Characterizing Heterogeneity of Disease Incidence in a Spatial Hierarchy: A Case Study from a Decade of Observations of Fusarium Head Blight of Wheat

A multilevel analysis of heterogeneity of disease incidence was conducted based on observations of Fusarium head blight (caused by Fusarium graminearum) in Ohio during the 2002–11 growing seasons. Sampling consisted of counting the number of diseased and healthy wheat spikes per 0.3 m of row at 10 sites (about 30 m apart) in a total of 67 to 159 sampled fields in 12 to 32 sampled counties per year. Incidence was then determined as the proportion of diseased spikes at each site. Spatial heterogeneity of incidence among counties, fields within counties, and sites within fields and counties was characterized by fitting a generalized linear mixed model to the data, using a complementary log-log link function, with the assumption that the disease status of spikes was binomially distributed conditional on the effects of county, field, and site. Based on the estimated variance terms, there was highly significant spatial heterogeneity among counties and among fields within counties each year; magnitude of the estimated variances was similar for counties and fields. The lowest level of heterogeneity was among sites within fields, and the site variance was either 0 or not significantly greater than 0 in 3 of the 10 years. Based on the variances, the intracluster correlation of disease status of spikes within sites indicated that spikes from the same site were somewhat more likely to share the same disease status relative to spikes from other sites, fields, or counties. The estimated best linear unbiased predictor (EBLUP) for each county was determined, showing large differences across the state in disease incidence (as represented by the link function of the estimated probability that a spike was diseased) but no consistency between years for the different counties. The effects of geographical location, corn and wheat acreage per county, and environmental conditions on the EBLUP for each county were not significant in the majority of years.

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Quantifying the Effects of Fusarium Head Blight on Grain Yield and Test Weight in Soft Red Winter Wheat

Phytopathology ◽

10.1094/phyto-08-14-0215-r ◽

2015 ◽

Vol 105 (3) ◽

pp. 295-306 ◽

Cited By ~ 39

Author(s):

Jorge David Salgado ◽

Laurence V. Madden ◽

Pierce A. Paul

Keyword(s):

Winter Wheat ◽

Grain Yield ◽

Fusarium Head Blight ◽

Fixed Effects ◽

Mixed Model ◽

Linear Mixed Model ◽

Test Weight ◽

Head Blight ◽

Soft Red Winter Wheat ◽

Red Winter Wheat

Fusarium head blight (FHB), caused by the fungus Fusarium graminearum, is known to negatively affect wheat grain yield (YLD) and test weight (TW). However, very little emphasis has been placed on formally quantifying FHB–YLD and FHB–TW relationships. Field plots of three soft red winter wheat cultivars—‘Cooper’ (susceptible to FHB), ‘Hopewell’ (susceptible), and ‘Truman’ (moderately resistant)—were grown during the 2009, 2010, 2011, and 2012 seasons, and spray inoculated with spore suspensions of F. graminearum and Parastagonospora nodorum to generate a range of FHB and Stagonospora leaf blotch (SLB) levels. FHB index (IND) and SLB were quantified as percent diseased spike and flag leaf area, respectively, and YLD (kg ha−1) and TW (kg m−3) data were collected. Using IND as a continuous covariate and cultivar (CV) and SLB as categorical fixed effects, linear mixed-model regression analyses (LMMR) were used to model the IND–YLD and IND–TW relationship and to determine whether these relationships were influenced by CV and SLB. The final models fitted to the data were of the generic form y = a + b (IND), where a (intercept) or b (slope) could also depend on other factors. LMMR analyses were also used to estimate a and b by combining the studies from these 4 years with an additional 16 experiments conducted from 2003 to 2013, and bivariate random-effects meta-analysis was used to estimate population mean b ([Formula: see text]) and a (ā) for the IND–YLD relationship. YLD and TW decreased as IND increased, with b ranging from −3.2 to −2.3 kg m−3 %−1 for TW. For the IND–YLD relationship, [Formula: see text] was −51.7 kg ha−1 %IND−1 and ā was 4,426.7 kg ha−1. Neither cultivar nor SLB affected the IND–YLD relationship but SLB affected a of the IND–TW regression lines, whereas cultivar affected b. Plots with the highest levels of SLB (based on ordinal categories for SLB) had the lowest a and Hopewell had the highest b. The level of IND at which a 50-kg m−3 reduction in TW was predicted to occur was 19, 16, and 22% for Cooper, Hopewell, and Truman, respectively. A yield loss of 1 MT ha−1 was predicted to occur at 19% IND. The rate of reduction in relative TW or YLD per unit increase in IND was between −0.39 and −0.32%−1 for TW and −1.17%−1 for YLD. Results from this study could be integrated into more general models to evaluate the economics of FHB management strategies.

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Efficacy and Economics of Integrating In-Field and Harvesting Strategies to Manage Fusarium Head Blight of Wheat

Plant Disease ◽

10.1094/pdis-01-14-0093-re ◽

2014 ◽

Vol 98 (10) ◽

pp. 1407-1421 ◽

Cited By ~ 27

Author(s):

Jorge David Salgado ◽

Laurence V. Madden ◽

Pierce A. Paul

Keyword(s):

Fusarium Head Blight ◽

Mixed Model ◽

Linear Mixed Model ◽

Management Program ◽

Cash Income ◽

Head Blight ◽

Fungicide Treatment ◽

Fungicide Application ◽

Moderate Resistance ◽

Moderately Resistant

Fusarium head blight (FHB), a fungal disease of wheat caused by Fusarium graminearum, and its associated toxins, particularly deoxynivalenol (DON), are best managed by integrating multiple strategies. Experiments were established in 2011 and 2013 to evaluate the effects of integrating cultivar resistance, fungicide application, and grain harvesting strategy on FHB index (IND; field severity), DON, grain yield (YLD), and grain test weight (TW; weight per unit volume). Plots of two moderately resistant and two susceptible cultivars were either treated with 19% tebuconazole + 19% prothioconazole or left untreated, and then inoculated with F. graminearum. IND was rated as the mean percentage of diseased spikelets per spike. Separate subsets of the plots of each cultivar–treatment combination were harvested with one of two combine harvester configuration: C1 (the default, set at a fan speed of 1,375 rpm and a shutter opening of 70 mm) and C4 (modified, with the same fan speeds but a wider shutter opening of 90 mm). YLD and TW data were collected, and grain samples were rated for percent Fusarium-damaged kernels (FDK) and tested for DON. Results from linear mixed-model analyses showed that the cultivar–treatment interaction was significant for all FHB-related responses, with the magnitude of the difference in mean arcsine-square-root-transformed IND and FDK (arcIND and arcFDK) and log-transformed DON (logDON) between treated and untreated being higher for susceptible than moderately resistant cultivars. Plots harvested with the C4 combine configuration had significantly higher mean TW than those harvested with C1. Treated plots had significantly higher YLD and TW than untreated plots, regardless of cultivar and configuration. Relative to the reference management program (untreated, susceptible cultivar, harvested with C1), the greatest percent reduction in FDK and DON and increase in YLD was observed for programs that included moderate resistance and fungicide treatment. The greatest percent increase in TW relative to the reference was observed when C4 adjusted combine setting was integrated with resistance and fungicide. Overall, the most effective management programs all included fungicide treatment, two included moderate resistance, and two included C4 combine setting. Relative to the reference management program, these programs resulted in 30 to 51% reduction in total estimated price discount, $127 to 312 ha−1 increase in gross cash income, and economic benefit of $31 to 272 ha−1, depending on the level of FHB IND (5 to 15%), grain price ($118 to 276 metric ton−1), and fungicide application cost ($40 to 96 ha−1).

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Heterogeneity of Fusarium Head Blight of Wheat: Multi-scale Distributions and Temporal Variation in Relation to Environment

Plant Health Progress ◽

10.1094/php-2012-0723-01-rs ◽

2012 ◽

Vol 13 (1) ◽

pp. 30

Author(s):

Alissa B. Kriss ◽

Laurence V. Madden ◽

Pierce A. Paul ◽

Xiangming Xu

Keyword(s):

Temporal Variation ◽

Fusarium Head Blight ◽

Mixed Model ◽

Linear Mixed Model ◽

Climate Index ◽

Head Blight ◽

Spatial And Temporal Scales ◽

Multi Scale ◽

Spatio Temporal ◽

Serious Disease

Fusarium head blight (FHB) is a serious disease of wheat, which is highly variable at several spatial and temporal scales. Different statistical approaches were used to either quantify or partially explain this heterogeneity. First, a generalized linear mixed model was fitted to hierarchical survey data for the incidence of FHB in Ohio. Estimated variance terms indicated large and significant spatial heterogeneity among counties and among fields within counties, with substantially lower variation among sites within fields. Second, window-pane analysis was used to investigate the effects of environment on the inter-annual variation in FHB in four United States (US) states and the spatio-temporal variation across three European countries. Moisture- or wetness-related variables (e.g., average daily relative humidity) were positively associated with FHB intensity for multiple window lengths and starting times, especially for the last 2 months of the growing season. Third, cross-spectral analysis was used to determine whether there was coherency between variation in FHB in Ohio and global climatic patterns. There were significant coherencies at one or more inter-annual time scales (i.e., periods), with peaks in FHB following lows in the climate index (a reflection of a La Niña event) by about 1 year. Accepted for publication 27 April 2012. Published 23 July 2012.

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Fusarium Head Blight Development and Deoxynivalenol Accumulation in Wheat as Influenced by Post-Anthesis Moisture Patterns

Phytopathology ◽

10.1094/phyto-04-14-0104-r ◽

2015 ◽

Vol 105 (2) ◽

pp. 210-219 ◽

Cited By ~ 12

Author(s):

Kelsey F. Andersen ◽

Laurence V. Madden ◽

Pierce A. Paul

Keyword(s):

Fusarium Head Blight ◽

Mixed Model ◽

Linear Mixed Model ◽

Regression Line ◽

Disease Spread ◽

Marginal Effect ◽

Head Blight ◽

Critical Thresholds ◽

Regression Slopes ◽

Treatment Window

Mist chamber experiments were conducted to quantify and model the effects of post-anthesis moisture on Fusarium head blight (FHB) index (IND) and deoxynivalenol (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) in 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; 2 days of mist at the beginning and end of the treatment window) had significantly higher infection efficiency (estimated diseased spikelets per spore) than the check; however, 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 %−1 IND for the point- and spray-inoculated experiments, respectively. Mist treatment did not have a significant effect on the slope but had a significant effect on the intercept. The height of the regression line (logDON after adjusting for IND) 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 experiments, 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.

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Screening of Durum Wheat (Triticum turgidum L. subsp. durum (Desf.) Husn.) Italian Cultivars for Susceptibility to Fusarium Head Blight Incited by Fusarium graminearum

Plants ◽

10.3390/plants10010068 ◽

2020 ◽

Vol 10 (1) ◽

pp. 68

Author(s):

Gaetano Bentivenga ◽

Alfio Spina ◽

Karim Ammar ◽

Maria Allegra ◽

Santa Olga Cacciola

Keyword(s):

Durum Wheat ◽

Fusarium Head Blight ◽

Fusarium Graminearum ◽

Triticum Turgidum ◽

Disease Incidence ◽

Morphological Characteristics ◽

Pcr Amplification ◽

Conidial Suspension ◽

Head Blight ◽

Italian Origin

In 2009, a set of 35 cultivars of durum wheat (Triticum turgidum L. subsp. durum (Desf.) Husn.) of Italian origin was screened for fusarium head blight (FHB) susceptibility at CIMMYT (Mexico) and in the 2019–20 cropping season, 16 of these cultivars, which had been included in the Italian National Plant Variety Register, were tested again in southern and northern Italy. Wheat cultivars were artificially inoculated during anthesis with a conidial suspension of Fusarium graminearum sensu lato using a standard spray inoculation method. Inoculum was a mixture of mono-conidial isolates sourced in the same areas where the trials were performed. Isolates had been characterized on the basis of morphological characteristics and by DNA PCR amplification using a specific primer set and then selected for their virulence and ability to produce mycotoxins. The susceptibility to FHB was rated on the basis of the disease severity, disease incidence and FHB index. Almost all of the tested cultivars were susceptible or very susceptible to FHB with the only exception of “Duprì”, “Tiziana” and “Dylan” which proved to be moderately susceptible. The susceptibility to FHB was inversely correlated with the plant height and flowering biology, the tall and the late heading cultivars being less susceptible.

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Anthesis, the infectious process and disease progress curves for fusarium head blight in wheat

Summa Phytopathologica ◽

10.1590/0100-5405/2075 ◽

2016 ◽

Vol 42 (2) ◽

pp. 134-139 ◽

Cited By ~ 2

Author(s):

Erlei Melo Reis ◽

Cristina Boareto ◽

Anderson Luiz Durante Danelli ◽

Sandra Maria Zoldan

Keyword(s):

Fusarium Head Blight ◽

Disease Incidence ◽

Weather Conditions ◽

Gibberella Zeae ◽

Head Blight ◽

Infectious Process ◽

Disease Progress ◽

Winter Cereals ◽

Aggregation Pattern ◽

Adverse Weather

ABSTRACT Fusarium head blight of wheat (Triticum aestivum), caused by the fungus Gibberella zeae, is a floral infecting disease that causes quantitative and qualitative losses to winter cereals. In Brazil, the sanitary situation of wheat has led to research in order to develop strategies for sustainable production, even under adverse weather conditions. To increase the knowledge of the relationship among the presence of anthesis, the infectious process, the disease progress and the saprophytic fungi present in wheat anthers, studies were conducted in the experimental field of University of Passo Fundo (UPF), using the cultivar Marfim, in the 2011 growing season. The disease incidence in spikes and spikelets was evaluated. The presence of exserted anthers increased the spike exposure time to the inoculum. The final incidence of fusarium head blight, in the field, was dependent on the presence of exserted anthers. The disease followed an aggregation pattern and its evolution increased with time, apparently showing growth according to secondary cycles. The fungi isolated from exserted anthers (Alternaria sp., Fusarium sp., Drechslera spp. and Epicoccum sp.) did not compete for the infection site of fusarium head blight in wheat, not interfering with the incidence of F. graminearum.

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Full Credibility with Generalized Linear and Mixed Models

Astin Bulletin ◽

10.2143/ast.39.1.2038056 ◽

2009 ◽

Vol 39 (1) ◽

pp. 61-80 ◽

Cited By ~ 6

Author(s):

José Garrido ◽

Jun Zhou

Keyword(s):

Mixed Models ◽

Mixed Model ◽

Linear Mixed Model ◽

Linear Models ◽

Link Function ◽

Analysis Method ◽

Risk Class ◽

Statistical Analysis Method ◽

Car Insurance ◽

Insurance Data

AbstractGeneralized linear models (GLMs) are gaining popularity as a statistical analysis method for insurance data. For segmented portfolios, as in car insurance, the question of credibility arises naturally; how many observations are needed in a risk class before the GLM estimators can be considered credible? In this paper we study the limited fluctuations credibility of the GLM estimators as well as in the extended case of generalized linear mixed model (GLMMs). We show how credibility depends on the sample size, the distribution of covariates and the link function. This provides a mechanism to obtain confidence intervals for the GLM and GLMM estimators.

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Chemotype and aggressiveness evaluation of Fusarium graminearum and Fusarium culmorum isolates from wheat fields in Wisconsin

Plant Disease ◽

10.1094/pdis-06-20-1376-re ◽

2021 ◽

Author(s):

Brian Mueller ◽

Carol Groves ◽

Damon L. Smith

Keyword(s):

Growth Rate ◽

Fusarium Head Blight ◽

Fusarium Graminearum ◽

Fusarium Culmorum ◽

Head Blight ◽

Growing Seasons ◽

Progress Curve ◽

Sporulation Capacity ◽

Derivatives Of

Fusarium graminearum commonly causes Fusarium head blight (FHB) on wheat, barley, rice, and oats. Fusarium graminearum produces nivalenol and deoxynivalenol (DON) and forms derivatives of DON based on its acetylation sites. The fungus is profiled into chemotypes based on DON derivative chemotypes (3 acetyldeoxynivalenol (3ADON) chemotype; 15 acetyldeoxynivalenol (15ADON) chemotype) and/or the nivalenol (NIV) chemotype. The current study assessed the Fusarium population found on wheat and the chemotype profile of the isolates collected from 2016 and 2017 in Wisconsin. Fusarium graminearum was isolated from all locations sampled in both 2016 and 2017. Fusarium culmorum was isolated only from Door County in 2016. Over both growing seasons, 91% of isolates were identified as the 15ADON chemotype while 9% of isolates were identified as the 3ADON chemotype. Aggressiveness was quantified by area under disease progress curve (AUDPC). The isolates with the highest AUDPC values were from the highest wheat producing cropping districts in the state. Deoxynivalenol production in grain and sporulation and growth rate in vitro were compared to aggressiveness in the greenhouse. Our results showed that 3ADON isolates in Wisconsin were among the highest in sporulation capacity, growth rate, and DON production in grain. However, there were no significant differences in aggressiveness between the 3ADON and 15ADON isolates. The results of this research detail the baseline frequency and distribution of 3ADON and 15ADON chemotypes observed in Wisconsin. Chemotype distributions within populations of F. graminearum in Wisconsin should continue to be monitored in the future.

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Species and trichothecene genotype of pathogens causing Fusarium head blight of wheat in Nebraska, USA

Plant Health Progress ◽

10.1094/php-02-21-0020-rs ◽

2021 ◽

Author(s):

Esteban Valverde-Bogantes ◽

Andreia Bianchini ◽

Stephen Wegulo ◽

Heather Hallen-Adams

Keyword(s):

Fusarium Head Blight ◽

Fusarium Species ◽

Management Strategies ◽

Elongation Factor ◽

Head Blight ◽

Single Spore ◽

Additional Species ◽

Growing Seasons ◽

Worldwide Distribution ◽

Pathogen Populations

Fusarium head blight (FHB) is an economically important disease caused by several Fusarium species affecting wheat and other small grain cereals. In recent years, reports of shifts in populations of FHB pathogens around the world have shown that these populations are dynamic and change continuously, often resulting in increased yield losses or changes in the mycotoxins produced in the grain, which highlights the need for increased vigilance. The objective of this research was to identify the species and trichothecene genotypes of FHB pathogens in Nebraska in order to monitor their populations and the major toxigenic risks in the state. A total of 74 single-spore Fusarium isolates were obtained from 42 FHB symptomatic wheat spikes collected from Nebraska fields during the growing seasons in 2015-2018. Most of the isolates were identified as F. graminearum (n=67) based on translation elongation factor 1α (TEF1), trichothecene 3-O-acetyltransferase (TRI101), and reductase (RED) sequences. Additional species included F. boothii (n=3), F. poae (n=2), F. acuminatum (n=1), and one isolate was an F. graminearum × F. boothii interspecific hybrid. All F. graminearum and F. boothii isolates had the 15-ADON trichothecene genotype. This study shows that F. graminearum is not the only pathogen causing FHB in Nebraska and helps expand knowledge on the worldwide distribution of F. boothii. The information obtained from this survey will be useful in developing effective FHB management strategies in Nebraska, since different pathogen populations can cause varying levels of disease intensity and can be selectively sensitive to management tactics.

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A graphical model for skewed matrix-variate non-randomly missing data

Biostatistics ◽

10.1093/biostatistics/kxy056 ◽

2018 ◽

Author(s):

Lin Zhang ◽

Dipankar Bandyopadhyay

Keyword(s):

Mixed Model ◽

Graphical Model ◽

Linear Mixed Model ◽

Disease Status ◽

Epidemiological Studies ◽

Model Parameters ◽

Probit Regression ◽

Pocket Depth ◽

Cross Sectional ◽

Missing Responses

SummaryEpidemiological studies on periodontal disease (PD) collect relevant bio-markers, such as the clinical attachment level (CAL) and the probed pocket depth (PPD), at pre-specified tooth sites clustered within a subject’s mouth, along with various other demographic and biological risk factors. Routine cross-sectional evaluation are conducted under a linear mixed model (LMM) framework with underlying normality assumptions on the random terms. However, a careful investigation reveals considerable non-normality manifested in those random terms, in the form of skewness and tail behavior. In addition, PD progression is hypothesized to be spatially-referenced, i.e. disease status at proximal tooth-sites may be different from distally located sites, and tooth missingness is non-random (or informative), given that the number and location of missing teeth informs about the periodontal health in that region. To mitigate these complexities, we consider a matrix-variate skew-$t$ formulation of the LMM with a Markov graphical embedding to handle the site-level spatial associations of the bivariate (PPD and CAL) responses. Within the same framework, the non-randomly missing responses are imputed via a latent probit regression of the missingness indicator over the responses. Our hierarchical Bayesian framework powered by relevant Markov chain Monte Carlo steps addresses the aforementioned complexities within an unified paradigm, and estimates model parameters with seamless sharing of information across various stages of the hierarchy. Using both synthetic and real clinical data assessing PD status, we demonstrate a significantly improved fit of our proposition over various other alternative models.

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