Multiple mutations across the succinate dehydrogenase gene complex are associated with boscalid resistance in Didymella tanaceti in pyrethrum

Evolution of the Genetic Structure of the Didymella tanaceti Population During Development of Succinate Dehydrogenase Inhibitor Resistance

Emergence of pathogens with decreased sensitivity to succinate dehydrogenase inhibitor fungicides is a global agronomical issue. Analysis of Didymella tanaceti isolates (n = 173), which cause tan spot of pyrethrum (Tanacetum cinerariifolium), collected prior to (2004 to 2005) and after (2009, 2010, 2012, and 2014) the commercial implementation of boscalid in Tasmanian pyrethrum fields identified that insensitivity developed over time and has become widespread. To evaluate temporal change, isolates were characterized for frequency of mutations in the succinate dehydrogenase (Sdh) B, C, and D subunits associated with boscalid resistance, mating type, and SSR genotype. All isolates from 2004 and 2005 exhibited wild-type (WT) Sdh alleles. Seven known Sdh substitutions were identified in isolates collected from 2009 to 2014. In 2009, 60.7% had Sdh substitutions associated with boscalid resistance in D. tanaceti. The frequency of WT isolates decreased over time, with no WT isolates identified in 2014. The frequency of the SdhB-H277Y genotype increased from 10.7 to 77.8% between 2009 and 2014. Genotypic evidence suggested that a shift in the population structure occurred between 2005 and 2009, with decreases in gene diversity (uh; 0.51 to 0.34), genotypic evenness (E5; 0.96 to 0.67), genotypic diversity (G; 9.3 to 6.8), and allele frequencies. No evidence was obtained to support the rapid spread of Sdh genotypes by clonal expansion of the population. Thus, insensitivity to boscalid has developed and become widespread within a diverse population within 4 years of usage. These results suggest that D. tanaceti can disperse insensitivity through repeated frequent mutation, sexual recombination, or a combination of both.

Cross-Resistance of Succinate Dehydrogenase Inhibitors (SDHI) in Botrytis cinerea and Development of Molecular Diagnostic Tools for SDHI Resistance Detection

Succinate dehydrogenase inhibitors (SDHIs) are keystone synthetic fungicides used to manage Botrytis cinerea in several hosts. In this study, we investigated the cross-resistance between five new SDHIs (pyraziflumid, isofetamid, benzovindiflupyr, fluxapyroxad, and pydiflumetofen) with commonly used SDHIs boscalid and fluopyram. Different mutations were detected in the sdhB gene in B. cinerea collected from Michigan grapes, and their frequency and EC50 value were determined. Among 216 B. cinerea boscalid-resistant isolates, five different mutations were detected, including H272R/Y, P225F/H, and N230I, at frequencies of 82.6, 4.3, 11.5, 0.4, and 5.3%, respectively. Five isolates of each genotype were used to screen the cross-resistance of the SDHIs. We classified the resistance profile of our mutants into five patterns. We report that all tested mutants were sensitive to benzovindiflupyr, indicating that it can be used as an effective fungicide against all B. cinerea mutants identified in this study. In addition, fluopyram, pydiflumetofen, and isofetamid can provide effective control according to which type of mutation is present in the field. We also developed and compared two molecular diagnostic tools, rhAMP and TaqMan assays, for rapid detection of SDHI resistance-associated mutants in B. cinerea. We report that the TaqMan assay was more successful than the rhAMP assay in detecting the B. cinerea mutant DNA at ≤10 pg and in a single assay was capable of monitoring two amino acid positions. Our results provide essential information about new SDHIs and provide molecular tools for monitoring SDHI resistance mutations, which will assist in gray mold disease control.

Risk Evaluation of Benzovindiflupyr Resistance of Verticillium dahliae Population in Maine

Verticillium dahliae causes Verticillium wilt, resulting in significant losses to potato production. Benzovindiflupyr, a succinate dehydrogenase inhibitor, effectively controls V. dahliae. However, frequent applications of the chemical may expedite the development of fungicide resistance in the pathogen population. To evaluate the risk of benzovindiflupyr resistance, 38 V. dahliae strains were obtained from diseased potatoes in Maine. The sensitivity of the field population was determined based on effective concentration for 50% inhibition (EC₅₀), which ranged from 0.07 to 11.28 μg ml^-1 with a median of 1.08. Segregated clusters of EC₅₀ values indicated that Maine V. dahliae populations have developed benzovindiflupyr resistance. By exposing conidia of V. dahliae to a high concentration of benzovindiflupyr, 18 benzovindiflupyr-resistant mutants were obtained. To examine their fitness, the mutants were continuously subculture-transferred for up to 10 generations. Mycelial growth, conidial production, competitiveness, pathogenicity, and cross resistance of the 10th generation mutants were examined. Results showed that 50% of the resistant mutants retained an adaptive level in mycelial growth, and 60% maintained conidial production similar to their parents. Pathogenicity did not change for any of the mutants. No cross resistance was detected between benzovindiflupyr and either azoxystrobin, boscalid, fluopyram, or pyrimethanil. Thus, the resistance risk in V. dahliae to benzovindiflupyr should be considered in Maine potato production.

Identification of Putative SDHI Target Site Mutations in the SDHB, SDHC, and SDHD Subunits of the Grape Powdery Mildew Pathogen Erysiphe necator

Succinate dehydrogenase inhibitors (SDHIs) are fungicides used in control of numerous fungal plant pathogens, including Erysiphe necator, the causal agent of grapevine powdery mildew (GPM). Here, the sdhb, sdhc, and sdhd genes of E. necator were screened for mutations that may be associated with SDHI resistance. GPM samples were collected from 2017 to 2020 from the U.S. states of California, Oregon, Washington, and Michigan, and the Canadian province of British Columbia. Forty-five polymorphisms were identified in the three sdh genes, 17 of which caused missense mutations. Of these, the SDHC-p.I244V substitution was shown in this study to reduce sensitivity of E. necator to boscalid and fluopyram, whereas the SDHC-p.G25R substitution did not affect SDHI sensitivity. Of the other 15 missense mutations, the SDHC-p.H242R substitution was shown in previous studies to reduce sensitivity of E. necator toward boscalid, whereas the equivalents of the SDHB-p.H242L, SDHC-p.A83V, and SDHD-p.I71F substitutions were shown to reduce sensitivity to SDHIs in other fungi. Generally, only a single amino acid substitution was present in the SDHB, SDHC, or SDHD subunit of E. necator isolates, but missense mutations putatively associated with SDHI resistance were widely distributed in the sampled areas and increased in frequency over time. Finally, isolates that had decreased sensitivity to boscalid or fluopyram were identified but with no or only the SDHC-p.G25R amino acid substitution present in SDHB, SDHC, and SDHD subunits. This suggests that target site mutations probably are not the only mechanism conferring resistance to SDHIs in E. necator.

SDH mutations confer complex cross-resistance patterns to SDHIs in Corynespora cassiicola

Succinate dehydrogenase inhibitors (SDHIs) are one of the most frequently used fungicides in cucumber fields in China. Our previous studies indicated that the sensitivity profile of Corynespora cassiicola, the causal agent of Corynespora leaf spot, to different SDHIs varied greatly; however, the underlying mechanism remains unclear. The 50% effective concentration (EC₅₀) values of boscalid, fluopyram, fluxapyroxad and isopyrazam in C. cassiicola collected from 2017 to 2020 shifted, with resistance frequencies of 79.83%, 78.43%, 83.19% and 49.86%, respectively. The sequence alignment of sdhB/C/D of resistant strains revealed that eight single amino acid mutations (B-H278Y/L, B-I280V, C-S73P, C-N75S, C-H134R, D-D95E and D-G109V), and three dual-mutations (B-I280V&C-S73P, B-I280V&C-N75S and C-S73P&C-N75S) conferred various SDHI resistance levels and cross-resistance profiles. The expression level of the sdhB/C/D gene and succinate dehydrogenase (SDH) activity in the mutants were significantly altered by the presence of SDHIs, compared with the wild type strain. Additionally, molecular docking results suggested that the missense mutation influenced the crystal structure of SDH and subsequently interfered with the interaction bonds and bond distances among the target protein and chemicals. In brief, amino acid mutations altered the fungicide response of target gene expression, SDH activity and the binding features of SDH-ligand complexes and subsequently conferred multiple resistance levels and complex cross-resistance patterns to SDHIs in C. cassiicola. The evaluation of C. cassiicola resistance to SDHIs provided a significant foundation for efficient chemical development and integrated CLS management strategies.

Mutations in Sdh Gene Subunits Confer Different Cross-Resistance Patterns to SDHI Fungicides in Alternaria alternata Causing Alternaria Leaf Spot of Almond in California

Alternaria leaf spot caused by Alternaria alternata and A. arborescens is a common disease of almond in California. Succinate dehydrogenase inhibitors (SDHIs) are widely used for its management; however, we observed reduced performance of SDHI fungicides at some field sites. Thus, we evaluated the sensitivity to boscalid of 520 isolates of the main pathogen A. alternata collected from major production areas between 2006 and 2019, and also evaluated the sensitivity of a subset of 204 isolates to six members of the SDHIs belonging to six subgroups. Additionally, 97 isolates (14 sensitive and 83 with reduced sensitivity) of the 204 were used to determine the molecular mechanisms of resistance. A wide range of in vitro concentrations to effectively inhibit mycelial growth by 50% (EC₅₀ values) was determined for each fungicide using the spiral gradient dilution method. Some isolates were highly resistant (EC₅₀ values >10 μg/ml) to boscalid (a pyridine-carboxamide), pyraziflumid (a pyrazine-carboxamide), and fluxapyroxad (a pyrazole-4-carboxamide), but not to fluopyram (a pyridinyl-ethyl-benzamide), isofetamid (a phenyl-oxo-ethyl thiophene amide), and pydiflumetofen (a N-methoxy-(phenyl-ethyl)-pyrazole-carboxamide). There was no strong cross resistance among the fungicides tested, including for the two pyrazole-4-carboxamides fluxapyroxad and penthiopyrad (tested for 33 of the 204 isolates). The comparison of EC₅₀ values for fluopyram and isofetamid resulted in the highest coefficient of determination (R² = 0.582) among 10 pairwise comparisons between subgroups. Sequence analyses of the 97 isolates revealed five mutations in SdhB, SdhC, or SdhD subunits of the Sdh target gene among 73 isolates with reduced sensitivity to at least one SDHI. No mutations were detected in the 14 sensitive isolates and in 10 of the 83 isolates with reduced sensitivity. The most common mutation (59 isolates) was H134R in SdhC. Other mutations included H277Y (eight isolates) and H277L (two isolates) in SdhB, as well as G79R (two isolates) and S135R (two isolates) in SdhC. Mutations H277Y in SdhB and S135R in SdhC were only present in isolates collected in 2012 or earlier. Both conferred mostly high levels of resistance to boscalid and also reduced sensitivity to pyraziflumid, fluxapyroxad, and isofetamid with intermediate EC₅₀ levels. Mutations H277L in SdhB, as well as H134R and G79R in SdhC, found in isolates obtained after 2012 had very similar resistance phenotypes with different levels of resistance to boscalid, pyraziflumid, and fluxapyroxad, whereas sensitivity to fluopyram, isofetamid, and pydiflumetofen was mostly less affected. Our data for SDHI fungicides do not support the classical concept of positive cross resistance within a single mode of action. Because some mutations conferred resistance to multiple SDHI subgroups, however, resistance management needs to consider all SDHIs as a homogenous group that should be mixed or rotated with other modes of action to delay development of resistance.

Sensitivity assessment and SDHC-I86F mutation frequency of Phakopsora pachyrhizi populations to benzovindiflupyr and fluxapyroxad fungicides from 2015 to 2019 in Brazil

BACKGROUND

Fungicides of the succinate dehydrogenase inhibitors (SDHIs) group have been used in soybean to control Asian soybean rust (ASR) caused by Phakopsora pachyrhizi. Fungal populations with less sensitivity to SDHI fungicides have been reported since 2015.

RESULTS

In this study, fungal sensitivity to benzovindiflupyr (BZV) and fluxapyroxad (FXD) was assessed using a total of 770 P. pachyrhizi populations sampled over four soybean growing seasons. Cross-resistance, intrinsic activity, and frequency of SDHC-I86F mutation were also analyzed. The average effective concentration to inhibit 50% (EC₅₀ ) and SDHC-I86F frequency increased over the 2015/2016, 2016/2017, 2017/2018 and 2018/2019 soybean-seasons. Fourteen P. pachyrhizi populations had the EC₅₀ value above 10 mg L^-1 for both carboxamides. No difference was found in intrinsic active to BZV and FXD fungicides for sensitive P. pachyrhizi populations. For P. pachyrhizi classified as less sensitive BZV showed the highest fungitoxicity effect. High frequency of the C-I86F mutation was observed in samples collected in volunteer soybean plants. The maximum frequency of SDHC-I86F mutation in the population was 50% and resulting in ASR populations with low sensitivity to SDHIs. A low correlation between bioassay and SDHC-I86F mutation was observed possible due to the dikaryotic nature of rust fungi or other mutations in the other succinate dehydrogenase subunits.

CONCLUSION

The present work provides an overview of a large sampling size of P. pachyrhizi populations and their performance over the four crop seasons. The high frequency of SDHC-I86F mutation and low sensitivity to SDHIs are widely distributed in the main soybean growing regions in Brazil and present in volunteer plants in the soybean-free period. Further detailed studies are needed to identify novel point mutations affecting the effectiveness of SDHIs. © 2021 Society of Chemical Industry.

Beyond Sea Turtles: Fusarium keratoplasticum in Eggshells of Podocnemis unifilis, a Threatened Amazonian Freshwater Turtle

The endangered yellow-spotted river turtle (Podocnemis unifilis) has experienced a dramatic population decline in the Ecuadorian Amazonia, mainly due to overexploitation of its eggs. To reverse this trend, the Wildlife Conservation Society has developed a head-start program in Yasuní National Park since 2008, but the potential risk that microbes associated with its eggs might represent for hatching success has not been evaluated yet. Members of the Fusarium solani species complex (FSSC) are involved in egg failure in sea turtles under natural and hatchery conditions, but their role in infecting the eggs of P. unifilis is unknown. In this study, we collected eggshells of P. unifilis and obtained 50 fungal and bacterial isolates. Some potentially pathogenic fungi of the genera Fusarium, Penicillium and Rhizopus were identified based on molecular data. Most importantly, the sea turtle pathogenic species F. keratoplasticum not only was present, but it was the most frequently found. Conversely, we have also isolated other microorganisms, such as Pseudomonas or Phoma-like species, producing a wide spectrum of antifungal compounds that may have a protective role against fungal diseases. Our survey provides useful information on potential pathogens found in P. unifilis eggshells, upon which the success of conservation programs may depend.

No Evidence of Resistance to Trifloxystrobin, Triflumizole, and Boscalid in Podosphaera leucotricha Isolates From U.S. Commercial Apple Orchards

Apple powdery mildew, caused by Podosphaera leucotricha, continues to be a challenge in commercial apple orchards in the U.S. Pacific Northwest and worldwide. In this study, P. leucotricha isolates were collected in 2018 and 2019 from two organic (baseline) and eight conventional (exposed) apple orchards in Washington, New York, and Virginia, and assessed for their sensitivity to trifloxystrobin (TRI, n = 232), triflumizole (TFZ, n = 217), and boscalid (BOS, n = 240) using a detached leaf assay. Effective concentrations inhibiting 50% growth (EC₅₀) were not significantly different between baseline and exposed isolates, and ranged from 0.001 to 0.105, 0.09 to 6.31, and 0.05 to 2.18 µg/ml, for TRI, TFZ, and BOS, respectively. Reduction in sensitivity by factors of 105, 63, and 22 to TRI, TFZ, and BOS, respectively, were observed in some isolates, but all isolates were controlled by the commercial label rates of the three fungicides on detached leaves. Sequencing of the cytochrome b (cytb), cytochrome P450 sterol 14α-demethylase (CYP51), and the iron-sulfur protein subunit (SdhB) genes in isolates with high EC₅₀ revealed no mutation previously reported to confer resistance to these fungicides in other fungi, and presence of a group I intron after codon 143 in the cytb gene. Significant (P < 0.001) moderate positive correlations (r = 0.38) observed between sensitivity to TRI and TFZ warrant continuous rotations of fungicides with different modes of action in conventional orchards. The established baseline sensitivities and the molecular markers will help in selecting discriminatory doses and bypassing the challenging in vivo testing for future sensitivity monitoring in P. leucotricha.

Resistance to succinate dehydrogenase inhibitors in field isolates of Podosphaera xanthii on cucumber: Monitoring, cross-resistance patterns and molecular characterization

New succinate dehydrogenase inhibitor fungicides (SDHIs), isopyrazam, pyraziflumid and isofetamid were introduced in the Japanese market in 2017-2018 to control powdery mildew on cucumber. SDHI resistance of the disease fungus (Podosphaera xanthii) was first reported during 2008-2009 against boscalid. Then, penthiopyrad which belongs to SDHIs was introduced in 2010, but subsequent monitoring study was not performed. We investigated the sensitivity of P. xanthii field isolates from Ibaraki Prefecture, Japan, to SDHIs and SdhB, SdhC and SdhD gene mutations, using a leaf disc assay and SDH gene analysis. A total of 19 out of the 22 selected isolates showed resistance to SDHIs. The 19 isolates were phenotypically categorized into three types: Resistant I as moderately and Resistant II as highly resistant to penthiopyrad, isopyrazam and pyraziflumid but sensitive to isofetamid and Resistant III as highly resistant to isofetamid but sensitive to the other three SDHIs. SDH gene analysis revealed that Resistant I and III isolates carried a substitution in PxD-S121P and PxC-A86V, respectively. Resistant II carried three different substitutions: PxC-G151R, PxC-G172D, and PxD-H137R. Among 127 isolates sampled from 16 cucumber greenhouses, 54 exhibited Resistant I phenotype and carried only PxD-S121P. Fifty-six isolates exhibited Resistant II and carried PxC-G151R (four isolates), PxC-G172D (24), and PxD-H137R (28). Only two isolates expressed the Resistant III phenotype carrying PxC-A86V. To the best of our knowledge, this is the first report demonstrating cross-resistance patterns and the molecular characterization of SDHIs in P. xanthii.

Occurrence and Extent of Boscalid Resistance in Populations of Alternaria alternata from California Pistachio Orchards

Alternaria late blight (ALB) caused by Alternaria spp. is an annual disease problem in California pistachio and requires repeated applications of fungicides to prevent significant losses of pistachio foliage and nut quality. From 2003 onward, the succinate dehydrogenase inhibiting fungicide boscalid has played a key role in ALB management. The development of boscalid resistance in A. alternata populations was monitored from 2005 to 2012 in pistachio producing areas in California. A total of 1,765 single-spore isolates, collected from commercial and experimental pistachio orchards with or without a history of boscalid exposure, were tested in a radial growth assay in agar media amended with the discriminatory dose of 10 µg/ml of boscalid. The frequency of boscalid-resistant isolates in 2005 was 12% but increased significantly and remained stable toward the end of the survey period. Most of the resistant isolates exhibited a high level of resistance (R) to boscalid with percent of mycelial growth inhibition (PGI) values between 0 and 50%, whereas significantly fewer isolates had an intermediate level (IR) of resistance (50 < PGI < 75%). The frequency of sensitive (S) isolates (75 < PGI < 100%) was generally the highest in orchards with no history of boscalid usage, whereas mean incidences of boscalid-resistant populations of Alternaria were 81, 92.4, 80.2, and 98%, in 2006, 2007, 2011, and 2012, respectively, in orchards that received a high number (at least three per season) of boscalid spray applications. In comparison, none to relatively low frequencies (0 to 12%) of resistance were observed in populations with no or limited exposure to Pristine, suggesting an air-movement of resistant spores through wind from treated to nontreated areas. In 2012, boscalid-resistant isolates were found practically in every sampled location in all counties, with the orchards in Fresno, Madera, Tulare, and King Counties being the locations with the highest frequencies of resistance (100%). Monitoring of A. alternata AaSDHB, AaSDHC, and AaSDHD mutations in 286 boscalid-resistant phenotypes identified 11 mutations, leading to amino acid substitutions in AaSDHB (seven mutations: H277Y/R/L, P230A/R, N235D/T), AaSDHC (one mutation: H134R), and AaSDHD (three mutations: D123E, H133R/P), with AaSDHB mutations being the most prevalent (80%) ones throughout the survey period. The majority of isolates carrying these mutations exhibited the R phenotype toward boscalid. The increased prevalence of boscalid resistance in populations of A. alternata is a likely contributing factor to the inability of pistachio farmers to successfully control ALB with Pristine. Other factors implicated in the rapid and widespread occurrence of A. alternata boscalid-resistant populations in California pistachios are further discussed.