Evaluation of QoI Fungicide Application Strategies for Managing Fungicide Resistance and Potato Early Blight Epidemics in Wisconsin

CRISPR/Cas StNRL1 gene knockout increases resistance to late blight and susceptibility to early blight in potato

With the development of genome editing technologies, editing susceptible genes is a promising method to modify plants for resistance to stress. NPH3/RPT2-LIKE1 protein (NRL1) interacts with effector Pi02860 of Phytophthora infestans and creates a protein complex, promoting the proteasome-mediated degradation of the guanine nucleotide exchange factor SWAP70. SWAP70, as a positive regulator, enhances cell death triggered by the perception of the P. infestans pathogen-associated molecular pattern (PAMP) INF1. Using a clustered regularly interspaced short palindrome repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system, a construct was made to introduce four guide RNAs into the potato cultivar Agria. A total of 60 putative transgenic lines were regenerated, in which 10 transgenic lines with deletions were selected and analyzed. A mutant line with a four-allelic knockdown of StNRL1 gene was obtained, showing an ~90% reduction in StNRL1 expression level, resulting in enhanced resistance to P. infestans. Surprisingly, mutant lines were susceptible to Alternaria alternata, suggesting that StNRL1 may play a role as a resistance gene; hence, silencing StNRL1 enhances resistance to P. infestans.

Microbial consortium mediated acceleration of the defense response in potato against Alternaria solani through prodigious inflation in phenylpropanoid derivatives and redox homeostasis

The present study was carried out in a pot experiment to examine the bioefficacy of three biocontrol agents, viz., Trichoderma viride, Bacillus subtilis, and Pseudomonas fluorescens, either alone or in consortium, on plant growth promotion and activation of defense responses in potato against the early blight pathogen Alternaria solani. The results demonstrate significant enhancement in growth parameters in plants bioprimed with the triple-microbe consortium compared to other treatments. In potato, the disease incidence percentage was significantly reduced in plants treated with the triple-microbe consortium compared to untreated control plants challenged with A. solani. Potato tubers treated with the consortium and challenged with pathogen showed significant activation of defense-related enzymes such as peroxidase (PO) at 96 h after pathogen inoculation (hapi) while, both polyphenol oxidase (PPO), and phenylalanine ammonia-lyase (PAL) at 72 hapi, compared to the individual and dual microbial consortia-treated plants. The expression of antioxidant enzymes like superoxide dismutase (SOD) and catalase (CAT) and the accumulation of pathogenesis-related proteins such as chitinase and β-1,3-glucanase were observed to be highest at 72 hapi in the triple microbe consortium as compared to other treatments. HPLC analysis revealed significant induction in polyphenolic compounds in triple-consortium bioprimed plants compared to the control at 72 hapi. Histochemical analysis of hydrogen peroxide (H2O2) clearly showed maximum accumulation of H2O2 in pathogen-inoculated control plants, while the lowest was observed in triple-microbe consortium at 72 hapi. The findings of this study suggest that biopriming with a microbial consortium improved plant growth and triggered defense responses against A. solani through the induction of systemic resistance via modulation of the phenylpropanoid pathway and antioxidative network.

Farmers' perceptions on tomato early blight, fungicide use factors and awareness of fungicide resistance: Insights from a field survey in Kenya

Early blight (EB) caused by Alternaria solani is one of the most devastating tomato diseases in Kenya and is most often managed by application of synthetic fungicides. However, there have been reports from farmers about the declining efficacy of some fungicides. These reports suggest that A. solani populations in Kenya could be developing resistance to some of the commonly used fungicides. In this study, we surveyed 175 tomato fields, sampled in 3 major tomato producing counties in Kenya, to determine the status of EB, management practices, and fungicide use factors that could contribute to development of resistance to fungicides among A. solani populations in Kenya. Data was recorded on farm characteristics, EB prevalence, fungicide usage, and farmers' perceptions on fungicide efficacy. EB was prevalent in 85% of the fields and 90% of the farmers identified it as a major cause of yield loss. Tomato was grown all year round on 60% of the fields with only short fallow periods. All farmers reported that they were relying on fungicides for EB control and none among the cultivars grown was resistant to the disease. A total of 40 fungicide products, representing 20 active compounds with varying FRAC resistance risk levels were in use against EB. Majority (83%) of the farmers were applying fungicides at dosages and frequencies higher than those indicated on labels. Most farmers (81%) indicated that they had observed declines in effectiveness of at least one fungicide, used at EB control. This observation was more with fungicides in the strobilurin and triazole groups. These findings demonstrate that the current tomato production systems in Kenya do not take into account the risk of A. solani developing resistance to fungicides. Enhancing farmers' knowledge of the disease and their ability to properly select and apply fungicides is therefore crucial for effective control of EB and mitigating the high risk of fungicide resistance build up.

Assessment of Plant Extracts and their In vitro Efficacy against Potato Early Blight Incited by Alternaria solani

Botanicals obtained from the plants are well known for the suppression of inimical plant pathogens. The present study explores the efficacy of five locally available plant extracts for their antifungal activity against the early blight of potato incited by Alternaria solani. The extracts include Datura stramonium, Allium sativum, Azadirachta indica, Eucalyptus globulus, and Lantana camara. All extracts reduced mycelial growth and conidial germination of A. solani. In vitro studies showed that extracts obtained from A. sativum and A. indica have significant inhibition of mycelial growth of A. solani (88.80 and 86.62 percent) at 20 percent concentration. Higher concentrations of A. sativum extract caused a higher reduction of A. solani radial growth on potato dextrose agar medium. Extracts obtained from A. sativum and A. indica at 20 percent concentration, were found most effective for inhibition of conidial germination (85.50 and 80.04 percent) respectively of A. solani. Observations by scanning electron microscope (SEM) showed dramatic alteration in A. solani hyphae collapsed and spores shrinked when treated with extract of A. sativum at a 20 per cent concentration. The qualitative and quantitative analysis of various phytochemicals like flavonoids, alkaloids, saponins, tannins, steroids, terpenoids, glycosides, and phenols was showed A. sativum extract better than all the other plant extracts. Observation also revealed that 20 percent concentration of garlic extract has potential to inhibit to A. solani.

Large-scale study validates that regional fungicide applications are major determinants of resistance evolution in the wheat pathogen Zymoseptoria tritici in France

In modern cropping systems, the near-universal use of plant protection products selects for resistance in pest populations. The emergence and evolution of this adaptive trait threaten treatment efficacy. We identified determinants of fungicide resistance evolution and quantified their effects at a large spatiotemporal scale. We focused on Zymoseptoria tritici, which causes leaf blotch in wheat. Phenotypes of qualitative or quantitative resistance to various fungicides were monitored annually, from 2004 to 2017, at about 70 sites throughout 22 regions of France (territorial units of 25 000 km² on average). We modelled changes in resistance frequency with regional anti-Septoria fungicide use, yield losses due to the disease and the regional area under organic wheat. The major driver of resistance dynamics was fungicide use at the regional scale. We estimated its effect on the increase in resistance and relative apparent fitness of each resistance phenotype. The predictions of the model replicated the spatiotemporal patterns of resistance observed in field populations (R² from 0.56 to 0.82). The evolution of fungicide resistance is mainly determined at the regional scale. This study therefore showed that collective management at the regional scale could effectively complete local actions.

Spatiotemporal Distribution of Potato-Associated Alternaria Species in Wisconsin

Potato early blight caused by Alternaria solani and potato brown spot caused by Alternaria alternata are two common potato foliar diseases. Fungicide applications in Wisconsin target early blight with the expectation of managing brown spot simultaneously. However, distributions of the two pathogens over time and space have not been previously reported in Wisconsin. In this study, six potato fields in Wisconsin were systematically sampled during 2014 to 2017 to investigate the incidences of both pathogens; incidences of the pathogens were compared by location, timing, and year. Incidence of A. alternata had been recorded starting in late June in every field every year, whereas incidence of A. solani started later in some of the fields. At the end of each growing season throughout the four years, the highest incidence (100% most of the years) of A. solani was observed in a field in Plover, located in a concentrated potato production area of central Wisconsin, and a field in Arena, located in an isolated potato production area in southern Wisconsin. The highest incidence (100% every year) of A. alternata was observed in a field in Madison, an isolated potato field that was managed organically. Such distribution patterns could be a result of the different host ranges of the pathogens and abundance of inoculum in different geographic locations. In 2016, disease severity was correlated with the incidence of both pathogens (P < 0.0001 to P = 0.0299), but in 2017, disease severity was correlated with the incidence of A. solani in most of the fields (P < 0.0001 to P = 0.0799). These findings suggest that both Alternaria spp. are important for considering disease management strategies in central and southern Wisconsin.

Intact salicylic acid signalling is required for potato defence against the necrotrophic fungus Alternaria solani

KEY MESSAGE

Using disease bioassays and transcriptomic analysis we show that intact SA-signalling is required for potato defences against the necrotrophic fungal pathogen Alternaria solani.

ABSTRACT

Early blight, caused by the necrotrophic fungus Alternaria solani, is an increasing problem in potato cultivation. Studies of the molecular components defining defence responses to A. solani in potato are limited. Here, we investigate plant defence signalling with a focus on salicylic acid (SA) and jasmonic acid (JA) pathways in response to A. solani. Our bioassays revealed that SA is necessary to restrict pathogen growth and early blight symptom development in both potato foliage and tubers. This result is in contrast to the documented minimal role of SA in resistance of Arabidopsis thaliana against necrotrophic pathogens. We also present transcriptomic analysis with 36 arrays of A. solani inoculated SA-deficient, JA-insensitive, and wild type plant lines. A greater number of genes are differentially expressed in the SA-deficient mutant plant line compared to the wild type and JA- insensitive line. In wild type plants, genes encoding metal ion transporters, such as copper, iron and zinc transporters were upregulated and transferase-encoding genes, for example UDP-glucoronosyltransferase and Serine-glyoxylate transferase, were downregulated. The SA-deficient plants show upregulation of genes enriched in GO terms related to oxidoreductase activity, respiratory chain and other mitochondrial-related processes. Pathogenesis-related genes, such as genes encoding chitinases and PR1, are upregulated in both the SA-deficient and wild type plants, but not in the JA-insensitive mutants. The combination of our bioassays and the transcriptomic analysis indicate that intact SA signalling, and not JA signalling, is required for potato defences against the necrotrophic pathogen A. solani.

ELECTRONIC SUPPLEMENTARY MATERIAL

The online version of this article (10.1007/s11103-020-01019-6) contains supplementary material, which is available to authorized users.

Fungicide Sensitivity Monitoring of Alternaria spp. Causing Leaf Spot of Sugarbeet (Beta vulgaris) in the Upper Great Lakes

Alternaria leaf spot (ALS), caused by Alternaria spp., can occur wherever sugarbeet is grown. Infection by Alternaria spp. and disease management has historically been considered a minor issue in sugarbeet production in the United States. An increase of both incidence and severity in 2016 of ALS high enough to cause yield loss has been observed in Michigan. With a renewed need to consider potential management of this disease, the sensitivity was determined for populations of Alternaria spp. to three classes of fungicides currently labeled for management of leaf spot on sugarbeet, including demethylase inhibitor (DMI), quinone outside inhibitor (QoI), and organo-tin fungicides. Leaves with symptoms of ALS were sampled from sugarbeet fields in east-central Michigan and southwestern Ontario, Canada. Monoconidial isolates were obtained to determine sensitivity to each fungicide class above. A spiral gradient dilution method was used to estimate the fungicide effective concentration (in milligrams per liter) that caused a 50% inhibition of fungal growth in vitro for all isolates. Significant temporal shifts were detected in the frequencies of sensitivity phenotypes to DMI and QoI but not organo-tin fungicides from 2016 through 2017. Individual isolates of Alternaria spp. were recovered with cross-resistance to DMI and multiple resistance to DMI, QoI, and triphenyltin hydroxide fungicides. To our knowledge, this is the first report of a fungus other than Cercospora beticola with resistance to organo-tin fungicides. Fungicide sensitivity monitoring indicates that an effective integrated disease management approach combining fungicide efficacy trials and monitoring pathogen biology is essential for developing effective resistance management recommendations.

Distribution and Stability of Quinone Outside Inhibitor Fungicide Resistance in Populations of Potato Pathogenic Alternaria spp. in Wisconsin

Quinone outside inhibitor (QoI) fungicides have been an important class in managing potato early blight caused by Alternaria solani and brown spot caused by A. alternata. Because of the single-site mode of action character of QoI fungicides, which are relied on for management of diseases in Wisconsin, and the abundant asexual conidia production of the Alternaria species, pathogen isolates with QoI resistance have been detected after just a few years of QoI fungicide usage in commercial production fields. Resistance to QoIs has been attributed to amino acid substitutions F129L and G143A in cytochrome b of A. solani and A. alternata, respectively, as a result of point mutations. The aim of this study was to assess Alternaria populations in Wisconsin for QoI resistance before and after fungicide applications in order to evaluate resistance stability. A TaqMan single nucleotide polymorphism genotyping assay was designed based on the sequences of the cytochrome b gene from Alternaria isolates collected in Wisconsin to profile QoI resistance in Alternaria populations as well as to explore factors that may influence frequency of QoI resistance in the pathogen populations. This assay successfully identified the mutations conferring QoI resistance in isolates collected from four locations each year from 2015 to 2017. During the course of this study, the frequency of A. solani isolates with the F129L mutation was consistently high and showed primarily the TTA mutation type. The frequency of A. alternata isolates with the G143A mutation started relatively low and increased at the end of the production season in each year (P = 0.0109, P = 0.2083, and P = 0.0159). A potato field managed without use of QoI fungicides showed a significantly lower (P < 0.05) frequency of A. alternata isolates carrying G143A than conventionally managed potato fields. The overall frequency of A. alternata isolates carrying G143A in the four locations was similar over the 3 years (P = 0.2971). The QoI resistance characteristics of the isolates were stable even when QoI selection pressure was removed for at least five subculture transfers, and the mutation types of codons 129 and 143 in the cytochrome b gene in A. solani and A. alternata, respectively, remained the same. This indicated that the application of QoIs in the field is not the sole factor responsible for the variation of the frequency of QoI resistance in the pathogen populations.

Aerial Concentrations of Pathogens Causing Early Blight and Brown Spot Within Susceptible Potato Fields

Early blight caused by Alternaria solani and brown spot caused by A. alternata are two common foliar diseases of potato, with early blight typically predominating in incidence and severity. Renewed interest in these two diseases has arisen as a result of notable differences in fungicide resistance profiles of the pathogens and inconsistent outcomes of disease management tactics. The pathogens share similar disease cycles, but they differ in the shape and size of their conidia. A. solani has a host range that includes just the Solanaceae, whereas A. alternata has a broad host range spanning numerous plant families. Such differences may result in differences in dispersal of the pathogens and subsequently influence epidemiology and management outcomes. In the commercial potato fields investigated in this study, the aerial conidial concentrations of A. solani and A. alternata differed significantly, with those of A. alternata conidia being higher in number and more variable than those of A. solani. The aerial conidial concentration of A. solani almost always significantly decreased with height (0 to 3 m above the canopy), whereas such a decrease was only observed for 4 of 12 days for A. alternata. The atmospheric concentrations of A. alternata were higher than those of A. solani at both upwind and downwind edges of the field (P < 0.0001), indicating more potential for long-distance dispersal. A higher aerial concentration of conidia at the downwind than the upwind location was observed for A. solani (P < 0.05), whereas overall no such effect was observed for A. alternata. This indicated that the potato fields investigated were likely the source of A. solani conidia, but they may not be the sole source of A. alternata. Results are consistent with inoculum of A. solani coming primarily from within the potato crop, whereas that of A. alternata may be generated from diverse plant sources across the landscape.

Characterization of Early Blight Resistance in Potato Cultivars

Early blight, caused by the fungus Alternaria solani, is one of the most economically important foliar diseases of potatoes worldwide. In this study, 217 tetraploid old and modern potato cultivars were evaluated for foliar resistance to early blight in field experiments in Pennsylvania in 2016 and 2017. Relative area under the disease progress curve (RAUDPC) was calculated based on visual assessment of foliar disease during the growing season each year. RAUDPC ranged from 0.0090 to 0.7372 in 2016 and from 0.0215 to 0.7889 in 2017, respectively. Significant differences in resistance to A. solani among cultivars were found (P < 0.0001). A significant interaction was found between cultivar and environment (P < 0.0001). Cluster analysis classified the cultivars into five groups: resistant, moderately resistant, intermediate, moderately susceptible, and susceptible. Broad-sense heritability for early blight resistance was estimated as 0.89 with a 95% confidence interval of 0.86 to 0.92. All cultivars were also evaluated for foliage maturity in separate field trials in 2016 and 2017, and a strong negative correlation between early blight resistance and maturity was found. Maturity-adjusted RAUDPC was calculated by regressing maturity on RAUDPC; predicted values more than two standard deviations greater or less than observed values were used to identify cultivars with greater genetic susceptibility or resistance to early blight, respectively, independent of maturity. Although most resistant and moderately resistant cultivars showed late maturity and most susceptible cultivars showed early maturity, a few exceptions were found.

Diversity and Virulence of Alternaria spp. Causing Potato Early Blight and Brown Spot in Wisconsin

Early blight, caused by Alternaria solani, along with brown spot, caused by A. alternata, have the potential to reduce quality and yield in potato production globally. Prior to this study, the incidence, disease impact, and fungicide resistance attributes of A. alternata in Wisconsin were poorly understood. Potato pathogens were isolated from foliar lesions at three commercial locations in Wisconsin in 2012 and 2017 and were initially morphologically identified as A. solani (n = 33) and A. alternata (n = 40). Identifications were further corroborated with the phylogenetic analysis of the internal transcribed spacer (ITS), translation elongation factor 1 (TEF1), gapdh, Alt a 1, and OPA10-2. A multigene phylogeny of ITS, TEF1, gapdh, and Alt a 1 showed five genotypes of A. alternata and one single genotype of A. solani. We demonstrated that the A. alternata isolates were virulent on potato cultivars Russet Burbank (P < 0.013) and Atlantic (P < 0.0073), though they caused less disease than A. solani (P < 0.0001 and P < 0.0001, respectively). A. alternata caused little disease on the breeding line 24-24-12 (P = 0.9929), and A. solani caused fewer disease symptoms on 24-24-12 than on Russet Burbank (P < 0.0001) or Atlantic (P < 0.0001). Breeding line 24-24-12 may be a promising source of potential resistance for the two diseases. There was no significant difference in virulence of different A. alternata genotypes, and no significant difference in virulence or genotype clustering among isolates from the three locations. Isolates of A. alternata that induced chlorosis caused larger lesion areas than isolates that did not in Russet Burbank (P < 0.0001), Atlantic (P < 0.0001), and 24-24-12 (P = 0.0365). There was no significant difference in virulence between quinone outside inhibitor (QoI)-sensitive and QoI-resistant isolates of A. alternata. This study enhanced our understanding of potato early blight and brown spot in Wisconsin, and suggested that A. alternata in addition to A. solani should be carefully monitored and possibly uniquely managed in order to achieve overall disease control.

Discovering Novel Alternaria solani Succinate Dehydrogenase Inhibitors by in Silico Modeling and Virtual Screening Strategies to Combat Early Blight

Alternaria blight is an important foliage disease caused by Alternaria solani. The enzyme Succinate dehydrogenase (SDH) is a potential drug target because of its role in tricarboxylic acid cycle. Hence targeting Alternaria solani SDH enzyme could be efficient tool to design novel fungicides against A. solani. We employed computational methodologies to design new SDH inhibitors using homology modeling; pharmacophore modeling and structure based virtual screening. The three dimensional SDH model showed good stereo-chemical and structural properties. Based on virtual screening results twelve commercially available compounds were purchased and tested in vitro and in vivo. The compounds were found to inhibit mycelial growth of A. solani. Moreover in vitro trials showed that inhibitory effects were enhanced with increase in concentrations. Similarly increased disease control was observed in pre-treated potato tubers. Hence the applied in silico strategy led us to identify novel fungicides.

Current Status of Early Blight Resistance in Tomato: An Update

Early blight (EB) is one of the dreadful diseases of tomato caused by several species of Alternaria including Alternaria linariae (which includes A. solani and A. tomatophila), as well as A. alternata. In some instances, annual economic yield losses due to EB have been estimated at 79%. Alternaria are known only to reproduce asexually, but a highly-virulent isolate has the potential to overcome existing resistance genes. Currently, cultural practices and fungicide applications are employed for the management of EB due to the lack of strong resistant cultivars. Resistance sources have been identified in wild species of tomato; some breeding lines and cultivars with moderate resistance have been developed through conventional breeding methods. Polygenic inheritance of EB resistance, insufficient resistance in cultivated species and the association of EB resistance with undesirable horticultural traits have thwarted the effective breeding of EB resistance in tomato. Several quantitative trait loci (QTL) conferring EB resistance have been detected in the populations derived from different wild species including Solanum habrochaites, Solanum arcanum and S. pimpinellifolium, but none of them could be used in EB resistance breeding due to low individual QTL effects. Pyramiding of those QTLs would provide strong resistance. More research is needed to identify additional sources of useful resistance, to incorporate resistant QTLs into breeding lines through marker-assisted selection (MAS) and to develop resistant cultivars with desirable horticultural traits including high yielding potential and early maturity. This paper will review the current understanding of causal agents of EB of tomato, resistance genetics and breeding, problems associated with breeding and future prospects.

Genetic diversity and occurrence of the F129L substitutions among isolates of Alternaria solani in south-eastern Sweden

BACKGROUND

Early blight, caused by the fungus Alternaria solani, occurs on potato mainly in the south-eastern part of Sweden, but also in other parts of the country. The aim of this study was to investigate the genetic diversity of A. solani populations from different potato growing regions in south-eastern Sweden using AFLP marker analysis. In addition, the cultured isolates were examined for substitutions in the gene encoding cytochrome b, associated with loss of sensitivity against QoI fungicides.

RESULTS

Nei's gene diversity index for the Swedish populations of A. solani revealed a gene diversity of up to 0.20. Also genetic differentiation was observed among populations of A. solani from different locations in south-eastern Sweden. The mitochondrial genotype of the isolates of A. solani was determined and both known genotypes, GI (genotype 1) and GII (genotype 2), were found among the isolates. The occurrence of the F129L substitution associated with a loss of sensitivity to strobilurins was confirmed among the GII isolates. In vitro conidial germination tests verified that isolates containing the F129L substitution had reduced sensitivity to azoxystrobin and, at a lower extent, to pyraclostrobin.

CONCLUSIONS

Genetic diversity was relatively high among isolates of A. solani in south-eastern part of Sweden. F129L substitutions, leading to reduced sensitivity to strobilurins, have been established in field populations, which may have implications for the future efficacy of QoI fungicides.

Ex Vivo Application of Secreted Metabolites Produced by Soil-Inhabiting Bacillus spp. Efficiently Controls Foliar Diseases Caused by Alternaria spp

Bacterial biological control agents (BCAs) are largely used as live products to control plant pathogens. However, due to variable environmental and ecological factors, live BCAs usually fail to produce desirable results against foliar pathogens. In this study, we investigated the potential of cell-free culture filtrates of 12 different bacterial BCAs isolated from flower beds for controlling foliar diseases caused by Alternaria spp. In vitro studies showed that culture filtrates from two isolates belonging to Bacillus subtilis and Bacillus amyloliquefaciens displayed strong efficacy and potencies against Alternaria spp. The antimicrobial activity of the culture filtrate of these two biological control agents was effective over a wider range of pH (3.0 to 9.0) and was not affected by autoclaving or proteolysis. Comparative liquid chromatography-mass spectrometry (LC-MS) analyses showed that a complex mixture of cyclic lipopeptides, primarily of the fengycin A and fengycin B families, was significantly higher in these two BCAs than inactive Bacillus spp. Interaction studies with mixtures of culture filtrates of these two species revealed additive activity, suggesting that they produce similar products, which was confirmed by LC-tandem MS analyses. In in planta pre- and postinoculation trials, foliar application of culture filtrates of B. subtilis reduced lesion sizes and lesion frequencies caused by Alternaria alternata by 68 to 81%. Taken together, our studies suggest that instead of live bacteria, culture filtrates of B. subtilis and B. amyloliquefaciens can be applied either individually or in combination for controlling foliar diseases caused by Alternaria species.

Use of PCR-RFLP Analysis to Monitor Fungicide Resistance in Cercospora beticola Populations from Sugarbeet (Beta vulgaris) in Michigan, United States

Genetic resistance to Quinone outside inhibitor (QoI) and benzimidazole fungicides may be responsible for a recent decline in efficacy of chemical control management strategies for Cercospora leaf spot (CLS) caused by Cercospora beticola in Michigan sugarbeet (Beta vulgaris) fields. The target genes and fungicide resistance mutations are known for these two fungicides. Based on this, two standard polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) assays were developed to detect the G143A and E198A point mutations in the fungal mitochondrial cytochrome b and the β-tubulin genes, respectively. These mutations confer a high level of resistance to either QoI or benzimidazole fungicides. The presence of the G143A and E198A mutations was monitored within C. beticola populations recovered from Michigan sugarbeet production fields collected in 2012. Both the QoI-resistant cytochrome b allele and the benzimidazole-resistant β-tubulin allele were detected directly from leaf tissue following a PCR-RFLP assay. Using either detection assay, the G143A and E198A mutations were detected in over 90% of the 118 field samples originating from Michigan sugarbeet production under fungicide management programs for CLS control. Monitoring of the G143A and E198A mutations in fields located in 9 counties and 58 townships indicated that the mutations were widespread in Michigan sugarbeet production areas. The PCR-based assays used and developed in this study were effective in detecting the presence of the G143A and E198A mutations in C. beticola field populations from Michigan.

Baseline Sensitivity of Guignardia citricarpa Isolates from Florida to Azoxystrobin and Pyraclostrobin

Citrus black spot (CBS), caused by Guignardia citricarpa, is an emerging disease in Florida. Fungicide applications are the main control measure worldwide. The in vitro activity and baseline sensitivity of G. citricarpa isolates to quinone outside inhibitor (QoI) fungicides (azoxystrobin and pyraclostrobin) were evaluated. The effective concentration needed to reduce mycelial growth or spore germination by 50% (EC₅₀) was determined for 86 isolates obtained from Florida counties where CBS is found. The effect of salicylhydroxamic acid (SHAM) plus azoxystrobin and pyraclostrobin was also assessed for mycelial growth and conidial germination. The mean EC₅₀ for mycelial growth for azoxystrobin was 0.027 μg/ml and that for pyraclostrobin was significantly lower at 0.007 μg/ml (P < 0.0001). Similarly, the mean EC₅₀ for conidial germination for azoxystrobin was 0.016 μg/ml and that for pyraclostrobin was significantly lower at 0.008 μg/ml (P < 0.0001). There was no effect of SHAM on inhibition of mycelial growth or conidial germination by the QoI fungicides but SHAM slightly affected mycelium inhibition by pyraclostrobin. Cytochrome b was partially sequenced and three group 1 introns were found. One intron was immediately post G143, likely inhibiting resistance-conferring mutations at that site. It is surmised that the QoI resistance risk is low in the Florida G. citricarpa population.

Distribution of QoI Resistance in Populations of Tangerine-Infecting Alternaria alternata in Florida

Chemical control, based on copper and quinone outside inhibitor (QoI) fungicides, has been essential for the management of brown spot of citrus, caused by Alternaria alternata. However, QoI control failures were detected recently in Florida. From 2008 to 2012, 817 monoconidial isolates of A. alternata from 46 citrus orchards were examined for sensitivity to azoxystrobin (AZ) and pyraclostrobin (PYR). Of the isolates, 57.6% were resistant to both fungicides, with effective concentration to inhibit 50% growth (EC₅₀) values greater than 5 μg/ml for AZ and 1 μg/ml for PYR. The mean EC₅₀ values for sensitive isolates were 0.139 and 0.020 μg/ml for AZ and PYR, respectively. The EC₅₀ values of both fungicides were highly correlated (P < 0.0001), indicating cross resistance. The proportion of resistant isolates differed significantly (P < 0.0001) among cultivars and with QoI application frequency (P < 0.0001). However, resistance was not significantly related (P = 0.364) to disease severity in the field (low, moderate, and high) or isolate virulence (P = 0.397). The molecular basis for QoI resistance was determined for a subset of 235 isolates using polymerase chain reaction restriction fragment length polymorphism of the cytochrome b gene. All resistant isolates showed the point mutation G143A. Based on the presence of one or two introns, isolates were classified as profile I and profile II, respectively. The resistance frequency was significantly higher (P < 0.0001) in isolate profile II, suggesting a higher selection pressure for resistant population profile II.

A Rapid Resazurin-Based Microtiter Assay to Evaluate QoI Sensitivity for Alternaria alternata Isolates and Their Molecular Characterization

Chemical management of Alternaria brown spot of citrus is based upon the timely application of site-specific fungicides, many of which are vulnerable to the development of fungicide resistance. A rapid microtiter bioassay based on the colorimetric changes of resazurin (RZ) dye was developed to evaluate the sensitivity of Alternaria alternata to quinone outside inhibitor (QoI) fungicides. Four liquid media (complete medium, minimal medium, potato dextrose broth, and yeast peptone dextrose broth), five conidia concentrations (from 10¹ to 10⁵ conidia/ ml), and five RZ concentrations (10, 20, 30, 40, and 50 μM) were evaluated. Complete medium at 10⁵ conidia/ml and 40 μM RZ were identified as optimal for measuring RZ reduction. The effective concentration of two QoI fungicides (azoxystrobin and pyraclostrobin) needed to reduce RZ by 50% (EC₅₀) was calculated and compared with those obtained from conidia germination tests on fungicide-amended media. Concordant EC₅₀ values were observed (R² = 0.923; P < 0.0001) from both methods. Resistant phenotypes were further characterized by the partial sequencing of the cytochrome b gene. Genetic variability associated with the presence or absence of two introns was observed among isolates. The identified resistant isolates had the amino acid substitution G143A, typical of QoI resistance in other fungi.

Early Blight Control in Potato Using Disease-Orientated Threshold Values

Epidemics of early blight caused by Alternaria spp. can cause significant economic damage to potato production if not adequately controlled. In order to improve control of Alternaria spp. in potato, studies were conducted to identify the optimal fungicide strategy and, if possible, to reduce the number of fungicide applications per growing season. Therefore, a disease-threshold-based framework was tested to define the optimal timing of fungicide application. The initiation and subsequent applications of fungicides were based on increases in disease incidence or severity. Adequate disease control was achieved by a three-time application with azoxystrobin, given that the applications were carried out at pivotal times in the epidemic. Targeted applications of fungicides reduced the number of sprayings required to protect starch yield. Results indicate that early blight can be effectively managed by using fungicide application thresholds based on disease progress.