Do some IPM concepts contribute to the development of fungicide resistance? Lessons learned from the apple scab pathosystem in the United States

Phenotyping, genetics, and "-omics" approaches to unravel and introgress enhanced resistance against apple scab (Venturia inaequalis) in apple cultivars (Malus × domestica)

Apple scab disease, caused by the fungus Venturia inaequalis, endangers commercial apple production globally. It is predominantly managed by frequent fungicide sprays that can harm the environment and promote the development of fungicide-resistant strains. Cultivation of scab-resistant cultivars harboring diverse qualitative Rvi resistance loci and quantitative trait loci associated with scab resistance could reduce the chemical footprint. A comprehensive understanding of the host-pathogen interaction is, however, needed to efficiently breed cultivars with enhanced resistance against a variety of pathogenic strains. Breeding efforts should not only encompass pyramiding of Rvi loci and their corresponding resistance alleles that directly or indirectly recognize pathogen effectors, but should also integrate genes that contribute to effective downstream defense mechanisms. This review provides an overview of the phenotypic and genetic aspects of apple scab resistance, and currently known corresponding defense mechanisms. Implementation of recent "-omics" approaches has provided insights into the complex network of physiological, molecular, and signaling processes that occur before and upon scab infection, thereby revealing the importance of both constitutive and induced defense mechanisms. Based on the current knowledge, we outline advances toward more efficient introgression of enhanced scab resistance into novel apple cultivars by conventional breeding or genetic modification techniques. However, additional studies integrating different "-omics" approaches combined with functional studies will be necessary to unravel effective defense mechanisms as well as key regulatory genes underpinning scab resistance in apple. This crucial information will set the stage for successful knowledge-based breeding for enhanced scab resistance.

Postinfection Application of Fenhexamid at Lower Doses in Conjunction with Captan Slowed Fungicide Resistance Selection in Botrytis cinerea on Detached Grape Berries

Fungicide resistance is a limiting factor in sustainable crop production. General resistance management strategies such as rotation and mixtures of fungicides with different modes of action have been proven to be effective in many studies, but guidance on fungicide dose or application timing for resistance management remains unclear or debatable. In this study, Botrytis cinerea and the high-risk fungicide fenhexamid were used to determine the effects of fungicide dose, mixing partner, and application timing on resistance selection across varied frequencies of resistance via detached fruit assays. The results were largely consistent with the recent modeling studies that favored the use of the lowest effective fungicide dose for improved resistance management. In addition, even 10% resistant B. cinerea in the population led to about a 40% reduction of fenhexamid efficacy. Overall, our findings show that application of doses less than the fungicide label dose, mixture with the low-risk fungicide captan, and application postinfection seem to be the most effective management strategies in our controlled experimental settings. This somewhat contradicts the previous assumption that preventative sprays help resistance management.

Fungicide Use Patterns in Select United States Wine Grape Production Regions

Wine grape production (Vitis sp.) in the United States requires fungicide inputs for disease control. Currently, there is limited data available on vineyard fungicide use patterns. This information is important in developing tailored recommendations for disease management and fungicide stewardship. In this paper, we summarize the wine grape vineyard fungicide use patterns from four major regions: Napa and Sonoma valleys (California), Willamette Valley (Oregon), Columbia Valley (Washington), and several smaller regions east of the Mississippi River in years 2009 to 2020. We learned that the average in-season total fungicide applications ranged regionally from 5.6 to 8. The most commonly applied Fungicide Resistance Action Committee (FRAC) codes in spray programs were FRAC 3, 13, and M02 across all regions, with some variation to the top four groups in each region. Most applications were made on 14-day intervals; however, shorter intervals (7-day) were favored early season, and longer intervals (21-day) were favored late season. Tank-mixing multiple active ingredients was common east of the Mississippi River during all stages of grape development; this action was typically favored during the bloom period in other regions. In a subset of records that participated in FRAC 11 fungicide resistance testing, the average number of FRAC 11 applications after testing was reduced to either no applications or one application in Napa and Sonoma valleys. This survey provides regionally specific data related to fungicide stewardship practices that could be a focus for future stewardship messaging and fungicide resistance selection training, including total product use (selection events), spray intervals (selection pressure), and tank mixing (selection management).[Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Chromosome-level phased genome assembly of "Antonovka" identified candidate apple scab-resistance genes highly homologous to HcrVf2 and HcrVf1 on linkage group 1

Apple scab, a fungal disease caused by Venturia inaequalis, leads to losses in both yield and fruit quality of apples (Malus domestica Borkh.). Most commercial apple cultivars, including those containing the well-characterized Rvi6-scab-resistance locus on linkage group (LG) 1, are susceptible to scab. HcrVf2 and HcrVf1 are considered the main paralogs of the Rvi6 locus. The major apple scab-resistance loci Vhc1 in "Honeycrisp" and Rvi17 in "Antonovka," were identified in close proximity to HcrVf2. In this study, we used long-read sequencing and in silico gene sequence characterization to identify candidate resistance genes homologous to HcrVf2 and HcrVf1 in Honeycrisp and Antonovka. Previously published chromosome-scale phased assembly of Honeycrisp and a newly assembled phased genome of Antonovka 172670-B were used to identify HcrVf2 and HcrVf1 homologs spanning Vhc1 and Rvi17 loci. In combination with 8 available Malus assemblies, 43 and 46 DNA sequences highly homologous to HcrVf2 and HcrVf1, respectively, were identified on LG 1 and 6, with identity and coverage ranging between 87-95 and 81-95%, respectively. Among these homologs, 2 candidate genes in Antonovka and Honeycrisp haplome A are located in close physical proximity to the scab-resistance marker Ch-Vf1 on LG 1. They showed the highest identity and coverage (95%) of HcrVf2 and only minor changes in the protein motifs. They were identical by state between each other, but not with HcrVf2. This study offers novel genomic resources and insights into the Vhc1 and Rvi17 loci on LG 1 and identifies candidate genes for further resistance characterization.

Dose-Dependent Genetic Resistance to Azole Fungicides Found in the Apple Scab Pathogen

The evolution of azole resistance in fungal pathogens presents a major challenge in both crop production and human health. Apple orchards across the world are faced with the emergence of azole fungicide resistance in the apple scab pathogen Venturia inaequalis. Target site point mutations observed in this fungus to date cannot fully explain the reduction in sensitivity to azole fungicides. Here, polygenic resistance to tebuconazole was studied across a population of V. inaequalis. Genotyping by sequencing allowed Quantitative Trait Loci (QTLs) mapping to identify the genetic components controlling this fungicide resistance. Dose-dependent genetic resistance was identified, with distinct genetic components contributing to fungicide resistance at different exposure levels. A QTL within linkage group seven explained 65% of the variation in the effective dose required to reduce growth by 50% (ED50). This locus was also involved in resistance at lower fungicide doses (ED10). A second QTL in linkage group one was associated with dose-dependent resistance, explaining 34% of variation at low fungicide doses (ED10), but did not contribute to resistance at higher doses (ED50 and ED90). Within QTL regions, non-synonymous mutations were observed in several ATP-Binding Cassette and Major Facilitator SuperFamily transporter genes. These findings provide insight into the mechanisms of fungicide resistance that have evolved in horticultural pathogens. Identification of resistance gene candidates supports the development of molecular diagnostics to inform management practices.

Physical Modes of Action of Fungicides Against Apple Scab: Timing Is Everything, but Dose Matters

The efficacy of currently available fungicides against apple scab, caused by the fungal pathogen Venturia inaequalis, was investigated in relation to when growers spray (ahead, during, or after rain) and how the spray reaches the target. The adaxial surface of individual leaves of potted trees were sprayed and then inoculated with ascospores of V. inaequalis, to establish dose-response curves for each fungicide. Discriminatory doses providing 50 and 90% symptom inhibition (EC50 and EC90, respectively) in sprays mimicking applications ahead of rain were used for experiments imitating alternative spray timings. Sprays were either applied during the spore germination phase or early or late after infection onset (either 336 or 672 degree-hours after inoculation, respectively), corresponding to grower spray schedules. Experiments were also carried out with sprays applied on the abaxial leaf surface to investigate fungicide efficacy through the leaf lamina. For all fungicides, the best efficacy was observed when sprays were applied during germination, followed by applications ahead of inoculation. Some products maintained equal or better efficacy at early infection, while efficacy in late infection dropped for all products, clearly indicating that this spray timing should be avoided. Some products with postinfection efficacy also showed translaminar efficacy. The close relationship found between EC50 of the active ingredients on potted trees and the label rate could help improve spraying decisions and reduce costs.

Fifty Years of Fungicide Development, Deployment, and Future Use

Plant disease management has not significantly changed significantly in the past 50 years, even as great strides have been made in the understanding of fungal biology and the etiology of plant disease. Issues of climate change, supply chain failures, war, political instability, and exotic invasives have created even more serious implications for world food and fiber security, and the stability of managed ecosystems, underscoring the urgency for reducing plant disease-related losses. Fungicides serve as the primary example of successful, widespread technology transfer, playing a central role in crop protection, reducing losses to both yield and postharvest spoilage. The crop protection industry has continued to improve upon previous fungicide chemistries, replacing active ingredients lost to resistance and newly understood environmental and human health risks, under an increasingly stricter regulatory environment. Despite decades of advances, plant disease management continues to be a constant challenge that will require an integrated approach, and fungicides will continue to be an essential part of this effort.

Target Mechanism of Iturinic Lipopeptide on Differential Expression Patterns of Defense-Related Genes against Colletotrichum acutatum in Pepper

Bacillus subtilis KB21 is an isolate with broad spectrum antifungal activity against plant pathogenic fungi. Our aim was to produce and purify antifungal lipopeptides via fermentation using B. subtilis KB21 and verify their antifungal mechanism against pepper anthracnose. When the KB21 strain was cultured in tryptic soy broth medium, the antifungal activity against pepper anthracnose correlated with biosurfactant production. However, there was no antifungal activity when cultured in Luria-Bertani medium. KB21 filtrates showed the highest degree of inhibition of mycelia (91.1%) and spore germination (98.9%) of Colletotrichum acutatum via increases in the biosurfactant levels. Using liquid chromatography-mass spectrometry (LC-MS) and LC-tandem MS (LC-MS/MS) analyses, the component with antifungal activity in the fermentation medium of the KB21 strain was determined to be the cyclic lipopeptide (CLP) antibiotic, iturin A. When the iturin fractions were applied to pepper fruits inoculated with conidia of C. acutatum, the lesion diameter and hyphal growth on the fruit were significantly suppressed. In addition, iturin CLP elevated the gene expression of PAL, LOX, and GLU in the treatments both with and without following fungal pathogens. Overall, the results of this study show that iturin CLPs from B. subtilis KB21 may be potential biological control agents for plant fungal diseases.

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.

Fungicide Physical Mode of Action: Impacts on Suppression of Hop Powdery Mildew

Understanding of the physical mode of action of fungicides allows more efficient and effective application and can increase disease control. Greenhouse and field studies were conducted to explore the preinfection and postinfection duration and translocative properties of fungicides commonly used to control hop powdery mildew, caused by Podosphaera macularis. In greenhouse studies, applications made 24 h before inoculation were almost 100% effective at suppressing powdery mildew, regardless of the fungicide evaluated. However, percentage control of powdery mildew based on the number of pathogen colonies per leaf varied significantly between fungicides with increasing time from inoculation to application, ranging from 50 to 100% disease control depending on the fungicide. Fluopyram or fluopyram + trifloxystrobin was particularly efficacious, suppressing nearly all powdery mildew development independent of application timing. In translocation studies, fluopyram and flutriafol were the most effective treatments in each of two separate experiments, resulting in zones of inhibition of 1,036 and 246.3 mm², respectively, on adaxial leaf surfaces when a single droplet of each fungicide was applied to the abaxial surface of leaves. In field experiments, all fungicide treatments provided nearly complete control of powdery mildew infection when applied before inoculation. Levels of disease control decreased with time depending on treatment, showing trends similar to those observed in greenhouse studies. In the 2017 field experiments, high levels of disease control (>75%) were observed at postinoculation time points for all treatments tested, whereas the same fungicides were more sensitive to application timing in a different year. Findings from this research indicate that differences in efficacy between fungicides are small when applications are made preventively, but postinfection activity and translaminar movement of certain fungicides may render some more effective depending on application coverage and preexisting infection.

Assessment of Pesticide Content in Apples and Selected Citrus Fruits Subjected to Simple Culinary Processing

Over the span of the last decade, certain pesticides have been banned in apple tree and citrus tree cultivations. Hence, it is important to conduct research focused on estimating the occurrence of residues of pesticides from the perspective of compliance with the relevant legislative regulations. Equally important is to estimate the reduction in pesticide residues through simple procedures such as washing and peeling. This research was conducted in the years 2012 and 2020. An assessment was made of the effect of in-house processing, such as conventional washing with tap water and peeling, on the level of pesticide residues in apples and citrus fruits (oranges, grapefruits and lemons). The level of pesticide residue was determined with the use of the QuEChERS method of extraction in conjunction with LC-MS/MS analysis. One can clearly observe a smaller number of pesticides identified in the edible parts of fruits in 2020 (seven pesticides in apples and three in citrus fruits) compared to 2012 (26 pesticides in apples and 4 in citrus fruits). In apples from 2012, only in the case of disulfoton was the maximum residue limit (MRL) exceeded, while in samples of apples from 2020 no instance of exceeded MRL was noted. This study did not reveal exceeded MRL values in the edible parts of citrus fruits in the analysed years. The absence of detected instances of pesticides not approved for use in the analysed years indicates that the producers complied with the relevant legislative regulations. The results obtained indicate that conventional washing with water (about 1.5 L/one fruit) did not have any effect on the level of pesticide residues in the analysed fruits. Apple peeling allowed for a reduction in pesticide levels in the range of 24% (carbendazim) to 100% (triflumuron, thiodicarb, tebuconazole).

Different LED Light Wavelengths and Photosynthetic Photon Flux Density Effect on Colletotrichum acutatum Growth

The study aimed to evaluate the effect of different photon flux density (PFD) and light-emitting diodes (LED) wavelengths on strawberry Colletotrichum acutatum growth characteristics. The C. acutatum growth characteristics under the blue 450 nm (B), green 530 nm (G), red 660 nm (R), far-red 735 nm (FR), and white 5700 K (W) LEDs at PFD 50, 100 and 200 μmol m⁻² s⁻¹ were evaluated. The effect on C. acutatum mycelial growth evaluated by daily measuring until five days after inoculation (DAI). The presence of conidia and size (width and length) evaluated after 5 DAI. The results showed that the highest inhibition of fungus growth was achieved after 1 DAI under B and G at 50 μmol m⁻² s⁻¹ PFD. Additionally, after 1–4 DAI under B at 200 μmol m⁻² s⁻¹ PFD. The lowest conidia width was under FR at 50 μmol m⁻² s⁻¹ PFD and length under FR at 100 μmol m⁻² s⁻¹ PFD. Various LED light wavelengths influenced differences in C. acutatum colonies color. In conclusion, different photosynthetic photon flux densities and wavelengths influence C. acutatum growth characteristics. The changes in C. acutatum morphological and phenotypical characteristics could be related to its ability to spread and infect plant tissues. This study’s findings could potentially help to manage C. acutatum by LEDs in controlled environment conditions.

Optimizing the Integration of a Biopesticide (Bacillus subtilis QST 713) with a Single-Site Fungicide (Benzovindiflupyr) to Reduce Reliance on Synthetic Multisite Fungicides (Captan and Mancozeb) for Management of Apple Scab

Apple scab is one of the most economically important diseases of apple in temperate production regions. In the absence of durable host resistance in commercially preferred cultivars, considerable applications of fungicides are needed to manage this disease. With the sequential development of resistance to nearly all classes of single-site fungicides in the apple scab pathogen Venturia inaequalis, synthetic multisite fungicides, such as mancozeb and captan, often comprise the core of chemical management programs for apple scab. Although these fungicides have demonstrable benefits for both disease and fungicide resistance management, the sustainability movement within agriculture aims to reduce reliance on such fungicides because of their broader environmental impacts. In this study, we establish a framework to enhance the feasibility of chemical management programs that do not rely on use of synthetic multisite protectant fungicides to manage apple scab. Specifically, we wish to evaluate chemical programs that integrate the biopesticide Bacillus subtilis QST 713 (Serenade Opti) in rotation with benzovindiflupyr (Aprovia), a single-site fungicide belonging to the class of succinate dehydrogenase inhibitors (SDHI), to circumvent the need for applications of synthetic multisite fungicides. During implementation of these programs, disease incidence data were taken at biweekly intervals. Regardless of the seasonal challenges presented in the 2 years of this study, when Bacillus subtilis QST 713 was used in place of captan and mancozeb mixtures, we did not observe any significant differences (P > 0.05) in development of apple scab symptoms between any of the management programs for the vertical axis or super spindle orchards in either year. This potential for substituting synthetic multisite fungicides with biopesticides is best realized when the programs are used with a decision support system in a super spindle planting system, where trees have reduced canopy densities. This 2-year study shows the potential to achieve adequate disease control using the integration of SDHI fungicides and biological controls without the use of synthetic multisite fungicides.

Resistance to Boscalid, Fluopyram and Fluxapyroxad in Blumeriella jaapii from Michigan (U.S.A.): Molecular Characterization and Assessment of Practical Resistance in Commercial Cherry Orchards

Management of cherry leaf spot disease, caused by the fungus Blumeriella jaapii, with succinate dehydrogenase inhibitor (SDHI) fungicides has been ongoing in Michigan tart cherry orchards for the past 17 years. After boscalid-resistant B. jaapii were first isolated from commercial orchards in 2010, premixes of SDHI fungicides fluopyram or fluxapyroxad with a quinone outside inhibitor were registered in 2012. Here, we report widespread resistance to fluopyram (Fluo^R), fluxapyroxad (Flux^R), and boscalid (Bosc^R) in commercial orchard populations of B. jaapii in Michigan from surveys conducted between 2016 and 2019. A total of 26% of 1610 isolates from the 2016-2017 surveys exhibited the fully-resistant Bosc^R Fluo^R Flux^R phenotype and only 7% were sensitive to all three SDHIs. Practical resistance to fluopyram and fluxapyroxad was detected in 29 of 35 and 14 of 35 commercial tart cherry orchards, respectively, in surveys conducted in 2018 and 2019. Sequencing of the SdhB, SdhC, and SdhD target genes from 22 isolates with varying resistance phenotypes showed that Bosc^S Fluo^R Flux^S isolates harbored either an I262V substitution in SdhB or an S84L substitution in SdhC. Bosc^R Fluo^R Flux^R isolates harbored an N86S substitution in SdhC, or contained the N86S substitution with the additional I262V substitution in SdhB. One Bosc^R Fluo^R Flux^R isolate contained both the I262V substitution in SdhB and the S84L substitution in SdhC. These mutational analyses suggest that Bosc^R Fluo^R Flux^R isolates evolved from fully sensitive Bosc^S, Fluo^S, Flux^S isolates in the population and not from boscalid-resistant isolates that were prevalent in the 2010-2012 time period.

Spontaneous and Fungicide-Induced Genomic Variation in Sclerotinia sclerotiorum

Stress from exposure to sublethal fungicide doses may cause genomic instability in fungal plant pathogens, which may accelerate the emergence of fungicide resistance or other adaptive traits. In a previous study, five strains of Sclerotinia sclerotiorum were exposed to sublethal doses of four fungicides with different modes of action, and genotyping showed that such exposure induced mutations. The goal of the present study was to characterize genome-wide mutations in response to sublethal fungicide stress in S. sclerotiorum and study the effect of genomic background on the mutational repertoire. The objectives were to determine the effect of sublethal dose exposure and genomic background on mutation frequency/type, distribution of mutations, and fitness costs. Fifty-five S. sclerotiorum genomes were sequenced and aligned to the reference genome. Variants were called and quality filtered to obtain high confidence calls for single nucleotide polymorphisms (SNPs), insertions/deletions (INDELs), copy number variants, and transposable element (TE) insertions. Results suggest that sublethal fungicide exposure significantly increased the frequency of INDELs in two strains from one genomic background (P value ≤ 0.05), while TE insertions were generally repressed for all genomic backgrounds and under all fungicide exposures. The frequency and/or distribution of SNPs, INDELs, and TE insertions varied with genomic background. A propensity for large duplications on chromosome 7 and aneuploidy of this chromosome were observed in the S. sclerotiorum genome. Mutation accumulation did not significantly affect the overall in planta strain aggressiveness (P value > 0.05). Understanding factors that affect pathogen mutation rates can inform disease management strategies that delay resistance evolution.

The Effects of Succinate Dehydrogenase Inhibitor Fungicide Dose and Mixture on Development of Resistance in Venturia inaequalis

Understanding how fungicide application practices affect selection for fungicide resistance is imperative for continued sustainable agriculture. Here, we examined the effect of field applications of the succinate dehydrogenase inhibitor (SDHI) fluxapyroxad at different doses and mixtures on the SDHI sensitivity of Venturia inaequalis, the apple scab pathogen. Fungicide applications were part of selection programs involving different doses (high or low) and mixtures (with a second single-site fungicide or a multisite fungicide). These programs were tested in two apple orchards over 4 years to determine potential cumulative selection effects on resistance. Each year after program applications, apple scab lesions were collected, and relative growth assays were conducted to understand shifts in fluxapyroxad sensitivity. After 4 years, there was a trend toward a reduction in sensitivity to fluxapyroxad for most selection programs in comparison to that in the non-selective-pressure control. In most years, the selection program plots treated with low-dose fluxapyroxad applications resulted in a larger number of isolates with reduced sensitivity, supporting the use of higher doses for disease management. Few significant differences (P < 0.05) in fungicide sensitivity were observed between isolates collected from plots where fungicide mixtures were applied compared to that in untreated plots, supporting the use of multiple modes of action in field applications. In all, appropriate doses and mixtures may contribute to increased longevity of SDHI fungicides used on perennial crops like apples.IMPORTANCE Of much debate is the effect of fungicide application dose on resistance development, as fungicide resistance is a critical barrier to effective disease management in agricultural systems. Our field study in apples investigated the effect of fungicide application dose and mixture on the selection of succinate dehydrogenase inhibitor resistance in Venturia inaequalis, a fungal pathogen that causes the economically important disease apple scab. Understanding how to best delay the development of resistance can result in increased efficacy, fewer applications, and sustainable fungicide use. Results from this study may have relevance to other perennial crops that require multiple fungicide applications and that are impacted by the development of resistance.

Ten Years of VINQUEST: First Insight for Breeding New Apple Cultivars With Durable Apple Scab Resistance

Apple scab, caused by Venturia inaequalis, is a major fungal disease worldwide. Cultivation of scab-resistant cultivars would reduce the chemical footprint of apple production. However, new apple cultivars carrying durable resistances should be developed to prevent or at least slow the breakdown of resistance against races of V. inaequalis. One way to achieve durable resistance is to pyramid multiple scab resistance genes in a cultivar. The choice of the resistance genes to be combined in the pyramids should take into account the frequency of resistance breakdown and the geographical distribution of apple scab isolates able to cause such breakdowns. In order to acquire this information and to make it available to apple breeders, the VINQUEST project (www.vinquest.ch) was initiated in 2009. Ten years after launching this project, 24 partners from 14 countries regularly contribute data. From 2009 to 2018, nearly 9,000 data points have been collected. This information has been used to identify the most promising apple scab resistance genes for developing cultivars with durable resistance, which to date are: Rvi5, Rvi11, Rvi12, Rvi14, and Rvi15. As expected, Rvi1, together with Rvi3 and Rvi8, were often overcome, and have little value for scab resistance breeding. Rvi10 may also belong to this group. On the other hand, Rvi2, Rvi4, Rvi6, Rvi7, Rvi9, and Rvi13 are still useful for breeding, but their use is recommended only in extended pyramids of ≥3 resistance genes.

Cytological and Gene Profile Expression Analysis Reveals Modification in Metabolic Pathways and Catalytic Activities Induce Resistance in Botrytis cinerea Against Iprodione Isolated From Tomato

Grey mold is one of the most serious and catastrophic diseases, causing significant yield losses in fruits and vegetables worldwide. Iprodione is a broad spectrum agrochemical used as a foliar application as well as a seed protectant against many fungal and nematode diseases of fruits and vegetables from the last thirty years. The extensive use of agrochemicals produces resistance in plant pathogens and is the most devastating issue in food and agriculture. However, the molecular mechanism (whole transcriptomic analysis) of a resistant mutant of B. cinerea against iprodione is still unknown. In the present study, mycelial growth, sporulation, virulence, osmotic potential, cell membrane permeability, enzymatic activity, and whole transcriptomic analysis of UV (ultraviolet) mutagenic mutant and its wild type were performed to compare the fitness. The EC₅₀ (half maximal effective concentration that inhibits the growth of mycelium) value of iprodione for 112 isolates of B. cinerea ranged from 0.07 to 0.87 µg/mL with an average (0.47 µg/mL) collected from tomato field of Guangxi Province China. Results also revealed that, among iprodione sensitive strains, only B67 strain induced two mutants, M0 and M1 after UV application. The EC₅₀ of these induced mutants were 1025.74 μg/mL and 674.48 μg/mL, respectively, as compared to its wild type 1.12 μg/mL. Furthermore, mutant M0 showed higher mycelial growth sclerotia formation, virulence, and enzymatic activity than wild type W0 and M1 on potato dextrose agar (PDA) medium. The bctubA gene in the mutant M0 replaced TTC and GAT codon at position 593 and 599 by TTA and GAA, resulting in replacement of phenyl alanine into leucine (transversion C/A) and aspartic acid into glutamic acid (transversion T/C) respectively. In contrast, in bctubB gene, GAT codon at position 646 is replaced by AAT and aspartic acid converted into asparagine (transition G/A). RNA sequencing of the mutant and its wild type was performed without (M0, W0) and with iprodione treatment (M-ipro, W-ipro). The differential gene expression (DEG) identified 720 unigenes in mutant M-ipro than W-ipro after iprodione treatment (FDR ≤ 0.05 and log2FC ≥ 1). Seven DEGs were randomly selected for quantitative real time polymerase chain reaction to validate the RNA sequencing genes expression (log fold 2 value). The gene ontology (GO) enrichment and Kyoto encyclopedia genes and genomes (KEGG) pathway functional analyses indicated that DEG’s mainly associated with lysophopholipase, carbohydrate metabolism, amino acid metabolism, catalytic activity, multifunctional genes (MFO), glutathione-S transferase (GST), drug sensitivity, and cytochrome P450 related genes are upregulated in mutant type (M0, M-ipro) as compared to its wild type (W0, W-ipro), may be related to induce resistant in mutants of B. cinerea against iprodione.

Identification and characterization of Colletotrichum species causing apple bitter rot in New York and description of C. noveboracense sp. nov

Apple bitter rot caused by Colletotrichum species is a growing problem worldwide. Colletotrichum spp. are economically important but taxonomically un-resolved. Identification of Colletotrichum spp. is critical due to potential species-level differences in pathogenicity-related characteristics. A 400-isolate collection from New York apple orchards were morphologically assorted to two groups, C. acutatum species complex (CASC) and C. gloeosporioides species complex (CGSC). A sub-sample of 44 representative isolates, spanning the geographical distribution and apple varieties, were assigned to species based on multi-locus phylogenetic analyses of nrITS, GAPDH and TUB2 for CASC, and ITS, GAPDH, CAL, ACT, TUB2, APN2, ApMat and GS genes for CGSC. The dominant species was C. fioriniae, followed by C. chrysophilum and a novel species, C. noveboracense, described in this study. This study represents the first report of C. chrysophilum and C. noveboracense as pathogens of apple. We assessed the enzyme activity and fungicide sensitivity for isolates identified in New York. All isolates showed amylolytic, cellulolytic and lipolytic, but not proteolytic activity. C. chrysophilum showed the highest cellulase and the lowest lipase activity, while C. noveboracense had the highest amylase activity. Fungicide assays showed that C. fioriniae was sensitive to benzovindiflupyr and thiabendazole, while C. chrysophilum and C. noveboracense were sensitive to fludioxonil, pyraclostrobin and difenoconazole. All species were pathogenic on apple fruit with varying lesion sizes. Our findings of differing pathogenicity-related characteristics among the three species demonstrate the importance of accurate species identification for any downstream investigations of Colletotrichum spp. in major apple growing regions.

New North American Isolates of Venturia inaequalis Can Overcome Apple Scab Resistance of Malus floribunda 821

Apple scab, caused by Venturia inaequalis, is a destructive fungal disease of major apple cultivars worldwide, most of which are moderately to highly susceptible. Thus, development of scab resistant cultivars is one of the highest priorities of apple breeding programs. The principal source of resistance for breeding programs has been the scab resistance gene Rvi6 that originated from the Japanese crabapple Malus floribunda (Sieb.) sel. 821. Isolates of V. inaequalis able to overcome Rvi6 have been identified in Europe, but have not yet been reported on the American continents. We recently discovered scab infection on M. floribunda 821 trees in a research orchard at Geneva, NY, U.S.A., where approximately 10% of the leaves bore profusely sporulating apple scab lesions, many of which had coalesced to cover entire leaves. We observed both chlorosis, typical to Rvi6, and pinpoint pitting symptoms typical to failed infections by V. inaequalis on hosts bearing the Rvi7 gene. We assessed genetic diversity and population genetic structure of 11 V. inaequalis isolates in total, of North American and European origin, isolated from M. floribunda 821, 'Nova Easygro', 'Golden Delicious', TSR33T239, 'Schone van Boskoop', and 'Prima', using 16,321 genome-wide SNPs. Population genetic structure and PCA separated the isolates into distinct European and U.S. groups. The forgoing suggests that the new Rvi6 virulent isolates emerged within U.S. populations, rather than being transported from Europe. The complete resistance breakdown in M. floribunda 821 but not in descendant cultivars, which kept their field resistance, suggests that durable resistance to apple scab will require a more comprehensive understanding of Rvi6 mediated resistance in diverse genetic backgrounds.

Comparative Studies on the Effect of Adjuvants with Urea to Reduce the Overwintering Inoculum of Venturia inaequalis

A 2-year study on the use of organic and conventional adjuvants alone, or mixed with urea, was conducted for management of overwintering inoculum of the apple scab pathogen, Venturia inaequalis. Select adjuvants (LI 700, Bond Max, Latron B-1956, and Organic Wet Betty [OWB]) have the potential to hasten urea-driven leaf litter decomposition and reduce V. inaequalis overwintering inoculum comparable to urea, and that one organic surfactant could perform the same level of leaf decomposition as urea. Combinations of adjuvants with urea significantly improved leaf litter degradation compared with urea alone, concomitant with reducing the number of pseudothecia present and pseudothecium fertility. We demonstrate that the combination of urea with Bond Max or OWB reduced pseudothecia fertility and ascospore production to less than 5% in the remaining pseudothecia, a significantly greater reduction than with urea alone. These results suggest that conventional growers combine urea with Bond Max or OWB to more effectively reduce overwintering inoculum, and that the adjuvant OWB can provide organic growers with comparable performance to urea used in conventional orchards for improved sanitation.

Tank Mixing Fungicides for Effectiveness Against Eastern Filbert Blight of Hazelnut

Hazelnut (Corylus avellana) production in Oregon primarily occurs on cultivars susceptible to Anisogramma anomala, the causal agent of eastern filbert blight (EFB). Management of EFB involves planting resistant cultivars, removal of cankered limbs, and the application of fungicides. Tank mixes of demethylation-inhibiting (DMI; Fungicide Resistance Action Committee [FRAC] group 3) or quinone outside inhibitor (QoI; FRAC group 11) fungicides with chlorothalonil (FRAC group M5) at full or reduced rates were evaluated for effectiveness against A. anomala. The use of chlorothalonil in a mix with a DMI or QoI fungicide was an effective treatment for EFB even if each component of the mix was at half the labeled rate. Different liquid or dry formulations of chlorothalonil were equally effective in a tank mix for EFB control. The combination of propiconazole (FRAC group 3) tank mixed with trifloxystrobin (FRAC group 11) was not effective, whereas trees treated with propiconazole tank mixed with pyraclostrobin (FRAC group 11) resulted in significantly fewer EFB cankers compared with nontreated trees. When using tank mixes for EFB management, DMI fungicides should remain at full rates while mixing with a half-rate of chlorothalonil. In contrast, QoI fungicides and chlorothalonil could both be used at half-rates and still maintain acceptable EFB control. Tank mixing chlorothalonil with fungicides at risk of resistance development can help maintain consistent EFB control and should help prevent or delay the emergence of fungicide-resistant A. anomala isolates.

Incorporating Adjuvants with Captan to Manage Common Apple Diseases

Captan has become an increasingly important fungicide in the management of common apple diseases such as apple scab (Venturia inaequalis) and bitter rot (Colletotrichum spp.) due to the low risk of fungicide resistance evolving in either pathogen population to this product. Restrictions on the amount of captan that can be applied per season limits the amount and the number of applications a grower may use, resulting in control failures during high disease pressure years. This 3-year field study evaluated how adjuvants combined with captan affected the incidence and severity of apple scab and bitter rot on two different apple cultivars. Results showed that Li700 plus captan and Bond Max plus captan reduced disease incidence of apple scab and bitter rot in years with moderate to high disease pressure by increasing the coverage and retention of captan. The addition of these adjuvants also resulted in possible yield losses due to russetting caused by phytotoxicity. The overall benefits of incorporating adjuvants with captan based on this study could reduce disease incidence while potentially saving a grower up to $5,329 ha^-1 due to fungicide reduction.

Tree spacing impacts the individual incidence of Moniliophthora roreri disease in cacao agroforests

BACKGROUND

Using conventional pesticides in crop protection has raised serious environmental concerns and there is therefore a need for integrated pest management (IPM) methods. In this paper, we found that the spacing of trees can impact disease, which could result in a reduction in pesticide applications and may act as a potential IPM method. We studied Frosty Pod Rot (FPR) in 20 cacao agroforests in Costa Rica (Upala region).

RESULTS

Using a generalized linear mixed model, we analyzed the impact of the neighborhood composition and distance from a studied cacao individual on its individual FPR incidence. We found that the number of cacao tree neighbors in a radius of 3.7 m and the number of fruit trees in a radius of 4.3 m had a significant negative influence on the incidence of FPR on individual cacao trees. Moreover, cacao tree neighbors had the most significant local influence compared to the neighborhood of other taller categories such as fruit or forest trees.

CONCLUSION

The mechanisms involved are related to the barrier effect, due to the effectiveness of the cacao tree's architecture as an efficient barrier against FPR spore dispersal. This paper provides new insights into optimization of the spatial environment around each host as an original IPM method. © 2017 Society of Chemical Industry.

Effects of Fungicides and Spray Application Interval on Controlling Marssonina Blotch of Apple in the Loess Plateau Region of China

Marssonina blotch, caused by the fungus Marssonina coronariae, is a serious foliar disease on apple in East Asia as well as in other moist temperate regions in Asia, Europe, and South America. Several fungicides were investigated for their toxicity to mycelial growth and conidial germination of the pathogen in vitro. Tebuconazole, kresoxim-methyl, hexaconazole, propiconazole, and a mixture of tebuconazole and benziothiazolinone sharply inhibited mycelial growth but had less effect on conidial germination. Field tests were conducted in a commercial orchard in Baishui County, Shaanxi Province, China, during 2012, 2013, 2014, and 2015 in order to develop recommendations for apple growers. Three applications of tebuconazole, hexaconazole, propiconazole, or a mixture of tebuconazole and benziothiazolinone at 20-day intervals from early July to late August resulted in defoliation incidence of <5%. When sprays of Bordeaux mixture + tebuconazole, Bordeaux mixture + propiconazole, and Bordeaux mixture + tebuconazole and benziothiazolinone were alternated, the spray interval was extended to 25 days and defoliation incidence remained <5%. Based on historical records and our results, scouting for symptoms should begin in mid-June. We recommend commencing the spray period in early July in years with normal rainfall patterns, and spraying in mid- to late June in years with much rainfall. The findings of this study create a foundation for implementation of an efficient spray program against Marssonina leaf blotch in apple orchards in the Loess Plateau Region of China.

Effects of Sublethal Fungicides on Mutation Rates and Genomic Variation in Fungal Plant Pathogen, Sclerotinia sclerotiorum

Pathogen exposure to sublethal doses of fungicides may result in mutations that may represent an important and largely overlooked mechanism of introducing new genetic variation into strictly clonal populations, including acquisition of fungicide resistance. We tested this hypothesis using the clonal plant pathogen, Sclerotinia sclerotiorum. Nine susceptible isolates were exposed independently to five commercial fungicides with different modes of action: boscalid (respiration inhibitor), iprodione (unclear mode of action), thiophanate methyl (inhibition of microtubulin synthesis) and azoxystrobin and pyraclostrobin (quinone outside inhibitors). Mycelium of each isolate was inoculated onto a fungicide gradient and sub-cultured from the 50–100% inhibition zone for 12 generations and experiment repeated. Mutational changes were assessed for all isolates at six neutral microsatellite (SSR) loci and for a subset of isolates using amplified fragment length polymorphisms (AFLPs). SSR analysis showed 12 of 85 fungicide-exposed isolates had a total of 127 stepwise mutations with 42 insertions and 85 deletions. Most stepwise deletions were in iprodione- and azoxystrobin-exposed isolates (n = 40/85 each). Estimated mutation rates were 1.7 to 60-fold higher for mutated loci compared to that expected under neutral conditions. AFLP genotyping of 33 isolates (16 non-exposed control and 17 fungicide exposed) generated 602 polymorphic alleles. Cluster analysis with principal coordinate analysis (PCoA) and discriminant analysis of principal components (DAPC) identified fungicide-exposed isolates as a distinct group from non-exposed control isolates (PhiPT = 0.15, P = 0.001). Dendrograms based on neighbor-joining also supported allelic variation associated with fungicide-exposure. Fungicide sensitivity of isolates measured throughout both experiments did not show consistent trends. For example, eight isolates exposed to boscalid had higher EC₅₀ values at the end of the experiment, and when repeated, only one isolate had higher EC₅₀ while most isolates showed no difference. Results of this support the hypothesis that sublethal fungicide stress increases mutation rates in a largely clonal plant pathogen under in vitro conditions. Collectively, this work will aid our understanding how non-lethal fungicide exposure may affect genomic variation, which may be an important mechanism of novel trait emergence, adaptation, and evolution for clonal organisms.

Seasonal and Cross-Seasonal Timing of Fungicide Trunk Injections in Apple Trees to Optimize Management of Apple Scab

To optimize the number and timing of trunk injections for season-long control of apple scab (Venturia inaequalis), we evaluated 1 to 2 and 4 seasonal and cross-seasonal injections of potassium phosphites and synthetic fungicides and quantified residues in leaves and fruit. Phosphites accumulated in the canopy at the highest concentrations, aligned well in time with scab suppression, and gave better leaf scab control of 41.8 to 73.5% than propiconazole (16.9 to 51.5%) or cyprodinil + difenoconazole (5.4 to 17.4%). More injections of phosphites controlled leaf scab better than fewer (23.7% versus 48.2%), and more fungicide injections resulted in 21.9 to 51.1% better leaf scab control than fewer. Leaf scab control with phosphites was only 3.2 to 13.9% better with 4 cross-seasonal compared with 4 seasonal injections, while 1 to 2 seasonal compared with 1 to 2 cross-seasonal injections improved scab control only for 4.2 to 22.1%. On shoots, injected phosphites provided comparable or for 4.4 to 10.5% and 22.3 to 41.4% better scab control than spray standards. On fruit, injected phosphites slightly improved control compared with sprayed phosphites or the sprayed fungicide standard (33.4 to 40.8%). Two seasonal injections of phosphites controlled shoot scab 5.7% better than 9 spray applications. Five sprays of cyprodinil + difenoconazole controlled scab better than their injections. Fruit residues of phosphites reached 2.8 ppm and declined in all treatments except in 2 seasonal injections and phosphite sprays. Cyprodinil and difenoconazole fruit residues reached 0.02 and 0.07 ppm and declined sharply toward the end of the season. These were far below the United States, Codex, and EU MRL-s of 1, 0.8, and 0.5 ppm for difenoconazole, and 1.7, 2, and 1 ppm for cyprodinil, respectively.

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.

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.

Integrated Fruit Production and Pest Management in Europe: The Apple Case Study and How Far We Are From the Original Concept?

This review focuses on the process of adapting the original concept of Integrated Pest Management (IPM) to the wider conception of the Integrated Fruit Production (IFP) implemented in Europe. Even though most of the pest management strategies still rely on the use of synthetic pesticides, a wide array of innovative and environmentally friendly tools are now available as possible alternative to the pesticides within the modern apple production system. We also highlight how recent pest management strategies and tools have created an opening for research towards IPM improvement, including the use of biorational pesticides, semiochemicals and biological control. Forecasting models, new tree training systems and innovative spray equipment have also been developed to improve treatment coverage, to mitigate pesticide drift and to reduce chemical residues on fruits. The possible threats that jeopardize the effective implementation of IPM and particularly the risks related to the development of the pesticide resistance and the introduction of new invasive pests are also reviewed. With the directive 128/09, the European legislation recognizes IPM as a strategic approach for the sustainable use of pesticides. Within this context, IPM and related guidelines is called to meet different areas of concern in relation to the worker and bystander safety. Beside the traditional economic criteria of the market-oriented agriculture, sustainable agriculture includes the assessment of the environmental impact of the agronomic practices within the societal context where they take place. As a consequence of the raising consumer concerns about environmental impacts generated by the fruit production, IFP certification over product standards, including process aspects, are frequently required by consumers and supermarket chains.