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

Stereoisomeric developmental toxicity of orysastrobin and its isomeric metabolite in zebrafish (Danio rerio) embryos: Cardiac abnormal development by orysastrobin

Orysastrobin (OSB), a strobilurin fungicide, inhibits the normal redox reactions of cytochrome bc1 at the Qo site of target phytopathogenic fungal species. Its frequent detection and high concentrations in natural wetlands and rivers have raised concerns regarding its acute toxicity and potential effects on fish. Therefore, this study examined the acute toxicities of OSB and its stereoisomeric metabolite F001 on zebrafish (Danio rerio) embryos, an animal model. OSB and F001 did not induce substantial mortality or inhibit hatching in the treated embryos. However, OSB exhibited acute toxicities, including pericardial and yolk sac edemas, spine curvature, and bleeding, at 5.0 mg/L concentration. In contrast, F001 did not induce such abnormalities in zebrafish embryos within the tested concentration ranges. Additionally, OSB induced abnormal cardiac development and significantly impaired heart function in embryos, likely due to the up-regulation of key heart development genes, such as kcnn6a and amhc. In OSB-treated embryos, a developmental delay in liver formation was observed. OSB-induced reactive oxygen species in zebrafish embryos. Overall, this study underscores the importance of gathering comprehensive toxicological data on OSB and F001 in fish to fully understand their environmental impacts, emphasizing the urgent need for repeated periodic monitoring to mitigate the environmental risks posed in agricultural waters, reservoirs, and other aquatic ecosystems.

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

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

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

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

Fungicide Sensitivity and Nontarget Site Resistance in Rhizoctonia zeae Isolates Collected from Corn and Soybean Fields in Nebraska

Rhizoctonia zeae was recently identified as the major Rhizoctonia species in corn and soybean fields in Nebraska and was shown to be pathogenic on corn and soybean seedlings. Fungicide seed treatments commonly used to manage seedling diseases include prothioconazole (demethylation inhibitor), fludioxonil (phenylpyrrole), sedaxane (succinate dehydrogenase inhibitor), and azoxystrobin (quinone outside inhibitor [QoI]). To establish the sensitivity of R. zeae to these fungicides, we isolated this pathogen from corn and soybean fields in Nebraska during 2015 to 2017 and estimated the relative effective concentration for 50% inhibition (EC50) of a total of 91 R. zeae isolates from Nebraska and Illinois. Average EC50 for prothioconazole, fludioxonil, sedaxane, and azoxystrobin was 0.219, 0.099, 0.078, and >100 µg ml-1, respectively. In planta assays showed that azoxystrobin did not significantly reduce the disease severity on soybean (P > 0.05). The cytochrome b gene of R. zeae did not harbor any mutation known to confer QoI resistance and had a type I intron directly after codon 143, suggesting that a G143A mutation is unlikely to evolve in this pathogen. For prothioconazole, fludioxonil, and sedaxane, the EC50 of the isolates did not differ significantly among the years of collection (P > 0.05), and their single discriminatory concentrations were identified as 0.1 µg ml-1. This is the first study to establish nontarget site resistance of R. zeae to azoxystrobin and the sensitivity of R. zeae to commonly used seed treatment fungicides in Nebraska. This information will help to guide strategies for chemical control of R. zeae and monitor sensitivity shifts in the future.

From Natural Hosts to Agricultural Threats: The Evolutionary Journey of Phytopathogenic Fungi

Since the domestication of plants, pathogenic fungi have consistently threatened crop production, evolving genetically to develop increased virulence under various selection pressures. Understanding their evolutionary trends is crucial for predicting and designing control measures against future disease outbreaks. This paper reviews the evolution of fungal pathogens from natural habitats to agricultural settings, focusing on eight significant phytopathogens: Pyricularia oryzae, Botrytis cinerea, Puccinia spp., Fusarium graminearum, F. oxysporum, Blumeria graminis, Zymoseptoria tritici, and Colletotrichum spp. Also, we explore the mechanism used to understand evolutionary trends in these fungi. The studied pathogens have evolved in agroecosystems through either (1) introduction from elsewhere; or (2) local origins involving co-evolution with host plants, host shifts, or genetic variations within existing strains. Genetic variation, generated via sexual recombination and various asexual mechanisms, often drives pathogen evolution. While sexual recombination is rare and mainly occurs at the center of origin of the pathogen, asexual mechanisms such as mutations, parasexual recombination, horizontal gene or chromosome transfer, and chromosomal structural variations are predominant. Farming practices like mono-cropping resistant cultivars and prolonged use of fungicides with the same mode of action can drive the emergence of new pathotypes. Furthermore, host range does not necessarily impact pathogen adaptation and evolution. Although halting pathogen evolution is impractical, its pace can be slowed by managing selective pressures, optimizing farming practices, and enforcing quarantine regulations. The study of pathogen evolution has been transformed by advancements in molecular biology, genomics, and bioinformatics, utilizing methods like next-generation sequencing, comparative genomics, transcriptomics and population genomics. However, continuous research remains essential to monitor how pathogens evolve over time and to develop proactive strategies that mitigate their impact on agriculture.

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

BACKGROUND

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

RESULTS

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

CONCLUSION

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

Resistance of the Ginseng Gray Mold Pathogen, Botrytis cinerea, to Boscalid and Pyraclostrobin Fungicides in China

Gray mold caused by Botrytis cinerea severely threatens the yield of ginseng (Panax ginseng). Various categories of fungicides have been utilized to control gray mold on this crop. In this study, the resistance of 102 isolates of B. cinerea from 11 commercial ginseng-growing regions in China to fungicides was examined. A total of 32.4% were resistant to boscalid, with EC50 values that ranged from 12.26 to 235.87 μg/ml, and 94.1% were resistant to pyraclostrobin, with EC50 values that ranged from 5.88 to 487.72 μg/ml. Except for sdhA and sdhD, the amino acid substitutions of P225F, P225L, N230I, H272Y, and H272R in the sdhB subunit from 24 (4 sensitive [S] and 20 resistant [R]), 5 (1 S and 4 R), 1 (S), 1 (R), and 8 (4 S and 4 R) strains, respectively, and the concurrent amino acid substitutions of G85A + I93V + M158V + V168I in the sdhC subunit from 5 (4 S and 1 R) strains were identified. A G143A substitution in cytochrome b was identified in 96 isolates that were resistant to pyraclostrobin and three that were sensitive to it. The Bcbi-143/144 intron was identified in the other three isolates sensitive to pyraclostrobin, but it was absent in the isolates that harbored the G143A mutation. The results showed that the populations of B. cinerea on ginseng have developed strong resistance to pyraclostrobin. Therefore, it is not recommended to continue using this fungicide to control gray mold on P. ginseng. Boscalid is still effective against most isolates. However, to prevent fungicide resistance, it is recommended to use a mixture of boscalid with other categories of fungicides.

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

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

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

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

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

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

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

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

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

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

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

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

Functional annotation and comparative analysis of four Botrytis cinerea mitogenomes reported from Punjab, Pakistan

Botrytis cinerea is one of the top phytopathogenic fungus which ubiquitously cause grey mold on a variety of horticultural plants. The mechanism of respiration in the fungus occurs within the mitochondria. Mitogenomes serve as a key molecular marker for the investigation of fungal evolutionary patterns. This study aimed at the complete assembly, characterization, and comparative relationship of four mitogenomes of Botrytis cinerea strains including Kst5C, Kst14A, Kst32B, Kst33A, respectively. High throughput sequencing of four mitogenomes allowed the full assembly and annotation of these sequences. The total genome length of these 4 isolates Kst5C Kst14A, Kst32B, Kst33A was 69,986 bp, 77,303 bp, 76,204 bp and 55, 226 bp respectively. The distribution of features represented 2 ribosomal RNA genes,14 respiration encoding proteins, 1 mitochondrial ribosomal protein-encoding gene, along with varying numbers of transfer RNA genes, protein-coding genes, mobile intronic regions and homing endonuclease genes including LAGLIDADG and GIY-YIG domains were found in all four mitogenomes. The comparative analyses performed also decipher significant results for four mitogenomes among fungal isolates included in the study. This is the first report on the detailed annotation of mitogenomes as a proof for investigation of variation patterns present with in the B. cinerea causing grey mold on strawberries in Pakistan. This study will also contribute to the rapid evolutionary analysis and population patterns present among Botrytis cinerea.

Exploration of Novel Scaffolds Targeting Cytochrome b of Pyricularia oryzae

The fulfilment of the European "Farm to Fork" strategy requires a drastic reduction in the use of "at risk" synthetic pesticides; this exposes vulnerable agricultural sectors-among which is the European risiculture-to the lack of efficient means for the management of devastating diseases, thus endangering food security. Therefore, novel scaffolds need to be identified for the synthesis of new and more environmentally friendly fungicides. In the present work, we employed our previously developed 3D model of P. oryzae cytochrome bc1 (cyt bc1) complex to perform a high-throughput virtual screening of two commercially available compound libraries. Three chemotypes were selected, from which a small collection of differently substituted analogues was designed and synthesized. The compounds were tested as inhibitors of the cyt bc1 enzyme function and the mycelium growth of both strobilurin-sensitive (WT) and -resistant (RES) P. oryzae strains. This pipeline has permitted the identification of thirteen compounds active against the RES cyt bc1 and five compounds that inhibited the WT cyt bc1 function while inhibiting the fungal mycelia only minimally. Serendipitously, among the studied compounds we identified a new chemotype that is able to efficiently inhibit the mycelium growth of WT and RES strains by ca. 60%, without inhibiting the cyt bc1 enzymatic function, suggesting a different mechanism of action.

Identification of Quinone Outside Inhibitor Fungicide-Resistant Isolates of Parastagonospora nodorum from Illinois and Kentucky

Stagonospora leaf and glume blotch, caused by Parastagonospora nodorum, is a major disease of winter wheat (Triticum aestivum) in the United States capable of significantly reducing grain yield and quality. Pathogens such as P. nodorum that overwinter in crop residue are often an increased concern in cropping systems that utilize no-till farming. In addition, the lack of wheat cultivars with complete resistance to P. nodorum has led to the reliance on foliar fungicides for disease management. Quinone outside inhibitor (QoI) fungicides (Fungicide Resistance Action Committee group 11) are one of the major classes used to manage foliar diseases in wheat. Use of the QoI class of fungicides tends to select isolates of fungal pathogens with resistance due to mutations in the fungal cytochrome b gene. Isolates of P. nodorum were collected from Illinois in 2014 and Kentucky in 2018, 2019, and 2020. Amplification and sequencing of a segment of the cytochrome b gene from these isolates revealed a mutation at codon 143 that confers a change from glycine to alanine in the amino acid sequence (known as the G143A mutation). In vitro plate assays and greenhouse trials were used to confirm and characterize the QoI resistance caused by the G143A mutation. The frequency of the tested isolates with the G143A mutation was 46% (57 of 123 isolates) and 5% (3 of 60 isolates) for Kentucky and Illinois, respectively. This research is the first to identify the G143A mutation in P. nodorum isolates with resistance to QoI fungicides in Illinois and Kentucky.

The G143A/S substitution of mitochondrially encoded cytochrome b (Cytb) in Magnaporthe oryzae confers resistance to quinone outside inhibitors

BACKGROUND

Rice blast, caused by Magnaporthe oryzae, is a destructive disease threatening the production of staple foods worldwide. Quinone outside inhibitors (QoIs) are a group of chemicals exhibiting excellent activity against a majority of plant pathogens, with the disadvantage that pathogens can easily develop resistance to QoIs.

RESULTS

Here, we investigated the activity of picoxystrobin against M. oryzae, which showed a great inhibitory effect on 100 strains of M. oryzae with half-maximal effective concentrations (EC₅₀ ) ranging from 0.0251 to 0.1337 μg ml^-1 . The EC₅₀ values showed a continuous unimodal distribution that was identical to the normal distribution, suggesting the potency of our study to represent baseline sensitivity. In addition, nine resistant mutants were obtained by exposing M. oryzae to a high dosage of picoxystrobin in the laboratory; all of them showed cross-resistance to the other five QoI fungicides. Although some mutants showed a decreased resistance factor after ten successive cultures on fungicide-free medium, the resistance to picoxystrobin was still inheritable. Amino acid substitution of G143S was detected in eight of nine picoxystrobin-resistant mutants, and G143A was detected in only one of nine mutants. A fitness penalty was found in the mutants carrying G143S rather than G143A.

CONCLUSION

Our findings suggested that M. oryzae had a mid to high risk of resistance to picoxystrobin. Considering this, we should be vigilant to the resistance risk and apply picoxystrobin sensibly in the field. © 2022 Society of Chemical Industry.

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

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

Synthesis and Antifungal Activity of New butenolide Containing Methoxyacrylate Scaffold

In order to improve the antifungal activity of new butenolides containing oxime ether moiety, a series of new butenolide compounds containing methoxyacrylate scaffold were designed and synthesized, based on the previous reports. Their structures were characterized by ¹H NMR, ¹³C NMR, HR-MS spectra, and X-ray diffraction analysis. The in vitro antifungal activities were evaluated by the mycelium growth rate method. The results showed that the inhibitory activities of these new compounds against Sclerotinia sclerotiorum were significantly improved, in comparison with that of the lead compound 3-8; the EC₅₀ values of V-6 and VI-7 against S. sclerotiorum were 1.51 and 1.81 mg/L, nearly seven times that of 3-8 (EC₅₀ 10.62 mg/L). Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) observation indicated that compound VI-3 had a significant impact on the structure and function of the hyphal cell of S. sclerotiorum mycelium and the positive control trifloxystrobin. Molecular simulation docking results indicated that the introduction of methoxyacrylate scaffold is beneficial to improving the antifungal activity of these compounds against S. sclerotiorum, which can be used as the lead for further structure optimization.

Identification of Septoria glycines Isolates from Soybean with Resistance to Quinone Outside Inhibitor Fungicides

Brown spot, caused by Septoria glycines, is a common foliar disease of soybean (Glycine max). Applications of fungicide products that contain quinone outside inhibitor (QoI) active ingredients to soybean fields have contributed to the selection and development of QoI-resistant populations of S. glycines. We investigated the molecular mechanisms of QoI-resistance in these populations through targeted analysis of the cytochrome b gene. Isolates of S. glycines collected from several soybean fields over different seasons varied in sensitivity to QoI fungicides. Characterization of the cytochrome b gene revealed a mutation that changed an amino acid from glycine to alanine at codon 143 - one that is generally associated with QoI fungicide resistances. A PCR assay was developed that allowed successful discrimination of QoI-sensitive and -resistant isolates based on the G143A mutation. Results of this study demonstrated that 47.5% of S. glycines isolates tested were resistant to QoI fungicides. Accurate monitoring of this mutation will help slow the spread of QoI resistance and will be important for fungicide resistant management in this pathosystem.

Analysis of resistance risk and resistance-related point mutations in Cyt b of QioI fungicide ametoctradin in Phytophthora litchii

BACKGROUND

Litchi downy blight, caused by Phytophthora litchii, is one of the most important diseases of litchi. Ametoctradin, as the only QioI (quinone inside and outside inhibitor) fungicide, has been registered in China in 2019. However, the ametoctradin-resistance risk and molecular basis in Phytophthora litchii have not been reported.

RESULTS

In this study, the sensitivity profile of 144 Phytophthora litchii strains to ametoctradin was determined, with a mean median effective concentration (EC₅₀ ) value of 0.1706 ± 0.091 μg mL^-1 . Nine stable resistant Phytophthora litchii mutants [resistance factor (RF) > 400] were derived from sensitive isolates using fungicide adaption. The compound fitness index of three resistant-mutants (HN10-1-1, HN10-1-2 and HN10-2-1) was similar or higher than that of their parental isolates in vitro. All these ametoctradin-resistant mutants were sensitive to metalaxyl, dimethomorph, oxathiapiprolin and cyazofamid. Two point mutations, leading to the S33L and D228N changes in PlCyt b (cytochrome b) were found in ametoctradin-resistant mutants. Eight ametoctradin-resistant mutants containing S33L showed increased sensitivity to azoxystrobin and amisulbrom, and one mutant containing D228N exhibited increased sensitivity to cyazofamid. In vitro enzyme activity test showed that ametoctradin could not inhibit the activity of cytochrome bc1 complex with S33L and D228N point mutation. AS-PCR primers were designed based on the S33L change to detect the ametoctradin-resistant strains in the future.

CONCLUSION

These results suggest that Phytophthora litchii has a medium to high resistance risk to ametoctradin in the laboratory. Two changes, S33L and D228N, in PlCyt b are likely to be associated with the observed ametoctradin resistance. © 2022 Society of Chemical Industry.

Development of a LAMP method for detecting F129L mutant in azoxystrobin-resistant Pyricularia oryzae

Azoxystrobin has been widely used since 1996 to control rice blast caused by Pyricularia oryzae. Azoxystrobin resistance related to mutations at the P. oryzae target protein (F129L of Cytb) has been reported worldwide. To quickly identify and detect resistant strains in the field, this research established a rapid loop-mediated isothermal amplification (LAMP) detection system for the F129L mutation. The system could detect the P. oryzae F129L (TTC-TTA) mutation at 62 °C within 60 min, with a detection limit of 100 fg/μL, which is 10 times higher than for conventional PCR. The method had high specificity and repeatability and could detect the F129L (TTC-TTA) mutation in plant tissues within 3 h. The LAMP method established in this study will be useful to detect azoxystrobin-resistant P. oryzae F129L mutant strains and generate significant data for the management of resistant P. oryzae isolates.

Molecular Mechanisms Underlying Fungicide Resistance in Citrus Postharvest Green Mold

The necrotrophic fungus Penicillium digitatum (Pd) is responsible for the green mold disease that occurs during postharvest of citrus and causes enormous economic losses around the world. Fungicides remain the main method used to control postharvest green mold in citrus fruit storage despite numerous occurrences of resistance to them. Hence, it is necessary to find new and more effective strategies to control this type of disease. This involves delving into the molecular mechanisms underlying the appearance of resistance to fungicides during the plant–pathogen interaction. Although mechanisms involved in resistance to fungicides have been studied for many years, there have now been great advances in the molecular aspects that drive fungicide resistance, which facilitates the design of new means to control green mold. A wide review allows the mechanisms underlying fungicide resistance in Pd to be unveiled, taking into account not only the chemical nature of the compounds and their target of action but also the general mechanism that could contribute to resistance to others compounds to generate what we call multidrug resistance (MDR) phenotypes. In this context, fungal transporters seem to play a relevant role, and their mode of action may be controlled along with other processes of interest, such as oxidative stress and fungal pathogenicity. Thus, the mechanisms for acquisition of resistance to fungicides seem to be part of a complex framework involving aspects of response to stress and processes of fungal virulence.

Azole Use in Agriculture, Horticulture, and Wood Preservation - Is It Indispensable?

Plant pathogens cause significant damage to plant products, compromising both quantities and quality. Even though many elements of agricultural practices are an integral part of reducing disease attacks, modern agriculture is still highly reliant on fungicides to guarantee high yields and product quality. The azoles, 14-alpha demethylase inhibitors, have been the fungicide class used most widely to control fungal plant diseases for more than four decades. More than 25 different azoles have been developed for the control of plant diseases in crops and the group has a world market value share of 20-25%. Azoles have proven to provide long-lasting control of many target plant pathogens and are categorized to have moderate risk for developing fungicide resistance. Field performances against many fungal pathogens have correspondingly been stable or only moderately reduced over time. Hence azoles are still, to date, considered the backbone in many control strategies and widely used as solo fungicides or as mixing partners with other fungicide groups, broadening the control spectrum as well as minimizing the overall risk of resistance development. This review describes the historic perspective of azoles, their market shares and importance for production of major crops like cereals, rice, oilseed rape, sugar beet, banana, citrus, and soybeans. In addition, information regarding use in amenity grass, in the wood preservation industry and as plant growth regulators are described. At the end of the review azoles are discussed in a wider context including future threats following stricter requirements for registration and potential impact on human health.

Fungicide Management of Pasmo Disease of Flax and Sensitivity of Septoria linicola to Pyraclostrobin and Fluxapyroxad

Among the diseases that have the potential to cause damage to flax (Linum usitatissimum L.) every year, the fungal disease pasmo, caused by Septoria linicola, is the most important. Fungicide application and a diverse crop rotation are the most important strategies to control this disease because there is little variation in resistance among flax cultivars. However, few fungicide products are available to flax growers. Field studies were conducted at four locations in Western Canada in 2014, 2015, and 2016 to determine the effect of two fungicide active ingredients applied singly and in combination: pyraclostrobin, fluxapyroxad, and fluxapyroxad + pyraclostrobin; and two application timings (early-flower, mid-flower, and at both stages) on pasmo disease severity, seed yield, and quality of flaxseed. The results indicated that among the three fungicide treatments, both pyraclostrobin and fluxapyroxad + pyraclostrobin controlled pasmo effectively; however, fluxapyroxad + pyraclostrobin was the most beneficial to improve the quality and quantity of the seed for most of the site-years. Disease severity in the fungicide-free control was 70%, and application of fluxapyroxad + pyraclostrobin decreased disease severity to 18%, followed by pyraclostrobin (23%) and fluxapyroxad (48%). Application of fluxapyroxad + pyraclostrobin also improved seed yield to 2,562 kg ha^-1 compared with 1,874 kg ha^-1 for the fungicide-free control, followed by pyraclostrobin (2,391 kg ha^-1) and fluxapyroxad (2,340 kg ha^-1). Fungicide application at early and mid-flowering stage had the same effects on disease severity and seed yield; however, seed quality was improved more when fungicide was applied at mid-flowering stage. Continuous use of the same fungicide may result in the development of fungicide insensitivity in the pathogen population. Thus, sensitivity of S. linicola isolates to pyraclostrobin and fluxapyroxad fungicides was determined by the spore germination and microtiter assay methods. Fungicide insensitivity was not detected among the 73 isolates of S. linicola tested against either of these fungicides.

Sensitivity of Pyricularia oryzae Populations to Fungicides Over a 26-Year Time Frame in Brazil

The long-term dynamics of fungicide resistance of the rice blast fungus Pyricularia oryzae was monitored by examining the reaction of the fungal field isolates, collected over a period of 26 years, to the active ingredients of commercially relevant fungicides. The in vitro sensitivity of all isolates was measured against quinone outside inhibitors (QoI), melanin biosynthesis inhibitors, and sterol demethylation inhibitor (DMI) fungicides, namely azoxystrobin (as a QoI), tricyclazole (as a melanin biosynthesis inhibitor), tebuconazole (as a DMI), and trifloxystrobin + tebuconazole (QoI + DMI). Over the 26-year collection period, a gradual rise in the EC₅₀ estimates for mycelial growth sensitivity was observed for all fungicides, but most strikingly for azoxystrobin. A rise in conidial germination and appressorium formation was also noted, most markedly for azoxystrobin. Consistently, the earlier isolates were much more sensitive to the active ingredients than the more contemporary isolates. The sequencing of the amplified cyt b fragment distinguished two haplotypes, H1 and H2. Haplotype H1 (six isolates) contained the G to C transversion at codon 143 (resulting in change G143A), linked to the resistant phenotype QoI-R. Haplotype H2 (40 isolates), gathered the isolates sensitive to QoI. This work documents the gradual rise in the frequency of fungicide-resistant isolates in P. oryzae rice populations on a long-term basis.

Molecular Identification of Mutations Conferring Resistance to Azoxystrobin in Cercospora nicotianae

Cercospora nicotianae, the causal agent of frogeye leaf spot (FLS) of tobacco, has been exposed to quinone outside inhibitor (QoI) fungicides for more than a decade through azoxystrobin applications targeting other major foliar diseases. From 2016 to 2018, a total of 124 isolates were collected from tobacco fields throughout Kentucky. Sensitivity of these isolates to azoxystrobin was previously characterized by determining the effective concentration to inhibit 50% conidial germination (EC₅₀). Based on azoxystrobin EC₅₀, isolates were categorized into three discrete groups: high sensitivity (<0.08 µg/ml), moderate sensitivity (0.14 to 0.64 µg/ml), and low sensitivity (>1.18 µg/ml). Variability in sensitivity in a limited number of C. nicotianae isolates was previously shown to be a result of resistance mutations in the fungicide target gene. To improve understanding of C. nicotianae cytochrome b (cytb) structure, the gene was cloned from three isolates representing each EC₅₀ group, and sequences were compared. Our analysis showed that cytb gene in C. nicotianae consists of 1,161 nucleotides encoding 386 amino acids. The cytb sequence among the cloned isolates was identical with the exception of the F129L and G143A point mutations. To more rapidly determine the resistance status of C. nicotianae isolates to azoxystrobin, a polymerase chain reaction (PCR) assay was developed to screen for mutations. According to this assay, 80% (n = 99) of tested C. nicotianae isolates carried an F129L mutation and were moderately resistant to azoxystrobin, and 7% (n = 9) carried the G143A mutation and were highly resistant. A receiver operating characteristic curve analysis suggested the PCR assay was a robust diagnostic tool to identify C. nicotianae isolates with different sensitivity to azoxystrobin in Kentucky tobacco production. The prevalence of both the F129L and G143A mutations in C. nicotianae from Kentucky differs from that of other pathosystems where resistance to QoI fungicides has been identified, in which the majority of sampled isolates of the pathogen species have a broadly occurring cytb mutation.

Difenoconazole Resistance Shift in Botrytis cinerea From Tomato in China Associated With Inducible Expression of CYP51

Gray mold caused by Botrytis cinerea is one of the most important diseases in tomato. It can be controlled effectively by demethylation inhibitor (DMI) fungicides, but their resistance status after long-term use in the field is unclear. The baseline sensitivity to difenoconazole of 142 B. cinerea isolates from China with no history of DMI usage was characterized, with a mean effective concentration for 50% mycelial growth inhibition (EC₅₀) of 0.97 ± 0.50 μg/ml. EC₅₀ values for difenoconazole sensitivity of another 248 isolates collected in 2011 and 2016 ranged from 0.04 to 11.99 μg/ml, and the frequency of difenoconazole sensitivity formed a nonnormal distribution curve. Detached fruit studies revealed that isolates with EC₅₀ values of approximately 6.00 μg/ml were not controlled effectively. The mean EC₅₀ of the resistant isolates changed from 6.74 to 8.65 μg/ml between 2011 and 2016. Positive cross-resistance was only observed between difenoconazole and two DMIs. One dual resistant isolate and one triple resistant isolate were found among the difenoconazole-resistant isolates collected in 2016, associated with point mutations in corresponding target proteins of the fungicides azoxystrobin and fludioxonil. This indicated that B. cinerea not only showed higher difenoconazole resistance levels but gradually changed from single to multiple fungicide resistance over time. No amino acid variation was found in the CYP51 protein. In the absence of difenoconazole, the relative expression of CYP51 was not significantly different in sensitive and resistant isolates. Induced expression of CYP51 is an important determinant of DMI resistance in B. cinerea from tomato. However, nucleotide variants found in the upstream region had no association with the fungicide resistance phenotype. These results will be helpful for the management of B. cinerea in the field.

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

BACKGROUND

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

RESULTS

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

CONCLUSION

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

Colonization of human opportunistic Fusarium oxysporum (HOFo) isolates in tomato and cucumber tissues assessed by a specific molecular marker

Fusarium oxysporum is a large complex cosmopolitan species composed of plant pathogens, human opportunistic pathogens, and nonpathogenic isolates. Many plant pathogenic strains are known based on host plant specificity and the large number of plant species attacked. F. oxysporum is an opportunistic pathogen in humans with a compromised immune system. The objectives of this study were: (1) to develop a specific marker to detect human opportunistic F. oxysporum (HOFo) isolates; (2) to determine whether or not HOFo isolates can colonize and cause disease symptoms in plants; and (3) to assess Taiwan isolates sensitivity to two agro-fungicides. The primer pair, Primer 5/ST33-R, specifically amplifying Taiwan and international reference HOFo isolates was developed and used to detect and assess the distribution of a Taiwan isolate in inoculated tomato plants and tomato and cucumber fruit. Taiwan HOFo isolate MCC2074 was shown to colonize tomato roots, hypocotyls, and cotyledons, but did not show any visible symptoms. Four days after surface inoculation of tomato and cucumber fruit with the same isolate, MCC2074 was detected in the pericarp and locular cavities of both tomato and cucumber fruit and in columella of tomato fruit. Three Taiwan HOFo isolates were found to be moderately sensitive to azoxystrobin and highly sensitive to difenconazole.

Cytochrome b Mutations F129L and G143A Confer Resistance to Azoxystrobin in Cercospora nicotianae, the Frogeye Leaf Spot Pathogen of Tobacco

Azoxystrobin is the only synthetic, systemic fungicide labeled in the United States for management of frogeye leaf spot (FLS) of tobacco (Nicotiana tabacum L.), caused by Cercospora nicotianae. Though traditionally considered a minor disease in the United States, FLS has recently become yield and quality limiting. In 2016 and 2017, 100 C. nicotianae isolates were collected from symptomatic tobacco from eight counties in Kentucky, United States. Prior to azoxystrobin sensitivity testing, some C. nicotianae isolates were found to utilize the alternative oxidase pathway and, after assay comparisons, conidial germination was utilized to evaluate sensitivity in C. nicotianae as opposed to mycelial growth. Azoxystrobin sensitivity was determined by establishing the effective concentration to inhibit 50% conidial germination (EC50) for 47 (in 2016) and 53 (in 2017) C. nicotianae isolates. Distributions of C. nicotianae EC50 values indicated three qualitative levels of sensitivity to azoxystrobin. Partial cytochrome b sequence, encompassing the F129L and G143A mutation sites, indicated single-nucleotide polymorphisms (SNPs) conferring the F129L mutation in C. nicotianae of moderate resistance (azoxystrobin at 0.177 ≤ EC50 ≤ 0.535 µg/ml) and the G143A mutation in isolates with an azoxystrobin-resistant phenotype (azoxystrobin EC50 > 1.15 µg/ml). Higher frequencies of resistant isolates were identified from greenhouse transplant (4 of 17) and conventionally produced (58 of 62) tobacco samples, as compared with field-grown tobacco (<4 weeks prior to harvest; 4 of 62) or organically produced samples (1 of 7), respectively. Together, these results suggest that resistance to azoxystrobin in C. nicotianae occurs broadly in Kentucky, and generate new hypotheses about selection pressure affecting resistance mutation frequencies.

Fungal Evolution in Anthropogenic Environments: Botrytis cinerea Populations Infecting Small Fruit Hosts in the Pacific Northwest Rapidly Adapt to Human-Induced Selection Pressures

Many fungal pathogens have short generation times, large population sizes, and mixed reproductive systems, providing high potential to adapt to heterogeneous environments of agroecosystems. Such adaptation complicates disease management and threatens food production. A better understanding of pathogen population biology in such environments is important to reveal key aspects of adaptive divergence processes to allow improved disease management. Here, we studied how evolutionary forces shape population structure of Botrytis cinerea, the causal agent of gray mold, in the Pacific Northwest agroecosystems. Populations of B. cinerea from adjacent fields of small fruit hosts were characterized by combining neutral markers (microsatellites) with markers that directly respond to human-induced selection pressures (fungicide resistance). Populations were diverse, without evidence for recombination and association of pathogen genotype with host. Populations were highly localized with limited migration even among adjacent fields within a farm. A fungicide resistance marker revealed strong selection on population structure due to fungicide use. We found no association of resistance allele with genetic background, suggesting de novo development of fungicide resistance and frequent extinction/recolonization events by different genotypes rather than the spread of resistance alleles among fields via migration of a dominant genotype. Overall our results showed that in agroecosystems, B. cinerea populations respond strongly to selection by fungicide use with greater effect on population structure compared to adaptation to host plant species. This knowledge will be used to improve disease management by developing strategies that limit pathogen local adaptation to fungicides and other human-induced selection pressures present in Pacific Northwest agroecosystems and elsewhere.IMPORTANCE Agroecosystems represent an efficient model for studying fungal adaptation and evolution in anthropogenic environments. In this work, we studied what evolutionary forces shape populations of one of the most important fungal plant pathogens, B. cinerea, in small fruit agroecosystems of the Pacific Northwest. We hypothesized that host, geographic, and anthropogenic factors of agroecosystems structure B. cinerea populations. By combining neutral markers with markers that directly respond to human-induced selection pressures, we show that pathogen populations are highly localized and that selection pressure caused by fungicide use can have a greater effect on population structure than adaptation to host. Our results give a better understanding of population biology and evolution of this important plant pathogen in heterogeneous environments but also provide a practical framework for the development of efficient management strategies by limiting pathogen adaptation to fungicides and other human-induced selection pressures present in agroecosystems of the Pacific Northwest and elsewhere.

Widespread QoI Fungicide Resistance Revealed Among Corynespora cassiicola Tomato Isolates in Florida

Target spot of tomato caused by Corynespora cassiicola is one of the most economically destructive diseases of tomato in Florida. A collection of 123 isolates from eight counties in Florida were evaluated for sensitivity to azoxystrobin and fenamidone based on mycelial growth inhibition (MGI), spore germination (SG), detached leaflet assays (DLAs), and sequence-based analysis of the cytochrome b gene (cytb). Cleavage of cytb by restriction enzyme (Fnu4HI) revealed the presence of a mutation conferring a glycine (G) to alanine (A) mutation at amino acid position 143 (G143A) in approximately 90% of the population, correlating with quinone outside inhibitor (QoI) resistance based on MGI (<40% at 5 μg/ml), SG (<50% at 1 and 10 μg/ml), and DLA (<10% severity reduction). The mutation conferring a phenylalanine (F) to leucine (L) substitution at position 129 (F129L) was confirmed in moderately resistant isolates (#9, #19, and #74) based on MGI (40 to 50% at 5 μg/ml), SG (<50% at 1 μg/ml and >50% at 10 μg/ml), and DLA (>10% and <43% severity reduction) for both QoI fungicides, whereas sensitive isolates (#1, #4, #7, #28, #29, #46, #61, #74, #75, #76, #91, #95, and #118) based on MGI (>50% at 5 μg/ml), SG (>50% at 1 μg/ml and 10 μg/ml), and DLA (>50% severity reduction) correlated to non-mutation-containing isolates or those with a silent mutation. This study indicates that QoI resistance among C. cassiicola isolates from tomato is widespread in Florida and validates rapid screening methods using MGI or molecular assays to identify resistant isolates in future studies.

Emergence of Stemphylium Leaf Blight of Onion in New York Associated With Fungicide Resistance

A complex of foliar diseases affects onion production in New York, including Botrytis leaf blight (Botrytis squamosa), purple blotch (Alternaria porri), Stemphylium leaf blight (SLB; Stemphylium vesicarium), and downy mildew (Peronospora destructor). Surveys were conducted in 2015 and 2016 to evaluate the cause of severe premature foliar dieback in New York onion fields. SLB was the most prevalent disease among fields with the greatest incidence, surpassing downy mildew, purple blotch, and Botrytis leaf blight. Sequencing of the internal transcribed spacer region of ribosomal DNA and the glyceraldedyhe-3-phosphate dehydrogenase and calmodulin genes identified S. vesicarium as the species most commonly associated with SLB. S. vesicarium was typically associated with a broad range of necrotic symptoms but, most commonly, dieback of leaf tips and asymmetric lesions that often extended over the entire leaf. Because of the intensive use of fungicides for foliar disease control in onion crops in New York, the sensitivity of S. vesicarium populations to various fungicides with site-specific modes of action was evaluated. Sensitivity of S. vesicarium isolates collected in 2016 to the quinone outside inhibitor (QoI) fungicide, azoxystrobin, was tested using a conidial germination assay. Isolates representing a broad range of QoI sensitivities were selected for sequencing of the cytochrome b gene to evaluate the presence of point mutations associated with insensitivity to azoxystrobin. The G143A mutation was detected in all 74 S. vesicarium isolates with an azoxystrobin-insensitive phenotype (effective concentrations reducing conidial germination by 50%, EC₅₀ = 0.2 to 46.7 µg of active ingredient [a.i.]/ml) and was not detected in all 31 isolates with an azoxystrobin-sensitive phenotype (EC₅₀ = 0.01 to 0.16 µg a.i./ml). The G143A mutation was also associated with insensitivity to another QoI fungicide, pyraclostrobin. Sensitivity to other selected fungicides commonly used in onion production in New York was evaluated using a mycelial growth assay and identified isolates with insensitivity to boscalid, cyprodinil, and pyrimethanil, but not difenoconazole. The frequency of isolates sensitive to iprodione, fluxapyroxad, and fluopyram was high (93.5 to 93.6%). This article discusses the emergence of SLB as dominant in the foliar disease complex affecting onion in New York and the complexities of management posed by resistance to fungicides with different modes of action.

Polyphenols from Rheum Roots Inhibit Growth of Fungal and Oomycete Phytopathogens and Induce Plant Disease Resistance

A growing world population requires an increase in the quality and quantity of food production. However, field losses due to biotic stresses are currently estimated to be between 10 and 20% worldwide. The risk of resistance and strict pesticide legislation necessitate innovative agronomical practices to adequately protect crops in the future, such as the identification of new substances with novel modes of action. In the present study, liquid chromatography mass spectrometry was used to characterize Rheum rhabarbarum root extracts that were primarily composed of the stilbenes rhaponticin, desoxyrhaponticin, and resveratrol. Minor components were the flavonoids catechin, epicatechin gallate, and procyanidin B1. Specific polyphenolic mixtures inhibited mycelial growth of several phytopathogenic fungi and oomycetes. Foliar spray applications with fractions containing stilbenes and flavonoids inhibited spore germination of powdery mildew in Hordeum vulgare with indications of synergistic interactions. Formulated extracts led to a significant reduction in the incidence of brown rust in Triticum aestivum under field conditions. Arabidopsis thaliana mutant and quantitative reverse-transcription polymerase chain reaction studies suggested that the stilbenes induce salicylic acid-mediated resistance. Thus, the identified substances of Rheum roots represent an excellent source of antifungal agents that can be used in horticulture and agriculture.

Diversity in species composition and fungicide resistance profiles in Colletotrichum isolates from apples

Outbreaks of bitter rot were observed in three commercial apple orchards in Illinois despite best management efforts during the 2018 production season. Three isolates from symptomatic fruit from these orchards and two isolates from an orchard in South Carolina were identified to the species level using morphological tools and calmodulin, glyceraldehyde-3-phosphate dehydrogenase, and beta-tubulin gene sequences. The isolates from Illinois were identified as Colletotrichum siamense of the Colletotrichum gloeosporioides species complex and the ones from South Carolina as Colletotrichum fioriniae and Colletotrichum fructicola of the Colletotrichum acutatum and the C. gloeosporioides species complex, respectively. Two of the three C. siamense isolates from Illinois were resistant to azoxystrobin and thiophanate-methyl as determined in mycelial growth tests in vitro. EC₅₀ values were >100 μg/ml for both fungicides. One isolate was only resistant to azoxystrobin. None of the isolates from South Carolina was resistant to either of the two compounds. All five isolates were sensitive to fludioxonil (EC₅₀ values <0.1 μg/ml), propiconazole (EC₅₀ values ranged from 0.15 to 0.36 μg/ml), and benzovindiflupyr (EC₅₀ values ranged from <0.1 to 0.33 μg/ml). Resistance in C. siamense to azoxystrobin and thiophanate-methyl was confirmed in detached fruit studies using apples treated with label rates of registered product. Resistance to thiophanate-methyl in C. siamense was based on E198A mutation in b-tubulin gene, whereas resistance to azoxystrobin was based on G143A in cytochrome b (CYTB). One isolate resistant to azoxystrobin possessed no amino acid variation in CYTB. This study shows that quinone outside inhibitor fungicide resistance in Colletotrichum from apple has emerged and is being selected for in Illinois apple orchards by current spray strategies. Resistance monitoring may alert growers to potential threats, but the employment of molecular tools based on current knowledge of resistance mechanisms will provide incomplete results.

MoMCP1, a Cytochrome P450 Gene, Is Required for Alleviating Manganese Toxin Revealed by Transcriptomics Analysis in Magnaporthe oryzae

Manganese, as an essential trace element, participates in many physiological reactions by regulating Mn associated enzymes. Magnaporthe oryzae is a serious pathogen and causes destructive losses for rice production. We identified a cytochrome P450 gene, MoMCP1, involving the alleviation of manganese toxin and pathogenicity. To identify the underlying mechanisms, transcriptomics were performed. The results indicated that many pathogenicity related genes were regulated, especially hydrophobin related genes in ∆Momcp1. Furthermore, the Mn²⁺ toxicity decreased the expressions of genes involved in the oxidative phosphorylation and energy production, and increased the reactive oxygen species (ROS) levels, which might impair the functions of mitochondrion and vacuole, compromising the pathogenicity and development in ∆Momcp1. Additionally, our results provided further information about Mn associated the gene network for Mn metabolism in cells.

Natamycin, a New Biofungicide for Managing Crown Rot of Strawberry Caused by QoI-Resistant Colletotrichum acutatum

Anthracnose crown rot of strawberry, caused by Colletotrichum acutatum, is an important disease affecting California nursery and fruit production. Preplant dip treatments of transplants with fludioxonil-cyprodinil or azoxystrobin are industry standards for managing the disease and have been used extensively. Following reports of reduced efficacy of azoxystrobin in the field, high levels of quinone outside inhibitor (QoI) resistance were detected in California isolates of the pathogen. Resistance was associated with the G143A mutation in the cytochrome b gene, similar to a previous report from Florida, and there were no detected fitness penalties in pathogenicity or virulence. Therefore, several alternative fungicides were investigated in laboratory and field studies. Subsequently, the new biofungicide natamycin was identified. Baseline sensitivities of 74 isolates of C. acutatum to natamycin were determined to be unimodal, with a range from 0.526 to 1.996 μg/ml (mean 0.973 μg/ml). Although this toxicity was considerably lower than that of azoxystrobin (using sensitive isolates), fludioxonil, or cyprodinil, dip treatments of transplants with natamycin (at 500 or 1000 mg/liter) were highly effective. Disease severity and plant mortality in field studies with inoculated transplants were reduced to similarly low levels as treatments containing fludioxonil, whereas azoxystrobin failed in inoculations with QoI-resistant isolates of C. acutatum. Fruit yield was also significantly increased by natamycin as compared with the inoculated control. Differences in disease susceptibility were observed among cultivars evaluated, with Monterey and Portola more susceptible than Fronteras. Natamycin has a unique mode of action that is different from other fungicides registered on strawberry and, based on this research, was registered in the United States as a preplant, biofungicide dip treatment of strawberry transplants for management of anthracnose crown rot.

Meta-Analytic Modeling of the Decline in Performance of Fungicides for Managing Soybean Rust after a Decade of Use in Brazil

An apparent decline of fungicide performance for the control of soybean rust in Brazil has been reported but the rate at which it has occurred has not been formally quantified. Control efficacy and yield response to three fungicides applied as single active ingredients (a.i.)-azoxystrobin (AZOX), cyproconazole (CYPR), and tebuconazole (TEBU)-and four applied as mixtures-AZOX+CYPR, picoxystrobin + CYPR, pyraclostrobin + epoxiconazole, and trifloxystrobin + prothioconazole (TRIF+PROT)-were summarized using network meta-analytic models fitted to mean severity and yield data from 250 trials (10-year period). The effect of year was tested on both variables in a meta-regression model. Overall control efficacy ranged from 56 to 84%; the three single-a.i. fungicides performed the poorest (56 to 62%). Yield increase for single-a.i. fungicides was as low as 30% but ranged from 47 to 65% for the premixes. Significant declines in both variables were detected for all fungicides except TRIF+PROT. For TEBU, control efficacy (yield response) declined the most: 78% (18%) to 54% (8%) from 2004-05 to 2013-14. The recent surge of resistant populations of Phakopsora pachyrhizi to both demethylation inhibitor and quinone outside inhibitor fungicides is likely the driving force behind a significant decline after 4 years of fungicide use.

The mitochondrial genome of the plant-pathogenic fungus Stemphylium lycopersici uncovers a dynamic structure due to repetitive and mobile elements

Stemphylium lycopersici (Pleosporales) is a plant-pathogenic fungus that has been associated with a broad range of plant-hosts worldwide. It is one of the causative agents of gray leaf spot disease in tomato and pepper. The aim of this work was to characterize the mitochondrial genome of S. lycopersici CIDEFI-216, to use it to trace taxonomic relationships with other fungal taxa and to get insights into the evolutionary history of this phytopathogen. The complete mitochondrial genome was assembled into a circular double-stranded DNA molecule of 75,911 bp that harbors a set of 37 protein-coding genes, 2 rRNA genes (rns and rnl) and 28 tRNA genes, which are transcribed from both sense and antisense strands. Remarkably, its gene repertoire lacks both atp8 and atp9, contains a free-standing gene for the ribosomal protein S3 (rps3) and includes 13 genes with homing endonuclease domains that are mostly located within its 15 group I introns. Strikingly, subunits 1 and 2 of cytochrome oxidase are encoded by a single continuous open reading frame (ORF). A comparative mitogenomic analysis revealed the large extent of structural rearrangements among representatives of Pleosporales, showing the plasticity of their mitochondrial genomes. Finally, an exhaustive phylogenetic analysis of the subphylum Pezizomycotina based on mitochondrial data reconstructed their relationships in concordance with several studies based on nuclear data. This is the first report of a mitochondrial genome belonging to a representative of the family Pleosporaceae.

The Detection and Characterization of QoI-Resistant Didymella rabiei Causing Ascochyta Blight of Chickpea in Montana

Ascochyta blight (AB) of pulse crops (chickpea, field pea, and lentils) causes yield loss in Montana, where 1.2 million acres was planted to pulses in 2016. Pyraclostrobin and azoxystrobin, quinone outside inhibitor (QoI) fungicides, have been the choice of farmers for the management of AB in pulses. However, a G143A mutation in the cytochrome b gene has been reported to confer resistance to QoI fungicides. A total of 990 isolates of AB-causing fungi were isolated and screened for QoI resistance. Out of these, 10% were isolated from chickpea, 81% were isolated from field peas, and 9% isolated from lentil. These were from a survey of grower's fields and seed lots (chickpea = 17, field pea = 131, and lentil = 21) from 23 counties in Montana sent to the Regional Pulse Crop Diagnostic Laboratory, Bozeman, MT, United States for testing. Fungicide-resistant Didymella rabiei isolates were found in one chickpea seed lot each sent from Daniels, McCone and Valley Counties, MT, from seed produced in 2015 and 2016. Multiple alignment analysis of amino acid sequences showed a missense mutation that replaced the codon for amino acid 143 from GGT to GCT, introducing an amino acid change from glycine to alanine (G143A), which is reported to be associated with QoI resistance. Under greenhouse conditions, disease severity was significantly higher on pyraclostrobin-treated chickpea plants inoculated with QoI-resistant isolates of D. rabiei than sensitive isolates (p-value = 0.001). This indicates that where resistant isolates are located, fungicide failures may be observed in the field. D. rabiei-specific polymerase chain reaction primer sets and hydrolysis probes were developed to efficiently discriminate QoI- sensitive and - resistant isolates.

Reduced Sensitivity to Azoxystrobin of Monilinia fructicola Isolates From Brazilian Stone Fruits is Not Associated With Previously Described Mutations in the Cytochrome b Gene

Quinone-outside inhibitor (QoI) fungicides are effective tools for preharvest control of brown rot of stone fruit. These fungicides have a very specific site of action so the risk of resistance selection is high. The sensitivity of Monilinia fructicola (G. Winter) Honey isolates to azoxystrobin (QoI) was investigated in 143 isolates collected between 2002 and 2011 from four Brazilian states in orchards with different frequencies of fungicide use (0 to 6 fungicides sprays/season). Sensitivity of the isolates to azoxystrobin was determined in vitro, by inhibition of mycelial growth and spore germination on fungicide-amended media or ex vivo by pathogen inoculation in untreated or treated fruit with azoxystrobin. Potential mutations in codons 143, 137, and 129 of the cytochrome b (Cyt b) gene and the occurrence of an intron immediately after codon 143 were analyzed in a subpopulation of the isolates. The M. fructicola population of São Paulo State was less sensitive to the fungicide than the population from the states of Paraná, Santa Catarina, and Rio Grande do Sul. The low sensitivity of the isolates was confirmed also by comparing to the sensitivity of the baseline isolates. Mutations in G143A, F129L, and G137R in Cyt b gene were not found. In addition, 58 isolates tested showed an intron after codon 143 in Cyt b gene. Our results indicate that other mechanisms of selection for low sensitivity to QoI fungicides should be investigated.

Early Detection of Airborne Inoculum of Magnaporthe oryzae in Turfgrass Fields Using a Quantitative LAMP Assay

Gray leaf spot (GLS) is a destructive disease of perennial ryegrass caused by a host specific pathotype of the ascomycete Magnaporthe oryzae. Early diagnosis is crucial for effective disease management and the implementation of Integrated Pest Management practices. However, a rapid protocol for the detection of low levels of airborne inoculum is still missing. We developed a pathogen-specific quantitative loop-mediated isothermal amplification (qLAMP) assay coupled with a spore trap system for rapid detection and quantification of airborne inoculum of the M. oryzae perennial ryegrass pathotype, and tested its suitability for implementation in GLS-infected turfgrass fields. In summer 2015, two perennial ryegrass plots were artificially inoculated with the pathogen, with four continuously running custom impaction spore traps placed in each plot. Sampling units were replaced daily and tested with the developed qLAMP assay, while plots were monitored for symptom development. Results confirmed that the qLAMP assay-trap system was able to detect as few as 10 conidia up to 12 days before symptoms developed in the field. LAMP technology is particularly appropriate for field implementation by nontechnical users, and has the potential to be a powerful decision support tool to guide timing of fungicide applications for GLS management.

Resistance in Strawberry Isolates of Colletotrichum acutatum from Florida to Quinone-Outside Inhibitor Fungicides

Anthracnose fruit rot of strawberry, caused by Colletotrichum acutatum, is a major disease in Florida and frequent quinone-outside inhibitor (QoI) fungicide applications are needed for disease control. From 1994 to 2014, 181 C. acutatum isolates were collected from multiple strawberry fields in Florida with or without QoI spray history. Sensitivity to azoxystrobin and pyraclostrobin was tested based upon mycelial growth and germ tube elongation inhibition. Mean effective concentration where growth was reduced by 50% (EC₅₀) values for isolates collected prior to 2013 based upon mycelial growth were 0.22 and 0.013 μg/ml and upon germ tube elongation were 0.57 and 0.03 μg/ml for azoxystrobin and pyraclostrobin, respectively. Mycelial growth and germ tube elongation of 48 isolates collected in 2013 and 2014 were not inhibited with azoxystrobin at 3 μg/ml and pyraclostrobin at 0.110 μg/ml. A fungicide discriminatory dose assay indicated that 43 of the 48 isolates had EC₅₀ values higher than 100 and 10 μg/ml for azoxystrobin and pyraclostrobin, respectively. Azoxystrobin and pyraclostrobin sprayed preventively on strawberry fruit inoculated with C. acutatum failed to control resistant isolates. Sequencing of the cytochrome b gene of sensitive and resistant isolates showed that QoI-resistant isolates contained either G143A or F129L amino acid substitutions.