Forecasting the spread of aerially transmitted crop diseases with a binary classifier for inoculum survival

The risk of between‐field spread of disease is typically omitted from crop disease warning systems, as it is difficult to know the number and location of inoculum sources and thus predict the abundance of inoculum arriving at healthy crops. This study explores the utility of a simple approach to predicting risk of between‐field spread, based on the estimated probability that inoculum will survive the transportation process. Using potato late blight as a case study, the effect of solar radiation on the viability of detached Phytophthora infestans sporangia was assessed. A model to estimate the probability of spore survival was derived using a binomial generalized linear mixed model (GLMM), and receiver operating characteristic (ROC) curve analysis and cross‐validation were used to evaluate the global performance of the model as a binary classifier for discriminating between viable and nonviable sporangia. The model yielded an area under the ROC curve of 0.92 (95% CI = 0.90–0.93), signifying an excellent classification algorithm. Inspection of the curve provided a number of suitable decision threshold (or cut‐off) probabilities for discriminating between viable and nonviable sporangia. The classifier was tested as a forecasting system for potato late blight outbreaks using 10 years of outbreak data from across Great Britain. There was a marked differentiation among the cut‐offs, but the best prediction outcome was an accuracy of 89% with an alert frequency of 1 in 7 days. This model can be easily modified or the methodology replicated for other pathosystems characterized by airborne inoculum.     

Use of SADIE statistics to study spatial dynamics of plant disease epidemics

Using a previously developed stochastic simulation model for plant disease epidemics, the relationship of the SADIE aggregation statistic I _a with initial epidemic conditions, spore dispersal distance, sampling quadrat size and other spatial statistics was investigated. Most variation in I _a was attributable to the initial spatial pattern of infected plants and sampling quadrat size. The importance of initial spatial pattern on SADIE clustering indices (for patches and gaps) was also demonstrated using a number of selected data sets. Correlation of I _a with clustering indices was close to 1·0. Epidemics arising from the regular and random initial patterns resulted in the smallest and greatest I _a values, respectively, at sampling times after disease spread had occurred. Furthermore, the variability in I _a between simulation runs also varied greatly with initial patterns, being lowest and greatest for the clumped and random initial patterns, respectively. I _a increased initially and then decreased with increasing incidence, especially for the clumped and random initial patterns. Overall, the effect of median spore dispersal distance on I _a was very small, especially for the random initial pattern. The correlation between I _a and intraclass correlation was generally small and varied greatly between initial patterns. However, there was a high positive correlation between I _a and a parameter describing the rate of decline of autocorrelation over spatial lags, indicating that I _a, clustering indices and autocorrelations measure some common properties of patterns.     

植物病害时空流行动态模拟模型的构建

 一个描述在二维空间中单一种植或混合种植的植物群体内病害时、空流行动态的计算机随机模拟模型构建完成。模型由寄主、病原2个组分和病斑产孢、孢子传播、孢子着落、孢子侵染、病斑潜育、寄主生长、病害控制等一系列代表病害流行生物学过程的子模型构成。模型采用了面向对象的程序设计方法,用C++语言编写,能以病害流行曲线图、空间分布图、数据列表等方式显示模拟结果。测试结果表明:模型能反映植物病害流行过程的本质规律,既可作为植物病害流行学教学工具,帮助学生理解病害流行的时、空动态规律和不同因子对病害流行的影响,也可以作为研究工具,对流行学的某些理论问题进行模拟研究     

Current knowledge on plant/canopy architectural traits that reduce the expression and development of epidemics

To reduce the use of pesticides, innovative studies have been developed to introduce the plant as the centre of the crop protection system. The aim of this paper is to explain how architectural traits of plants and canopies induce a more or less severe epidemic and how they may be modified in order to reduce disease development. In particular, it focuses on three key questions: i) which processes linked to epidemics can be influenced by architecture ii) how can architecture be characterized relative to these modes of action, and iii) how can these effects be explored and exploited? The roles of plant/canopy architecture on inoculum interception, on epidemic development via the microclimate and on tissue receptivity are discussed. In addition, the concepts of disease avoidance, canopy porosity and an ideotype unfavourable for disease development are described. This paper shows that many advances have already been made, but progress is still required in four main fields: microclimatology, mathematical modelling of plants, molecular genetics and ideotype conception.     

Effects of initial epidemic conditions, sporulation rate, and spore dispersal gradient on the spatio-temporal dynamics of plant disease epidemics

ABSTRACT A stochastic model that simulates the spread of disease over space and time was developed to study the effects of initial epidemic conditions (number of initial inocula and their spatial pattern), sporulation rate, and spore dispersal gradient on the spatio-temporal dynamics of plant disease epidemics. The spatial spread of disease was simulated using a half-Cauchy distribution with median dispersal distance mu (units of distance). The rate of temporal increase in disease incidence (beta(I), per day) was influenced jointly by mu and by the sporulation rate lambda (spores per lesion per day). The relationship between beta(I) and mu was nonlinear: the increase in beta(I) with increasing mu was greatest when mu was small (i.e., when the dispersal gradient was steep). The rate of temporal increase in disease severity of diseased plants (beta(S)) was affected mainly by lambda: beta(S) increased directly with increasing lambda. Intraclass correlation (kappa(t)), the correlation of disease status of plants within quadrats, increased initially with disease incidence, reached a peak, and then declined as disease incidence approached 1.0. This relationship was well described by a power-law model that is consistent with the binary form of the variance power law. The amplitude of the model relating kappa(t) to disease incidence was affected mainly by mu: kappa(t) decreased with increasing mu. The shape of the curve was affected mainly by initial conditions, especially the spatial pattern of the initial inocula. Generally, the relationship of spatial autocorrelation (rho(t,k)), the correlation of disease status of plants at various distances apart, to disease incidence and distance was well described by a four-parameter power-law model. rho(t,k) increased with disease incidence to a maximum and then declined at higher values of disease incidence, in agreement with a power-law relationship. The amplitude of rho(t,k) was determined mainly by initial conditions and by mu: rho(t,k) decreased with increasing mu and was lower for regular patterns of initial inocula. The shape of the rho(t,k) curve was affected mainly by initial conditions, especially the spatial pattern of the initial inocula. At any level of disease incidence, autocorrelation declined exponentially with spatial lag; the degree of this decline was determined mainly by mu: it was steeper with decreasing mu.     

Influence of crop growth and structure on the risk of epidemics by Mycosphaerella graminicola (Septoria tritici) in winter wheat

Generally, it is recognized that inocula of Septoria tritici present on the basal leaves of winter wheat crops are spread towards the top of the canopy by splashy rainfall. This mechanism of inoculum dispersal is commonly accepted to be a key limit on disease progression. Therefore, attempts to forecast epidemics of S. tritici often quantify rainfall by some means, but largely ignore measurement of pathogen and host variables. In the present study, we show that new wheat leaves emerge initially at a height below established leaves that can contain sporulating lesions of S. tritici . This presents the possibility of horizontal inoculum transfer, even without splashy rainfall. The extent and duration of overlap between emergent and established leaves was found to differ considerably with cultivar and sowing date. Nitrogen application had little effect on overlap, because differences in crop phenology, e.g. leaf area and nodal length, were relative. However, estimates of raindrop penetration to the base of crop canopies suggested that vertical movement of inoculum is affected by nitrogen application. Crops receiving more nitrogen are denser, and therefore less rainfall reaches the base of the canopy. The interactions between crop and pathogen development are discussed with reference to the implications for predicting disease risk. In particular, cultivar traits that promote disease escape are quantified.     

Effect of various crop establishment methods practised by Asian farmers on epidemics of rice sheath blight caused by Rhizoctonia solani

Establishment methods for rice crops in tropical Asia are very diverse, leading to variation in the structure of rice canopies. Differences in canopy structure can in turn affect the spread of the rice sheath blight pathogen, Rhizoctonia solani . Rice sheath blight epidemics were compared during two seasons in crops established by different methods: direct broadcasting of pregerminated rice seeds, and transplanting of rice seedlings at spacings of 20 × 20 cm, 13 × 25 cm and 25 × 25 cm between hills (i.e. along and between rows, respectively). In both years, the apparent infection rate based on incidence data and the terminal severity of sheath blight were lower in the direct-seeded crops than in any of the transplanted ones, regardless of spacing. The frequency of leaf-to-leaf contacts ( CF ) between hills (or plants) was highest in direct-seeded rice, and lowest in rice transplanted at a spacing of 25 × 25 cm. Larger CF is known to favour rice sheath blight epidemics. The apparent contradiction between higher incidence and lower CF in the transplanted stands than in the direct-seeded stands is interpreted in terms of accessibility of healthy host tissues to the spread of the pathogen in the canopy, and accounts for within-host (rice hill or plant) and between-host (hill or plant) disease spread. The analysis of incidence-severity relationships indicated a less aggregated distribution of the disease in direct-seeded rice, which was related to the spatial distribution of the tillers. These findings have direct implications for the management of the disease.     

植物真菌和卵菌病暴发的起源和传播

传染病暴发在植物、动物和人群中很常见。除了少数已发展为流行病和大流行病外,在很大程度上大多数传染病暴发的原因仍未知,植物真菌和卵菌病暴发尤其如此。所有流行病和大流行病都是从局部暴发开始,然后蔓延到更广泛的地理区域,因此了解其初始暴发的原因对于有效预防和控制植物病害流行病和大流行病至关重要。该文首先描述疾病暴发的定义和检测,随后简要描述导致植物传染病暴发的主要原因,包括寄主植物、病原体及其相关的环境因素,以一种真菌和一种卵菌病原体为例简要概述宿主病原体系统,并强调分子工具在帮助揭示病原体的起源和传播及其暴发及大流行方面的作用。由于人为活动及气候的加速变化,植物病害暴发的可能性越来越大,最后提出应该如何应对其暴发。     

A theoretical assessment of the effects of vector-virus transmission mechanism on plant virus disease epidemics

ABSTRACT A continuous-time and deterministic model was used to characterize plant virus disease epidemics in relation to virus transmission mechanism and population dynamics of the insect vectors. The model can be written as a set of linked differential equations for healthy (virus-free), latently infected, infectious, and removed (postinfectious) plant categories, and virus-free, latent, and infective insects, with parameters based on the transmission classes, vector population dynamics, immigration/emigration rates, and virus-plant interactions. The rate of change in diseased plants is a function of the density of infective insects, the number of plants visited per time, and the probability of transmitting the virus per plant visit. The rate of change in infective insects is a function of the density of infectious plants, the number of plants visited per time by an insect, and the probability of acquiring the virus per plant visit. Numerical solutions of the differential equations were used to determine transitional and steady-state levels of disease incidence (d*); d* was also determined directly from the model parameters. Clear differences were found in disease development among the four transmission classes: nonpersistently transmitted (stylet-borne [NP]); semipersistently transmitted (foregut-borne [SP]); circulative, persistently transmitted (CP); and propagative, persistently transmitted (PP), with the highest disease incidence (d) for the SP and CP classes relative to the others, especially at low insect density when there was no insect migration or when the vector status of emigrating insects was the same as that of immigrating ones. The PP and CP viruses were most affected by changes in vector longevity, rates of acquisition, and inoculation of the virus by vectors, whereas the PP viruses were least affected by changes in insect mobility. When vector migration was explicitly considered, results depended on the fraction of infective insects in the immigration pool and the fraction of dying and emigrating vectors replaced by immigrants. The PP and CP viruses were most sensitive to changes in these factors. Based on model parameters, the basic reproductive number (R(0))-number of new infected plants resulting, from an infected plant introduced into a susceptible plant population-was derived for some circumstances and used to determine the steady-state level of disease incidence and an approximate exponential rate of disease increase early in the epidemic. Results can be used to evaluate disease management strategies.     

种植模式与施磷深度对蚕豆群体冠层结构及其产量的影响

在小区试验与大田生产试验条件下,采用三个种植密度(12 000株·667m-2,13 000株·667m-2,14000株·667m-2)、两个留苗方式(一穴单株,一穴双株)及三个施磷深度(10 cm,15 cm,20 cm)处理,通过裂区试验研究了高产蚕豆群体冠层结构指标及其对产量的影响,结果表明,13 000株·667m-2、15 cm施磷深度、双株三角留苗种植模式下,盛花期蚕豆群体叶面积指数、叶绿素SPAD值,主根长均维持在较高水平,冠层结构较优,产量最高,达到275.2 kg·667m-2;生产试验显示,"一穴双株"能有效提高蚕豆结荚率,提高产量,较常规栽培增产14%以上。提出以"深松增密,减穴加距,中层施磷"为主要内容的蚕豆高产栽培技术。     

作物冠层对喷灌水分分布影响的研究进展

喷灌水分到达冠层以后,经过冠层的截留和水分再分配过程,主要以两种方式到达地面,即穿过冠层直接落入土壤和通过叶片的集水,然后以茎秆为通道流入土壤.以不同方式进入土壤中的水量与作物的种类、冠层结构、种植密度,以及喷灌系统和喷灌时的农田小气候等因素有关.本文根据喷灌水分在农田的分布特点,把喷灌系统和作物结合起来,提出了喷灌有效灌水均匀系数的概念.该系数能综合反映灌溉水经过冠层再分配过程以后,田间水分的有效性.     

Predicting epidemics of yellow rust (Puccinia striiformis) on the upper canopy of wheat from disease observations on lower leaves

Data from field experiments were used to test whether disease observations on lower leaves of wheat were good predictors of future epidemic development in the upper canopy. Fungicide treatments to replicated plots in 1994 and 1995 caused variation in levels of initial inoculum of urediniospores of yellow rust ( Puccinia striiformis ). Observations of symptom severity were made on individual leaf layers throughout the season. Sporulating lesions on lower leaves were considered to be a measure of inoculum source strength for transfer to upper culm leaves. Low source strengths were associated with delays in epidemic development on the upper leaves, as quantified by a location parameter, t _m, the time at which severity reached half of the asymptote value in logistic fits to disease progress data on the upper leaves. However, there was much unexplained variation, probably due to extraneous variation in upward transfer efficiency of inoculum and rates of epidemic development. Vanderplank's sanitation ratio theory was used to account for variation in inoculum transfer and epidemic rate. The analysis revealed that if the aim is to predict disease on a newly emerged culm leaf, during the period when it can be treated effectively with fungicide, then observations of disease two leaves further down the culm were of the greatest predictive value ( R ² = 86%). These observations, however, need to be integrated with information about factors affecting upward inoculum transfer and rates of epidemic development if acceptable predictive precision is to be achieved.     

基质中添加西兰花残体对大丽轮枝菌GFP标记菌株在棉花体内扩展的影响

 由大丽轮枝菌引起的棉花黄萎病是一种难以防治的土传病害,西兰花残体还对其有一定的防治作用,防效为62.82%。为解析西兰花残体对棉花黄萎病的防治机制,本研究通过土壤杆菌转化的方法构建了大丽轮枝菌的绿色荧光标记菌株,采用共聚焦显微镜观察标记菌株在添加西兰花残体营养基质中和空白对照营养基质种植的棉花体内的侵染和扩展情况。结果表明构建的标记菌株gfp-wx-1与野生菌株wx-1的生物学特性无显著性差异。同时发现大丽轮枝菌在添加西兰花残体营养基质中棉花体内扩展较慢,具体表现为:在空白营养基质种植的棉花体内,大丽轮枝菌在接种第2 d时就可侵染根尖表层及根内部,第3 d到达茎部维管束,第5 d叶片可观察到少量病原菌,第7 d第一片子叶呈现大量病原菌,后期迅速扩展,叶片出现黄萎病斑;而在营养基质中添加西兰花残体种植的棉花体内,大丽轮枝菌在接种第2 d时就可侵染根尖表层,第3 d侵染根尖内部,第5 d侵染茎部维管束,直到第7 d第一片子叶才出现少量病原菌,后期扩展慢,叶片病斑较少。本研究通过荧光定量PCR方法检测了大丽轮枝菌在两个处理棉花根部定殖情况,结果表明西兰花残体能够显著降低大丽轮枝菌在棉花根部定殖的量。该研究初步明确了西兰花残体对棉花黄萎病的防治机制,为棉花黄萎病的绿色防治提供了一条新的途径。     

基质中添加西兰花残体对大丽轮枝菌GFP标记菌株在棉花体内扩展的影响

 由大丽轮枝菌引起的棉花黄萎病是一种难以防治的土传病害,西兰花残体还对其有一定的防治作用,防效为62.82%。为解析西兰花残体对棉花黄萎病的防治机制,本研究通过土壤杆菌转化的方法构建了大丽轮枝菌的绿色荧光标记菌株,采用共聚焦显微镜观察标记菌株在添加西兰花残体营养基质中和空白对照营养基质种植的棉花体内的侵染和扩展情况。结果表明构建的标记菌株gfp-wx-1与野生菌株wx-1的生物学特性无显著性差异。同时发现大丽轮枝菌在添加西兰花残体营养基质中棉花体内扩展较慢,具体表现为:在空白营养基质种植的棉花体内,大丽轮枝菌在接种第2 d时就可侵染根尖表层及根内部,第3 d到达茎部维管束,第5 d叶片可观察到少量病原菌,第7 d第一片子叶呈现大量病原菌,后期迅速扩展,叶片出现黄萎病斑;而在营养基质中添加西兰花残体种植的棉花体内,大丽轮枝菌在接种第2 d时就可侵染根尖表层,第3 d侵染根尖内部,第5 d侵染茎部维管束,直到第7 d第一片子叶才出现少量病原菌,后期扩展慢,叶片病斑较少。本研究通过荧光定量PCR方法检测了大丽轮枝菌在两个处理棉花根部定殖情况,结果表明西兰花残体能够显著降低大丽轮枝菌在棉花根部定殖的量。该研究初步明确了西兰花残体对棉花黄萎病的防治机制,为棉花黄萎病的绿色防治提供了一条新的途径。     

河南小麦叶枯类病害春季流行的时间动态规律研究

1997～1998年的研究结果表明:小麦叶枯病害在河南麦田春季的流行曲线基本呈S型曲线。始发期一般在3月20日～4月10日,指数增长期大约10～20d,该期流行速率最高;4月10～20日以后该病进入逻辑斯蒂增长期,可持续30～40d,流行速率比指数增长期稍低,没有明显的衰退期;影响小麦叶枯类病害始发期的气象因子为3月份的日照、降水量和气温,4月份的气温、日照、降水日数、相对湿度与发生程度关系密切。河南主栽小麦品种中没有对叶枯类病害免疫的品种,70%以上的主栽小麦品种为感叶枯病品种。     

Relationship between disease severity and escape of Pseudoperonospora cubensis sporangia from a cucumber canopy during downy mildew epidemics

Fundamental to the development of models to predict the spread of cucurbit downy mildew is the ability to determine the escape of Pseudoperonospora cubensis sporangia from infected fields. Aerial concentrations of sporangia, C (sporangia m^?3), were monitored using Rotorod samplers deployed at 0·5 to 3·0 m above a naturally infected cucumber canopy in two sites in central and eastern North Carolina in 2011, where disease severity ranged from 1 to 40%. Standing crop of sporangia was assessed each morning at 07·00 h EDT and ranged from 320 to 16 170 sporangia m^?2. Disease severity and height above the canopy significantly (P < 0·0001) affected C with mean concentration (C_m) being high at moderate disease. Values of C_m decreased rapidly with canopy height and at a height of 2·0 m, C_m was only 7% of values measured at 0·5 m when disease was moderate. Daily total flux (F_D) was dependent on disease severity and ranged from 5·9 to 2242·3 sporangia m^?2. The fraction of available sporangia that escaped the canopy increased from 0·028 to 0·171 as average wind speed above the canopy for periods of high C increased from 1·7 to 3·6 m s^?1. Variations of C_m and F_D with increasing disease were well described (P < 0·0001) by a log‐normal model with 15% as the threshold above which C_m and F_D decreased as disease severity increased. These results indicate that disease severity should be used to adjust sporangia escape in spore transport simulation models that are used to predict the risk of spread of cucurbit downy mildew.     

Effect of resistance variation in a natural plant host–pathogen metapopulation on disease dynamics

Existing theory suggests that increasing the diversity of resistance and virulence types in host–pathogen interactions will result in qualitative shifts in spatial and temporal dynamics, and greater among-population asynchrony in disease dynamics and prevalence. Here, data are presented from a biologically realistic metapopulation model of gene-for-gene interactions that indicate that population level variation in resistance diversity will be negatively associated with disease prevalence (fraction of individuals infected). The model also predicts that disease incidence (presence/absence) will be positively related to total resistance diversity across the metapopulation, because high resistance diversity also selects for more virulent pathogens. These results are then contrasted with empirical data from a natural host–pathogen system. While the argument that high resistance diversity should generally lead to lower disease levels has been applied extensively in agricultural situations, the connection between genetic diversity, resistance and disease dynamics has never been demonstrated in natural systems. Here, through analysis of multiyear data on disease prevalence in the context of knowledge of resistance variation among host populations in a natural plant host–pathogen metapopulation, the first evidence is provided that observed levels of asynchrony in disease dynamics may indeed be related to resistance structure.     

Effect of male sterility on ergot disease spread in wheat

Cytoplasmic male-sterile winter wheat, grown in the field in England with a limited supply of pollen, set over 80% less seed than fertile wheat. Wheat ears precociously inoculated with ergot ( Claviceps purpurea ) initiated local natural epidemics of disease at flowering and, within 1-5m of primary foci, sclerotial abundance at harvest was correlated inversely with seed set, Sclerotial mass in poorly pollinated male-sterile wheat comprised more than 20% of the threshed grain yield, in contrast to only 0.7% in fertile wheat.