Diversity of Genetic and Vegetative Compatibility Group of Colletotrichum coccodes Isolates from Chile Using Amplified Fragment Length Polymorphism Markers.

Colletotrichum coccodes (Wallr.) Hughes is an asexual fungus with five vegetative compatibility groups. It was postulated that C. coccodes was isolated at the center of origin of potato at one time, and due to the movement of potato around the globe, the fungus was established on each continent but became bottlenecked and genetically unable to form stable heterokaryons via vegetative compatibility grouping (VCG) studies. The objectives of this study were (i) to determine if the VCGs around the world are related to the VCGs in Chile, (ii) to determine the diversity of C. coccodes populations in Chile, and (iii) to find any evidence for a cryptic sexual life cycle for this fungus. Worldwide C. coccodes populations have been found to be genetically correlated and belong to one or more C. coccodes-identified VCGs. The most distributed VCG in Chile was VCG2, which is the most common VCG in North America. We hypothesize that one or more VCGs had spread from Chile to the rest of the world. Precautions and further studies should be investigated by using other molecular markers and gene sequencing.

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.

Phylogenetics of tobacco rattle virus isolates from potato (Solanum tuberosum L.) in the USA: a multi-gene approach to evolutionary lineage.

Tobacco rattle virus (TRV) is an important soil-borne virus of potato that is transmitted by stubby-root nematodes. TRV causes corky ringspot, a tuber disease of economic importance to potato production. Utilizing protein-coding regions of the whole genome and a range of computational tools, the genetic diversity, and population structure of TRV isolates from several potato-growing regions (Colorado, Idaho, Indiana, Minnesota, Nebraska, North Dakota, and Washington State) in the USA were determined. Phylogenetic analyses based on RNA2 nucleotide sequences, the coat protein (CP) and nematode transmission (2b) genes, showed geographical clustering of USA isolates with previously known American isolates, while European isolates grouped in a distinct cluster. This was corroborated by the observed genetic differentiation and infrequent gene flow between American and European isolates. Low genetic diversity was revealed among American isolates compared to European isolates. Phylogenetic clustering based on RNA1 genes (RdRp, RdRp-RT, and 1a) were all largely incongruent to that of 1b gene (virus suppressor of RNA silencing). This genetic incongruence suggested the influence of recombination. Furthermore, the RdRp, RdRp-RT, and 1a genes were predicted to be more conserved and under negative selection, while the 1b gene was less constrained. Different evolutionary lineages between TRV RNA1 and RNA2 genomic segments were revealed.

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.

Development and Application of a Real-Time Reverse-Transcription PCR and Droplet Digital PCR Assays for the Direct Detection of Potato mop top virus in Soil.

Potato mop top virus (PMTV) is a continuing threat to potato production throughout the world. It has the potential to persist in the soil for long periods in the sporosori of its vector Spongospora subterranea f. sp. subterranea, which is as an important source for PMTV infection and dissemination. In this study, we used real-time quantitative reverse-transcription PCR (qRT-PCR) and reverse-transcription droplet digital PCR (RT-ddPCR) assays of the total RNA extracted directly from the soil to develop a simple, fast, and sensitive method to detect PMTV in soil samples using a specific primer with high efficiency despite a minimal amount of viral RNA. The designed primers are resilient in the presence of various PCR inhibitors in the soil when RNA is extracted. Both assays detected PMTV in all soil types used and supported the detection of <10 PMTV copies µl-1 in the RNA sample. With qRT-PCR, detection was linear, with amplification efficiencies ranging from 93.3 to 105.3% for silt loam, loamy sand, sand, and sandy loam in various experiments with R2 > 0.99. Furthermore, the RT-ddPCR assay also demonstrated a high degree of linearity (R2 > 0.99 and P < 0.0001) with the RNA extracted from the soil samples representing different textures and physiochemical characteristics that were artificially spiked with infested S. subterranea f. sp. subterranea sporosori. Additionally, both assays successfully detected PMTV in different types of naturally infested soil with PMTV carrying S. subterranea f. sp. subterranea sporosori levels ranging from 6.2 × 102 g-1 to 1.2 × 106 g-1 in soils with pH ranging from 4.9 to 7.5 and organic matter ranging from 0.9 to 5.1%, demonstrating the potential to detect PMTV in a wide variety of soils. To our knowledge, this is the first report of the development of real-time PCR and ddPCR methods for the direct detection of a soilborne virus in soil.

Detection and Quantification of Spongospora subterranea Sporosori in Soil by Quantitative Real-Time PCR.

Powdery scab on potato tubers is caused by the obligate soilborne biotroph Spongospora subterranea and is known to cause substantial losses in potato production. The pathogen also infects roots of susceptible hosts, forming galls which can negatively affect root function. S. subterranea is also the vector of Potato mop-top virus, which causes a tuber necrosis disease that can, depending on temperature and cultivar, render potato tubers unmarketable. In this study, we adapted a published protocol to develop a sensitive and robust quantitative real-time PCR (qPCR) assay using specific primers and probes for detecting and quantifying S. subterranea sporosori in soil types that differ in physical properties, including organic matter content and soil pH. For the first time, an external control was utilized and applied directly to the soil prior to DNA extraction, which facilitated normalization of S. subterranea sporosori soil levels from sample to sample. The duplex qPCR protocol was demonstrated to be highly sensitive, capable of detecting and quantifying as few as 1 sporosorus/g of soil, with consistently high qPCR efficiency and the coefficient of determination (R2) values ranging from 94 to 99% and 0.98 to 0.99, respectively. The protocol was successfully implemented in enumerating S. subterranea sporosori in naturally infested field soil collected from several states and in artificial potting mixes with high organic matter content ranging from 64 to 71%. The qPCR method developed can be useful for potato growers to avoid agricultural soils highly infested with S. subterranea and in the development of risk assessment models in the future that incorporate cultivar susceptibility to powdery scab and soil infestation levels.

Assessment of Factors Associated with Molecular Quantification of Stubby Root Nematode Paratrichodorus allius from Field Soil DNA.

Factors relating to SYBR Green-based quantitative real-time PCR (qPCR) quantification of stubby root nematode Paratrichodorus allius using soil DNA were evaluated in this study. Soils used were loamy sand from potato fields in North Dakota and Idaho. Results showed that the largest nematode individuals (body length >720 µm) produced significant lower Cq values than the smallest individuals (<359 µm), indicating more total DNA amount in the largest nematodes. Soil pre-treatments showed that autoclaved field soil had significantly reduced DNA amount and quality. The air- or oven-dried soil yielded a lower amount of DNA with similar purity, compared with natural field soil. PCR inhibitors were detected in soil DNA substrates targeting pBluescript II SK(+)-plasmid DNA. Al(NH4)(SO4)2 treatment during DNA preparation significantly reduced the inhibitors compared with post-treatment of soil DNA with polyvinylpolypyrrolidone column. The effect of PCR inhibitors on qPCR was suppressed by bovine serum albumin. Quantification results did not significantly change when increasing the number of DNA extractions from three to six per soil sample when soil grinding and grid sampling strategies were used. Two standard curves, generated from serial dilutions of plasmid DNA containing P. allius ITS1 rDNA and soil DNA containing known nematode numbers, produced similar correlations between Cq values and amount of targets. The targets in soil DNA quantified by qPCR using either standard curve correlated well with microscopic observations using both artificially and naturally infested field soils. This is the first study for assessing various factors that may affect qPCR quantification of stubby root nematodes. Results will be useful during the setup or optimization of qPCR-based quantification of plant-parasitic nematodes from soil DNA.

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.

Assessments of Temporal Variations in Haplotypes of 'Candidatus Liberibacter solanacearum' and Its Vector, the Potato Psyllid, in Potato Fields and Native Vegetation.

The potato psyllid, Bactericera cockerelli (Sulc) (Hemiptera: Triozidae), had been known for nearly a century to cause psyllid yellows of solanaceous crops. However, it has only been a decade since the insect was discovered to transmit the bacterium 'Candidatus Liberibacter solanacearum' (Lso), which putatively causes potato zebra chip disease. This project was initiated to quantify temporal incidences of haplotypes of the psyllid (Central, Southwestern, and Western) and Lso (A, B) in potato fields and in native vegetation. Psyllids were collected from native vegetation in Texas (2011-2014), and from potato fields in Texas and New Mexico (2014-2017). Psyllids were tested for Lso and haplotypes of both psyllid and Lso. In Texas, the Central psyllid haplotype was overwhelmingly dominant both in potato fields and in native vegetation regardless of location and time of collection. However, in New Mexico potato fields, although the Southwestern haplotype was overall dominant, the ratios of individual haplotypes varied among years and within a season. The Southwestern psyllid haplotype was greater in incidence than the Central early but declined later in the season in each of the 4 yr, while the Central haplotype was low in incidence early but increased over time. Lso was detected in all three psyllid haplotypes representing the first report in Southwestern psyllid haplotype. In Texas, Lso haplotype A was more frequently detected than B, but in New Mexico the incidence of positive psyllids was not high enough to make definitive conclusions regarding predominant Lso haplotype.

Assessing Potato Cultivar Sensitivity to Tuber Necrosis Caused by Potato mop-top virus.

Potato mop-top virus (PMTV) causes mop top disease in potato. This disease can result in a decline in tuber quality causing economic losses to growers due to the production of necrotic lesions and discolored tissue in infected tubers. Due to the soilborne nature of PMTV, identifying and developing host resistance against the virus is considered the best disease management option. Very little is known about the sensitivity of U.S. potato cultivars to PMTV-induced tuber necrosis. The current study is aimed at investigating the sensitivity of a large number of potato cultivars to PMTV-induced tuber necrosis. Sixty-three cultivars representing all market-types were evaluated in North Dakota over a 2-year period for virus-induced tuber necrosis incidence and severity. PMTV-induced tuber necrosis (P < 0.0001) and severity (P < 0.0001) were significantly different among cultivars. Cultivars were categorized into sensitive, insensitive, and moderately sensitive/insensitive groups based on the virus-tuber induced necrosis data from both years. Based on data from ND trials, six cultivars (Red Endeavor, Viking, Dakota Jewel, Dark Red Norland, Nicolet, and Modoc) were rated as sensitive and 43 were rated as insensitive to PMTV-induced tuber necrosis. Four cultivars, including Bannock Russet, Gemstar Russet, Lelah, and Waneta showed zero PMTV incidence over 2 years. These results will help growers in making individual or coordinated decisions for the management of PMTV-induced tuber necrosis under field and storage conditions.

Potential Impact of Fluopyram on the Frequency of the D123E Mutation in Alternaria solani.

Succinate dehydrogenase-inhibiting (SDHI) fungicides have been widely applied in commercial potato (Solanum tuberosum L.) fields for the control of early blight, caused by Alternaria solani Sorauer. Five-point mutations on three AsSdh genes in A. solani have been identified as conferring resistance to SDHI fungicides. Recent work in our laboratory determined that A. solani isolates possessing the D123E mutation, or the substitution of aspartic acid for glutamic acid at position 123 in the AsSdhD gene, were collected at successively higher frequencies throughout a 3-year survey. In total, 118 A. solani isolates previously characterized as possessing the D123E mutation were evaluated in vitro for boscalid and fluopyram sensitivity. Over 80% of A. solani isolates with the D123E mutation evaluated were determined to be highly resistant to boscalid in vitro. However, effective concentration at which the fungal growth is inhibited by 50% values of isolates with the D123E mutation to fluopyram, ranging from 0.2 to 3 µg/ml, were sensitive and only slightly higher than those of baseline isolates to fluopyram, which ranged from 0.1 to 0.6 µg/ml. Five A. solani isolates with the D123E mutation were further evaluated in vivo for percent disease control obtained from boscalid and fluopyram compared with two wild-type isolates, three isolates possessing the F129L mutation, two isolates possessing the H134R mutation, two isolates possessing the H133R mutation, and one isolate with the H278R mutation. Relative area under the dose response curve values for boscalid and fluopyram were significantly lower for all five D123E-mutant isolates, demonstrating reduced disease control in vivo. In field trials, the frequency of A. solani isolates with the D123E mutation recovered from treatments receiving an in-furrow application of fluopyram ranged from 5 to 37%, which was significantly higher compared with treatments receiving foliar applications of standard protectants, in which the frequency of the D123E mutation in isolates ranged from 0 to 2.5%. Results suggest that A. solani isolates possessing the D123E mutation have a selective advantage under the application of fluopyram compared with SDHI-sensitive isolates, as well as isolates possessing other mutations conferring SDHI resistance. These data illustrate the importance of implementing fungicide resistance management strategies and cautions the use of fluopyram for in-furrow applications that target other pathogens of potato.

Parasitic Fitness of Fungicide-Resistant and -Sensitive Isolates of Alternaria solani.

Resistance to chemistries of the succinate dehydrogenase inhibiting (SDHI) and quinone outside inhibiting (QoI) fungicides has developed rapidly in populations of Alternaria solani, the cause of early blight of potato. Reduced sensitivity to the anilinopyrimidine (AP) fungicide pyrimethanil has also been identified recently, determining that resistance to three chemical classes of fungicides is present within the A. solani population. Although no mutations have been characterized to confer resistance to APs, in A. solani five point mutations on three AsSdh genes have been determined to convey resistance to SDHIs, and the substitution of phenylalanine with leucine at position 129 (F129L) in the cytb gene confers resistance to QoIs. The objective of this study was to investigate the parasitic fitness of A. solani isolates with resistance to one or more of these chemical classes. A total of 120 A. solani isolates collected from various geographical locations around the United States were chosen for in vitro assessment, and 60 of these isolates were further evaluated in vivo. Fitness parameters measured were (i) spore germination in vitro, (ii) mycelial expansion in vitro, and (iii) aggressiveness in vivo. No significant differences in spore germination or mycelial expansion (P = 0.44 and 0.51, respectively) were observed among wild-type and fungicide-resistant isolates in vitro. Only A. solani isolates possessing the D123E mutation were shown to be significantly more aggressive in vivo (P < 0.0001) compared with wild-type isolates. These results indicate that fungicide-resistant A. solani isolates have no significant fitness penalties compared with sensitive isolates under the parameters evaluated regardless of the presence or absence of reduced sensitivity to multiple chemical classes. Results of these studies suggest that A. solani isolates with multiple fungicide resistances may compete successfully with wild-type isolates under field conditions.

Spatial and Temporal Distribution of Mutations Conferring QoI and SDHI Resistance in Alternaria solani Across the United States.

The application of succinate dehydrogenase inhibiting (SDHI) and quinone outside inhibiting (QoI) fungicide chemistries is a primary tactic in the management of early blight of potato, caused by Alternaria solani. Resistance to QoIs in A. solani has been attributed to the F129L mutation, while resistance to SDHIs is conferred by five different known point mutations on three AsSdh genes. In total, 1,323 isolates were collected from 2013 through 2015 across 11 states to determine spatial and temporal frequency distribution of these mutations. A real-time polymerase chain reaction (PCR) was used to detect the presence of the F129L mutation. Molecular detection of SDHI-resistant isolates was performed using SDH multiplex PCR specific for point mutations in AsSdhB, AsSdhC, or AsSdhD genes and mismatch amplification analysis PCR detecting the point mutations in AsSdhB. Previous work in our research group determined that substitutions of histidine for tyrosine (H278Y) or arginine (H278R) at codon 278 on the AsSdhB gene were the most prevalent mutations, detected in 46 and 21% of A. solani isolates, respectively, collected in 2011 to 2012, and uniformly distributed among six sampled states. In contrast, the substitution of histidine for arginine (H134R) at codon 134 in the AsSdhC gene was the most prevalent mutation in 2013 through 2015, identified in 36% of isolates, compared with 7.5% of isolates recovered in 2011 to 2012. Substitutions of histidine for arginine (H133R) at codon 133 and aspartic acid for glutamic acid (D123E) at codon 123 in the AsSdhD gene were detected in 16 and 12%, respectively, in the A. solani population by 2015 and were recovered across a wide range of states, compared with 15 and 1.5% of isolates collected in 2011 to 2012, respectively. Overall, SDHI- and QoI-resistant isolates were detected at high frequencies across all years, with evidence of significant spatial variability. Future research will investigate whether these results are due to differences in parasitic fitness.

Assessing Potato Cultivar Sensitivity to Tuber Necrosis Caused by Tobacco rattle virus.

Tobacco rattle virus (TRV) causes the economically important corky ring spot disease in potato. Chemical control is difficult due to the soilborne nature of the TRV-transmitting nematode vector, and identifying natural host resistance against TRV is considered to be the optimal control measure. The present study investigated the sensitivity of 63 cultivars representing all market types (evaluated at North Dakota and Washington over 2 years) for the incidence of TRV-induced tuber necrosis and severity. This article also investigates the cultivar-location interaction (using a mixed-effects model) for TRV-induced necrosis. TRV-induced tuber necrosis (P < 0.0001) and severity (P < 0.0001) were significantly different among cultivars evaluated separately in North Dakota and Washington trials. Mixed-effects model results of pooled data (North Dakota and Washington) demonstrated that the interaction of cultivar and location had a significant effect (P = 0.03) on TRV-induced necrosis. Based on the virus-induced tuber necrosis data from both years and locations, cultivars were categorized into sensitive, moderately sensitive, insensitive, and moderately insensitive groups. Based on data from North Dakota, 10 cultivars, including Bintje, Centennial Russet, Ciklamen, Gala, Lelah, Oneida Gold, POR06V12-3, Rio Colorado, Russian Banana, and Superior, were rated as insensitive to TRV-induced tuber necrosis. Similar trials assessing TRV sensitivity among cultivars conducted in Washington resulted in a number of differences in sensitivity rankings compared with North Dakota trials. A substantial shift in sensitivity of some potato cultivars to TRV-induced tuber necrosis was observed between the two locations. Four cultivars (Centennial Russet, Oneida Gold, Russian Banana, and Superior) ranked as insensitive for North Dakota trials were ranked as sensitive for Washington trials. These results can assist the potato industry in making cultivar choices to reduce the economic impact of TRV-induced tuber necrosis.

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.

Genomes of 'Candidatus Liberibacter solanacearum' Haplotype A from New Zealand and the United States Suggest Significant Genome Plasticity in the Species.

'Candidatus Liberibacter solanacearum' contains two solanaceous crop-infecting haplotypes, A and B. Two haplotype A draft genomes were assembled and compared with ZC1 (haplotype B), revealing inversion and relocation genomic rearrangements, numerous single-nucleotide polymorphisms, and differences in phage-related regions. Differences in prophage location and sequence were seen both within and between haplotype comparisons. OrthoMCL and BLAST analyses identified 46 putative coding sequences present in haplotype A that were not present in haplotype B. Thirty-eight of these loci were not found in sequences from other Liberibacter spp. Quantitative polymerase chain reaction (qPCR) assays designed to amplify sequences from 15 of these loci were screened against a panel of 'Ca. L. solanacearum'-positive samples to investigate genetic diversity. Seven of the assays demonstrated within-haplotype diversity; five failed to amplify loci in at least one haplotype A sample while three assays produced amplicons from some haplotype B samples. Eight of the loci assays showed consistent A-B differentiation. Differences in genome arrangements, prophage, and qPCR results suggesting locus diversity within the haplotypes provide more evidence for genetic complexity in this emerging bacterial species.

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.

Aspects of pathogen genomics, diversity, epidemiology, vector dynamics, and disease management for a newly emerged disease of potato: zebra chip.

An overview is provided for the aspects of history, biology, genomics, genetics, and epidemiology of zebra chip (ZC), a destructive disease of potato (Solanum tuberosum) that represents a major threat to the potato industries in the United States as well as other potato-production regions in the world. The disease is associated with a gram-negative, phloem-limited, insect-vectored, unculturable prokaryote, 'Candidatus Liberibacter solanacearum', that belongs to the Rhizobiaceae family of α-Proteobacteria. The closest cultivated relatives of 'Ca. L. solanacearum' are members of the group of bacteria known as the α-2 subgroup. In spite of the fact that Koch's postulates sensu stricto have not been fulfilled, a great deal of progress has been made in understanding the ZC disease complex since discovery of the disease. Nevertheless, more research is needed to better understand vector biology, disease mechanisms, host response, and epidemiology in the context of vector-pathogen-plant interactions. Current ZC management strategies focus primarily on psyllid control. The ultimate control of ZC likely relies on host resistance. Unfortunately, all commercial potato cultivars are susceptible to ZC. Elucidation of the 'Ca. L. solanacearum' genome sequence has provided insights into the genetic basis of virulence and physiological and metabolic capability of this organism. Finally, the most effective, sustainable management of ZC is likely to be based on integrated strategies, including removal or reduction of vectors or inocula, improvement of host resistance to the presumptive pathogen and psyllid vectors, and novel gene-based therapeutic treatment.

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).