Optimizing Use of DMI Fungicides for Management of Apple Powdery Mildew Caused by Podosphaera leucotricha in New York State.

Powdery mildew, caused by the ascomycete Podosphaera leucotricha, is an endemic disease found wherever apples are grown that reduces both tree vigor and fresh market yield. In the absence of durable host resistance, chemical management is the primary means of disease control. Demethylation inhibitor (DMI) fungicides are widely used to manage apple powdery mildew, but members within this fungicide class have been observed to differ in efficacy with respect to disease control. Moreover, debate exists as to the optimal timing of DMI fungicide applications for management of apple powdery mildew. In this regard, the goal of this study was to determine the best-use practices for DMI fungicides to manage apple powdery mildew in New York State. Multiyear trials were conducted to evaluate the potential differential efficacy performance of four common DMI fungicides, and additional trials were conducted to assess optimal application timing. In all years, we observed that treatments of flutriafol and myclobutanil consistently had the lowest incidences of powdery mildew compared with difenoconazole and fenbuconazole. In the 2018 and 2021 trials, the newly registered mefentrifluconazole was more comparable to the difenoconazole program with respect to powdery mildew disease incidence. We hypothesize that differences in DMI efficacy may result from each fungicide's water solubility and lipophilicity characteristics and thus their ability to move systemically in the host or more easily penetrate the surface of germinating conidia. Applications timed between petal fall and first cover resulted in the lowest incidence of powdery mildew on terminal leaves of apple shoots compared with applications timed before petal fall. These observations are contrary to previous studies conducted in regions with differing climates. We also found that the incidence of secondary powdery mildew observed 2 weeks after petal fall was influenced by applications of DMI fungicides during the previous season. For example, management programs consisting of applications of flutriafol or myclobutanil in the previous season tended to have lower incidence of apple powdery in the next spring, presumably because of reductions in overwintering inoculum. Despite reports of DMI resistance in other apple pathosystems, the DMI fungicide class is still relevant for the successful management of apple powdery mildew in New York State.

A Genome Resource for Several North American Venturia inaequalis Isolates with Multiple Fungicide Resistance Phenotypes.

The apple scab pathogen, Venturia inaequalis, is among the most economically important fungal pathogens that affects apples. Fungicide applications are an essential part of disease management. Implementation of cultural practices and genetic sources of resistance in the host are vital components of scab management. This is the first presentation of multiple, high quality, well-annotated genomes of four North American V. inaequalis isolates having both sensitive and multiple fungicide resistance phenotypes. We envision that these isolates will enable investigations into fungicide resistance mechanisms, exploring fungal virulence factors and delineating phylogenomic relationships among apple scab isolates from around the world.

Characterization of the VisdhC and VisdhD Genes in Venturia inaequalis, and Sensitivity to Fluxapyroxad, Pydiflumetofen, Inpyrfluxam, and Benzovindiflupyr.

Succinate dehydrogenase inhibitors (SDHI) are an important class of fungicides for management of apple scab, especially as resistance to other classes of fungicides has become prevalent in the northeastern United States. Considering their single-site mode of action, there is high risk of resistance development to SDHI fungicides. Such risk mandates the need for proper monitoring of shifts in population sensitivity. This study aims to provide a means for phenotypic and genotypic characterization of SDHI fungicide resistance for Venturia inaequalis, the causal agent of apple scab. To complement the published sequence of VisdhB, target genes VisdhC and VisdhD were identified using sequences of homologous genes in other fungal organisms and a draft genome of V. inaequalis. Using mycelial growth and conidial germination assays, baseline sensitivities and cross sensitivities of V. inaequalis were determined for several SDHI fungicides. Mean baseline EC50 values for conidial germination of benzovindiflupyr, fluxapyroxad, pydiflumetofen, and inpyrfluxam were found to be 0.0021, 0.0284, 0.014, and 0.0137 µg ml-1, respectively. Mean baseline EC50 values for mycelial growth of benzovindiflupyr, fluxapyroxad, pydiflumetofen, and inpyrfluxam were found to be 0.0575, 0.228, 0.062, and 0.0291 µg ml-1, respectively. A significant and positive correlation in sensitivity was found between benzovindiflupyr, fluxapyroxad, pydiflumetofen, and inpyrfluxam as well as penthiopyrad and fluopyram, with the highest correlation between benzovindiflupyr and penthiopyrad for mycelial inhibition of V. inaequalis (r = 0.950, P < 0.001). For inhibition of conidial germination, the highest correlation was observed between penthiopyrad and fluopyram (r = 0.775, P < 0.001). Furthermore, the sequences of the VisdhC and VisdhD genes were identified and characterized for baseline isolates of V. inaequalis. Residues of similar position to mutations found in other systems that confer resistance to SDHI fungicides were identified in baseline isolates, but no mutations were identified in baseline isolates or those previously exposed to SDHI fungicides. This study will serve as a reference for future monitoring of resistance to SDHI fungicides in V. inaequalis at both a phenotypic and genotypic level.

Xylosandrus germanus (Coleoptera: Curculionidae: Scolytinae) Occurrence, Fungal Associations, and Management Trials in New York Apple Orchards.

Xylosandrus germanus (Blandford) has caused increasing damage in high-density New York apple orchards since 2013, resulting in tree decline and death. We documented their occurrence and timing in > 50 orchards using ethanol-baited traps from 2014 to 2016. First captures ranged from 48 to 83 degree days (base 10 °C) from 1 January. Captures were numerically higher at the orchard-woods interface than within the orchard interior, but differences were not significant in locations with lower populations. Control using insecticide trunk sprays was tested in potted, waterlogged apple trees placed in orchards and nurseries, and inside wooded areas adjacent to orchards. A verbenone repellent was used in combination with trunk sprays to improve control. Overall, insecticide sprays were inconsistent and marginal in preventing new infestations. Chlorpyrifos significantly reduced infestations versus lambda-cyhalothrin and untreated trees at one location in the 2015 orchard trials, and versus untreated trees at one location in the 2016 nursery trials, but otherwise performed no better than other treatments. The addition of verbenone to either the check or permethrin treatments resulted in significantly fewer attack sites containing brood at one orchard site in 2016. Chlorpyrifos, lambda-cyhalothrin, and permethrin significantly reduced the number of attack sites containing adults compared with untreated trees at one nursery trial location in 2016, but were otherwise ineffective in reducing numbers of trees in other locations and infestation categories. We found several fungal and bacterial species associated with X. germanus and its infestation of apples. These microbes likely play a minimal role in apple decline.

Overexpression of the CYP51A1 Gene and Repeated Elements are Associated with Differential Sensitivity to DMI Fungicides in Venturia inaequalis.

The involvement of overexpression of the CYP51A1 gene in Venturia inaequalis was investigated for isolates exhibiting differential sensitivity to the triazole demethylation inhibitor (DMI) fungicides myclobutanil and difenoconazole. Relative expression (RE) of the CYP51A1 gene was significantly greater (P < 0.0001) for isolates with resistance to both fungicides (MRDR phenotype) or with resistance to difenoconazole only (MSDR phenotype) compared with isolates that were resistant only to myclobutanil (MRDS phenotype) or sensitive to both fungicides (MSDS phenotype). An average of 9- and 13-fold increases in CYP51A1 RE were observed in isolates resistant to difenoconazole compared with isolates with MRDS and MSDS phenotypes, respectively. Linear regression analysis between isolate relative growth on myclobutanil-amended medium and log10 RE revealed that little to no variability in sensitivity to myclobutanil could be explained by CYP51A1 overexpression (R(2) = 0.078). To investigate CYP51A1 upstream anomalies associated with CYP51A1 overexpression or resistance to difenoconazole, Illumina sequencing was conducted for three isolates with resistance to difenoconazole and one baseline isolate. A repeated element, "EL 3,1,2", with the properties of a transcriptional enhancer was identified two to four times upstream of CYP51A1 in difenoconazole-resistant isolates but was not found in isolates with the MRDS phenotype. These results suggest that different mechanisms may govern resistance to different DMI fungicides in the triazole group.

Molecular Characterization of the sdhB Gene and Baseline Sensitivity to Penthiopyrad, Fluopyram, and Benzovindiflupyr in Venturia inaequalis.

The succinate dehydrogenase inhibiting (SDHI) fungicides are a class of single-site fungicides that are increasingly important in the management of Venturia inaequalis. In this study, the baseline sensitivity of V. inaequalis to penthiopyrad, fluopyram, and benzovindiflupyr was investigated. In all, 35 to 70 isolates with no prior exposure to single-site fungicides were used to determine the effective concentration at which growth was inhibited by 50% (EC50). Mean EC50 values for the conidial germ tube growth stage for penthiopyrad, fluopyram, and benzovindiflupyr were 0.086, 0.176, and 0.0016 µg ml-1, respectively. Linear correlation analysis revealed a significant and positive correlation between fluopyram and penthiopyrad (P ≤ 0.0001, r = 0.66) and fluopyram and benzovindiflupyr (P = 0.0014, r = 0.52). Baseline sensitivities of V. inaequalis during the mycelial growth stage were also determined for fluopyram and benzovindiflupyr. EC50 values were higher for fluopyram and benzovindiflupyr during this stage compared with the conidial germ tube growth stage, with means of 0.043 and 2.02 µg ml-1, respectively. In addition, the sdhB gene was characterized for three isolates of V. inaequalis collected from a research, baseline, and commercial orchard population. No common mutation sites associated with SDHI resistance in other phytopathogenic fungi were discovered in these isolates or isolates that were recovered following field applications of SDHI fungicides. The results of this study suggest that SDHI fungicides have a high level of activity during the conidial germ tube elongation stage in V. inaequalis and provide a basis for phenotypic and genotypic monitoring of shifts toward resistance of V. inaequalis populations to the SDHI fungicide class.

Impact of White Pine Blister Rust on Resistant Cultivated Ribes and Neighboring Eastern White Pine in New Hampshire.

To determine the impact of white pine blister rust (WPBR) following the recent breakdown of the Cr resistance dominant gene in cultivated Ribes spp., 255 plants of 19 Ribes cultivars and 445 neighboring eastern white pine (Pinus strobus) from 42 sites across New Hampshire were evaluated. Of the 19 Ribes cultivars evaluated, 15 were WPBR resistant, and 4 of these were labeled as black currant (Ribes nigrum) with the Cr gene (Cr Ribes cultivars). Incidence of WPBR ranged from 0 to 88% for WPBR-resistant Ribes cultivars. Mean WPBR severity was 14 and <6% of leaf area for Cr Ribes and partially resistant cultivars, respectively. The presence of Cronartium ribicola was confirmed on 17 of the 19 Ribes cultivars screened with polymerase chain reaction analysis and DNA sequencing. Reference accessions of Cr Ribes cultivars from the Canadian Clonal Genebank were successfully infected with C. ribicola inoculum collected in New Hampshire from Cr Ribes cultivars and P. strobus, confirming that the vCr race of C. ribicola that has overcome the Cr resistance dominant gene in cultivated Ribes spp. is present in New Hampshire. The probability of finding pine trees with WPBR was greater for trees neighboring infected Cr Ribes cultivars (0.18) than trees neighboring WPBR-free Ribes cultivars (0.02). Results from this study suggest that the breakdown of Cr-based resistance in Ribes spp. poses a threat to the white pine resource and to cultivated Ribes production.

Prevalence of Myclobutanil Resistance and Difenoconazole Insensitivity in Populations of Venturia inaequalis.

Demethylation inhibitors (DMIs) are a class of single-site fungicides with high levels of protective and curative efficacy against Venturia inaequalis, the causal agent of apple scab. To determine the prevalence of resistance to the DMI fungicide myclobutanil, 3,987 single-lesion conidial V. inaequalis isolates from 141 commercial, research, and baseline orchard populations were examined throughout New England, the mid-Atlantic, and the Midwest from 2004 to 2013. Of these orchard populations, 63% had practical resistance, 13% had reduced sensitivity, and 24% were sensitive to myclobutanil. A sensitivity baseline for the recently introduced DMI fungicide difenoconazole was established to make comparisons with myclobutanil sensitivity in orchard populations. The mean effective concentration of difenoconazole at which mycelial growth was inhibited by 50% (EC50) was determined to be 0.002 µg ml-1 for 44 baseline isolates of V. inaequalis. From 2010 to 2013, 1,012 isolates of V. inaequalis from 37 of the 141 orchard populations above were screened for sensitivity to difenoconazole. In all, 1 orchard population had reduced sensitivity to difenoconazole, while the remaining 36 orchard populations were sensitive to the fungicide. In field experiments, difenoconazole demonstrated high levels of apple scab control on mature apple fruit, despite the fact that the population of V. inaequalis had practical resistance to difenoconazole. Although our results indicate widespread resistance to myclobutanil but not difenoconazole, due to the propensity for cross-sensitivity among DMI fungicides, growers with myclobutanil resistance should be cautious when using difenoconazole for disease management.

The Effect of Delayed-Dormant Chemical Treatments on Demethylation Inhibitor (DMI) Sensitivity in a DMI-resistant Population of Venturia inaequalis.

Demethylation inhibitor (DMI) fungicides are an effective means to manage apple scab caused by Venturia inaequalis. Unfortunately, practical resistance to DMI fungicide chemistries is prevalent in populations in New York and the New England states. Management practices that delay the development of DMI resistance in V. inaequalis populations are highly desired by regional apple producers. Trials were conducted in a New York apple orchard during the 2011 and 2012 growing seasons to determine the impact of delayed-dormant (after bud break, but prior to green tissue) chemical treatments on the DMI sensitivity of a V. inaequalis population with stable resistance to DMI fungicides. Delayed-dormant treatment programs consisted of either an application of a copper fungicide, a manganese sanitation product, a DMI fungicide (myclobutanil), or no fungicide. Sensitivity to the DMI fungicide myclobutanil was evaluated for a minimum of 25 V. inaequalis single lesion conidial isolates from each of four replicated treatment blocks. In both years, mean percent relative growth on myclobutanil amended media for V. inaequalis isolates from the copper treatment program were significantly (P < 0.05) lower than isolates from blocks did not receive a delayed dormant fungicide treatment. The effect of the manganese treatment was inconsistent between years. V. inaequalis isolates collected from the myclobutanil treatment program were not significantly (P > 0.05) different in myclobutanil sensitivity from isolates collected from the blocks that did not receive a delayed dormant fungicide treatment. Overall, the results suggest that delayed dormant treatments of copper may favorably impact the myclobutanil sensitivity for a population of V. inaequalis with resistance to DMI fungicides, and should be considered as a standard management practice in apple production.

Heteroplasmy of the cytochrome b gene in Venturia inaequalis and its involvement in quantitative and practical resistance to trifloxystrobin.

Quantitative (partial) and qualitative (complete) resistance responses to quinone outside inhibitor (QoI) fungicides have been documented for the apple scab pathogen Venturia inaequalis. Resistance monitoring efforts have traditionally focused on the detection of qualitative resistance based on a single point mutation, G143A, within the cytochrome b (cyt b) gene. In order to better understand the role of heteroplasmy of the cyt b gene in the QoI resistance response for isolates and populations of V. inaequalis, an allele-specific quantitative polymerase chain reaction was developed to quantify the relative abundance of the A143 (resistant) allele in 45 isolates of V. inaequalis with differing in vitro resistance responses to the QoI fungicide trifloxystrobin. Although a high relative abundance of the A143 allele (>62%) was associated with isolates with high resistance responses (50 to 100% relative growth on trifloxystrobin-amended medium), heteroplasmy of the cyt b gene was not the primary factor involved in isolates with moderate resistance responses (29 to 49% relative growth). The relative abundance of the A143 allele in isolates with moderate resistance to trifloxystrobin rarely exceeded 8%, suggesting that other resistance mechanisms are involved in moderate resistance and, therefore, that the Qol resistance response is polygenic. In research orchards where QoI fungicides failed to control apple scab (practical resistance), field trials were conducted to demonstrate the link between practical resistance and the abundance of the A143 allele. Relative abundance of the A143 allele in these orchard populations exceeded 20% in 2011 and 2012. Similarly, of the eight additional commercial orchards screened in 2011, the relative abundance of the A143 allele always exceeded 20% in those with QoI practical resistance. Although heteroplasmy of the cyt b gene did not entirely explain the response of isolates with moderate resistance to QoIs, the relative abundance of A143 in orchard populations of V. inaequalis helps to explain the point of emergence for practical resistance to trifloxystrobin across several orchard populations with differing production histories.

Prevalence and Stability of Qualitative QoI Resistance in Populations of Venturia inaequalis in the Northeastern United States.

Quinone-outside-inhibitor (QoI) fungicides are a safe and effective means of managing apple scab caused by Venturia inaequalis. To determine the prevalence of both quantitative (partial) and qualitative (complete) QoI resistance in V. inaequalis in the northeastern United States, we sampled single-lesion conidial isolates (n = 4,481) from 120 commercial and research orchards from 2004 to 2011 with a range of exposure to QoI fungicides from none to several applications a year. In all, 67% of these orchard populations of V. inaequalis were sensitive to QoI fungicides, 28% exhibited QoI practical resistance, and 5% were not sensitive QoI fungicides but had not become practically resistant. Isolates with qualitative QoI resistance, conferred by the G143A cytochrome b gene mutation, were found in 13 of the 34 QoI-resistant orchard populations. To evaluate the stability of the G143A mutation, 27 isolates were selected from different orchard populations to represent the scope of regional populations. These isolates were subcultured continuously in the presence or absence of the QoI fungicide trifloxystrobin. All isolates that initially possessed qualitative resistance maintained the resistant genotype (G143A) for six transfers over 6 months in both the absence and presence of trifloxystrobin. Given the observed QoI resistance in orchard populations of V. inaequalis and the stability of the G143A mutation in individual isolates, apple scab management paradigms must encompass strategies to limit selection of QoI resistance in the sensitive orchard populations remaining in the region.

Characterization of the cytochrome b (cyt b) gene from Monilinia species causing brown rot of stone and pome fruit and its significance in the development of QoI resistance.

BACKGROUND: Quinone outside inhibitor (QoI) resistance as a consequence of point mutations in the cytochrome b (cyt b) gene has been reported in numerous plant pathogenic fungi. To examine the potential for QoI resistance development in those Monilinia species causing brown rot of stone and pome fruits [Monilinia fructicola (G Winter) Honey, M. laxa (Aderhold & Ruhland) Honey and M. fructigena (Aderhold & Ruhland) Honey], an examination was made of the sequence and exon/intron structure of their cyt b genes for the presence of any point mutations and/or introns commonly associated with resistance to QoIs in fungal plant pathogens. RESULTS: None of the point mutations typically linked to QoI resistance was present in any of the Monilinia isolates examined. Furthermore, the cyt b genes from M. fructicola and M. laxa, but not M. fructigena, possessed a group-I-like intron directly after codon 143. Based on the results obtained, a simple PCR assay using a single primer pair was developed, allowing discrimination between the three Monilinia species without the need for culturing. CONCLUSIONS: Results suggest that resistance to QoI fungicides based on the G143A mutation is not likely to occur in M. fructicola or M. laxa. Conversely, M. fructigena may be at higher risk for developing QoI resistance owing to the absence of a G143-associated intron.

Characterizing Fenbuconazole and Propiconazole Sensitivity and Prevalence of 'Mona' in Isolates of Monilinia fructicola from New York.

Demethylation inhibitor (DMI) resistant populations of Monilinia fructicola, the causal agent of brown rot of stone fruit, and the presence of the genetic DMI resistance determinant 'Mona' have been reported throughout the eastern United States. In this study, we endeavored to conduct a comprehensive investigation of DMI sensitivity, the prevalence of 'Mona', and implications of DMI use for M. fructicola populations from New York and Pennsylvania. Of the 18 orchards surveyed, only 9 were primarily composed of isolates with either resistance or reduced sensitivity to fenbuconazole and propiconazole. The DMI resistance determinant 'Mona' was only found in 5 orchards, present in isolates with a range of sensitivity phenotypes, and not always present in resistant isolates. These results suggested that 'Mona' only contributes to a portion of the quantitative resistance response to DMI fungicides. On detached blossoms and fruit, protective applications of fenbuconazole (Indar 2F) against isolates with resistance or reduced sensitivity resulted in significantly (P < 0.05) lower brown rot incidence compared to applications of propiconazole (Orbit 3.6EC) and water controls. By comparison, therapeutic applications of fenbuconazole and propiconazole against isolates with resistance or reduced sensitivity provided little to no reduction in brown rot incidence on blossoms and fruit.