Characterization of Fusarium oxysporum f. sp. pisi Associated with Root Rot of Field Pea in North Dakota and the Effects of Temperature on Aggressiveness

Fusarium root rot is an important disease of field pea (Pisum sativum var. sativum L.) that occurs everywhere pea is grown, causing yield loss of up to 75%. Fusarium root rot is caused by a complex of Fusarium species, most notably Fusarium solani in the Pacific Northwest of the United States and F. avenaceum in the northern Great Plains of the United States and Canada. F. oxysporum f. sp. pisi (Fop) was frequently isolated from peas exhibiting root rot symptoms in North Dakota during recent surveys. Fop causes wilt (races 1, 5, and 6) and near wilt (race 2) on pea. However, its contribution to pea root rot remains unclear. Fop race was determined for isolates from North Dakota pea root rot surveys. ND Fop isolates were evaluated for root rot pathogenicity and aggressiveness at standard and elevated temperatures. Results from greenhouse wilt assays indicated that all Fop races exist in North Dakota, with race 2 most prevalent among the 25 North Dakota isolates evaluated. Root rot evaluations conducted at 21/18°C and 25/19°C day/night temperatures demonstrated that most Fop isolates were as aggressive or more aggressive than F. solani and F. avenaceum under both temperature regimes. Aggressiveness of Fop isolates tended to increase at elevated assay temperatures. Results from these experiments indicate that Fop may be an important contributor to the root rot complex of field pea in North Dakota and should be considered in integrated pest management strategies, including pea breeding efforts to improve resistance to Fusarium root rot.[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.

Ascochyta blight in North Dakota field pea: the pathogen complex and its fungicide sensitivity

Worldwide, Ascochyta blight is caused by a complex of host-specific fungal pathogens, including Ascochyta pisi, Didymella pinodes, and Didymella pinodella. The application of foliar fungicides is often necessary for disease management, but a better understanding of pathogen prevalence, aggressiveness, and fungicide sensitivity is needed to optimize control. Leaf and stem samples were obtained from 56 field pea production fields in 14 counties in North Dakota from 2017 to 2020 and isolates were collected from lesions characteristic of Ascochyta blight. Based on fungal characteristics and sequencing the ITS1-5.8S-ITS2 region, 73% of isolates were confirmed to be D. pinodes (n = 177) and 27% were A. pisi (n = 65). Across pathogens, aggressiveness was similar among some isolates in greenhouse assays. The in vitro pyraclostrobin sensitivity of all D. pinodes isolates collected from 2017 to 2020 was lower than that of the three baseline isolates. Sensitivity of 91% of A. pisi isolates collected in 2019 and 2020 was lower than the sensitivity of two known sensitive isolates. Resistance factors (Rf) from mean EC50 values of pyraclostrobin baseline/known sensitive isolates to isolates collected from 2017 to 2020 ranged from 2 to 1,429 for D. pinodes and 1 to 209 for A. pisi. In vitro prothioconazole sensitivity of 91% of D. pinodes isolates collected from 2017 to 2020 was lower than the sensitivity of the baseline isolates and 98% of A. pisi isolates collected from 2019 to 2020 was lower than the sensitivity of the known sensitive isolates. Prothioconazole Rf ranged from 1 to 338 for D. pinodes and 1 to 127 for A. pisi. Based on in vitro results, 92% of D. pinodes and 98% of A. pisi isolates collected displayed reduced-sensitivity/resistance to both fungicides when compared to baseline/known sensitive isolates. Disease control under greenhouse conditions of both pathogens provided by both fungicides was significantly lower in isolates determined to be reduced-sensitive or resistant in in vitro assays when compared to sensitive. Results reported here reinforce growers desperate need of alternative fungicides and/or management tools to fight Ascochyta blight in North Dakota and neighboring regions.

Aggressiveness of Small-Spored Alternaria spp. and Their Sensitivity to Succinate Dehydrogenase Inhibitor Fungicides

Brown leaf spot of potato is caused by a number of small-spored Alternaria spp. Alternaria alternata sensu stricto, A. arborescens, and A. tenuissima have been reported with increasing frequency in commercial potato fields. Potato cultivars with resistance to small-spored Alternaria spp. have yet to be developed; therefore, the application of foliar fungicides is a primary management strategy. Greenhouse inoculation assays demonstrated that isolates of these three small-spored Alternaria spp. were pathogenic. Significant differences in aggressiveness were observed across isolates; however, there was no trend in aggressiveness based on species. Significant fungicide by isolate interactions in in vitro fungicide sensitivity and significant differences between baseline and nonbaseline isolates were observed in all three small-spored Alternaria spp. The ranges of in vitro sensitivity of A. alternata baseline isolates to boscalid (EC₅₀ <0.010 to 0.89 µg/ml), fluopyram (<0.010 to 1.14 µg/ml) and solatenol (<0.010 to 1.14 µg/ml) were relatively wide when compared with adepidyn (<0.010 to 0.023 µg/ml). The baseline sensitivities of A. arborescens and A. tenuissima isolates to all four fungicides were <0.065 µg/ml. Between 10 and 21% of nonbaseline A. alternata isolates fell outside the baseline range established for the four succinate dehydrogenase inhibitor (SDHI) fungicides evaluated. In A. arborescens, 10 to 80% of nonbaseline isolates had higher sensitivities than the baseline. A. tenuissima isolates fell outside the baseline for boscalid (55%), fluopyram (14%), and solatenol (14%), but none fell outside the baseline range for adepidyn. Evaluations of in vivo fungicide efficacy demonstrated that most isolates were equally controlled by the four SDHI fungicides. However, reduced boscalid efficacy was observed for four isolates (two each of A. arborescens and A. tenuissima) and reduced fluopyram control was observed in one A. alternata isolate. Results of these studies demonstrate that isolates of all three species could be contributing to the brown leaf spot pathogen complex and that monitoring both species diversity and fungicide sensitivity could be advantageous for the management of brown leaf spot in potatoes with SDHI fungicides.

Pea seed-borne mosaic virus (PSbMV) Risk Analysis of Field Pea Based on Susceptibility, Yield Loss, and Seed Transmission

Pea seed-borne mosaic virus (PSbMV), a nonpersistently aphid-transmitted potyvirus, has been reported in field pea (Pisum sativum L.)-growing regions worldwide. In 2014, PSbMV was first identified in field peas in North Dakota, U.S.A. Susceptibility and yield losses attributed to PSbMV infection are influenced by viral pathotype and host genotype. Isolate ND14-1, recovered from North Dakota infected seed and identified as pathotype 4 (P4), was mechanically inoculated onto 20 field pea cultivars under greenhouse conditions. PSbMV susceptibility, number of seeds and pods per plant, yield, symptom expression, and PSbMV seed transmission rates were assessed by cultivar. A risk assessment was developed based on cultivar susceptibility, yield reduction, and PSbMV seed transmission. Risk factors were weighted based on perceived importance to commercial field pea producers. Three cultivars were classified as low risk, seven cultivars were classified as intermediate risk, and 10 cultivars were classified as high risk. Two of the low-risk cultivars, Aragorn and Cruiser, were confirmed to be resistant to this isolate of PSbMV. Cultivar Arcadia was susceptible to PSbMV infection with mild expression of symptoms, but was classified as low risk based on a low seed transmission rate and diminished yield losses. This risk assessment could prove a useful tool for growers in field pea cultivar selection where PSbMV is prevalent.

Impact of SDH Mutations in Alternaria solani on Recently Developed SDHI Fungicides Adepidyn and Solatenol

Early blight, caused by Alternaria solani, is observed annually in all midwestern potato production areas. The use of foliar fungicides remains a primary management strategy. However, A. solani has developed reduced sensitivity or resistance to many single-site fungicides such as quinone outside inhibitor (QoI, FRAC group 11), succinate dehydrogenase inhibitor (SDHI, FRAC group 7), demethylation inhibitor (DMI, FRAC group 3), and anilinopyrimidine (AP, FRAC group 9) fungicides. Boscalid, fluopyram, solatenol, and adepidyn are EPA-registered SDHI fungicides used commercially on a variety of crops, including potato. Five SDH mutations have been characterized previously in A. solani that affect the efficacy of boscalid while only one of these mutations has been demonstrated to negatively affect fluopyram efficacy. Conidial germination assays were used to determine if a shift in sensitivity has occurred in these SDHI fungicides. A. solani isolates collected prior to the commercial application of SDHI fungicides (baseline) were compared with recently collected isolates (nonbaseline). Greenhouse evaluations were conducted also to evaluate the efficacy of boscalid, fluopyram, solatenol, and adepidyn on A. solani isolates possessing individual SDH mutations. Additionally, field trials were conducted to determine the effects of application of these SDHI fungicides on the frequency of SDH mutations. Fluopyram, solatenol, and adepidyn had high intrinsic activity against A. solani when compared with boscalid, based on in vitro assays. The application of adepidyn and solatenol resulted in greater early blight control than the application of boscalid and fluopyram in greenhouse experiments. Molecular characterization of A. solani isolates collected from the field trials determined that the frequency of the H134R-mutation can increase in response to more recently developed SDHI fungicides. In contrast, the H278R/Y- and H133R-mutations decreased to the point of being nearly absent in these field experiments.

Using Breeding Populations With a Dual Purpose: Cultivar Development and Gene Mapping-A Case Study Using Resistance to Common Bacterial Blight in Dry Bean (Phaseolus vulgaris L.)

Dry bean (Phaseolus vulgaris L.) is an important worldwide legume crop with low to moderate levels of resistance to common bacterial blight (CBB) caused by Xanthomonas axonopodis pv. phaseoli. A total of 852 genotypes (cultivars, preliminary and advanced breeding lines) from the North Dakota State University dry bean breeding program were tested for their effectiveness as populations for genome-wide association studies (GWAS) to identify genomic regions associated with resistance to CBB, to exploit the associated markers for marker-assisted breeding (MAB), and to identify candidate genes. The genotypes were evaluated in a growth chamber for disease resistance at both the unifoliate and trifoliate stages. At the unifoliate stage, 35% of genotypes were resistant, while 25% of genotypes were resistant at the trifoliate stage. Libraries generated from each genotype were sequenced using the Illumina platform. After filtering for sequence quality, read depth, and minor allele frequency, 41,998 single-nucleotide polymorphisms (SNPs) and 30,285 SNPs were used in GWAS for the Middle American and Andean gene pools, respectively. One region near the distal end of Pv10 near the SAP6 molecular marker from the Andean gene pool explained 26.7-36.4% of the resistance variation. Three to seven regions from the Middle American gene pool contributed to 25.8-27.7% of the resistance, with the most significant peak also near the SAP6 marker. Six of the eight total regions associated with CBB resistance are likely the physical locations of quantitative trait loci identified from previous genetic studies. The two new locations associated with CBB resistance are located at Pv10:22.91-23.36 and Pv11:52.4. A lipoxgenase-1 ortholog on Pv10 emerged as a candidate gene for CBB resistance. The state of one SNP on Pv07 was associated with susceptibility. Its subsequent use in MAB would reduce the current number of lines in preliminary and advanced field yield trial by up to 14% and eliminate only susceptible genotypes. These results provide a foundational SNP data set, improve our understanding of CBB resistance in dry bean, and impact resource allocation within breeding programs as breeding populations may be used for dual purposes: cultivar development as well as genetic studies.

Dry Bean and Anthracnose Development From Seeds With Varying Symptom Severity

Anthracnose, caused by the fungal pathogen Colletotrichum lindemuthianum, is a damaging seed-transmitted disease of dry beans that causes reduced seed quality and yield. Seed-to-seedling transmission of C. lindemuthianum has been documented as high as 15% in asymptomatic seeds under greenhouse conditions. Increasing pathogen colonization in seeds has been correlated with increasing anthracnose seed symptoms via quantitative PCR (qPCR), but stem colonization has not been quantified. Previous studies also have characterized seed yield and quality losses caused by planting C. lindemuthianum-infected seeds, but none evaluated the effect of growing asymptomatic seeds on disease and plant development under field conditions. A real-time qPCR assay was developed in this study and used to detect C. lindemuthianum in the stems of seedlings as early as 15 days after planting. Field trials measured the seed-to-seedling transmission of C. lindemuthianum across levels of anthracnose symptoms in seeds ranging from healthy to severely discolored. Results from these two field trials indicated that emergence and yield decreased and foliar symptoms, pathogen detection, and incidence of symptoms on progeny seeds increased as the severity of infection in planted seeds increased. In both years, planting asymptomatic seeds resulted in higher anthracnose severity than planting healthy seeds. Yield, seed weight, and incidence of symptoms on progeny seeds were not higher in asymptomatic seeds than in healthy seeds in 2014, when moderate disease pressure was observed. However, these factors were significantly different in 2015, when anthracnose severity was driven up to 75% by conducive weather conditions. This serves as a strong warning to growers that planting seed grown in a field where anthracnose was present, even if those seeds are asymptomatic, can result in yield and quality losses. Planting certified dry bean seed is always recommended.

Sources of Resistance to Fusarium solani and Associated Genomic Regions in Common Bean Diversity Panels

Common bean (Phaseolus vulgaris L.) production worldwide is hampered by Fusarium root rot (FRR), which is caused by Fusarium solani. Screening for FRR resistance on a large scale is notoriously difficult and often yields inconsistent results due to variability within the environment and pathogen biology. A greenhouse screening assay was developed incorporating multiple isolates of F. solani to improve assay reproducibility. The Andean (ADP; n = 270) and Middle American (MDP; n = 280) Diversity Panels were screened in the greenhouse to identify genetic factors associated with FRR resistance. Forty-seven MDP and 34 ADP lines from multiple market classes were identified as resistant to FRR. Greenhouse phenotyping repeatability was confirmed via five control lines. Genome-wide association mapping using ∼200k SNPs was performed on standard phenotyping score 1–9, as well as binary and polynomial transformation of score data. Sixteen and seven significant genomic regions were identified for ADP and MDP, respectively, using all three classes of phenotypic data. Most candidate genes were associated with plant immune/defense mechanisms. For the ADP population, ortholog of glucan synthase-like enzyme, senescence-associated genes, and NAC domain protein, associated with peak genomic region Pv08:0.04–0.18 Mbp, were the most significant candidate genes. For the MDP population, the peak SNPs Pv07:15.29 Mbp and Pv01:51 Mbp mapped within gene models associated with ethylene response factor 1 and MAC/Perforin domain-containing gene respectively. The research provides a basis for bean improvement through the use of resistant genotypes and genomic regions for more durable root rot resistance.

Quantifying Control Efficacy of Fungicides Commonly Applied for Potato Early Blight Management

Early blight is an economically important foliar disease of potato in the United States. Because of the lack of resistant potato cultivars, fungicides are applied extensively to obtain adequate control. To manage early blight, standard protectant fungicides and single-site mode-of-action "specialty" fungicides are applied either alone or incorporated into a fungicide rotation program. Control efficacy at two crop growth stages (tuber initiation/early bulking and late bulking/tuber maturation) and the overall tuber yield response to standard and specialty fungicides were assessed using network metaanalytic models. Control efficacy of fungicides ranged from moderate to very high (>30 to 75%) compared with the nontreated control. For both potato growth stages, specialty fungicides performed better than standard protectant fungicides. Furthermore, control efficacy of both fungicides was higher (3 to 9%) at late bulking and tuber maturation when compared with early bulking crop growth stage. Specialty fungicide programs increased overall tuber yields by 4 and 9% over standard fungicides and nontreated control, respectively. Based on the results, more precise fungicide use recommendations and fungicide programs can be developed for early blight management.

Genotypes and Genomic Regions Associated With Rhizoctonia solani Resistance in Common Bean

Rhizoctonia solani Kühn (teleomorph Thanatephorus cucumeris) is an important root rot pathogen of common bean (Phaseolus vulgaris L.). To uncover genetic factors associated with resistance to the pathogen, the Andean (ADP; n = 273) and Middle American (MDP; n = 279) diversity panels, which represent much of the genetic diversity known in cultivated common bean, were screened in the greenhouse using R. solani anastomosis group 2-2. Repeatability of the assay was confirmed by the response of five control genotypes. The phenotypic data for both panels were normally distributed. The resistance responses of ∼10% of the ADP (n = 28) and ∼6% of the MDP (n = 18) genotypes were similar or higher than that of the resistant control line VAX 3. A genome-wide association study (GWAS) was performed using ∼200k single nucleotide polymorphisms to discover genomic regions associated with resistance in each panel, For GWAS, the raw phenotypic score, and polynomial and binary transformation of the scores, were individually used as the input data. A major QTL peak was observed on Pv02 in the ADP, while a major QTL was observed on Pv01 with the MDP. These regions were associated with clusters of TIR-NB_ARC-LRR (TNL) gene models encoding proteins similar to known disease resistance genes. Other QTL, unique to each panel, were mapped within or adjacent to a gene model or cluster of related genes associated with disease resistance. This is a first case study that provides evidence for major as well as minor genes involved in resistance to R. solani in common bean. This information will be useful to integrate more durable root rot resistance in common bean breeding programs and to study the genetic mechanisms associated with root diseases in this important societal legume.

The Detection and Characterization of QoI-Resistant Didymella rabiei Causing Ascochyta Blight of Chickpea in Montana

Ascochyta blight (AB) of pulse crops (chickpea, field pea, and lentils) causes yield loss in Montana, where 1.2 million acres was planted to pulses in 2016. Pyraclostrobin and azoxystrobin, quinone outside inhibitor (QoI) fungicides, have been the choice of farmers for the management of AB in pulses. However, a G143A mutation in the cytochrome b gene has been reported to confer resistance to QoI fungicides. A total of 990 isolates of AB-causing fungi were isolated and screened for QoI resistance. Out of these, 10% were isolated from chickpea, 81% were isolated from field peas, and 9% isolated from lentil. These were from a survey of grower's fields and seed lots (chickpea = 17, field pea = 131, and lentil = 21) from 23 counties in Montana sent to the Regional Pulse Crop Diagnostic Laboratory, Bozeman, MT, United States for testing. Fungicide-resistant Didymella rabiei isolates were found in one chickpea seed lot each sent from Daniels, McCone and Valley Counties, MT, from seed produced in 2015 and 2016. Multiple alignment analysis of amino acid sequences showed a missense mutation that replaced the codon for amino acid 143 from GGT to GCT, introducing an amino acid change from glycine to alanine (G143A), which is reported to be associated with QoI resistance. Under greenhouse conditions, disease severity was significantly higher on pyraclostrobin-treated chickpea plants inoculated with QoI-resistant isolates of D. rabiei than sensitive isolates (p-value = 0.001). This indicates that where resistant isolates are located, fungicide failures may be observed in the field. D. rabiei-specific polymerase chain reaction primer sets and hydrolysis probes were developed to efficiently discriminate QoI- sensitive and - resistant isolates.

Identifying and Managing Root Rot of Pulses on the Northern Great Plains

Pulse crops (annual grain legumes such as field pea, lentil, dry bean, and chickpea) have become an important component of the cropping system in the northern Great Plains of North America over the last three decades. In many areas, the intensity of damping-off, seedling blight, root rot, and premature ripening of pulse crops is increasing, resulting in reduction in stand establishment and yield. This review provides a brief description of the important pathogens that make up the root rot complex and summarizes root rot management on pulses in the region. Initially, several specific Fusarium spp., a range of Pythium spp., and Rhizoctonia solani were identified as important components of the root rot disease complex. Molecular approaches have recently been used to identify the importance of Aphanomyces euteiches on pulses, and to demonstrate that year-to-year changes in precipitation and temperature have an important effect on pathogen prevalence. Progress has been made on management of root rot, but more IPM tools are required to provide effective disease management. Seed-treatment fungicides can reduce damping-off and seedling blight for many of the pathogens in this disease complex, but complex cocktails of active ingredients are required to protect seedlings from the pathogen complex present in most commercial fields. Partial resistance against many of the pathogens in the complex has been identified, but is not yet available in commercial cultivars. Cultural practices, especially diversified cropping rotations and early, shallow seeding, have been shown to have an important role in root rot management. Biocontrol agents may also have potential over the long term. Improved methods being developed to identify and quantify the pathogen inoculum in individual fields may help producers avoid high-risk fields and select IPM packages that enhance yield stability.

Beta Regression Model for Predicting the Development of Pink Rot in Potato Tubers During Storage

Pink rot is an important disease of potato with worldwide distribution. Severe yield and quality losses have been reported at harvest and in postharvest storage. Under conditions favoring disease development, pink rot severity can continue to increase from the field to storage and from storage to transit, causing further losses. Prediction of pink rot disease development in storage has great potential for growers to intervene at an earlier stage of disease development to minimize economic losses. Pink rot disease is estimated as percent rot confined on the interval (0 or 1, corresponding to 0% as no disease and 100% as maximum disease). In this study, beta regression is considered over the traditional ordinary least squares regression (linear regression) for fitting continuous response variables bounded on the unit interval (0,1). This method is considered a good alternative to data transformation and analysis by linear regression. The percentages of incidence of pink rot in tubers at harvest, yield, and days after harvest were used as study covariates to predict pink rot development from 32 to 78 days postharvest. Results demonstrate that the interaction between percentage of pink rot at harvest and yield is a significant predictor (P < 0.0001) of the beta regression model. A linear regression model was also designed to compare the results with the proposed beta regression model. Linear predictors observed in diagnostic plots with linear regression model was found to not be constant and an adjusted R² (0.49) was obtained. The pseudo R² (0.56) and constant variance for this study suggests that the beta regression function is adequate for predicting the development of pink rot during storage. The use of the beta prediction model could help growers decide whether to apply a fungicide to tubers going into storage or to market their crop before significant storage losses are incurred.

Individual Participant Data Meta-Analysis of Foliar Fungicides Applied for Potato Early Blight Management

Foliar fungicides continue to be the primary means of early blight management on potato in the United States. Both premium-priced, single-site mode-of-action "specialty" fungicides and standard protectant multisite fungicides are applied, either alone or incorporated into fungicide rotation programs to combat early blight. Individual participant data meta-analysis was conducted to compare overall fungicide efficacy against early blight on potato, quantify tuber yields, and identify the most efficacious timing for fungicide applications. In this study, the specialty fungicide-based applications were compared against the standard fungicides chlorothalonil and mancozeb applied alone. Type 3 fixed effects indicated that there was a significant difference (P < 0.0001) in overall efficacy and yield among the treatments applied to manage early blight in potato. There was a significant difference (P < 0.0001) among treatments in early blight development during the growing season. Applications incorporating specialty fungicides, when compared with standard fungicides, significantly affected disease severity from vegetative growth initiation (P = 0.0139) to tuber maturation (P = 0.0009). Results demonstrate that the higher cost, specialty-fungicide-based applications were most effective for early blight management in North Dakota and Minnesota.

Etiology of a Tuber Rot and Foliar Blight of Potato Caused by Phytophthora nicotianae

Although Phytophthora nicotianae is not normally considered to be an important pathogen of potato (Solanum tuberosum), intermittent outbreaks of a foliar blight and tuber rot have been reported in the United States over the past 75 years. Due to the sporadic nature of these reports, little is known about the etiology of the disease in potato. However, foliar disease and tuber rots caused by this pathogen are usually centered near areas of standing water in the field and along pivot tracks. Moreover, soil particles adhering to the foliage of infected potato plants suggest that water splash is involved in P. nicotianae dissemination and infection. Soil infestation and water splash dissemination studies were conducted under greenhouse conditions to examine the role that zoospores of P. nicotianae may play in disease on potato. In the soil infestation study, inoculum of P. nicotianae was added to soil at four rates (0.0, 1.0 × 10³, 5.0 × 10³, and 4.0 × 10⁴ zoospores/ml) and three timings (at planting and 7 and 14 days after planting). Direct infection of aboveground plant tissues was achieved via splash dissemination of inoculum onto potato foliage. All soil infestations significantly reduced emergence, with the exception of the 1.0 × 10³ zoospores/ml treatment, and no plants emerged from soil infested with 4.0 ×10⁴ zoospores/ml. Significant reductions in stem number were observed with infestations of 1.0 × 10³ and 5.0 × 10³ zoospores/ml at planting and 5.0 × 10³ zoospores/ml at 7 days after planting. Progeny tuber infections were confirmed with infestations at 1.0 × 10³ zoospores/ml at planting and 7 days after planting. Lesions developed on leaflets, petioles, leaf axils, and stems in all water splash dissemination treatments within 3 days of inoculation, significant differences in the lesion number were observed, and disease severity generally was proportional to inoculum concentration. Relative area under the disease progress curve of the 5.0 × 10³ and 4.0 × 10⁴ zoospores/ml splash dissemination treatments was significantly greater than the 0.0 zoospore and 1.0 × 10³ zoospores/ml treatments. Progeny tuber infections were observed with all water splash dissemination treatments but infection rates did not differ significantly among treatments. These studies confirm the hypothesis that water splash dissemination of P. nicotianae inoculum is a likely means by which infections of this pathogen are initiated in potato.

Molecular characterization and detection of mutations associated with resistance to succinate dehydrogenase-inhibiting fungicides in Alternaria solani

Early blight, caused by Alternaria solani, is an economically important foliar disease of potato in several production areas of the United States. Few potato cultivars possess resistance to early blight; therefore, the application of fungicides is the primary means of achieving disease control. Previous work in our laboratory reported resistance to the succinate dehydrogenase-inhibiting (SDHI) fungicide boscalid in this plant pathogen with a concomitant loss of disease control. Two phenotypes were detected, one in which A. solani isolates were moderately resistant to boscalid, the other in which isolates were highly resistant to the fungicide. Resistance in other fungal plant pathogens to SDHI fungicides is known to occur due to amino acid exchanges in the soluble subunit succinate dehydrogenase B (SdhB), C (SdhC), and D (SdhD) proteins. In this study, the AsSdhB, AsSdhC, and AsSdhD genes were analyzed and compared in sensitive (50% effective concentration [EC50] < 5 μg ml(-1)), moderately resistant (EC50 = 5.1 to 20 μg ml(-1)), highly resistant (EC50 = 20.1 to 100 μg ml(-1)), and very highly resistant (EC50 > 100 μg ml(-1)) A. solani isolates. In total, five mutations were detected, two in each of the AsSdhB and AsSdhD genes and one in the AsSdhC gene. The sequencing of AsSdhB elucidated point mutations cytosine (C) to thymine (T) at nucleotide 990 and adenine (A) to guanine (G) at nucleotide 991, leading to an exchange from histidine to tyrosine (H278Y) or arginine (H278R), respectively, at codon 278. The H278R exchange was detected in 4 of 10 A. solani isolates moderately resistant to boscalid, exhibiting EC50 values of 6 to 8 μg ml(-1). Further genetic analysis also confirmed this mutation in isolates with high and very high EC50 values for boscalid of 28 to 500 μg ml(-1). Subsequent sequencing of AsSdhC and AsSdhD genes confirmed the presence of additional mutations from A to G at nucleotide position 490 in AsSdhC and at nucleotide position 398 in the AsSdhD, conferring H134R and H133R exchanges in AsSdhC and AsSdhD, respectively. The H134R exchange in AsSdhC was observed in A. solani isolates with sensitive, moderate, highly resistant, and very highly resistant boscalid phenotypes, and the AsSdhD H133R exchange was observed in isolates with both moderate and very high EC50 value boscalid phenotypes. Detection and differentiation of point mutations in AsSdhB resulting in H278R and H278Y exchanges in the AsSdhB subunit were facilitated by the development of a mismatch amplification mutation assay. Detection of these two mutations in boscalid-resistant isolates, in addition to mutations in AsSdhC and AsSdhD resulting in an H134R and H133R exchange, respectively, was achieved by the development of a multiplex polymerase chain reaction to detect and differentiate the sensitive and resistant isolates based on the single-nucleotide polymorphisms present in all three genes. A single A. solani isolate with resistance to boscalid did not contain any of the above-mentioned exchanges but did contain a substitution of aspartate to glutamic acid at amino acid position 123 (D123E) in the AsSdhD subunit. Among A. solani isolates possessing resistance to boscalid, point mutations in AsSdhB were more frequently detected than mutations in genes coding for any other subunit.

Prevalence and Impact of SDHI Fungicide Resistance in Alternaria solani

Early blight, caused by Alternaria solani, is an important chronic foliar disease of potato (Solanum tuberosum) present every growing season in the Midwestern United States. Most currently grown potato cultivars lack resistance to early blight; therefore, foliar fungicides are relied upon for disease management. Foliar fungicides with high efficacy against the pathogen, such as boscalid, frequently are used under high disease pressure situations, such as potatoes grown under overhead irrigation. Boscalid is a member of the succinate dehydrogenase inhibiting (SDHI) fungicide group and was registered for use on potato in 2005. Baseline sensitivity of A. solani to the SDHI fungicides boscalid, penthiopyrad, and fluopyram using a spore germination assay demonstrated similar intrinsic activity against A. solani with mean EC₅₀ values of 0.33, 0.38, and 0.31 μg/ml, respectively. However, isolates varied in their sensitivity to each of these fungicides, resulting in very low correlations (r) among isolate sensitivity to each fungicide. Resistance to boscalid in A. solani was detected in the states of North Dakota, Minnesota, Nebraska, Texas, Idaho, Wisconsin, and Florida from early blight samples collected in 2010 and 2011. Two phenotypes of boscalid resistance were detected. Approximately 80% of all A. solani assayed were found to have some level of resistance to boscalid with about 5 and 75% of the population moderately resistant (5 to 20 μg/ml) and highly resistant (>20 μg/ml), respectively, to the fungicide. Nearly 99% of all boscalid resistant isolates possessed the F129L mutation in the cytrochrome b gene, indicating that an A. solani population with dual fungicide resistance predominates in the states surveyed. However, A. solani isolates resistant to boscalid remained sensitive to fluopyram, and a large proportion of moderately resistant and resistant isolates were sensitive to penthiopyrad. Disease control data from in vivo trials demonstrated a significant loss of fungicide efficacy when boscalid and fluxapyroxad were used to control moderately and highly resistant isolates of A. solani relative to the control these fungicides provided wild-type isolates. Fluopyram, however, controlled boscalid resistant isolates as well as it controlled wild-type isolates of A. solani. These data will assist potato growers in regions where boscalid resistance is prevalent by assisting them in avoiding fungicides that do not effectively control early blight and in selecting SDHI fungicide molecules that remain efficacious.

Development and Validation of a Real-Time PCR Assay for the Quantification of Verticillium dahliae in Potato

An increase in the stringency for higher quality potato tubers and restrictions on the use of soil fumigants, among other factors, has garnered renewed interest in Verticillium wilt, particularly in russet-skinned cultivars grown for processing. In response to the needs of producers, breeders have increased efforts in the development of potato cultivars with resistance to Verticillium dahliae Kleb., the primary cause of Verticillium wilt. These efforts have resulted in the release of numerous russet-skinned cultivars with purported resistance to the pathogen. However, because efficient and effective methods to screen germplasm for true resistance do not exist, breeders typically have reported resistance based on the development of wilt symptoms alone. The studies reported here demonstrate the efficiency and practicality of a QPCR method for quantification of V. dahliae in potato stem tissue. This method, developed to detect the target trypsin protease gene of the pathogen, was compared with traditional methods for V. dahliae quantification which involve plating stem tissue or sap onto semi-selective media, as well as to a recently developed QPCR assay which amplifies a region of the β-tubulin gene of V. dahliae. The QPCR assay developed in the studies reported here was demonstrated to be sensitive to 0.25 pg of DNA. Use of the duplex real-time PCR assay, utilizing the potato actin gene to normalize quantification, resulted in clearer differentiation of levels of resistance among eight russet-skinned potato cultivars inoculated in greenhouse trials when compared with traditional plating assays. However, relative levels of resistance among cultivars were similar between traditional plating and QPCR methods, resulting in correlation coefficients greater than 0.93. The assay described here also detected the pathogen in inoculated stem tissue at higher frequencies than both traditional plating assays and a previously developed QPCR assay. The QPCR assay developed here demonstrates rapid, efficient, and accurate quantification of V. dahliae, providing a tool amenable for use by breeding programs on large numbers of clones and selections, and will aid researchers evaluating other control strategies for Verticillium wilt.

Tuber Rot of Potato Caused by Phytophthora nicotianae: Isolate Aggressiveness and Cultivar Susceptibility

A study was undertaken in 2008 and 2009 to examine potato (Solanum tuberosum) cultivar susceptibility, the potential of other host species to act as sources of inoculum for potato infections, and other aspects of potato-Phytophthora nicotianae interactions. Twelve isolates of P. nicotianae collected from five leaf, one petiole, and six tuber infections of potato from five states, as well as isolates from a variety of other host species, were evaluated for ability to cause tuber rot of potato via inoculation studies. Additionally, the susceptibility of 27 potato cultivars commonly grown in the United States to tuber infection by P. nicotianae was determined. Eighty-three percent of the isolates recovered from potato were highly aggressive, infecting tubers at nearly four times greater incidences than isolates originating from nonpotato hosts. With the exception of two tobacco isolates, zoospores of all isolates recovered from nonpotato hosts were able to infect potato tubers. Russet cultivars were significantly less susceptible to P. nicotianae than red and white cultivars in 2008, and red cultivars in 2009. Umatilla Russet was the most resistant cultivar in both years, whereas Red Norland and Dakota Rose were the most susceptible in both years. Results of a survey for P. nicotianae conducted in four states from 2008 through 2010 confirmed previous observations of naturally occurring infections of potato in Missouri, Nebraska, and Texas, as well as infections of potato in Michigan (documented for the first time). All isolates recovered in the survey were sensitive to mefenoxam (EC₅₀ < 1.0 μg/ml).

Effect of Application Method and Rate on Residual Efficacy of Mefenoxam and Phosphorous Acid Fungicides in the Control of Pink Rot of Potato

Experiments were conducted to examine the effectiveness of rate and method of phosphorous acid application for controlling pink rot of potato (Solanum tuberosum) caused by Phytophthora erythroseptica. Replicated small-plot and replicated split commercial field trials were established in commercial production fields in Minnesota from 2006 to 2009. Fungicides were applied in-furrow at planting, or as one, two, or three foliar applications via ground sprayer, irrigation system (chemigation), or fixed-wing aircraft. Phosphorous acid efficacy was compared to mefenoxam, the fungicide commonly utilized to manage pink rot, either by determining natural infections in the field or by inoculating eyes of harvested tubers using a mefenoxam-sensitive and -resistant isolate of P. erythroseptica via postharvest challenge inoculation. In replicated small plot trials, both in-furrow and two foliar applications of mefenoxam controlled tuber rot in the field, and significantly controlled tuber rot in storage. Phosphorous acid also reduced tuber rot in the field when applied two or three times to the foliage. Although phosphorous acid was ineffective when applied in-furrow, one, two, and three foliar applications and a postharvest application of phosphorous acid controlled mefenoxam-sensitive and -resistant isolates of P. erythroseptica during storage for 187 days, while mefenoxam failed to control the resistant isolate. In replicated split commercial field trials, two aerial applications of phosphorous acid were as effective as three applications in reducing pink rot incidence in tubers inoculated postharvest. Three aerial applications were as effective as three chemigation applications in replicated split commercial field trials in 2008, but provided significantly greater protection than chemigation in 2009.

Competitive Parasitic Fitness of Mefenoxam-Sensitive and -Resistant Isolates of Phytophthora erythroseptica under Fungicide Selection Pressure

A 2-year field and laboratory experiment was initiated to study the competitive parasitic fitness of mefenoxam-resistant (50% effective concentration [EC₅₀] > 100 μg ml^-1) and mefenoxam-sensitive (EC₅₀ = 0.07 μg ml^-1) isolates of Phytophthora erythroseptica with equal aggressiveness. The competitive ability of the mefenoxam-resistant and -sensitive isolates was tested under no selection pressure (nonfungicide treated) as well as under the influence of mefenoxam and non-mefenoxam (phosphorous acid) fungicides. P. erythroseptica isolates were combined in four ratios of mefenoxam-resistant (R) to mefenoxam-susceptible (S) (0R:0S, 1R:1S, 3R:1S, and 1R:3S) and subsequently infested into the soil at the time of planting. In-furrow mefenoxam applications were applied to the soil immediately following infestation with P. erythroseptica. Phosphorous acid was applied at tuber initiation and 14 days after tuber initiation. Noninfested, nonfungicide-treated plots served as controls. P. erythroseptica isolates recovered from field-infected pink rot tubers at harvest and 3 to 4 weeks after harvest were tested for mefenoxam sensitivity in vitro. In vivo studies were performed by challenge inoculating a zoospore suspension in the four ratios described above onto potato tubers harvested from nontreated, phosphorous acid-treated, or mefenoxam-treated field plots. These field plots were not infested with P. erythroseptica at planting. Results from both field and in vivo studies demonstrate that mefenoxam-resistant isolates of P. erythroseptica are as fit as sensitive isolates in the absence of selection pressure or in the presence of a phosphorous acid fungicide treatment. Under mefenoxam selection pressure, mefenoxam-resistant P. erythroseptica isolates were more parasitically fit than -sensitive isolates. These studies suggest the lack of an apparent fitness penalty in mefenoxam-resistant P. erythroseptica populations under field conditions and that these isolates could be stable in most agroecological systems. Based on these results, mefenoxam-based fungicides are no longer recommended for the management of pink rot once mefenoxam-resistant P. erythroseptica populations are detected in a specific field.

Colonization of Potato by Colletotrichum coccodes: Effect of Soil Infestation and Seed Tuber and Foliar Inoculation

Colonization of potato (Solanum tuberosum) tissue, including roots, stolons, and above and below ground stems, by Colletotrichum coccodes, the causal agent of black dot, was evaluated following soil infestation, inoculation of seed tubers and foliage, and every combination thereof, in field trials over two growing seasons in North Dakota and Minnesota. A total of 107,520 isolations for C. coccodes performed across four site-years allowed for an extensive comparison of fungal colonization of the host plant and disease severity. The black dot pathogen was detected in potato stems at the first sampling date in all four site-years, as early as 14 days prior to emergence. Colonization of above and below ground stems occurred at a higher frequency than in roots and stolons in all four site-years, resulting in significantly higher relative area under the colonization progress curves (RAUCPCs) (α = 0.05). Although fungal colonization and disease incidence were higher in inoculated and/or infested treatments, sufficient natural inoculum was present to result in substantial levels of disease in noninoculated and noninfested plots. However, noninoculated and noninfested plots displayed the lowest RAUCPC values across three of four site-years and those treatments with multiple inoculation events tended to have higher RAUCPC values. Isolates belonging to vegetative compatibility group (VCG)2 and -5 were recovered from plants sampled in 2004 more frequently than isolates belonging to VCG1 and -3. A significant difference in disease incidence on stems was observed only in North Dakota in 2004 and Minnesota in 2003 (α = 0.05). Noninoculated and noninfested plots displayed the lowest disease incidence, whereas those treatments with more than one inoculation and/or infestation event tended to have higher disease incidence. Results of this study, including the disease severity and yield data, provide a better understanding of colonization of potato plants by C. coccodes and its impact.

Characterization and Epidemiological Significance of Potato Plants Grown from Seed Tubers Affected by Zebra Chip Disease

An emerging disease of potato in the United States, known as "Zebra Chip" or "Zebra Complex" (ZC), is increasing in scope and threatens to spread further. Here, we report on studies performed to understand the role of tuberborne ZC in the epidemiology of this disease. Depending on variety, up to 44% of ZC-affected seed tubers (ZCST) were viable, producing hair sprouts and weak plants. Chip discoloration in progeny tubers of ZCST was more severe than those from ZC-asymptomatic seed tubers but varied depending on whether progeny tubers or foliage were positive or negative for 'Candidatus Liberibacter solanacearum'. A low percentage of greenhouse-grown plants produced by ZCST tested positive for 'Ca. Liberibacter'. No adult potato psyllids became infective after feeding upon these plants but they did acquire 'Ca. Liberibacter' from field-grown plants produced by ZCST. Plants with new ZC infections near plants produced by ZCST were not significantly different from healthy plants, whereas plants affected with ZC from infectious potato psyllids had significantly more ZC infections near either plants produced by ZCST or healthy plants. We conclude that, in areas where ZC is currently established, plants produced by ZCST do not significantly contribute to ZC incidence and spread within potato fields.

Detection, Distribution, and Genetic Variability of 'Candidatus Liberibacter' Species Associated with Zebra Complex Disease of Potato in North America

The specificity and sensitivity of polymerase chain reaction (PCR) primers developed for 'Candidatus Liberibacter solanacearum' and 'Candidatus Liberibacter psyllaurous' were evaluated in conventional and real-time PCR assays. All PCR primers were specific for 'Ca. L. psyllaurous' and 'Ca. L. solanacearum' insomuch as they did not detect other prokaryotic plant pathogens that affect potato except for the putative pathogens associated with psyllid-yellows and haywire. Conventional PCR assays were capable of detecting 0.19 to 1.56 ng of total DNA per reaction, and real-time PCR was found capable of detecting 1.56 to 6.25 ng of total DNA per reaction, depending on the specific PCR primer set used. 'Ca. Liberibacter' species associated with zebra complex disease (ZC) was confirmed in plants affected by this disease throughout Texas from 2005 to 2008, in seed tubers produced in Wyoming in 2007, and in Colorado, Kansas, Nebraska, and Mexico in 2008. A multiplex PCR assay using 'Ca. L. solanacearum'-specific primers and primers specific for the β-tubulin DNA regions from potato was developed, providing possible utility of the multiplex assay for 'Ca. Liberibacter' detection in different solanaceous plant species. Preliminary studies suggest silverleaf nightshade (Solanum elaeagnifolium), wolfberry (Lycium barbarum), black nightshade (S. ptychanthum), and jalapeno pepper (Capsicum annuum) as additional solanaceous hosts for the ZC-associated bacterium. The 'Ca. Liberibacter' species detected in all samples divided into two clusters sharing similarity of 99.8% in their partial 16S rRNA gene sequences and 99.3% in their partial intergenic spacer region (ISR)-23S rRNA gene sequences. Genetic variation in the 16S rDNA region consistently matched that of the ISR-23S rDNA region. In this partial 16S-ISR-23S rDNA region, there was a total of eight single nucleotide polymorphisms among 'Ca. L. psyllaurous' and 'Ca. L. solanacearum' "strains" investigated in this study. 'Ca. L. solanacearum' and 'Ca. L. psyllaurous' were shown to be very closely related bacteria, if not the same, by successful amplification using a combination of forward primer of 'Ca. L. solanacearum' and reverse primer of 'Ca. L. psyllaurous' in ZC-affected potato samples. This finding clarifies the current taxonomic status of 'Ca. L. solanacearum' and 'Ca. L. psyllaurous'. The detection of 'Ca. L. solanacearum' from haywire-symptomatic potato samples demonstrates that this bacterium might also be associated with this disease.

A Real-Time PCR Assay for the Detection of Clavibacter michiganensis subsp. sepedonicus Based on the Cellulase A Gene Sequence

Clavibacter michiganensis subsp. sepedonicus, causal agent of bacterial ring rot (BRR) of potato (Solanum tuberosum), is a globally important quarantine pathogen that is managed in North America using zero tolerance regulations in the certified seed industry. C. michiganensis subsp. sepedonicus is well documented to cause symptomless infections in potato, contributing to its persistence in certified seed stocks. Reliable laboratory methods to detect symptomless infections with a high degree of sensitivity could assist in the reduction of inoculum in certified seed potato stocks. A real-time polymerase chain reaction (PCR) assay was developed using the cellulase A (CelA) gene sequence as the basis for primer design. CelA primers were specific to C. michiganensis subsp. sepedonicus grown in vitro and did not detect any other coryneform bacteria or potato pathogenic bacteria but did detect 69 strains of C. michiganensis subsp. sepedonicus. The CelA real-time PCR assay was more sensitive than immunofluorescence (IFA) and Cms50/72a PCR assays in detecting C. michiganensis subsp. sepedonicus in infected potato tuber cores blended with healthy tuber cores in simulated seed lot contamination experiments. CelA primers detected nonmucoid and mucoid strains with equivalent sensitivity. In naturally infected seed lots, CelA PCR primers also were more sensitive in detecting symptomless infections of C. michiganensis subsp. sepedonicus in seed tubers prior to planting compared to Cms50/72a PCR primers, IFA, and enzyme-linked immunosorbent assay. A real-time PCR format using the newly developed CelA primers proved to be a very robust detection tool for C. michiganensis subsp. sepedonicus with the added advantage of detecting only virulent strains of the ring rot bacterium.

Resistance to QoI Fungicides in Ascochyta rabiei from Chickpea in the Northern Great Plains

Ascochyta blight, caused by Ascochyta rabiei (teleomorph: Didymella rabiei), is an important fungal disease of chickpea (Cicer arietinum). A monitoring program was established in 2005 to determine the sensitivity of A. rabiei isolates to the QoI (strobilurin) fungicides azoxystrobin and pyraclostrobin. A total of 403 isolates of A. rabiei from the Northern Great Plains and the Pacific Northwest were tested. Ninety-eight isolates collected between 2005 and 2007 were tested using an in vitro spore germination assay to determine the effective fungicide concentration at which 50% of conidial germination was inhibited (EC₅₀) for each isolate-fungicide combination. A discriminatory dose of 1 μg/ml azoxystrobin was established and used to test 305 isolates from 2006 and 2007 for in vitro QoI fungicide sensitivity. Sixty-five percent of isolates collected from North Dakota in 2005, 2006, and 2007 and from Montana in 2007 were found to exhibit a mean 100-fold decrease in sensitivity to both azoxystrobin and pyraclostrobin when compared to sensitive isolates, and were considered to be resistant to azoxystrobin and pyraclostrobin. Under greenhouse conditions, QoI-resistant isolates of A. rabiei caused significantly higher amounts of disease than sensitive isolates on azoxystrobin- or pyraclostrobin-amended plants. These results suggest that disease control may be inadequate at locations where resistant isolates are present.

First Report of Reduced Sensitivity to a QoI Fungicide in Isolates of Alternaria solani Causing Early Blight of Potato in Canada

Early blight of potato (Solanum tuberosum L.) caused by Alternaria solani Sorauer is a frequent concern for potato growers in Canada. Management of early blight has relied on foliar fungicides that often include quinone outside inhibitor (QoI) fungicides such as azoxystrobin. In recent years, isolates of A. solani with reduced sensitivity to QoI fungicides, conferred by the presence of the F129L mutation (in the cytochrome b gene causing amino acid substitution of phenylalanine with leucine at position 129), have become widespread in potato-production areas of the United States, leading to a reduced efficacy of these products (3). Observations of reduced fungicide efficacy, following application of QoI fungicides to commercial fields in Manitoba, Canada in 2007, prompted an examination of the fungicide sensitivity of isolates of A. solani collected from fields in this province. Nine isolates of A. solani were obtained from potato foliage with typical early blight symptoms from four fields in Manitoba using standard protocols (2). Isolates were maintained on clarified V8 agar (1) and identified to species level based on conidial morphology (4). The sensitivity of each isolate to azoxystrobin was determined by assessing conidial germination on water agar plates amended with 0, 0.001, 0.01, 0.1, 1.0, or 10.0 mg/liter of azoxystrobin with protocols described previously (1). Two reference isolates of A. solani from North Dakota with known sensitivities to azoxystrobin and one isolate from Prince Edward Island (PEI), Canada, (a province yielding only isolates sensitive to azoxystrobin in previous surveys; R. D. Peters, unpublished data) were included in the assays. Calculated effective concentration (EC₅₀) values (azoxystrobin concentration inhibiting conidial germination by 50%) were determined for each isolate response from two replications of the assays. The reference isolates of A. solani from North Dakota were sensitive or had reduced sensitivity to azoxystrobin with mean EC₅₀ values of 0.02 and 0.2 mg/liter, respectively. The isolate from PEI was sensitive to azoxystrobin with a mean EC₅₀ value of 0.04 mg/liter. By contrast, isolates of A. solani from Manitoba had reduced sensitivity to azoxystrobin with mean EC₅₀ values from 0.2 to 0.8 mg/liter. Real-time PCR analysis of each isolate was performed (2) and confirmed the presence of the F129L mutation in the Manitoba isolates and the isolate with reduced sensitivity to azoxystrobin from North Dakota. The F129L mutation was absent in the azoxystrobin-sensitive wild-type isolates from PEI and North Dakota. To our knowledge, this is the first report of isolates of A. solani with reduced sensitivity to azoxystrobin in Canada. Since cross resistance among QoI fungicides has been demonstrated in A. solani isolates with the F129L mutation (3), adoption of resistance management strategies, including alternating QoI fungicides with fungicides having different modes of action and further monitoring pathogen populations for QoI sensitivity in Canadian production areas, is recommended. References: (1) J. S. Pasche et al. Plant Dis. 88:181, 2004. (2) J. S. Pasche et al. Plant Dis. 89:269, 2005. (3) J. S. Pasche and N. C. Gudmestad. Crop Prot. 27:427, 2008. (4) J. Rotem. The Genus Alternaria: Biology, Epidemiology, and Pathogenicity. The American Phytopathological Society, St. Paul, MN, 1994.

Variability in morphology and aggressiveness among North American vegetative compatibility groups of Colletotrichum coccodes

North American isolates of Colletotrichum coccodes, representing six vegetative compatibility groups (NA-VCG), were used to study morphological and pathogenic variability. The objective was to determine if variability in conidial and microsclerotial size was related to pathogenicity. Significant differences were detected in length, width, and length/width ratios of conidia as well as in the length and width of microsclerotia among the NA-VCGs. The longest and widest conidia were produced by isolates belonging to NA-VCG1 and the largest microsclerotia were produced by isolates of NA-VCG2. Conidial and microsclerotial lengths and widths also were affected significantly by type of growth medium. There was no relationship between the size of conidia and the size of microsclerotia among the NA-VCGs studied. Conidial and microsclerotial size may affect inoculum potential and survival as isolates of NA-VCG2 have been demonstrated to occur more frequently than other NA-VCGs. Aggressiveness of 17 isolates of C. coccodes representing six NA-VCG's was studied on three potato cultivars using foliar and root inoculation methods. C. coccodes infection reduced tuber weight in all cultivars with both inoculation methods although tuber weight reductions were significantly higher following root inoculations than foliar inoculations. Pathogenic aggressiveness varied among NA-VCGs. Isolates belonging to NA-VCG2 and 3 were the least aggressive on potato foliage and isolates of NA-VCG1, 2, 3, 4, and 5 produced higher microsclerotial density on all three cultivars compared with isolates of NA-VCG6. Across inoculation methods, isolates of C. coccodes belonging to NA-VCG2 and 6 were the most aggressive based on reductions in tuber weight. Umatilla Russet was the most susceptible cultivar to C. coccodes compared to other cultivars regardless of inoculation method. These results demonstrate variability in morphology and pathogenic aggressiveness among the NA-VCGs of C. coccodes but these traits are not related.

First Report of Tobacco rattle virus Causing Corky Ringspot in Potatoes Grown in Minnesota and Wisconsin

In July 2007, potato tubers cv. Russet Burbank (RB) with necrotic arcs and spots were detected in three fields in Buffalo County, Wisconsin and one field in Benson County, Minnesota. Umatilla Russet (UR) potatoes harvested from the west half of a field in Swift County, MN had similar, but visually distinct necrotic lesions. Portions of one field in Minnesota were abandoned, and the stored potato crop from two fields in Wisconsin was rejected by processors, representing a total crop loss due to tuber necrosis. Tuber symptoms displayed in both cultivars resembled those described for corky ringspot caused by Tobacco rattle virus (TRV) (4). Total RNA was isolated from necrotic tuber tissue crushed in liquid nitrogen and extracted using the Total RNA Isolation Kit (Promega Corp., Madison, WI). These extracts were tested for the presence of TRV by reverse transcription (RT)-PCR using primers complementary to nucleotides 6555 to 6575 and identical to nucleotides 6113 to 6132 within the 3' terminal open reading frame of TRV RNA-1 (3). The expected 463-bp fragments were amplified from RB tubers. Nucleotide sequences from a Wisconsin and Minnesota isolate (GenBank Accession Nos. EU569290 and EU569291, respectively) were 99 to 100% identical to the corresponding region in a published TRV sequence (GenBank Accession No. AF055912). A 396-bp fragment was amplified from UR tubers and sequence data (GenBank Accession No. EU569292) indicated a unique 63 nucleotide sequence was substituted for a 129 nucleotide sequence spanning residues 227 to 357 of the 463-bp amplicon from the RB TRV isolates. Seven fragments were sequenced from different UR tubers and the 396-bp fragment was identical among them. The sequence outside the substituted region had 92% identity to the published TRV sequence. Amplification of the full-length TRV RNA2 using primers 179/180 located in the 5' and 3' untranslated regions (2) was successful for 28 and 0% of the RB and UR samples, respectively, suggesting that the RNA2 is not present in these strains or has undergone significant mutation. TRV-infected sap from both potato cultivars was mechanically transmitted to tobacco cv. Samsun NN and these plants subsequently tested positive for TRV by ELISA using ATCC antiserum PVAS 820. Ninety tubers exhibiting mild to severe symptoms of TRV were planted in the greenhouse. Each tuber was bisected laterally; necrotic tissue was removed from one half of the tuber and tested for the presence of TRV using RT-PCR protocols described above for RNA1. The remaining half was bisected horizontally and both sections were planted. Foliage from each emerged plant was subsequently also tested by RT-PCR for TRV RNA1. All RB tubers from Wisconsin tested positive for TRV, but only 7 of 24 emerged plants tested positive. Only 72% of the UR tubers and 4 of 25 emerged plants tested positive. TRV has been confirmed in California, Colorado, Florida, Idaho, Michigan (1), Oregon, and Washington. To our knowledge, this is the first report of corky ringspot in potato caused by TRV in Minnesota and Wisconsin. References: (1) W. W. Kirk et al. Plant Dis. 92:485, 2008. (2) S. A. MacFarlane. J. Virol. Methods. 56:91, 1996. (3) D. J. Robinson. J. Virol. Methods 40:57, 1992. (4) S. A. Slack. Tobacco rattle virus. Page 71 in: Compendium of Potato Diseases. 2nd ed. W. R. Stevenson et al., eds. The American Phytopathological Society, St. Paul, MN, 2001.

A Foliar Blight and Tuber Rot of Potato Caused by Phytophthora nicotianae: New Occurrences and Characterization of Isolates

Phytophthora spp. are pathogenic to many plant species worldwide, and late blight, caused by Phytophthora infestans, and pink rot, caused by P. erythroseptica, are two important diseases of potato. Another Phytophthora sp., P. nicotianae, was recovered from pink-rot-symptomatic tubers collected from commercial fields in Nebraska, Florida, and Missouri in 2005, 2006, and 2007, respectively. P. nicotianae also was recovered from foliage obtained from commercial potato fields in Nebraska and Texas exhibiting symptoms very similar to those of late blight. Isolates of P. cactorum also were recovered from foliar infections in a commercial potato field in Minnesota in 2005. Natural infection of potato foliage by P. cactorum and infection of wounded potato tuber tissue via inoculation with zoospores of P. capsici are reported here for the first time. Isolates of P. nicotianae, regardless of origin, were primarily of the A1 mating type. All isolates of P. nicotianae and P. cactorum were sensitive to the fungicide mefenoxam. Optimum growth of P. nicotianae, P. erythroseptica, and P. cactorum in vitro occurred at 25°C; however, only P. nicotianae sustained growth at 35°C. Regardless of the tissue of origin, all isolates of P. nicotianae and P. cactorum were capable of infecting potato tubers and leaves. However, isolates of P. nicotianae were less aggressive than P. erythroseptica isolates only when tubers were not wounded prior to inoculation. Pink rot incidence varied significantly among potato cultivars following inoculation of nonwounded tubers with zoospores of P. nicotianae, ranging from 51% in Red Norland to 19% in Atlantic. Phytophthora spp. also differed significantly in their ability to infect potato leaves. Highest infection frequencies were obtained with P. infestans and levels of infection varied significantly among P. nicotianae isolates. The rate of foliar lesion expansion was similar among isolates of P. nicotianae and P. infestans. Whereas P. infestans infections yielded profuse sporulation, no sporulation was observed with foliar infections of P. nicotianae.

Baseline Sensitivity of Ascochyta rabiei to Azoxystrobin, Pyraclostrobin, and Boscalid

Ascochyta rabiei, causal agent of Ascochyta blight on chickpea (Cicer arietinum), can cause severe yield loss in the United States. Growers rely on applications of fungicides with site-specific modes of action such as the quinone outside inhibiting (QoI) fungicides azoxystrobin and pyraclostrobin, and the carboximide fungicide boscalid, to manage disease. In all, 51 isolates collected prior to QoI fungicide registration and 71 isolates collected prior to boscalid registration in the United States were tested in an in vitro assay to determine the effective fungicide concentration at which 50% of conidial germination was inhibited (EC₅₀) for each isolate-fungicide combination. The effect of salicylhydroxamic acid (SHAM) on conidia of A. rabiei in the presence and absence of azoxystrobin also was assessed to determine whether the fungus is capable of using alternative respiration. Five of nine A. rabiei isolates tested had significantly higher (P ≤ 0.05) EC₅₀ values when SHAM was not included in media amended with azoxystrobin, indicating that A. rabiei has the potential to use alternative respiration to overcome fungicide toxicity in vitro. EC₅₀ values of azoxystrobin and pyraclostrobin ranged from 0.0182 to 0.0338 μg/ml and from 0.0012 to 0.0033 μg/ml, with mean values of 0.0272 and 0.0023 μg/ml, respectively. EC₅₀ values of boscalid ranged from 0.0177 to 0.4960 μg/ml, with a mean of 0.1903 μg/ml. Establishment of these baselines is the first step in developing a monitoring program to determine whether shifts in sensitivity to these fungicides are occurring in the A. rabiei pathogen population.

NE-11 represents a new strain variant class of Potato virus Y

This report describes the characterization by whole-genome sequencing of four PVY isolates with unique combinations of molecular and symptomatic characteristics. Three of these four isolates were of type PVY(N:O) (ID-1, OR-1, PN10A), including one of "type B", which contains an extra recombination event in the 5'UTR/P1 cistron; the other (NE-11) represents a novel PVY molecular genotype, previously misclassified as a PVY(NA-NTN) isolate. The full genome sequence of this latter isolate is unique inasmuch as it is nearly identical to that of PVY(N) isolates for the first 2,000 nucleotides (nts), after which it very strongly resembles PVY(NA-NTN) isolates for the next 600 nts. For the final 7,000 nts of its genome, NE-11 shares intermediate identity with these other two previously reported classes of PVY(N) genomes, except for a portion of the capsid protein region in which it resembles neither. Recombination in each of the four isolates was verified by a suite of recombination detection programs. PN10A represents the first complete sequence of a PVY strain variant of the class reported as PVY(N)-W (or PVY(N:O)) type B. Specific PCR assays for two unique regions of NE-11 are presented that will allow the identification of this strain variant by other researchers.

Genetic Variability in the Potato Pathogen Colletotrichum coccodes as Determined by Amplified Fragment Length Polymorphism and Vegetative Compatibility Group Analyses

ABSTRACT Amplified fragment length polymorphism (AFLP) using three primer sets was used to characterize 211 Colletotrichum coccodes isolates from North America, 112 of which were assigned to six vegetative compatibility groups (VCGs) using nitrate nonutilizing (nit) mutants. These isolates clustered into five corresponding groups by unweighted pairgroup method with arithmetic means-based cluster analysis of AFLP banding patterns. Isolates of C. coccodes belonging to NA-VCG1 and NA-VCG3 were closely related, as were isolates belonging to NA-VCG2 and NA-VCG5. Based on bootstrap analysis of AFLP data, the two isolates originally assigned to NA-VCG4 clustered with isolates belonging to NA-VCG2 and NA-VCG5. C. coccodes isolates that clustered with two isolates belonging to NA-VCG6 were the most diverged from other groups, including seven isolates collected from hosts other than potato. As opposed to the bootstrap analysis, a quadratic discriminant analysis (QDA) of AFLP data correctly categorized the two isolates of NA-VCG4. Furthermore, in isolates where VCG determinations had been made, this model correctly classified isolates of all VCGs. QDA classifications were identical to those made by the bootstrap analysis, with the exception of VCG4. Overall, classifications made by the QDA model were strongly correlated (r = 0.970, P < 0.001) to the VCGs assigned by traditional methods. All 99 C. coccodes isolates evaluated only by AFLP also were subjected to QDA, leading to the assignment of a presumptive VCG for each isolate. No isolates of VCG4 or VCG6 were identified by QDA within this population. Symptoms of black dot developed in plants inoculated with isolates collected from both potato and non-potato hosts. However, total yield was not significantly reduced by infection with non-potato isolates. The lack of any additional groups identified by AFLP analysis may be an indicator of a limited level of genetic variation among North American C. coccodes isolates. AFLP is a much more efficient technique for subspecific characterization in C. coccodes than VCG analysis utilizing nit mutants and will provide an effective means by which the population biology of this pathogen can be further investigated worldwide.

Biological Significance of Mefenoxam Resistance in Phytophthora erythroseptica and Its Implications for the Management of Pink Rot of Potato

Tubers from plants treated with in-furrow and foliar applications of mefenoxam were inoculated with eight isolates of Phytophthora erythroseptica having varying levels of sensitivity to the fungicide. Two isolates with effective concentration causing 50% reduction of mycelial growth (EC₅₀) values of 0.02 and 0.04 μg ml^-1 were categorized as being mefenoxam sensitive. Isolates with EC₅₀ values >1.0 μg ml^-1 were designated as insensitive to mefenoxam and were grouped two each into low intermediate (EC₅₀ = 1.1 and 5.3 μg ml^-1), high intermediate (EC₅₀ = 26 and 74 μg ml^-1), and resistant (EC₅₀ ≥ 100 μg ml^-1). The biological significance of these isolates was examined by quantifying disease control. P. erythroseptica isolates classified in the resistant group infected a significantly greater proportion of untreated tubers than isolates in any other group. Mefenoxam reduced infection frequency of sensitive isolates by as much as 37%. Mefenoxam did not provide disease control of any isolate possessing insensitivity to the fungicide, with the greatest decrease in control observed with the low intermediate group. Aggressiveness indices, representing tuber infection frequency and depth of penetration, were calculated for untreated and mefenoxam-treated tubers. According to these indices, both isolates classified in the resistant group and high intermediate isolate 252-4 were more aggressive than sensitive isolates in the absence of mefenoxam pressure, and significantly so in the presence of mefenoxam. These results suggest that pink rot may become more severe in fields known to contain P. erythroseptica populations with mefenoxam EC₅₀ values >1.0 μg ml^-1 if the fungicide is applied. These factors should be considered when developing strategies to manage pink rot and mefenoxam-resistant populations of P. erythroseptica.

Effect of the F129L Mutation in Alternaria solani on Fungicides Affecting Mitochondrial Respiration

Isolates of Alternaria solani previously collected from throughout the Midwestern United States and characterized as being azoxystrobin sensitive or reduced sensitive were tested for sensitivity to the Quinone outside inhibitor (Q_oI) fungicides famoxadone and fenamidone and the carboxamide fungicide boscalid. All three fungicides affect mitochondrial respiration: famoxadone and fenamidone at complex III, and boscalid at complex II. A. solani isolates possessing reducedsensitivity to azoxystrobin also were less sensitive in vitro to famoxadone and fenamidone compared with azoxystrobin-sensitive isolates, but the shift in sensitivity was of lower magnitude, approximately 2- to 3-fold versus approximately 12-fold for azoxystrobin. The in vitro EC₅₀ values, the concentration that effectively reduces germination by 50% relative to the untreated control, for sensitive A. solani isolates were significantly lower for famoxadone and azoxystrobin than for fenamidone and boscalid; whereas, for reduced-sensitive isolates, famoxadone EC₅₀ values were significantly lower than all other fungicides. Isolates of A. solani with reducedsensitivity to azoxystrobin were twofold more sensitive in vitro to boscalid than were azoxystrobin-sensitive wild-type isolates, displaying negative cross-sensitivity. All isolates determined to have reduced-sensitivity to azoxystrobin also were determined to possess the amino acid substitution of phenylalanine with leucine at position 129 (F129L mutation) using real-time polymerase chain reaction. In vivo studies were performed to determine the effects of in vitro sensitivity shifts on early blight disease control provided by each fungicide over a range of concentrations. Reduced-sensitivity to azoxystrobin did not significantly affect disease control provided by famoxadone, regardless of the wide range of in vitro famoxadone EC₅₀ values. Efficacy of fenamidone was affected by some azoxystrobin reduced-sensitive A. solani isolates, but not others. Boscalid controlled azoxystrobin-sensitive and reduced-sensitive isolates with equal effectiveness. These results suggest that the F129L mutation present in A. solani does not convey cross-sensitivity in vivo among all Q_oI or related fungicides, and that two- to threefold shifts in in vitro sensitivity among A. solani isolates does not appreciably affect disease control.

Shift in Sensitivity of Alternaria solani in Response to QoI Fungicides

Isolates of Alternaria solani, cause of potato early blight, collected in 1998 through 2001 from various potato growing areas across the midwestern United States, were tested for sensitivity to azoxystrobin. Isolates collected in 1998, prior to the introduction of azoxystrobin, were tested to establish the baseline sensitivity of the fungus to this fungicide. Isolates collected in subsequent years, not necessarily from the same sites as baseline isolates, were tested to determine if populations of A. solani had become less sensitive to azoxystrobin. Azoxystrobin sensitivity was determined utilizing an in vitro spore germination assay. The effective fungicide concentration that inhibited spore germination by 50% (EC₅₀) was determined for each isolate. There was no significant difference in mean EC₅₀ values between baseline isolates and all other isolates collected through 1999. Mean azoxystrobin EC₅₀ values of A. solani isolates collected in 2000 and 2001 were significantly higher compared with means from previous years, and mean azoxystrobin EC₅₀ values from 2001 were significantly higher than means from isolates collected in 2000. A subset of 54 A. solani isolates was evaluated in vitro for cross-sensitivity to pyraclostrobin and trifloxystrobin. A highly significant and strong correlation among the isolates tested for fungicide cross-sensitivity was detected between azoxystrobin and pyraclostrobin; however, the correlation between azoxystrobin and trifloxystrobin, and between trifloxystrobin and pyraclostrobin, was significant but weak. A second subset of five isolates was chosen for in vivo assessment of azoxystrobin, pyraclostrobin, and trifloxystrobin sensitivity. Disease severity on plants treated with azoxystrobin and pyraclostrobin was significantly greater with reduced-sensitive A. solani isolates compared with sensitive isolates. Disease severity was not statistically different between azoxystrobin reduced-sensitive and sensitive A. solani isolates on plants treated with trifloxystrobin. This is the first report of a shift in sensitivity to Q_oI fungicides in a fungus possessing only an anamorphic stage.