Spatial and Temporal Sensitivity of Alternaria Species Associated With Potato Foliar Diseases to Demethylation Inhibiting and Anilino-Pyrimidine Fungicides

A Novel Strain of Fusarium oxysporum Alternavirus 1 Isolated from Fusarium oxysporum f. sp. melonis Strain T-BJ17 Confers Hypovirulence and Increases the Sensitivity of Its Host Fungus to Difenoconazole and Pydiflumetofen

In the current study, a novel strain of Fusarium oxysporum alternavirus 1 (FoAV1) was identified from the Fusarium oxysporum f. sp. melonis (FOM) strain T-BJ17 and was designated as Fusarium oxysporum alternavirus 1-FOM (FoAV1-FOM). Its genome consists of four dsRNA segments of 3515 bp (dsRNA1), 2663 bp (dsRNA2), 2368 bp (dsRNA3), and 1776 bp (dsRNA4) in length. Open reading frame 1 (ORF1) in dsRNA1 was found to encode a putative RNA-dependent RNA polymerase (RdRp), whose amino acid sequence was 99.02% identical to that of its counterpart in FoAV1; while ORF2 in dsRNA2, ORF3 in dsRNA3, and ORF4 in dsRNA4 were all found to encode hypothetical proteins. Strain T-BJ17-VF, which was verified to FoAV1-FOM-free, was obtained using single-hyphal-tip culture combined with high-temperature treatment to eliminate FoAV1-FOM from strain T-BJ17. The colony growth rate, ability to produce spores, and virulence of strain T-BJ17 were significantly lower than those of T-BJ17-VF, while the dry weight of the mycelial biomass and the sensitivity to difenoconazole and pydiflumetofen of strain T-BJ17 were greater than those of T-BJ17-VF. FoAV1-FOM was capable of 100% vertical transmission via spores. To our knowledge, this is the first time that an alternavirus has infected FOM, and this is the first report of hypovirulence and increased sensitivity to difenoconazole and pydiflumetofen induced by FoAV1-FOM infection in FOM.

Inhibitory Effects of Endemic Thyme's Thymol-Carvacrol Chemotype Essential Oil on Aspergillus Species with Free Radical Scavenging Properties

There is a burgeoning focus on utilizing the antifungal and antioxidant properties of essential oils derived from various plants as a modern and natural approach to combat the growth of fungi that contaminate food. In this study, we used essential oils extracted from Thymus daenensis Celak. subsp. daenensis to address three mycotoxin-producing species of Aspergillus, specifically A. flavus, A. parasiticus, and A. niger, all of which are recognized contaminants of food and agricultural products. Concurrently, the antioxidant properties of the essential oils were evaluated, revealing their noteworthy role in the antifungal activity. Essential oils were derived from T. daenensis subsp. daenensis was observed to have a significant inhibitory effect on all three species of Aspergillus, as evidenced by the minimum inhibitory concentration (MIC) ranging from 575 to 707 ppm and the half-maximal inhibitory concentration (IC50) ranging from 237 to 280 ppm. These results confirm the strong antifungal activity of the essential oils. Furthermore, the essential oil exhibited free radical scavenging activity, resulting in an EC50 value of 37.1 μg/ml. In summary, T. daenensis subsp. daenensis essential oil demonstrated a competitive advantage over other similar plants and synthetic antibiotics. This indicates the promising potential of this essential oil as a natural antifungal agent to control Aspergillus growth and mycotoxin contamination. It offers an alternative or complementary approach to conventional antifungal agents and could be a valuable addition to the arsenal of natural remedies to address fungal contamination in food and agricultural products.

A Novel Strain of Fusarium oxysporum Virus 1 Isolated from Fusarium oxysporum f. sp. niveum Strain X-GS16 Influences Phenotypes of F. oxysporum Strain HB-TS-YT-1hyg

A novel strain of Fusarium oxysporum virus 1 (FoV1) was identified from the Fusarium oxysporum f. sp. niveum strain X-GS16 and designated as Fusarium oxysporum virus 1-FON (FoV1-FON). The full genome of FoV1-FON is 2902 bp in length and contains two non-overlapping open reading frames (ORFs), ORF1 and ORF2, encoding a protein with an unknown function (containing a typical -1 slippery motif G_GAU_UUU at the 3'-end) and a putative RNA-dependent RNA polymerase (RdRp), respectively. BLASTx search against the National Center for the Biotechnology Information (NCBI) non-redundant database showed that FoV1-FON had the highest identity (97.46%) with FoV1. Phylogenetic analysis further confirmed that FoV1-FON clustered with FoV1 in the proposed genus Unirnavirus. FoV1-FON could vertically transmit via spores. Moreover, FoV1-FON was transmitted horizontally from the F. oxysporum f. sp. niveum strain X-GS16 to the F. oxysporum strain HB-TS-YT-1hyg. This resulted in the acquisition of the F. oxysporum strain HB-TS-YT-1hyg-V carrying FoV1-FON. No significant differences were observed in the sporulation and dry weight of mycelial biomass between HB-TS-YT-1hyg and HB-TS-YT-1hyg-V. FoV1-FON infection significantly increased the mycelial growth of HB-TS-YT-1hyg, but decreased its virulence to potato tubers and sensitivity to difenoconazole, prochloraz, and pydiflumetofen. To our knowledge, this is the first report of hypovirulence and reduced sensitivity to difenoconazole, prochloraz, and pydiflumetofen in F. oxysporum due to FoV1-FON infection.

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.

A Botybirnavirus Isolated from Alternaria tenuissima Confers Hypervirulence and Decreased Sensitivity of Its Host Fungus to Difenoconazole

Alternaria alternata botybirnavirus 1 (AaBRV1) was isolated from a strain of Alternaria alternata, causing watermelon leaf blight in our previous research. The effect of AaBRV1 on the phenotype of its host fungus, however, was not determined. In the present study, a novel strain of AaBRV1 was identified in A. tenuissima strain TJ-NH-51S-4, the causal agent of cotton Alternaria leaf spot, and designated as AaBRV1-AT1. A mycovirus AaBRV1-AT1-free strain TJ-NH-51S-4-VF was obtained by protoplast regeneration, which eliminated AaBRV1-AT1 from the mycovirus AaBRV1-AT1-infected strain TJ-NH-51S-4. Colony growth rate, spore production, and virulence of strain TJ-NH-51S-4 were greater than they were in TJ-NH-51S-4-VF, while the sensitivity of strain TJ-NH-51S-4 to difenoconazole, as measured by the EC50, was lower. AaBRV1-AT1 was capable of vertical transmission via asexual spores and horizontal transmission from strain TJ-NH-51S-4 to strain XJ-BZ-5-1hyg (another strain of A. tenuissima) through hyphal contact in pairing cultures. A total of 613 differentially expressed genes (DEGs) were identified in a comparative transcriptome analysis between TJ-NH-51S-4 and TJ-NH-51S-4-VF. Relative to strain TJ-NH-51S-4-VF, the number of up-regulated and down-regulated DEGs in strain TJ-NH-51S-4 was 286 and 327, respectively. Notably, the expression level of one DEG-encoding cytochrome P450 sterol 14α-demethylase and four DEGs encoding siderophore iron transporters were significantly up-regulated. To our knowledge, this is the first documentation of hypervirulence and reduced sensitivity to difenoconazole induced by AaBRV1-AT1 infection in A. tenuissima.

Aggressiveness of Small-Spored Alternaria spp. and Their Sensitivity to Succinate Dehydrogenase Inhibitor Fungicides

Brown leaf spot of potato is caused by a number of small-spored Alternaria spp. Alternaria alternata sensu stricto, A. arborescens, and A. tenuissima have been reported with increasing frequency in commercial potato fields. Potato cultivars with resistance to small-spored Alternaria spp. have yet to be developed; therefore, the application of foliar fungicides is a primary management strategy. Greenhouse inoculation assays demonstrated that isolates of these three small-spored Alternaria spp. were pathogenic. Significant differences in aggressiveness were observed across isolates; however, there was no trend in aggressiveness based on species. Significant fungicide by isolate interactions in in vitro fungicide sensitivity and significant differences between baseline and nonbaseline isolates were observed in all three small-spored Alternaria spp. The ranges of in vitro sensitivity of A. alternata baseline isolates to boscalid (EC₅₀ <0.010 to 0.89 µg/ml), fluopyram (<0.010 to 1.14 µg/ml) and solatenol (<0.010 to 1.14 µg/ml) were relatively wide when compared with adepidyn (<0.010 to 0.023 µg/ml). The baseline sensitivities of A. arborescens and A. tenuissima isolates to all four fungicides were <0.065 µg/ml. Between 10 and 21% of nonbaseline A. alternata isolates fell outside the baseline range established for the four succinate dehydrogenase inhibitor (SDHI) fungicides evaluated. In A. arborescens, 10 to 80% of nonbaseline isolates had higher sensitivities than the baseline. A. tenuissima isolates fell outside the baseline for boscalid (55%), fluopyram (14%), and solatenol (14%), but none fell outside the baseline range for adepidyn. Evaluations of in vivo fungicide efficacy demonstrated that most isolates were equally controlled by the four SDHI fungicides. However, reduced boscalid efficacy was observed for four isolates (two each of A. arborescens and A. tenuissima) and reduced fluopyram control was observed in one A. alternata isolate. Results of these studies demonstrate that isolates of all three species could be contributing to the brown leaf spot pathogen complex and that monitoring both species diversity and fungicide sensitivity could be advantageous for the management of brown leaf spot in potatoes with SDHI fungicides.

Genetic Structure and Triazole Antifungal Susceptibilities of Alternaria alternata from Greenhouses in Kunming, China

Alternaria alternata is an opportunistic human fungal pathogen and a ubiquitous phytopathogen capable of causing diseases to >100 agricultural crops and ornamental plants. To control plant diseases caused by A. alternata, triazole fungicides have been widely used both in open crop and vegetable fields and in indoor growth facilities such as greenhouses. At present, the effect of fungicide use on triazole resistance development in A. alternata populations is not known. Here, we isolated 237 A. alternata strains from nine greenhouses around metropolitan Kunming in Yunnan, southwest China, determined their genotypes using 10 short tandem repeat markers, and quantified their susceptibility to four triazoles (difenoconazole, tebuconazole, itraconazole, and voriconazole). Abundant allelic and genotypic diversities were detected among these A. alternata strains. Significantly, over 17% of the strains were resistant to difenoconazole, and both known and new drug-resistance mutations were found in the triazole target gene cyp51. Our findings of high-level genetic variation of A. alternata in greenhouses coupled with high-frequency fungicide resistance call for greater attention to continued monitoring and to developing alternative plant fungal disease management strategies in greenhouses. IMPORTANCE Alternaria alternata is among the most common fungi in our environments, such as indoor facilities, the soil, and outdoor air. It can cause diseases in >100 crop and ornamental plants. Furthermore, it can cause human infections. However, our understanding of its genetic diversity and antifungal susceptibility is very limited. Indeed, the critical threshold values for resistance have not been defined for most antifungal drugs in this species. Greenhouses are known to have heavy applications of agricultural fungicides. In this study, we analyzed strains of A. alternata from nine greenhouses near metropolitan Kunming in southwestern China. Our study revealed very high genetic diversity and identified strains with high MIC values against two agricultural and two medical triazole antifungals within each of the nine greenhouses. Our study calls for greater attention to this emerging threat to food security and human health.

Fungicide Resistance in Alternaria alternata from Blueberry in California and Its Impact on Control of Alternaria Rot

Alternaria rot caused by Alternaria alternata is one of the major postharvest diseases affecting blueberries in California. The sensitivity profiles of A. alternata from blueberry field to quinone outside inhibitors (QoIs), boscalid, fluopyram, fludioxonil, cyprodinil, and polyoxin D in California were examined in this study. EC₅₀ values of 51 A. alternata isolates for boscalid varied greatly among the isolates, ranging from 0.265 to >100 μg/ml. EC₅₀ values of 51 A. alternata isolates to fluopyram, fludioxonil, cyprodinil, and polyoxin D were 5.188 ± 7.118, 0.078 ± 0.021, 0.465 ± 0.302, and 6.238 ± 7.352 μg/ml, respectively. In total, 143 isolates were screened for resistance at 5 and 10 μg/ml for fludioxonil, cyprodinil, and fluopyram, 10 μg/ml for polyoxin D, and 10 and 50 μg/ml for boscalid. Based on the published discriminatory concentrations for phenotyping resistance, of the 143 isolates, all were considered resistant to boscalid; 32, 69, and 42 were sensitive, low resistant, and resistant to fluopyram, respectively; and all were sensitive to fludioxonil and cyprodinil. In a PCR-restriction fragment length polymorphism method for phenotyping, 60 out of the 143 isolates were classified as resistant to QoIs. Control tests on detached blueberry fruit inoculated with different Alternaria isolates showed that fludioxonil and cyprodinil significantly reduced disease incidence and severity; however, pyraclostrobin, boscalid, fluopyram, and polyoxin D significantly reduced only disease severity. The obtained results will be helpful in making decisions on fungicide programs to control A. alternata isolates with resistance or reduced sensitivities to multiple fungicides.

Detection and Biological Characteristics of Alternaria alternata Resistant to Difenoconazole from Paris polyphylla var. chinensis, an Indigenous Medicinal Herb

Black spot caused by Alternaria alternata (BSAA) is one of the most common diseases of Paris polyphylla var. chinensis, causing yield losses in China. Demethylation inhibitors (DMIs) have been used to control this disease in China for decades. Some farmers have complained about the decreased efficacy of DMIs against BSAA. The objective of this study was to detect and characterize the resistance of A. alternata against difenoconazole from P. polyphylla var. chinensis during 2018. Of the 22 isolates of A. alternata obtained from Sichuan Province in the southwest of China, 20 were resistant to difenoconazole. Mycelial growth rates and sporulation of the difenoconazole-resistant (Dfn^R) isolates were not different from those of the difenoconazole-sensitive (Dfn^S) isolates. No cross resistance between difenoconazole and tebuconazole or propiconazole was observed. Mutations were identified at gene AaCYP51 of Dfn^R isolates based on the sequence alignment of the Dfn^R and Dfn^S isolates. All of the mutations could be divided into three resistant genotypes, I (K715R + Y781C), II (K715R + D1140G + T1628A), and III (no mutation). The docking total score of the Dfn^S isolates was 5.6020, higher than the resistant genotype I (4.4599) or the resistant genotype II (3.8651), suggesting that the DMI resistance of A. alternata may be caused by the decreased affinity between AaCYP51 and difenoconazole.

Enantioselective effects of the fungicide metconazole on photosynthetic activity in Microcystis flos-aquae

Enantiomers of chiral fungicides usually display different toxic effects on nontarget organisms in the surrounding environment, although there are rare reports on the enantioselective toxicity of metconazole (MEZ) to aquatic organisms, such as Microcystis flos-aquae (M. flos-aquae). To explore the enantioselective toxicity of MEZ in algae, the impact of various concentrations (0.001, 0.003, 0.01, 0.03 and 0.1 mg/L) of MEZ on M. flos-aquae over 8 days was investigated. Significant differences were observed between the four enantiomers in chlorophyll a (Chl a) contents, carotenoids, photochemical efficiency (F_v/F_m), rapid light-response curves (RLCs), utilization efficiency of light energy (α) and protein contents during treatment time. MEZ can enantioselectively stimulate the chlorophyll fluorescence parameters (RLCs, F_v/F_m and α) and carotenoid and Chl a contents of M. flos-aquae, especially at low concentrations (0.001 or 0.003 mg/L). At high concentrations of 0.03 or 0.1 mg/L, the chlorophyll fluorescence parameters (RLCs, F_v/F_m and α), protein and Chl a contents of M. flos-aquae exposed to cis-enantiomers were lower than those of M. flos-aquae exposed to trans-enantiomers. These observations indicated that the enantiomers of MEZ pose different toxicities to M. flos-aquae, with the cis-enantiomers more toxic than the trans-enantiomers. These results are beneficial for understanding the enantioselective effects of MEZ enantiomers on nontarget organisms and helpful for evaluating their eco-environment risk.

Evaluation of the antifungal and biochemical activities of mefentrifluconazole against Botrytis cinerea

Mefentrifluconazole is the first product of a new sub-class of triazoles fungicides, i.e., the isopropanol triazoles, with the broad spectrum and high activity. In this study, the potential and biochemical activities of mefentrifluconazole against Botrytis cinerea were investigated. The frequency distribution of all EC₅₀ values of mefentrifluconazole against mycelial growth and germ tube elongation of 106 isolates formed unimodal curve, with the mean EC₅₀ values of 0.124 ± 0.025 and 0.015 ± 0.008 μg/mL, respectively. The effect of mefentrifluconazole against gray mold was determined on detached leaves of cucumber in vivo, the treatment of mefentrifluconazole at 200 μg/mL provided 100% preventative efficacy and 72.7% curative efficacy. No evident correlation was detected between the sensitivity of B. cinerea to mefentrifluconazole and that to tebuconazole, difenoconazole, myclobutanil, hexaconazole, triadimefon, flusilazole and pyrisoxazole (P > 0.05). Mefentrifluconazole treatment resulted in the increase of mycelium branch, the decrease of ergosterol content and the changes of the permeability of cell membrane. These studies evaluated the potential of mefentrifluconazole to control gray mold and helped us to understand the possible biochemical activity of mefentrifluconazole against B.cinerea.

Pathogenicity and Control of Phacidium lacerum, an Emerging Pome Fruit Pathogen in Washington State

Phacidium lacerum (anamorph Ceuthospora pinastri) is a recently reported quarantine fungal pathogen responsible for postharvest rot in apples and pears. Very little is known about its pathogenicity, epidemiology, and best management practices. We screened pathogenicity of P. lacerum on twigs from seven and fruit from nine major commercial apple cultivars. Among the nine cultivars tested, detached fruit of Honeycrisp and Gala cultivars were the most susceptible, whereas WA38 (Cosmic Crisp) was the least susceptible (P < 0.05). Effective concentrations to inhibit 50% growth (EC₅₀) were determined in 41 baseline P. lacerum isolates. The mean EC₅₀ values for four postharvest fungicides, i.e., fludioxonil (FDL), difenoconazole (DIF), thiabendazole (TBZ), and pyrimethanil (PYRI) were 0.16, 0.38, 0.54, and 0.72 µg/ml, respectively. The mean EC₅₀ values for four preharvest fungicides, i.e., pyraclostrobin (PYRA), fluxapyroxad (FLUX), boscalid (BOSC), and fluopyram (FLUP) were 0.96, 12.64, 16.54, and 44.46 µg/ml, respectively. In situ efficacy trials were conducted on detached Gala apples treated preventively and curatively with the aforementioned fungicides. After 6 months of storage at 1°C, FDL and DIF provided full control followed by TBZ and PYRI, whereas the other preharvest fungicides provided fair or low efficacies. Findings of this study shed light on pathogenicity of this emerging pathogen and provide necessary knowledge for effective management of Phacidium rot.

Unconventional Yeasts Are Tolerant to Common Antifungals, and Aureobasidium pullulans Has Low Baseline Sensitivity to Captan, Cyprodinil, and Difenoconazole

Many yeasts have demonstrated intrinsic insensitivity to certain antifungal agents. Unlike the fungicide resistance of medically relevant yeasts, which is highly undesirable, intrinsic insensitivity to fungicides in antagonistic yeasts intended for use as biocontrol agents may be of great value. Understanding how frequently tolerance exists in naturally occurring yeasts and their underlying molecular mechanisms is important for exploring the potential of biocontrol yeasts and fungicide combinations for plant protection. Here, yeasts were isolated from various environmental samples in the presence of different fungicides (or without fungicide as a control) and identified by sequencing the internal transcribed spacer (ITS) region or through matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. Among 376 isolates, 47 taxa were identified, and Aureobasidium pullulans was the most frequently isolated yeast. The baseline sensitivity of this yeast was established for 30 isolates from different environmental samples in vitro to captan, cyprodinil, and difenoconazole. For these isolates, the baseline minimum inhibitory concentration (MIC₅₀) values for all the fungicides were higher than the concentrations used for the control of plant pathogenic fungi. For some isolates, there was no growth inhibition at concentrations as high as 300 µg/mL for captan and 128 µg/mL for cyprodinil. This information provides insight into the presence of resistance among naturally occurring yeasts and allows the choice of strains for further mechanistic analyses and the assessment of A. pullulans for novel applications in combination with chemical agents and as part of integrated plant-protection strategies.

Induced expression of CYP51 associated with difenoconazole resistance in the pathogenic Alternaria sect. on potato in China

BACKGROUND

Early blight caused by Alternaria spp. is amongst the most important diseases in potato. Demethylation inhibitor (DMI) fungicides are widely used to control the disease but long-term use may decrease its control efficacy due to fungicide resistance. This study investigated the occurrence of difenoconazole resistance in Alternaria spp. and molecular resistant mechanisms.

RESULTS

EC₅₀ values of 160 isolates to difenoconazole ranged from 0.026 μg mL^-1 to 15.506 μg mL^-1 and the frequency of difenoconazole sensitivity formed a non-normal distribution curve with a major and a minor peak. Isolates with EC₅₀ values of 4.121 and 5.461 μg mL^-1 were not controlled effectively at fungicide doses of 50 and 100 μg mL^-1 . Cross-resistance was observed between DMI fungicides difenoconazole and propiconazole, but not between difenoconazole and other fungicide groups, including boscalid, iprodione, or carbendazim. The CYP51gene was 1673 bp encoding 525 amino acids in length and contained two introns. All sensitive and resistant isolates had the identical amino acid sequence of CYP51, with the exception of one resistant isolate carrying a mutation of R511W. A 6 bp insertion in the upstream region was observed in half of the resistant isolates. In the absence of propiconazole, the relative expression of CYP51 was not significantly different in sensitive and resistant isolates. In the presence of difenoconazole, expression of CYP51 gene was induced significantly in the DMI-resistant isolates but not in the sensitive ones.

CONCLUSION

Induced expression of CYP51 in resistant isolates exposed to difenoconazole is an important determinant for DMI resistance in potato pathogens Alternaria sect. © 2019 Society of Chemical Industry.

Constraining Evolution of Alternaria alternata Resistance to a Demethylation Inhibitor (DMI) Fungicide Difenoconazole

Evolution of fungicide resistance in plant pathogens is one of major concerns in sustainable plant disease management. In this study, the genetics and potential of developing resistance to a demethylation inhibitor (DMI) fungicide, difenoconazole, in the fungal pathogen Alternaria alternata was investigated using a comparative analysis of genetic variation in molecular (Single Sequence Repeats, SSR) and phenotypic (fungicide tolerance) markers. No difenoconazole resistance was found in the 215 A. alternata isolates sampled from seven different ecological zones in China despite the widespread use of the fungicide for more than 20 years. This result suggests that the risk of developing resistance to difenoconazole in A. alternata is low and we hypothesize that the low risk is likely caused by fitness penalties incurred by resistant mutants and the multiple mechanisms involving in developing resistance. Heritability and plasticity account for ∼24 and 3% of phenotypic variation, respectively, indicating that genetic adaptation by sequence variation plays a more important role in the evolution of difenoconazole resistance than physiological adaptation by altering gene expression. Constraining selection in the evolution of A. alternata resistance to difenoconazole was documented by different patterns of population differentiation and isolate-by-distance between SSR markers and difenoconazole tolerance. Though the risk of developing resistance is low, the findings of significant differences in difenoconazole tolerance among isolates and populations, and a skewing distribution toward higher tolerance suggests that a stepwise accumulation of tolerance to the fungicide might be occurring in the pathogen populations. As a consequence, dynamic management programs guided by evolutionary principles such as spatiotemporal rotations of fungicides with different modes of action are critical to prevent the continued accumulation of tolerance or the evolution of resistance to difenoconazole and other DMI fungicides.

Selection Pressure Pathways and Mechanisms of Resistance to the Demethylation Inhibitor-Difenoconazole in Penicillium expansum

Penicillium expansum causes blue mold, the most economically important postharvest disease of pome fruit worldwide. Beside sanitation practices, the disease is managed through fungicide applications at harvest. Difenoconazole (DIF) is a new demethylation inhibitor (DMI) fungicide registered recently to manage postharvest diseases of pome fruit. Herein, we evaluated the sensitivity of 130 P. expansum baseline isolates never exposed to DIF and determined the effective concentration (EC50) necessary to inhibit 50% germination, germ tube length, and mycelial growth. The respective mean EC50 values of 0.32, 0.26, and 0.18 μg/ml indicate a high sensitivity of P. expansum baseline isolates to DIF. We also found full and extended control efficacy in vivo after 6 months of storage at 1°C. We conducted a risk assessment for DIF-resistance development using ultraviolet excitation combined with or without DIF-selection pressure to generate and characterize lab mutants. Fifteen DIF-resistant mutants were selected and showed EC50 values of 0.92 to 1.4 μg/ml and 1.7 to 3.8 μg/ml without and with a DIF selection pressure, respectively. Resistance to DIF was stable in vitro over a 10-week period without selection pressure. Alignment of the full CYP51 gene sequences from the three wild-type and 15 mutant isolates revealed a tyrosine to phenylalanine mutation at codon 126 (Y126F) in all of the 15 mutants but not in the wild-type parental isolates. Resistance factors increased 5 to 15-fold in the mutants compared to the wild-type-isolates. DIF-resistant mutants also displayed enhanced CYP51 expression by 2 to 14-fold and was positively correlated with the EC50 values (R 2 = 0.8264). Cross resistance between DIF and fludioxonil, the mixing-partner in the commercial product, was not observed. Our findings suggest P. expansum resistance to DIF is likely to emerge in commercial packinghouse when used frequently. Future studies will determine whether resistance to DIF is qualitative or quantitative which will be determinant in the speed at which resistance will develop and spread in commercial packinghouses and to develop appropriate strategies to extend the lifespan of this new fungicide.

Parasitic Fitness of Fungicide-Resistant and -Sensitive Isolates of Alternaria solani

Resistance to chemistries of the succinate dehydrogenase inhibiting (SDHI) and quinone outside inhibiting (QoI) fungicides has developed rapidly in populations of Alternaria solani, the cause of early blight of potato. Reduced sensitivity to the anilinopyrimidine (AP) fungicide pyrimethanil has also been identified recently, determining that resistance to three chemical classes of fungicides is present within the A. solani population. Although no mutations have been characterized to confer resistance to APs, in A. solani five point mutations on three AsSdh genes have been determined to convey resistance to SDHIs, and the substitution of phenylalanine with leucine at position 129 (F129L) in the cytb gene confers resistance to QoIs. The objective of this study was to investigate the parasitic fitness of A. solani isolates with resistance to one or more of these chemical classes. A total of 120 A. solani isolates collected from various geographical locations around the United States were chosen for in vitro assessment, and 60 of these isolates were further evaluated in vivo. Fitness parameters measured were (i) spore germination in vitro, (ii) mycelial expansion in vitro, and (iii) aggressiveness in vivo. No significant differences in spore germination or mycelial expansion (P = 0.44 and 0.51, respectively) were observed among wild-type and fungicide-resistant isolates in vitro. Only A. solani isolates possessing the D123E mutation were shown to be significantly more aggressive in vivo (P < 0.0001) compared with wild-type isolates. These results indicate that fungicide-resistant A. solani isolates have no significant fitness penalties compared with sensitive isolates under the parameters evaluated regardless of the presence or absence of reduced sensitivity to multiple chemical classes. Results of these studies suggest that A. solani isolates with multiple fungicide resistances may compete successfully with wild-type isolates under field conditions.

Potential Impact of Fluopyram on the Frequency of the D123E Mutation in Alternaria solani

Succinate dehydrogenase-inhibiting (SDHI) fungicides have been widely applied in commercial potato (Solanum tuberosum L.) fields for the control of early blight, caused by Alternaria solani Sorauer. Five-point mutations on three AsSdh genes in A. solani have been identified as conferring resistance to SDHI fungicides. Recent work in our laboratory determined that A. solani isolates possessing the D123E mutation, or the substitution of aspartic acid for glutamic acid at position 123 in the AsSdhD gene, were collected at successively higher frequencies throughout a 3-year survey. In total, 118 A. solani isolates previously characterized as possessing the D123E mutation were evaluated in vitro for boscalid and fluopyram sensitivity. Over 80% of A. solani isolates with the D123E mutation evaluated were determined to be highly resistant to boscalid in vitro. However, effective concentration at which the fungal growth is inhibited by 50% values of isolates with the D123E mutation to fluopyram, ranging from 0.2 to 3 µg/ml, were sensitive and only slightly higher than those of baseline isolates to fluopyram, which ranged from 0.1 to 0.6 µg/ml. Five A. solani isolates with the D123E mutation were further evaluated in vivo for percent disease control obtained from boscalid and fluopyram compared with two wild-type isolates, three isolates possessing the F129L mutation, two isolates possessing the H134R mutation, two isolates possessing the H133R mutation, and one isolate with the H278R mutation. Relative area under the dose response curve values for boscalid and fluopyram were significantly lower for all five D123E-mutant isolates, demonstrating reduced disease control in vivo. In field trials, the frequency of A. solani isolates with the D123E mutation recovered from treatments receiving an in-furrow application of fluopyram ranged from 5 to 37%, which was significantly higher compared with treatments receiving foliar applications of standard protectants, in which the frequency of the D123E mutation in isolates ranged from 0 to 2.5%. Results suggest that A. solani isolates possessing the D123E mutation have a selective advantage under the application of fluopyram compared with SDHI-sensitive isolates, as well as isolates possessing other mutations conferring SDHI resistance. These data illustrate the importance of implementing fungicide resistance management strategies and cautions the use of fluopyram for in-furrow applications that target other pathogens of potato.

Sensitivity of Phacidiopycnis spp. Isolates from Pome Fruit to Six Pre- and Postharvest Fungicides

Phacidiopycnis washingtonensis and P. pyri cause speck rot and Phacidiopycnis rot on apple and pear, respectively. Infection occurs in the orchard and remains latent, and symptoms appear after months of storage. Decay management relies on orchard sanitation and pre- and postharvest fungicides. In a 2017 survey, speck rot accounted for 6.4% of apple decay in central Washington, whereas Phacidiopycnis rot accounted for 3.9 and 6.7% of total pear decay in Washington and Oregon, respectively. Sensitivities of baseline populations of 110 P. washingtonensis and 76 P. pyri isolates collected between 2003 and 2005 to preharvest fungicides pyraclostrobin (PYRA) and boscalid (BOSC) and to postharvest fungicides thiabendazole (TBZ), fludioxonil (FDL), pyrimethanil (PYRI), and difenoconazole (DFC) were evaluated using a mycelial growth inhibition assay. Mean effective concentrations necessary to inhibit 50% growth (EC₅₀) of P. washingtonensis were 0.1, 0.3, 0.8, 1.8, 2.1, and 4.8 µg/ml for FDL, PYRI, TBZ, DFC, PYRA, and BOSC, respectively. Respective mean EC₅₀ values for P. pyri were 0.2, 0.6, 1.6, 1.1, 0.4, and 1.8 µg/ml. The sensitivity of exposed P. washingtonensis and P. pyri populations collected in 2017 revealed potential shifts toward BOSC and PYRA resistance. The efficacy of the six fungicides to control isolates of each pathogen with different in vitro sensitivity levels was evaluated on apple and pear fruit. FDL, DFC, and PYRI controlled both Phacidiopycnis spp. regardless of their EC₅₀ values after 5 months of storage at 0°C in a regular atmosphere. The consistent occurrence of Phacidiopycnis spp. will require continuous monitoring and development of disease management strategies based on fungicide phenotypes and efficacy of existing fungicides assessed herein.

Spatial and Temporal Distribution of Mutations Conferring QoI and SDHI Resistance in Alternaria solani Across the United States

The application of succinate dehydrogenase inhibiting (SDHI) and quinone outside inhibiting (QoI) fungicide chemistries is a primary tactic in the management of early blight of potato, caused by Alternaria solani. Resistance to QoIs in A. solani has been attributed to the F129L mutation, while resistance to SDHIs is conferred by five different known point mutations on three AsSdh genes. In total, 1,323 isolates were collected from 2013 through 2015 across 11 states to determine spatial and temporal frequency distribution of these mutations. A real-time polymerase chain reaction (PCR) was used to detect the presence of the F129L mutation. Molecular detection of SDHI-resistant isolates was performed using SDH multiplex PCR specific for point mutations in AsSdhB, AsSdhC, or AsSdhD genes and mismatch amplification analysis PCR detecting the point mutations in AsSdhB. Previous work in our research group determined that substitutions of histidine for tyrosine (H278Y) or arginine (H278R) at codon 278 on the AsSdhB gene were the most prevalent mutations, detected in 46 and 21% of A. solani isolates, respectively, collected in 2011 to 2012, and uniformly distributed among six sampled states. In contrast, the substitution of histidine for arginine (H134R) at codon 134 in the AsSdhC gene was the most prevalent mutation in 2013 through 2015, identified in 36% of isolates, compared with 7.5% of isolates recovered in 2011 to 2012. Substitutions of histidine for arginine (H133R) at codon 133 and aspartic acid for glutamic acid (D123E) at codon 123 in the AsSdhD gene were detected in 16 and 12%, respectively, in the A. solani population by 2015 and were recovered across a wide range of states, compared with 15 and 1.5% of isolates collected in 2011 to 2012, respectively. Overall, SDHI- and QoI-resistant isolates were detected at high frequencies across all years, with evidence of significant spatial variability. Future research will investigate whether these results are due to differences in parasitic fitness.