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.

Cercospora leaf spot (CLS), caused by Cercospora beticola, is one of the major diseases affecting productivity and profitability of beet production worldwide. Fungicides are critical for the control of this disease and one of the most commonly used products is the quinone outside inhibitor (Q_OI) azoxystrobin. In total, 150 C. beticola isolates were collected from two commercial processing table beet fields in Batavia, NY in 2014. The mating types of the entire population were determined, and genetic diversity of a subset of samples (n = 48) was assessed using five microsatellite loci. Sensitivity to azoxystrobin was tested using a spore germination assay. The cytochrome b gene was sequenced to check for the presence of point mutations known to confer Q_OI resistance in fungi. High allelic diversity (H_e= 0.50) and genotypic diversity (D* = 0.96), gametic equilibrium of the microsatellite loci, and equal ratios of mating types were suggestive of a mixed mode of reproduction for C. beticola. Resistance to azoxystrobin was prevalent because 41% of the isolates had values for effective concentrations reducing spore germination by 50% (EC₅₀) > 0.2 μg/ml. The G143A mutation, known to cause Q_OI resistance in C. beticola, was found in isolates with EC₅₀values between 0.207 and 19.397 μg/ml. A single isolate with an EC₅₀of 0.272 μg/ml carried the F129L mutation, known to be associated with low levels of Q_OI resistance in fungi. This is the first report of the F129L mutation in C. beticola. The implications of these findings for the epidemiology and control of CLS in table beet fields in New York are discussed.

Root-knot nematodes (Meloidogyne fallax and M. hapla) cause significant reductions in potato yield by reducing tuber quality. Concentrations of M. fallax and M. hapla DNA in soil were determined by quantitative polymerase chain reaction following sampling at planting and harvest within 78 fields across 3 years in Australia. Meloidogyne spp. were also detected using a tomato bioassay. M. fallax was more prevalent than M. hapla and DNA concentrations of M. fallax in soil were significantly higher in samples collected at harvest compared with those at planting. In contrast, M. hapla DNA in soil did not significantly change from planting to harvest. Using receiver operating characteristic curve analysis, M. fallax DNA in soil at planting and harvest was a highly accurate predictor of tuber damage at harvest and galling on tomato. Prediction accuracy for tuber damage was highest for M. fallax DNA compared with M. hapla or M. fallax + M. hapla. Both Meloidogyne spp. were detected in the peel of asymptomatic certified seed. For M. fallax, the addition of seedborne inoculum did not improve tuber damage predictions. This suggested that soilborne M. fallax populations contributed most substantially to tuber damage. These findings highlight the utility of this approach for predicting risk of crop damage from nematodes. The use of this technique as a practical management tool is discussed.

Stemphylium leaf blight caused by Stemphylium vesicarium was recently identified as an emerging disease and dominant in the foliar disease complex affecting onion in New York. Here, we report the genomes of two isolates of S. vesicarium, On16-63 and On16-391. The availability of the genomes will accelerate genomic studies of S. vesicarium, including population biology, sexual reproduction, and fungicide resistance. Additionally, comparative genomics with the other published genome of S. vesicarium causing brown spot of pear will help understand pathogen biology and underpin the development of management strategies for this disease.

Stemphylium leaf blight (SLB) caused by Stemphylium vesicarium is the dominant foliar disease affecting large-scale onion production in New York. The disease is managed by fungicides, but control f...

In late July and August 2015, foliar disease was observed in three hop (Humulus lupulus; unknown cultivars) yards in Ontario, Otsego, and Putnam counties, New York (NY). Disease incidence ranged be...