A complex of foliar diseases affects onion production in New York, including Botrytis leaf blight (Botrytis squamosa), purple blotch (Alternaria porri), Stemphylium leaf blight (SLB; Stemphylium vesicarium), and downy mildew (Peronospora destructor). Surveys were conducted in 2015 and 2016 to evaluate the cause of severe premature foliar dieback in New York onion fields. SLB was the most prevalent disease among fields with the greatest incidence, surpassing downy mildew, purple blotch, and Botrytis leaf blight. Sequencing of the internal transcribed spacer region of ribosomal DNA and the glyceraldedyhe-3-phosphate dehydrogenase and calmodulin genes identified S. vesicarium as the species most commonly associated with SLB. S. vesicarium was typically associated with a broad range of necrotic symptoms but, most commonly, dieback of leaf tips and asymmetric lesions that often extended over the entire leaf. Because of the intensive use of fungicides for foliar disease control in onion crops in New York, the sensitivity of S. vesicarium populations to various fungicides with site-specific modes of action was evaluated. Sensitivity of S. vesicarium isolates collected in 2016 to the quinone outside inhibitor (QoI) fungicide, azoxystrobin, was tested using a conidial germination assay. Isolates representing a broad range of QoI sensitivities were selected for sequencing of the cytochrome b gene to evaluate the presence of point mutations associated with insensitivity to azoxystrobin. The G143A mutation was detected in all 74 S. vesicarium isolates with an azoxystrobin-insensitive phenotype (effective concentrations reducing conidial germination by 50%, EC50 = 0.2 to 46.7 µg of active ingredient [a.i.]/ml) and was not detected in all 31 isolates with an azoxystrobin-sensitive phenotype (EC50 = 0.01 to 0.16 µg a.i./ml). The G143A mutation was also associated with insensitivity to another QoI fungicide, pyraclostrobin. Sensitivity to other selected fungicides commonly used in onion production in New York was evaluated using a mycelial growth assay and identified isolates with insensitivity to boscalid, cyprodinil, and pyrimethanil, but not difenoconazole. The frequency of isolates sensitive to iprodione, fluxapyroxad, and fluopyram was high (93.5 to 93.6%). This article discusses the emergence of SLB as dominant in the foliar disease complex affecting onion in New York and the complexities of management posed by resistance to fungicides with different modes of action.

Prior to harvest, maize kernels are invaded by a diverse population of fungal organisms that comprise the microbiome of the grain mass. Poor post-harvest practices and improper drying can lead to the growth of mycotoxigenic storage fungi and deterioration of grain quality. Hermetic storage bags are a low-cost technology for the preservation of grain during storage, which has seen significant adoption in many regions of Sub-Saharan Africa. This study explored the use of high-throughput DNA sequencing of the fungal Internal Transcribed Spacer 2 (ITS2) region for characterization of the fungal microbiome before and after 3 months of storage in hermetic and non-hermetic (woven) bags in the United States and Kenya. Analysis of 1,377,221 and 3,633,944 ITS2 sequences from the United States and Kenya, respectively, resulted in 251 and 164 operational taxonomic units (OTUs). Taxonomic assignment of these OTUs revealed 63 and 34 fungal genera in the US and Kenya samples, respectively, many of which were not detected by traditional plating methods. The most abundant genus was Fusarium, which was identified in all samples. Storage fungi were detected in the grain mass prior to the storage experiments and increased in relative abundance within the woven bags. The results also indicate that storage location had no effect on the fungal microbiome of grain stored in the United States, while storage bag type led to significant changes in fungal composition. The fungal microbiome of the Kenya grain also underwent significant changes in composition during storage and fungal diversity increased during storage regardless of bag type. Our results indicated that extraction of DNA from ground kernels is sufficient for identifying the fungi associated with the maize. The results also indicated that bag type was the most important factor influencing changes in fungal microbiome during storage. The results also support the recommended use of hermetic storage for reducing food safety risks, especially from mycotoxigenic fungi.

Downy mildew disease, caused by the obligate oomycete pathogen Peronospora effusa, is the most important economic constraint for spinach production. Three races (races 12, 13, and 14) of P. effusa have been sequenced and assembled. The draft genomes of these three races have been deposited to GenBank and provide useful resources for dissecting the interaction between the host and the pathogen and may provide a framework for determining the mechanism by which new races of the pathogen are rapidly emerging.

Cercospora leaf spot (CLS), caused by the fungus Cercospora beticola, is the dominant foliar disease affecting table-beet production in New York. CLS epidemics occur annually and, if uncontrolled, will rapidly lead to defoliation. In broad-acre production, season-long maintenance of healthy leaves is important to facilitate harvest by top-pulling. Fungicides are the dominant means of CLS control and applications are initiated at an action threshold of 1 CLS lesion/leaf. Regular fungicide application occurs thereafter without regard for scheduling based on weather-based risk. The current action threshold was evaluated with selected fungicides in two replicated field trials. Copper oxychloride + copper hydroxide and propiconazole significantly improved CLS control if initiated prior to infection. Pydiflumetofen + difenoconazole significantly reduced area under the disease progress stairs compared with other fungicides tested and was most efficacious when applications began at 1 CLS lesion/leaf. Six replicated field trials also evaluated the utility of scheduling fungicides on weather-based risk rather than a calendar approach. Two risk thresholds (moderate and high) integrating the accumulation of daily infection values based on temperature and relative humidity from a forecaster for CLS in sugar beet were evaluated. Applications of pydiflumetofen + difenoconazole were reduced from three to two by using the forecaster at either risk threshold compared with calendar applications without affecting CLS control. For propiconazole, the moderate risk threshold provided CLS control equivalent to calendar applications and saved one spray per season. Thus, there was substantial scope to reduce spray frequency by scheduling based on weather-based risk rather than calendar applications. The optimal risk thresholds for pydiflumetofen + difenoconazole and propiconazole were high and moderate, respectively. In these trials, periods of high risk occurred less frequently than moderate risk, increasing the reapplication intervals and, hence, represented a less conservative approach to disease management.

Stemphylium leaf blight (SLB), caused by Stemphylium vesicarium, is a foliar disease of onion worldwide, and has recently become an important disease in the northeastern United States and Ontario, Canada. The symptoms begin as small, tan to brown lesions on the leaves that can progress to defoliate plants. Crop loss occurs through reduced photosynthetic area, resulting in smaller, lower-quality bulbs. Leaf necrosis caused by SLB also can compromise bulb storage, as green leaves are required for the uptake of sprout inhibitors applied prior to harvest. The pathogen can overwinter on infested onion residue and infected volunteer plants. Asymptomatic weedy hosts near onion fields may also be a source of inoculum. Production of ascospores of the teleomorph (Pleospora allii) peaks in early spring in northeastern North America, often before the crop is planted, and declines rapidly as daily mean air temperatures rise. Conidia usually are present throughout the growing season. Application of fungicides is a standard practice for management of the complex of fungi that can cause foliar diseases of onion in this region. Recent assessments have shown that populations of S. vesicarium in New York and Ontario are resistant to at least three single-site mode-of-action fungicides. Three disease prediction systems have been developed and evaluated that may enable growers to reduce the frequency and/or number of fungicide applications, but the loss of efficacious fungicides due to resistance development within S. vesicarium populations threatens sustainability. The lack of commercially acceptable onion cultivars with sufficient resistance to reduce the number of fungicides for SLB also limits the ability to manage SLB effectively. Integrated disease management strategies for SLB are essential to maintain profitable, sustainable onion production across eastern North America.