specificity, stability and simplicity, the RPA-LFD assay could be a promising tool for rapid on-site diagnosis of fungicide-resistant isolates. © 2021 Society of Chemical Industry.

Advances in Understanding Fungicide Resistance in Botrytis cinerea in China

Gray mold, caused by Botrytis cinerea, is a devastating disease that causes significant yield losses in various economically important plants. Fungicide application is one of the main strategies for management of gray mold; however, B. cinerea has developed resistance to various groups of fungicide. In China, benzimidazole-, dicarboximide-, and quinone outside inhibitor-resistant populations of B. cinerea have become dominant. Substitute mutations in fungicide target genes are responsible for resistance in B. cinerea. Based on known resistance mechanisms, molecular methods including loop-mediated isothermal amplification have been developed for rapid detection of resistant isolates of B. cinerea. Because B. cinerea is able to quickly develop resistance to various fungicides, various integrated strategies have been implemented in the last decade, including biological and agricultural practices, to manage fungicide resistance in B. cinerea.

Evolution of the Resistance of Botrytis cinerea to Carbendazim and the Current Efficacy of Carbendazim Against Gray Mold After Long-Term Discontinuation

Gray mold caused by Botrytis cinerea is a fungal disease that critically threatens agricultural production, and carbendazim was the first fungicide used to control B. cinerea. However, B. cinerea developed serious resistance to carbendazim, and this fungicide has thus rarely been used in the past decade in China. Due to the extended discontinuation of carbendazim use, the evolution of the resistance of B. cinerea to carbendazim in recent years is unclear, and whether carbendazim can effectively control gray mold is largely unknown. Therefore, this study determined the sensitivity of 407 B. cinerea isolates collected from 2014 to 2018 to carbendazim and the ability of carbendazim to control gray mold in the field. The results showed that the frequency of B. cinerea isolates resistant to carbendazim remained above 95%. Three different mutation types responsible for the resistance of B. cinerea to carbendazim were identified at codon 198 in the β-tubulin gene sequence: E198V (changed from GAG to GTG), E198A (changed from GAG to GCG), and E198K (changed from GAG to AAG). Over the last 5 years, E198V was the major mutation. However, an analysis of its evolution revealed that the percentage of the E198V mutation declined after 2017 to 56.5% in 2018. In addition, the proportion of isolates with the E198K mutation decreased over time, and no isolates with this mutation were found in either 2017 or 2018. The proportion of the E198A mutation increased over the 5-year test period to reach 43.5% in 2018. Furthermore, three greenhouse experiments demonstrated that carbendazim has lost its ability to control gray mold. We attribute the above findings to our results showing that the carbendazim-resistant isolates had no fitness penalties compared with the carbendazim-sensitive isolates for sporulation and mycelial growth. In particular, the E198A mutant isolates exhibited a strong ability to sporulate, suggesting that the E198A mutation might become dominant in the future. Interestingly, the results showed that carbendazim-sensitive isolates could be easily controlled by four conventional fungicides, namely boscalid, procymidone, iprodione, and pyrimethanil, with mean EC₅₀ values of 0.71 ± 0.2 mg liter^-1, 1.33 ± 0.39 mg liter^-1, 0.59 ± 0.33 mg liter^-1, and 6.02 ± 3.02 mg liter^-1, respectively. In conclusion, carbendazim has lost its application value and is ineffective for the control of gray mold.

Development of a LAMP method for detecting the N75S mutant in SDHI-resistant Corynespora cassiicola

The replacement of asparagine with serine at codon 75 of the sdhC gene (N75S) confers succinate dehydrogenase inhibitor resistance in Corynespora cassiicola, which caused by consecutive fungicide application. To rapidly detect the mutation of N75S, a method based on loop-mediated isothermal amplification (LAMP) was developed in this study. The optimal primer set among the six primer sets designed could clearly identify N75S from the wild-type genotype. The detection threshold of the optimized LAMP mixture (10 μL) was 8.8 fg of target DNA at 63 °C within 60 min. This method specifically showed a color change and ladder-like band only when DNA extracted from isolates containing the N75S mutation was added. The results of stability tests suggested a satisfactory repeatability of this method. Additionally, the assay could positively distinguish N75S mutants from crude DNA isolated from conidia and mycelia of C. cassiicola. Given the high efficiency, sensitivity, specificity, repeatability and simplicity of operation, the LAMP method established here could be useful to evaluate the shift in the sensitivity of C. cassiicola to SDHIs and will provide significant data for the management of Corynespora leaf spot.

Carbendazim Resistance of Fusarium graminearum From Henan Wheat

Fusarium head blight, also called scab, is caused by Fusarium graminearum and is one of the most important destructive diseases of wheat. The frequency of carbendazim resistance in 1,132 isolates of F. graminearum recovered from fields in different regions of Henan Province in 2016, 2017, and 2018 was determined. A total of 31 F. graminearum isolates resistant to carbendazim were detected, including 30 moderately resistant isolates and one highly resistant isolate. The frequency of resistance of F. graminearum isolates to carbendazim was 2.7%. The range of effective concentration (EC₅₀) values of 1,101 sensitive isolates and 30 moderately resistant isolates was 0.08 to 0.98 μg ml^-1 and 2.73 to 13.28 μg ml^-1, respectively. The mean ± SD EC₅₀ value was 0.55 ± 0.13 μg ml^-1 and 5.61 ± 2.58 μg ml^-1, respectively. The EC₅₀ value of the highly resistant isolate was 21.12 μg ml^-1. Point mutation types of the carbendazim-resistant isolates were characterized by cloning the β₂-tubulin gene of 31 resistant isolates. Three point mutation types at amino acids F167Y, E198Q, and E198L in the β₂-tubulin gene of resistant isolates were identified. Among 31 resistant isolates, the frequency of point mutation types in F167Y, E198Q, and E198L of the β₂-tubulin gene was 71.0, 25.8, and 3.2%, respectively. The data indicate that F. graminearum has developed resistance to carbendazim in Henan Province, and single point mutations at amino acid F167Y were the predominant type of mutation detected.

Monitoring Methyl Benzimidazole Carbamate-Resistant Isolates of the Cucurbit Powdery Mildew Pathogen, Podosphaera xanthii, Using Loop-Mediated Isothermal Amplification

Powdery mildew, caused by the fungus Podosphaera xanthii, is one of the most economically important diseases affecting cucurbit crops in Spain. Currently, chemical control offers the most efficient management of the disease; however, P. xanthii isolates resistant to multiple classes of site-specific fungicides have been reported in the Spanish cucurbit powdery mildew population. In previous studies, resistance to the fungicides known as methyl benzimidazole carbamates (MBCs) was found to be caused by the amino acid substitution E198A on β-tubulin. To detect MBC-resistant isolates in a faster, more efficient, and more specific way than the traditional methods used to date, a loop-mediated isothermal amplification (LAMP) system was developed. In this study, three sets of LAMP primers were designed. One set was designed for the detection of the wild-type allele and two sets were designed for the E198A amino acid change. Positive results were only obtained with both mutant sets; however, LAMP reaction conditions were only optimized with primer set 2, which was selected for optimal detection of the E198A amino acid change in P. xanthii-resistant isolates, along with the optimal temperature and duration parameters of 65°C for 75 min, respectively. The hydroxynaphthol blue (HNB) metal indicator was used for quick visualization of results through the color change from violet to sky blue when the amplification was positive. HNB was added before the amplification to avoid opening the lids, thus decreasing the probability of contamination. To confirm that the amplified product corresponded to the β-tubulin gene, the LAMP product was digested with the enzyme LweI and sequenced. Our results show that the LAMP technique is a specific and reproducible method that could be used for monitoring MBC resistance of P. xanthii directly in the field.

Alternative Molecular-Based Diagnostic Methods of Plant Pathogenic Fungi Affecting Berry Crops-A Review

Increasing consumer awareness of potentially harmful pesticides used in conventional agriculture has prompted organic farming to become notably more prevalent in recent decades. Central European countries are some of the most important producers of blueberries, raspberries and strawberries in the world and organic cultivation methods for these fruits have a significant market share. Fungal pathogens are considered to be the most significant threat to organic crops of berries, causing serious economic losses and reducing yields. In order to ameliorate the harmful effects of pathogenic fungi on cultivations, the application of rapid and effective identification methods is essential. At present, various molecular methods are applied for fungal species recognition, such as PCR, qPCR, LAMP and NGS.

Benzimidazole- and QoI-resistance in Corynespora cassiicola populations from greenhouse-cultivated cucumber: An emerging problem in China

Target leaf spot caused by Corynespora cassiicola is an economically important foliar disease on cucumber. In recent years, this disease has caused a serious problem on greenhouse-cultivated cucumber in China. In this study, to explore the characteristics and possible causes of heavy occurrence of the disease, we monitored the resistance of C. cassiicola strains from different provinces of China to benzimidazole and quinone outside inhibitor (QoI) fungicides. The results from sequence comparison of target genes β-tubulin and Cytb of 619C. cassiicola strains indicate that resistance frequency to benzimidazoles and QoIs is up to 100%. Furtherly, molecular resistance mechanism of C. cassiicola to benzimidazoles and QoIs was analysed. One single mutation E198A and three double mutations E198A&M163I, E198A&F167Y and E198A&F200S were observed in target gene β-tubulin, which confers resistance to benzimidazoles. To our knowledge, this is the first report that double mutations of β-tubulin confer resistance to benzimidazoles in filamentous fungi. Compared with single mutation E198A, three double mutations significantly decreased sensitivity to benzimidazoles. Moreover, significant difference of sensitivity to benzimidazoles was observed among three double mutations. These mutation genotypes of β-tubulin have different geographical distribution and the mutation E198A&M163I is prevalent, occupying for 63.94%. In addition, strong cross resistance patterns between carbendazim, benomyl and thiabendazole were observed in C. cassiicola strains conferring different β-tubulin mutations. For QoI resistance, the only mutation G143A of Cytb was detected in tested 619C. cassiicola strains. Strong positive cross resistance was observed when comparing the EC₅₀ values of sensitive and resistant strains of C. cassiicola for six intrinsically different QoIs such as azoxystrobin, fluoxastrobin, pyraclostrobin, fenaminstrobin, picoxystrobin and coumoxystrobin. Taken together, all the results not only provide novel insights into understanding resistance mechanism to benzimidazoles and QoIs in filamentous fungi, but also provide some important references for resistance management of target leaf spot on cucumber.