A comparison between visual estimates and image analysis measurements to determine septoria leaf blotch severity in winter wheat

Methods to estimate disease severity vary in accuracy, reliability, ease of use and cost. Severity of septoria leaf blotch (SLB, caused by Zymoseptoria tritici) was estimated by four raters and by image analysis (assumed actual values) on individual leaves of winter wheat in order to explore accuracy and reliability of estimates, and to ascertain whether there were any general characteristics of error. Specifically, the study determined: (i) the accuracy and reliability of visual assessments of SLB over the full range of severity from 0 to 100%; (ii) whether certain 10% ranges in actual disease severity between 0 and 100% were more prone to estimation error compared with others; and (iii) whether leaf position affected accuracy within those ranges. Lin's concordance correlation analysis of all severities (0–100%) demonstrated that all raters had estimates close to the actual values (agreement: ρ_c = 0·92–0·99). However, agreement between actual SLB severities and estimates by raters was less good when compared over short 10% subdivisions within the 0–100% range (ρ_c = ?0·12 to 0·99). Despite common rater imprecision at estimating low and high SLB severities, individual raters differed considerably in their accuracy over the short 10% subdivisions. There was no effect of leaf position on accuracy or precision of severity estimate on separate leaves (L1–L3). Pursuing efforts in understanding error in disease estimation should aid in improving the accuracy of assessments, making visual estimates of disease severity more useful for research and applied purposes.     

Reliability and accuracy of visual estimation of phomopsis leaf blight of strawberry

ABSTRACT Six different individuals (raters) assessed the severity of Phomopsis leaf blight on strawberry leaflets in five experimental repetitions over 2 years by making a direct visual estimation of the percentage of diseased area of each leaflet or by using the Horsfall-Barratt (H-B) disease scale. Intra-rater and inter-rater reliability and accuracy were determined, and then the relationship between visually estimated severity values and actual severity values was evaluated. Agreement in estimated disease severity values between assessment times by the same raters (i.e., intra-rater reliability), and agreement in disease severity values among raters at a single assessment time (i.e., inter-rater reliability), were both high, with most correlation coefficients being greater than 0.85. The intra-class correlation for overall agreement among raters ranged from 0.80 to 0.96 for the five repetitions. Based on the concordance coefficient calculated for each rater in each repetition, agreement between estimated and actual severity (i.e., accuracy) was somewhat lower than reliability. The relationship between estimated and actual severity was linear, and there was a slight trend to overestimate disease severity. The H-B scale was not more reliable or accurate than direct estimation of severity, and the linear relationship between estimated and actual severity did not support the principles underling the H-B scale. Both size of leaflets and number of lesions per leaflet slightly affected the error in estimate of disease severity.     

Use of bayesian methods to improve prediction of panicle and shoot blight severity of pistachio in california

ABSTRACT Panicle and shoot blight, caused by a Fusicoccum sp., is one of the major aboveground diseases of pistachio in California. The effects of temperature, number of continuous rainy days in April and May, irrigation system, and incidence of latent infection of the Fusicoccum sp. on severity of panicle and shoot blight of pistachio leaves and fruit have been quantified previously, using data collected from 1999 through 2001. A predictive model for leaves and another model for fruit with good explanatory power were generated. In 2003 and 2004, newly collected data were used to evaluate the two models with non-Bayesian and Bayesian methods. The 95% credible (i.e., confidence) intervals of initial (before modification with non-Bayesian and Bayesian methods) and updated parameter estimates were used to investigate their prognostic validity. In 2003, the non-Bayesian analysis resulted in all parameter estimates, with the exception of cumulative daily mean temperature from 1 June until harvest, having different 95% confidence intervals than the parameter estimates of the original models. In addition, the parameter estimates for drip irrigation for the leaf infection and the parameter estimates for drip irrigation and number of continuous rainy days in April and May for fruit infection were not statistically significant. With Bayesian methods, the reestimated model parameters had overlapping 95% credible intervals with the initial estimated parameters, except for the number of continuous rainy days in April and May. When the two sets of modified parameter estimates were used to predict disease severity, statistically significant (alpha = 0.05) differences between observed and predicted disease severities were found with non-Bayesian analysis for leaf infection in three locations and with Bayesian analysis for fruit infection in one orchard. The parameter estimates were modified again at the end of the 2004 season and were all statistically significant with both non-Bayesian and Bayesian methods. Both sets of parameter estimates gave predictions that were not significantly different from observed disease severity on leaves and fruit in all monitored orchards in 2004. In summary, Bayesian methods gave more consistent results when used to update parameter estimates with new information and yielded predictions not statistically different from observed disease severity in more cases than the non-Bayesian analysis.     

Reliability and accuracy of visual methods to quantify severity of foliar bacterial spot symptoms on peach and nectarine

The objectives of this study were to assess the reliability and accuracy of visual methods used to quantify the severity of bacterial spot (Xanthomonas arboricola pv. pruni) symptoms and evaluate the effects of rater experience on the quality of disease estimates. Three cohorts of raters differing in experience with disease assessment rated three sets of peach or nectarine leaves (n ≥ 103; disease severity levels from 0% to 100%) by direct estimation of percentage leaf area with symptoms. Four of the experienced raters also rated the leaves using a 1–7 interval scale. Actual disease severity on the leaves was obtained with the APS assess image analysis software. Equivalence tests based on a bootstrap analysis were used to compare the rating scale and direct estimation methods, and to evaluate the effects of rater experience, computer training and human instruction on accuracy and reliability of disease estimates. In concordance analysis of continuous variables, with data from scale converted to percentage, the direct estimation method resulted in more accurate and reliable estimates than the interval scale. Analysing the scale data without conversion to percentage improved the concordance statistics for the scale but not sufficiently to match the direct estimation method. Accuracy was affected more by rater experience and intrinsic ability than reliability. Instruction on disease symptoms resulted in the largest improvement in estimates from inexperienced raters. Accurate and reliable direct estimation of bacterial spot severity on peach and nectarine can be made by raters with varying levels of experience provided they receive sufficient instruction.     

Standard area diagram set for assessment of severity and temporal progress of apple blotch

Apple blotch (Marssonina coronaria) is a foliar disease of increasing importance globally. Methods to quantify the disease and knowledge about epidemiology are required for new studies on the disease. The objectives of this study were to develop a standard area diagram set (SADs) to assess apple blotch severity and to describe the temporal progress of the disease under field conditions on older and younger leaves of two apple cultivars. For the development of SADs, symptomatic leaves were collected and scanned to obtain the actual severity. Based on the pattern of the disease, a SADs was elaborated and validated. Leaf severities were estimated without and with SADs by 12 raters to validate the tool. After validation, the SADs was used to assess apple blotch in older and younger leaves of selected shoots during the vegetative cycle of cvs. Eva and Gala. SADs severities ranged from 0.2 to 96%. Accuracy, precision, and reliability of the estimates were significantly improved when the SADs was used. In the field, the onset of apple blotch was in late spring and greater increases in severity occurred during summer. Rates of disease progress ranged from 0.09 to 0.13. Epidemics were different in older and younger leaves at the end of the apple vegetative cycle for both cultivars tested. Our work provided a tool for apple blotch quantification and described the disease progress curve under subtropical conditions, which can contribute as basis for future studies.

     

Development and validation of a set of standard area diagrams to estimate severity of potato early blight

Standard area diagrams (SADs) to assess the severity of potato early blight (Alternaria grandis) on leaves of potato (Solanum tuberosum L.) were developed and validated. The proposed SADs include images of leaves with 10 distinct disease severities (0.1, 1, 3, 5, 10, 20, 40, 60, 80 and 100 %). The SADs were validated by 12 raters who had no previous experience in evaluating plant disease. Lin’s concordance correlation analysis of estimated vs. actual disease severity (based on image analysis) showed that precision and accuracy improved for most raters using the SADs, compared to assessments made without the SADs. The SADs improved accuracy (coefficient of bias, C _b ?=?0.97 and 0.99, without and with SADs, respectively) and agreement (Lin’s concordance correlation coefficient, ρ _c ?=?0.91 and 0.98 without and with SADs, respectively) of the estimates of severity. Severity estimates were more reliable when using SADs (coefficient of determination, R ² ?=?0.80 unaided and R ² ?=?0.95 with SADs, and the intra-class correlation ρ?=?0.86 without SADs and ρ?=?0.97 using the SADs). The SADs improved raters’ ability to accurately, precisely and reliably estimate potato early blight severity, and as such can be used to assess severity for several purposes, including breeding for resistance, fungicide screening, and pathotype characterization.     

Application of image analysis in studies of quantitative disease resistance, exemplified using common bacterial blight-common bean pathosystem

The effectiveness of image analysis (IA) compared with an ordinal visual scale, for quantitative measurement of disease severity, its application in quantitative genetic studies, and its effect on the estimates of genetic parameters were investigated. Studies were performed using eight backcross-derived families of common bean (Phaseolus vulgaris) (n = 172) segregating for the molecular marker SU91, known to be associated with a quantitative trait locus (QTL) for resistance to common bacterial blight (CBB), caused by Xanthomonas campestris pv. phaseoli and X. fuscans subsp. fuscans. Even though both IA and visual assessments were highly repeatable, IA was more sensitive in detecting quantitative differences between bean genotypes. The CBB phenotypic difference between the two SU91 genotypic groups was consistently more than fivefold for IA assessments but generally only two- to threefold for visual assessments. Results suggest that the visual assessment results in overestimation of the effect of QTL in genetic studies. This may have been caused by lack of additivity and uneven intervals of the visual scale. Although visual assessment of disease severity is a useful tool for general selection in breeding programs, assessments using IA may be more suitable for phenotypic evaluations in quantitative genetic studies involving CBB resistance as well as other foliar diseases.     

Development and validation of a set of standard area diagrams to aid in estimation of spot blotch severity on wheat leaves

This study aimed to develop and validate a standard area diagram (SAD) set to quantify the severity of spot blotch, caused by Bipolaris sorokiniana, on wheat leaves. The proposed SAD set includes images of leaves with 11 distinct disease severities (0·1, 1, 5, 10, 20, 30, 40, 50, 60, 70 and 83%). The SAD set was validated by 12 raters without experience in evaluating plant disease. Lin's concordance correlation analysis of estimated versus actual disease severity (based on image analysis) showed that precision and accuracy improved for all raters using the SAD set in contrast to assessments made without it. The SAD set improved accuracy (coefficient of bias, C_b = 0·88 and 0·99, without and with the SAD set, respectively) and agreement (Lin's concordance correlation coefficient, ρ_c = 0·81 and 0·96 without and with the SAD set, respectively) of the estimates of severity. The severity estimates were also more reliable when using the SAD set (coefficient of determination, R² = 0·76 unaided and R² = 0·92 with the SAD set, and intra‐class correlation ρ = 0·79 without the SAD set and ρ = 0·95 using the SAD set). The SAD set proposed in this study will improve the accuracy and reliability of estimates of spot blotch severity on wheat leaves.     

Disease Assessment Concepts and the Advancements Made in Improving the Accuracy and Precision of Plant Disease Data

New concepts in phytopathometry continue to emerge, such as the evolution of the concept of pathogen intensity versus the well-established concept of disease intensity. The concept of pathogen severity, defined as the quantitative measurement of the amount of pathogen per sampling unit has also emerged in response to the now commonplace development of quantitative molecular detection tools. Although the concept of disease severity, i.e., the amount of disease per sampling unit, is a well-established concept, the accuracy and precision of visual estimates of disease severity is often questioned. This article will review disease assessment concepts, as well as the methods and assessment aides currently available to improve the accuracy and precision of visually-based disease severity data. The accuracy and precision of visual disease severity assessments can be improved by quantitatively measuring and comparing the accuracy and precision of rates and/or assessment methods using linear regression, by using computer-based disease assessment training programmes, and by developing and using diagrammatic keys (standard area diagrams).     

Microcomputer-Based Quantification of Maize Streak Virus Symptoms in Zea mays

ABSTRACT We investigated the use of computer-assisted image analysis techniques for the objective quantification of maize streak virus (MSV) symptoms in Zea mays. We compared independent duplicate evaluations of chlorotic lesion areas occurring on MSV-infected leaves using visual assessment, a commercial image analysis system, and a custom image analysis system employing software developed in our laboratory. Relative to visual assessments of disease severity, computer-assisted image analysis employing both the commercial and custom systems provided significant enhancements in the accuracy and precision of chlorotic area estimations. The commercial image analysis system afforded no significant improvement in precision or accuracy over the custom system. An important advantage of examining images using the custom-written software was that the software permitted a high degree of analysis automation. Digitized images of maize leaves could be automatically analyzed by the custom software five times faster than, and with the same precision and accuracy as, when the same images were analyzed with the commercial software. Because of the flexibility of the image analysis techniques described, they should be applicable to the measurement of symptom severity in other plant host-pathogen combinations.     

Effects of rater bias and assessment method on disease severity estimation with regard to hypothesis testing

The effects of bias (over‐ and underestimates) in estimates of disease severity on hypothesis testing using different assessment methods was explored. Nearest percentage estimates (NPE), the Horsfall–Barratt (H‐B) scale, and two linear category scales (10% increments, with and without additional grades at low severity) were compared using simulation modelling to assess effects of bias. Type I and type II error rates were used to compare two treatment differences. The power of the H‐B scale and the 10% scale were least for correctly testing a hypothesis compared with the other methods, and the effects of rater bias on type II errors were greater over specific severity ranges. Apart from NPEs, the amended 10% category scale was most often superior to other methods at all severities tested for reducing the risk of type II errors. It should thus be a preferred method for raters who must use a category scale for disease assessments. Rater bias and assessment method had little effect on type I error rates. The power of the hypothesis test using unbiased estimates was most often greater compared with biased estimates, regardless of assessment method. An unanticipated observation was the greater impact of rater bias compared with assessment method on type II errors. Knowledge of the effects of rater bias and scale type on hypothesis testing can be used to improve accuracy and reliability of disease severity estimates, and can provide a logical framework for improving aids to estimate severity visually, including standard area diagrams and rater training software.     

Improving sooty blotch and flyspeck severity estimation on apple fruit with the aid of standard area diagrams

Sooty blotch and flyspeck is caused by numerous species of fungi that colonize the surface of apple fruit and thereby lower its market value. Although this disease poses a substantial threat to apple growers’ profitability in some regions, reliable and cost-effective methods for epidemiological and disease control studies have not been validated, nor are they widely available. We modified a standard area diagram to aid sooty blotch and flyspeck severity assessments and quantified its impact on accuracy and precision of visual estimates. Samples of ‘Fuji’ and ‘Mutsu’ fruit were photographed both from the top and laterally. Severity was assessed from a sub-sample of 160 images using image analysis software. Validation of the diagram was performed by eight raters who independently assessed severity in two series of selected images representing the lateral view and the top view, initially unaided and subsequently with the aid of the scale. Severity estimates ranged from 0.4% to 98% (most fruit had <10% severity). Accuracy and precision of the estimates were significantly improved when using the diagrammatic scale; concordance correlation coefficient values increased from 0.81 to 0.95. A strong tendency to underestimate severity for the mid-range to high levels was minimized when using the aid, which also improved reproducibility of the estimates among raters. In addition to strengthening evidence that a standard area diagram can be used reliably in sooty blotch and flyspeck studies, we expanded its application to disease assessment in the peduncle region, which enhances the usefulness of the method for evaluating efficacy of management practices.     

Variation in resistance to Verticillium wilt within seedling populations of some varieties of lucerne (Medicago sativa)

Verticillium wilt was assessed in seedling populations of five lucerne varieties: Euver, Maris Kabul, Sabilt, Verneuil and Vertus. Visual assessments of disease severity in Vertus were compared with estimates of fungal biomass obtained by a maceration-dilution plate method and glucosamine assays. Symptom severity correlated with the amounts of fungus present only at the lower disease ratings. In contrast, direct correlations were obtained between visually assessed disease severities and the chlorophyll contents of plant shoots. Wide variation in disease reaction type were found within populations of all five varieties and disease development was found to differ in two environments with differing temperatures. The significance of these variations is discussed in relation to the genetic background of the host and studies on the biochemical basis of resistance to Verticillium wilt.     

A new standard area diagram set for assessment of severity of soybean rust improves accuracy of estimates and optimizes resource use

Soybean rust (SBR), caused by Phakopsora pachyrhizi, is the most important yield-damaging fungal disease of soybean due to severe reduction in healthy leaf area and acceleration of leaf fall. In experimental research, SBR severity is estimated visually aided/trained by a standard area diagram (SAD) developed and validated during the mid-2000s (Old SAD). In this study, we propose a new SAD set for SBR with six true-colour diagrams following linear increments (c. 15% increments) amended with four additional diagrams at low (<10%) severities, totalling 10 diagrams (0.2%, 1%, 3%, 5%, 10%, 25%, 40%, 55%, 70%, and 84%). For evaluation, 37 raters were split into two groups. Each assessed severity in a 50-image sample (0.25%–84%), first unaided and then using either the Old SAD or the New SAD. Accuracy, precision, and reliability of estimates improved significantly relative to unaided estimates only when aided by the New SAD (accuracy >0.95). Low precision (<0.78) and a trend of underestimation with an increase in severity were the main issues with the Old SAD, which did not differ from unaided estimates. Simulation to evaluate the impact of the errors by different methods on hypothesis tests, showed that the new SAD was more powerful for detecting the smallest difference in mean control (e.g., 70% vs. 65% disease reduction) than the Old SAD; the latter required a 2-fold increase in sample size to achieve the same power. There is a need to improve some SADs, taking advantage of new knowledge and technology to increase accuracy of the estimates, and to optimize both resource use efficiency and management decisions.     

Factors affecting the temporal progress of stem canker (Rhizoctonia solani ) on potatoes (Solanum tuberosum)

The effects of different densities of tuber-borne inoculum, selected agronomic treatments (date of planting, irrigation and size of seed tubers) and their interactions on the temporal progress of stem canker ( Rhizoctonia solani ) on potato plants ( Solanum tuberosum ) were investigated in a multifactorial experiment. Data comprising stem number and the incidence and severity of stem canker from planting until tuber initiation in two consecutive growing seasons were analysed using linear contrasts, quadratic contrasts and the area under the disease progress or host growth curve. Differences in the incidence and severity of stem canker were dominated by the effect of different densities of tuber-borne inoculum. The majority of disease progress curves were nonmonotonic for the incidence and severity of stem canker with a rapid rise in disease up to stem emergence and a decline thereafter. Most treatments affected the area under the curve and to a lesser extent the average rate of increase in disease. Of the agronomic treatments, later dates of planting and pre-emergence irrigation reduced the levels of stem canker whereas size of seed tubers did not affect the progress of disease. Little additional information was revealed by scoring for the severity rather than the incidence of stem canker.     

Systemic insecticides for control of Delphacodes kuscheli and the Mal de Río Cuarto virus on maize

Control of the Mal de Río Cuarto virus (MRCV) and its planthopper vector Delphacodes kuscheli was studied on maize hybrids whose seeds had been treated with systemic insecticides. Laboratory tests were performed to determine the effects of seed treatments with insecticides (acephate, carbofuran, imidacloprid) on the survival of the planthopper. Field experiments using four maize hybrids whose seeds had been treated with the insecticides were performed to establish the effect of the latter on MRCV incidence and severity, and on grain yield. MRCV infection was confirmed by DAS-ELISA. Carbofuran was the most effective insecticide in laboratory tests, independently of the hybrid tested, followed by imidacloprid and acephate. MRCV incidences were high in all treatments in the field test under natural planthopper infestations. Disease severity data analysis indicated that the insecticide - hybrid interaction was not significant. Maize hybrid Dekalb 664 and the imidacloprid treatments had the lowest severity means among the four hybrids and three insecticide treatments, respectively. Data for grain yield showed that the insecticide - hybrid interaction was significant and imidacloprid was generally the most effective in the field experiments. A negative correlation was observed between the mean disease severity index and mean grain yield. The results suggest that if an effective systemic insecticide is applied as a seed coating, it may be possible to obtain good control of D. kuscheli, decrease MRCV severity and increase grain yield under field conditions in areas at risk for MRCV.     

Temporal dynamics of root and foliar severity of soybean sudden death syndrome at different inoculum densities

Temporal dynamics of soybean sudden death syndrome (SDS) root and foliar disease severity were studied in growth chamber experiments on susceptible plants exposed to different inoculum densities (0, 10⁰, 10¹, 10², and 10³ conidia g⁻¹ soil) of Fusarium virguliforme. The monomolecular model provided the best fit to describe the progress of root and foliar disease severity over time. Disease severity and area under disease progress curve (AUDPC) both increased in response to increasing inoculum density (P < 0.01), particularly for foliar symptoms. Rate of disease progress increased as inoculum densities increased for both root and foliar disease severities. The incubation period for root and foliar disease severity ranged from 9 to 18 and 15 to 25 days, respectively. Significant differences in root rot severity were most easily detected during the early stages of infection, whereas root rot and foliar severities were only weakly correlated when both were assessed simultaneously at later stages of disease development. Root rot severity assessments performed 15 to 20 days after inoculation (DAI) were most highly correlated (r > 0.9, P < 0.01) with foliar disease severity assessments performed 30 to 50 DAI. Root biomass was reduced by up to 67% at the three highest inoculum densities, indicating the aggressiveness that F. virguliforme possesses as a root rot pathogen on soybeans.     

Glasshouse and field evaluation of benomyl and triadimefon applied at seeding to control take-all in wheat

The effects of two fungicides, benomyl and triadimefon, applied at seeding, on the incidence and severity of take-all ( Gaeumannomyces graminis var. tritici ) of wheat were investigated in the glasshouse and in the field. In glasshouse studies with an artificially inoculated and naturally infested sandy loam, both fungicides caused significantly less disease, whereas in a field study with a clay soil and artificial inoculum, triadimefon caused significantly less disease. In the field, both fungicides were more effective when placed near the seed as granules or as pellets than when applied as seed treatments.     

Fungicide seed treatment efficacy against Microdochium nivale and M. majus in vitro and in vivo

BACKGROUND: Seed-borne Microdochium majus (Wollenweber) and M. nivale Fries are the primary pathogens responsible for Fusarium seedling blight in the UK. The two species show differences in pathogenicity, host preference and sensitivities to temperature, but their relative sensitivities to fungicide seed treatments are unknown. The aim was firstly to determine the efficacy of fungicide seed treatments towards single-spore isolates of M. majus and M. nivale using in vitro experiments, and subsequently to determine efficacy in vivo over a range of temperatures. RESULTS: Differences in EC(50) values between all seed treatments were evident from the in vitro experiments and ranged from 0.028 mg L(-1) for fludioxonil to 22.8 mg L(-1) for carboxin + thiram. The two seed treatments that showed best performance in vitro were used to examine efficacy towards seed-borne infection in vivo at 4, 8, 12 and 16 degrees C. Generally, seedling emergence improved and the severity of stem-base disease symptoms on emerged seedlings was reduced for both species through the use of the fungicides. The combination of fludioxonil + difenconazole showed improved performance compared with fludioxonil alone. Significantly less severe symptoms were observed through the use of fludioxonil and fludioxonil + difenconazole compared with bitertanol + fuberidazole at 12 degrees C and for all except one M. nivale infected seed lot at 8 degrees C. CONCLUSIONS: Differences in fungicide sensitivity between the two species in vitro were not evident in vivo. This is the first report of the effect of fungicide seed treatments on the control of seedling blight caused by M. majus and M. nivale.     

Effects of sunlight exposure on grapevine powdery mildew development

Natural and artificially induced shade increased grapevine powdery mildew (Erysiphe necator) severity in the vineyard, with foliar disease severity 49 to 75% higher relative to leaves in full sun, depending on the level of natural shading experienced and the individual experiment. Cluster disease severities increased by 20 to 40% relative to those on check vines when ultraviolet (UV) radiation was filtered from sunlight reaching vines in artificial shading experiments. Surface temperatures of leaves in full sunlight averaged 5 to 8°C higher than those in natural shade, and in one experiment, filtering 80% of all wavelengths of solar radiation, including longer wavelengths responsible for heating irradiated tissues, increased disease more than filtering UV alone. In controlled environment experiments, UV-B radiation reduced germination of E. necator conidia and inhibited both colony establishment (hyphal formation and elongation) and maturity (latent period). Inhibitory effects of UV-B radiation were significantly greater at 30°C than at 20 or 25°C. Thus, sunlight appears to inhibit powdery mildew development through at least two mechanisms, i.e., (i) UV radiation's damaging effects on exposed conidia and thalli of the pathogen; and (ii) elevating temperatures of irradiated tissues to a level supraoptimal or inhibitory for pathogen development. Furthermore, these effects are synergistic at temperatures near the upper threshold for disease development.