Phytopathology (PHYTOPATHOLOGY )

Publisher: American Phytopathological Society


Phytopathology is the premier international journal of fundamental research regarding plant diseases, the agents that cause them, their spread, the losses they cause, and measures to control them. Subject areas include analytical and theoretical plant pathology, bacteriology, biochemistry and cell biology, biological control, disease control and pest management, ecology and population biology, epidemiology, etiology, genetics and resistance, mycology, nematology, plant stress and abiotic disorders, postharvest pathology and mycotoxins, techniques, and virology.

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Publications in this journal

  • [Show abstract] [Hide abstract]
    ABSTRACT: Early stage infections caused by fungal/oomycete spores may not be detected until signs or symptoms develop. Serological and molecular techniques are currently used for detecting these pathogens. Next-generation sequencing (NGS) has potential as a diagnostic tool, due to the capacity to target multiple unique signature loci of pathogens in an infected plant metagenome. NGS has significant potential for diagnosis of important eukaryotic plant pathogens. However, the assembly and analysis of huge amounts of sequence is laborious, time consuming, and not necessary for diagnostic purposes. Previous work demonstrated that a bioinformatic tool termed Electronic probe Diagnostic Nucleic acid Analysis (EDNA) had potential for greatly simplifying detecting Fungal and Oomycete plant pathogens in simulated metagenomes. The initial study demonstrated limitations for detection accuracy related to the analysis of matches between queries and metagenome reads. This study is a modification of EDNA demonstrating a better accuracy for detecting Fungal and Oomycete plant pathogens.
    Phytopathology 01/2015;
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    ABSTRACT: Bias (over and underestimates) in estimates of disease severity, and the impact of that inaccuracy on hypothesis testing using different disease scales was explored. Nearest percent estimates (NPE), the Horsfall-Barratt (H-B) scale and four different linear category scales (5% and 10% increments, with and without additional grades at low severity) were compared. Actual values and estimates by 4 different raters of the severity (0 to 100%) of Septoria leaf blotch on leaves of winter wheat were used to develop distributions for a simulation model. The simulations were based on i) all the 4 raters data combined, ii) only the most accurate rater estimates, and iii) only the most biased rater. Regardless of the effect of rater ability, we found that, there were lower type II error rates with NPEs as compared with the other category scales at severities of 80 to 100%. On the other hand, with lower severities (0 to 20%), the 5% and 10% scales with additional grades had type II error rates comparable to those for the NPEs. Raters who overestimated severity and used the H-B scale had the highest risk of a type II error when the mean disease severity was low. Knowledge of how rater ability and scale type can affect hypothesis testing can be used to improve disease assessment as well as to provide a logical framework for developing standard area diagrams.
    Phytopathology 10/2014; 104(11):26.
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    ABSTRACT: The accuracy and reliability of visual assessments of SLB severity by raters (i.e. one plant pathologist with extensive experience and three other raters trained prior to field observations using standard area diagrams and DISTRAIN) was determined by comparison with assumed actual values obtained by digital image analysis. Initially analyses were performed using SLB severity over the full 0-100% range; then, to explore error over short ranges of the 0-100% scale, the scale was divided into sequential 10%-increments based on the actual values. Lin’s concordance correlation (LCC) analysis demonstrated that all raters were accurate when compared over the whole severity range (LCC coefficient (ρc)= 0.92-0.99). However, agreement between actual and visual SLB severities was less good when compared over the short intervals of the 10×10% classes (ρc= -0.12-0.99), demonstrating that agreement will vary depending on the actual disease range over which it is compared. Inter-rater reliability between each pair of raters over the full 0-100% range (correlation analysis r= 0.970-0.992, P<0.0001), and inter-class correlation coefficient (ρ≥ 0.927) were very high. This study provides new insight into using a full range of actual disease severity vs limited ranges to ensure a realistic measure of rater accuracy and reliability, in addition to contributing to the ongoing debate on the use of visual disease estimates based on the 0-100% ratio scale for epidemiological research.
    Phytopathology 10/2014; 104(11):37.
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    ABSTRACT: Assessment of disease severity is most often made visually, and estimates can be inaccurate. Nearest percent estimates (NPEs) of Septoria leaf blotch on leaves of winter wheat by four raters (R1-R4) assessing non-treated (NT) and fungicide-treated (FT) plots were compared to true values using Lin’s concordance correlation coefficient (ρc) on two dates in 2006 and 2007. Estimates were converted to Horsfall-Barratt (HB) mid-points and again compared for accuracy and precision. Estimates of severity from FT and NT plots were analyzed to ascertain effects of rater using both the NPE and HB values. Regardless of method, all raters showed a range of agreement with true values on FT and NT plots (ρc = 0 to 1). Use of the HB scale most often reduced agreement (84.4% of the time), and did not improve rater-associated bias of treatment mean severity estimates. Consequently, estimates of mean severity differed significantly among raters and from true values (F=126 to 1260, P=0.002 to<0.0001). However, a comparison of treatment effects showed that the true values and R1 to R4 all demonstrated significant effects of fungicide (F=101 to 1952, P=0.002 to <0.00001). Ranking of raters differed on one occasion when HB values were used. These results demonstrate the effect of the HB scale, and the need for accurate disease assessment to minimize over or underestimates compared to true severity so as to minimize the potential for type II errors.
    Phytopathology 10/2014; 104(11):15.
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    ABSTRACT: ABSTRACT Asparagus virus 2 (AV-2) is a member of the genus Ilarvirus and thought to induce the asparagus decline syndrome. AV-2 is known to be transmitted by seed, and the possibility of pollen transmission was proposed 25 years ago but not verified. In AV-2 sequence analyses, we have unexpectedly found mixed infection by two distinct AV-2 isolates in two asparagus plants. Because mixed infections by two related viruses are normally prevented by cross protection, we suspected that pollen transmission of AV-2 is involved in mixed infection. Immunohistochemical analyses and in situ hybridization using AV-2-infected tobacco plants revealed that AV-2 was localized in the meristem and associated with pollen grains. To experimentally produce a mixed infection via pollen transmission, two Nicotiana benthamiana plants that were infected with each of two AV-2 isolates were crossed. Derived cleaved-amplified polymorphic sequence analysis identified each AV-2 isolate in the progeny seedlings, suggesting that pollen transmission could indeed result in a mixed infection, at least in N. benthamiana.
    Phytopathology 09/2014; 104(9):1001-1006.
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    ABSTRACT: This study was intended to analyze the photosynthetic performance of rice leaf blades infected with Monographella albescens by combining chlorophyll (Chl) a fluorescence images with gas exchange and photosynthetic pigment pools. The net CO2 assimilation rate, stomatal conductance, transpiration rate, total Chl and carotenoid pools and Chl a/b ratio all decreased, but the internal CO2 concentration increased, in the inoculated plants compared with their non-inoculated counterparts. The first detectable changes in the images of Chl a fluorescence from the leaves of inoculated plants were already evident at 24 hai and increased dramatically as the leaf scald lesions expanded. However, these changes were negligible for the photosystem II photochemical efficiency (Fv/Fm) at 24 hours after inoculation, in contrast with other Chl fluorescence traits, such as the photochemical quenching coefficient, yield of photochemistry and yield for dissipation by down-regulation, which were therefore much more sensitive than the Fv/Fm ratio in assessing the early stages of fungal infection. It was also demonstrated that M. albescens was able to impair the photosynthetic process in both symptomatic and asymptomatic leaf areas. Overall, it was proven that Chl a fluorescence imaging is an excellent tool to describe the loss of functionality of the photosynthetic apparatus occurring in rice leaves upon infection by M. albescens.
    Phytopathology 08/2014;
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    ABSTRACT: Mist chamber experiments were conducted to quantify and model the effects of post-anthesis moisture on FHB index (IND) and DON. Four mist treatments, one daily and three intermittent, were applied during an 8-day window immediately after anthesis, plus an untreated check. All intermittent mist treatments received moisture on 4 of the 8 days, but the distribution of the supplemental moisture during the treatment window varied among the treatments. Separate sets of spikes in each treatment were either spray- or point-inoculated with a spore suspension of Fusarium graminearum. Based on results from linear mixed model analyses, mist treatment had a significant effect on arcsine-square root-transformed IND (arcIND) and log-transformed DON (logDON) on spray-inoculated spikes, but only a marginal effect on DON in point-inoculated spikes. The daily mist treatments (Mist1) consistently had the highest mean IND and DON, but several of the 4-day intermittent mist treatments were not significantly different, particularly for point inoculations. Only Mist1 and one of the intermittent mist treatments (Mist2; two days of mist at the beginning and end of the treatment window) had significantly higher infection efficiency (estimated diseased spikelets/spore) than the check, but none of the treatments increased the rate of disease spread within the spike (based on visual symptoms) relative to the check. For all treatments, there was a significant, positive linear relationship between IND and logDON, with estimated mean regression slopes (rates of logDON increase per unit increase in IND) of 0.04 and 0.02 logDON %-1IND for the point- and spray-inoculated experiments, respectively. Mist treatment did not have a significant effect of the slope, but had a significant effect on the intercept. The height of the regression line (logDON after adjusting for FHB index) was consistently higher for Mist2 than for Mist1, for both point- and spray-inoculated spikes. Estimated mean back-transformed DON at a fixed level of IND was 4.9 and 2.9 ppm higher for Mist2 than Mist1 in the spray- and point-inoculation experiment, respectively. Generalized linear mixed models were used to estimate the risk of IND and DON exceeding critical thresholds, showing similar results among treatments in terms of estimated probabilities. The estimated probabilities of IND ≥ 10% at 20 days after inoculation and DON ≥ 2, 5, and 10 ppm were not significantly different between Mist1 and Mist2. These results suggest that post-anthesis moisture patterns may play a role in DON exceeding critical thresholds even when FHB level are relatively low.
    Phytopathology 08/2014;
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    ABSTRACT: Global climate change will have effects on diurnal temperature oscillations besides average temperatures. Studies on potato late blight (Phytophthora infestans) development have not considered daily temperature oscillations. We hypothesize that growth and development rates of P. infestans would be less influenced by change in average temperature as the magnitude of fluctuations in daily temperatures increases. We investigated the effects of seven constant (10, 12, 15, 17, 20, 23, 27°C) and diurnally oscillating temperatures (±5°C and ±10°C) around the same means on number of lesions, incubation period, latent period, radial lesion growth rate and sporulation intensity on detached potato leaves inoculated with two P. infestans isolates from clonal lineages US-8 and US-23. A four parameter thermodynamic model was used to describe relationships between temperature and disease development measurements. Incubation and latency progression accelerated with increasing oscillations at low mean temperatures, but slowed down with increasing oscillations at high mean temperatures (P<0.005), as hypothesized. Infection efficiency, lesion growth rate and sporulation increased under small temperature oscillations compared to constant temperatures but decreased when temperature oscillations were large. Thus, diurnal amplitude in temperature should be considered in models of potato late blight, particularly when predicting effects of global climate change on disease development.
    Phytopathology 08/2014;
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    ABSTRACT: Pathogen adaptation to different hosts can lead to specialization and, when coupled with reproductive isolation, genome-wide differentiation and ecological speciation. We tested the hypothesis of host specialization among California populations of Eutypa lata (causal fungus of Eutypa dieback of grapevine and apricot), which is reported from > 90 species. Genetic analyses of nine microsatellite loci in 182 isolates from three hosts (grapevine, apricot, willow) at three locations were complemented by cross-inoculations on cultivated hosts grapevine and apricot, to reveal patterns of host specialization. The cultivated hosts are likely more important sources of inoculum than the wild host willow, based on our findings of higher pathogen prevalence and allelic richness in grapevine and apricot. High levels of gene flow among all three hosts and locations, and no grouping by clustering analyses, suggest neither host nor geographic differentiation. Cross-inoculations revealed diversified phenotypes harboring various performance levels in grapevine and apricot, with no apparent correlation with their host of origin. Such phenotypic diversity may enable this pathogen to persist and reproduce as a generalist. Regular genetic reshuffling through sexual recombination, frequent immigration among hosts, and the lack of habitat choice in this passively-dispersed fungus may prevent fixation of alleles controlling host specialization.
    Phytopathology 08/2014;
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    ABSTRACT: Pepper is the third most important solanaceous crop in the U.S. and fourth most important worldwide. To identify sources of resistance for commercial breeding, one hundred-seventy pepper genotypes from 5 continents and 45 countries were evaluated for Phytophthora fruit rot resistance using two isolates of Phytophthora capsici. Genetic diversity and population structure were assessed on a subset of 157 genotypes using 23 polymorphic simple sequence repeats (SSRs). Partial resistance and isolate specific interactions were identified in the population at both 3 and 5 days post inoculation (dpi). PIs 640833 and 566811 were the most resistant lines evaluated at 5 dpi to isolates 12889 and OP97, with mean lesion areas less than Criollo de Morelos. Genetic diversity was moderate (0.44) in the population. The program STRUCTURE inferred four genetic clusters with moderate to very great differentiation among clusters. Most lines evaluated were susceptible or moderately susceptible at 5 dpi, and no lines evaluated were completely resistant to Phytophthora fruit rot. Significant population structure was detected when peppers were grouped by predefined categories of disease resistance, continent and country of origin. Moderately resistant/resistant PIs to both isolates of P. capsici at 5 dpi were in genetic clusters one and two.
    Phytopathology 07/2014;
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    ABSTRACT: Double-stranded RNAs purified from a cherry tree collected in Italy and a plum tree collected in Azerbaijan were submitted to deep sequencing. Contigs showing weak but significant identity with various members of the family Betaflexiviridae were reconstructed. Sequence comparisons led to the conclusion that the viral isolates identified in the analysed Prunus plants belong to the same viral species. Their genome organisation is similar to that of some members of the family Betaflexiviridae, with three overlapping ORFs (RNA polymerase, movement protein and capsid protein). Phylogenetic analyses of the deduced encoded proteins showed a clustering with the sole member of the genus Tepovirus, Potato virus T. Given these results, the name Prunus virus T (PrVT) is proposed for the new virus. It should be considered as a new member of the genus Tepovirus, even if the level of nucleotide identity with PVT is borderline with the genus demarcation criteria for the family Betaflexiviridae. An RT-PCR detection assay was developed and allowed the identification of two other PrVT isolates and an estimate of 1% prevalence in the large Prunus collection screened. Due to the mixed infection status of all hosts identified to date, it was not possible to correlate the presence of PrVT with specific symptoms.
    Phytopathology 07/2014;
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    ABSTRACT: Isolates in the Fusarium oxysporum species complex (FOSC) from soybean range from non-pathogenic to aggressive pathogens causing seedling damping-off, wilt, and root rot. The objective of this research was to characterize the genotype and phenotype of isolates within the FOSC recovered predominantly from soybean roots and seedlings. Sequence analyses of the translation elongation factor (tef1α) gene and the mitochondrial small subunit (mtSSU), PCR-RFLP analysis of the intergenic spacer (IGS) region, and identification of the mating type loci were conducted for 170 isolates. Vegetative compatibility (VC) tests were conducted for 114 isolates. Isolate aggressiveness was tested using a rolled towel assay for 159 isolates. Phylogenetic analysis of the tef1α and mtSSU and PCR-RFLP analysis of the IGS region separated the FOSC isolates into five clades, including F. commune. Both mating type loci, MAT1-1 or MAT1-2, were present in isolates from all clades. The VC tests were not informative, as most VC groups consisted of a single isolate. Isolate aggressiveness varied within and among clades; isolates in clade 2 were significantly less aggressive (P <0.0001) when compared to isolates from the other clades and F. commune. The results from this study demonstrate the high levels of genotypic and phenotypic diversity within the FOSC from soybean, but further work is needed to identify characteristics associated with pathogenic capabilities.
    Phytopathology 07/2014;
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    ABSTRACT: ABSTRACT Many plant pathogens are microscopic, cryptic, and difficult to diagnose. The new approach of ecometagenetics, involving ultrasequencing, bioinformatics, and biostatistics, has the potential to improve diagnoses of plant pathogens such as nematodes from the complex mixtures found in many agricultural and biosecurity situations. We tested this approach on a gradient of complexity ranging from a few individuals from a few species of known nematode pathogens in a relatively defined substrate to a complex and poorly known suite of nematode pathogens in a complex forest soil, including its associated biota of unknown protists, fungi, and other microscopic eukaryotes. We added three known but contrasting species (Pratylenchus neglectus, the closely related P. thornei, and Heterodera avenae) to half the set of substrates, leaving the other half without them. We then tested whether all nematode pathogens-known and unknown, indigenous, and experimentally added-were detected consistently present or absent. We always detected the Pratylenchus spp. correctly and with the number of sequence reads proportional to the numbers added. However, a single cyst of H. avenae was only identified approximately half the time it was present. Other plant-parasitic nematodes and nematodes from other trophic groups were detected well but other eukaryotes were detected less consistently. DNA sampling errors or informatic errors or both were involved in misidentification of H. avenae; however, the proportions of each varied in the different bioinformatic pipelines and with different parameters used. To a large extent, false-positive and false-negative errors were complementary: pipelines and parameters with the highest false-positive rates had the lowest false-negative rates and vice versa. Sources of error identified included assumptions in the bioinformatic pipelines, slight differences in primer regions, the number of sequence reads regarded as the minimum threshold for inclusion in analysis, and inaccessible DNA in resistant life stages. Identification of the sources of error allows us to suggest ways to improve identification using ecometagenetics.
    Phytopathology 07/2014; 104(7):749-761.