Recent advancement in plant disease management
Prem Pratap Singh, ... Bhanu Prakash, in Food Security and Plant Disease Management, 2021
Abstract
Plant Pathology is the science of studying plant diseases that renders the disease-management answers to the farmers. It ameliorates the disease-management approaches to attain food security and food safety for the world. Phytopathogens, with their rapid dispersibility and adaptiveness in variable domains, overcome all the active sources of disease management. The practices of monoculturing and intensive inputs of agrochemicals serve as the selection pressures for the pathogens adaptation and evolution. Therefore with the understanding of the dynamic nature of the plant diseases, the outsmart management approach must be in line with the environmental-acceptability and circumstances prevailing in the agriculture field and markets. The approaches of sustainable intensification with modern technical advancements offered new opportunities in the form of an integrated systems-based viewpoint for disease management. They unlash the molecular premises of the plant immunity by discovering some novel insights into the hostpathogen interactions. For the future aspects of plant pathology, more integrated management strategies are needed to increase the resilience of the crops against phytopathogens.
INTRODUCTION
GEORGE N. AGRIOS, in Plant Pathology [Fifth Edition], 2005
PROLOGUE: THE ISSUES
Plant pathology is a science that studies plant diseases and attempts to improve the chances for survival of plants when they are faced with unfavorable environmental conditions and parasitic microorganisms that cause disease. As such, plant pathology is challenging, interesting, important, and worth studying in its own right. It is also, however, a science that has a practical and noble goal of protecting the food available for humans and animals. Plant diseases, by their presence, prevent the cultivation and growth of food plants in some areas; or food plants may be cultivated and grown but plant diseases may attack them, destroy parts or all of the plants, and reduce much of their produce, i.e., food, before they can be harvested or consumed. In the pursuit of its goal, plant pathology is joined by the sciences of entomology and weed science.
It is conservatively estimated that diseases, insects, and weeds together annually interfere with the production of, or destroy, between 31 and 42% of all crops produced worldwide [Table 1-1]. The losses are usually lower in the more developed countries and higher in the developing countries, i.e., countries that need food the most. It has been estimated that of the 36.5% average of total losses, 14.1% are caused by diseases, 10.2% by insects, and 12.2% by weeds.
TABLE 1-1. Estimated Annual Crop Losses Worldwide
| Attainable crop production [2002 prices] | $1.5 trillion |
| Actual crop production [36.5%] | $950 billion |
| Production without crop protection | $455 billion |
| Losses prevented by crop protection | $415 billion |
| Actual annual losses to world crop production | $550 billion |
| Losses caused by diseases only [14.1%] | $220 billion |
Considering that 14.1% of the crops are lost to plant diseases alone, the total annual worldwide crop loss from plant diseases is about $220 billion. To these should be added 612% losses of crops after harvest, which are particularly high in developing tropical countries where training and resources such as refrigeration are generally lacking. Also, these losses do not include losses caused by environmental factors such as freezes, droughts, air pollutants, nutrient deficiencies, and toxicities.
Although impressive, the aforementioned numbers do not tell the innumerable stories of large populations in many poor countries suffering from malnutrition, hunger, and starvation caused by plant diseases; or of lost income and lost jobs resulting from crops destroyed by plant diseases, forcing people to leave their farms and villages to go to overcrowded cities in search of jobs that would help them survive.
Moreover, the need for measures to control plant diseases limits the amount of land available for cultivation each year, limits the kinds of crops that can be grown in fields already contaminated with certain microorganisms, and annually necessitates the use of millions of kilograms of pesticides for treating seeds, fumigating soils, spraying plants, or the postharvest treatment of fruits. Such control measures not only add to the cost of food production, some of them, e.g., crop rotation, necessarily limit the amount of food that can be produced, whereas others add toxic chemicals to the environment. It is therefore the duty and goal of plant pathology to balance all the factors involved so that the maximum amount of food can be produced with the fewest adverse side effects on the people and the environment.
Applications of Computational Methods in Plant Pathology
Keshavi Nalla, ... Shashank Kumar PhD, MSc, BSc, in Natural Remedies for Pest, Disease and Weed Control, 2020
Abstract
Plant pathology is a branch of study that deals with the interaction between pathogens and plants. It could be referred to as phytopathology. This study also involves the disease etiology, pathogenic identification and classification, disease cycles, plant disease epidemiology, disease resistance, and the effects of diseases on humans and other organisms. Monitoring plant health and diagnosing different plant diseases is essential to control the diseases in agriculture. Technology advances in terms of computer vision techniques have made the disease monitoring and study of pathogenic conditions in plants easier. Digital image processing, color space models, feature to feature extraction, low-level feature extraction, high-level feature extraction, support vector machine, k-means, neural networks, smart or precision agriculture, hyperspectral imaging, soft computing, image preprocessing are some of the computational techniques that are used for disease detection and plant health monitoring.
DISEASES | Plant Pathology, Principles
G.N. Agrios, in Encyclopedia of Applied Plant Sciences, 2003
Introduction
The principles of plant pathology are statements that hold true for a large number and variety of plant diseases that share some basic common characteristics, for example, they are all caused by microorganisms. Regardless of their specific cause, such diseases share the same principles, as opposed, for example, to the abiotic [environmental] diseases that are caused by physical or chemical nonliving factors. The principles, however, often need to be modified somewhat to accommodate changes caused by the extreme differences among pathogens, such as those between fungi and viruses. The principles of plant pathology also multiply as we consider the various stages [infection, defense, genetics, epidemiology, control] of disease initiation, development, and control. Nevertheless, the principles of plant pathology provide some true statements that unify the extraordinary variety of events accompanying plant diseases.
The Plant Microbiome: Diversity, Dynamics, and Role in Food Safety
Sarah M. Allard, Shirley A. Micallef, in Safety and Practice for Organic Food, 2019
6.2 Disease-Suppressive Soils
Central to plant pathology is the disease triangle, a model showing the interactions between host, pathogen, and environment that lead to disease [Scholthof, 2007]. For disease to occur, conditions for all of these components must be optimal. Disease-suppressive soils manipulate the environment, reducing conduciveness to disease despite the presence of a pathogen and susceptible host [Hadar and Papadopoulou, 2012]. Once established, disease suppressiveness persists in the long term, even with repeated reintroduction of a pathogen [Cook et al., 1995]. Composts with suppressive qualities include vermicompost, green waste, straw, animal manure, and soil amendments used in organic agriculture. Sterilization studies have shown that the disease-suppressive qualities of compost can be attributed primarily to microbial communities [Liu et al., 2007]. Microbes with known pathogen-suppressing potential, such as members of Xylariaceae, Lactobacillaceae, and Bacillus, are more abundant in disease-suppressive soils than nonsuppressive soils [Wu et al., 2008; Klein et al., 2013; Penton et al., 2014; Mendes et al., 2011].
Microbial communities associated with disease suppression may act through general or specific mechanisms. The general suppression effect is attributed to competition for nutrients and/or space as well as release of antibiotic compounds and toxins carried out by a large metabolically active community [Hadar and Papadopoulou, 2012]. Specific interactions between compost-dwelling microbes and pathogens, including parasitism and predation, also lead to disease suppression. Suppressive composts may enhance plant defense through ISR [Yogev et al., 2010; Zhang et al., 1998] and supporting plant growth and general health. In contrast to the application of a single biocontrol organism, suppressive composts contain a diverse community of microorganisms that may combine several of the strategies described to achieve disease suppression. The effectiveness of disease-suppressive soils may be enhanced by inoculation with biocontrol agents such as Trichoderma hamatum or Bacillus subtilis [Nakasaki et al., 1998; Kwok et al., 1987; Hadar and Papadopoulou, 2012].
Although disease suppression in amended soils has been observed in many different contexts, it is not easy to reproduce in the field [Bonanomi et al., 2010; Termorshuizen et al., 2006]. Due to the complexity and specificity of plant-pathogen-environment interactions, use of disease-suppressive soils will be most effective if tailored specifically based on host, pathogen, and environment in including consideration of interplay with the plant microbiome. With these concerns addressed, disease-suppressive composts have potential as an environmentally friendly, safe, and effective approach to disease control for organic agriculture.
Advanced methods of plant pathogen diagnostics
L.A. Shcherbakova, in Comprehensive and Molecular Phytopathology, 2007
RAPD-PCR
The modern plant pathology possesses a variety of PCR-based diagnostic tools. A researcher should have an idea of the target sequences that could be selected for DNA assay for a plant pathogen to be detected and identified. Therefore, availability of information derived on phytopathogen genome sequencing is essential. As the specificity of PCR is assured by the primers, a correct choice and design of the primers is a requirement for success of any PCR analysis. The primer choice is the first stage of PCR diagnostics.
As genomes of viruses and viroids are relatively small, full data on their sequences are available in databases and appropriate primers can be easily found. Less information has been accumulated about the genomes of bacteria, oomycetes, and fungi, although the volume of data is growing. For these pathogens, general approaches to selection of particular known DNA target fragments are available, and the techniques based on screening of random regions of DNA have been developed.
For bacteria, oomycetes, and fungi, DNA encoding ribosomal RNA [rDNA] is generally used as a target sequence. Several facts make rDNA suitable for diagnostic purpose. Many copies of rDNA are present in each cell, thus enhancing the sensitivity of detection. The genes are present in all organisms and contain highly conserved 5.8 S region that gives rDNA universal applicability. At the same time, there are highly variable regions, such as internal transcribed spacer [ITS] regions. The conserved regions can be used to design universal primers for the group detection of microorganisms within a taxon [for all oomycetes, fungi, or bacteria], while the presence of variable regions allows finding distinctions between races, strain, and isolates. Other target sequences which are used for detection of fungi are beta-tubulin genes which are connected with resistance to fungicides. DNAs contained in bacterial plasmids and pathogenicity-associated genes usually serve as the sources of the target fragments.
One of the techniques used if the target nucleotide sequence is unknown is random amplified polymorphic DNA PCR [RAPD-PCR], or arbitrary primed polymerase chain reaction [AP-PCR]. The RAPD-PCR is usually applied, alone or together with RFLP, in studying DNA polymorphism, in gene mapping, and in population and evolutionary biology. The RAPD-PCR is important for plant pathogen diagnostics as it enables screening the sequences specific for closely related species, strains, races, and isolates, and differentiate them.
In contrast to the described PCR analyses, where two primers restricting the amplified sequence are used, RAPD-PCR involves annealing of single primers. The primer binds to the random complementary sequences of the genomic DNA, and after amplification, RAPD-PCR product of arbitrary length, which is partially or completely homologous to the arbitrarily primed sequence at both ends, is generated. The DNA polymorphism, resulting from insertions, deletions, and base substitutions, influences generation of the RAPD-PCR product, which ultimately shows as presence or absence of bands in gel after RAPD-PCR. With this method, it is possible to amplify gene products from many organisms analyzed, and the pattern of the bands after electrophoresis will be specific for a particular organism. Many different primers have to be tested to identify a band that is specific for a target. Specific bands can be used for synthesis of highly specific primers.
Finishing, it should be noted that PCR is not the only amplification diagnostic technique. For instance, some plant pathogens have been detected with ligase chain reaction [LCR]. It is based on the ability of DNA-dependent DNA-ligase to ligate a DNA strand in the presence of adenosine triphosphate [ATP] and Mg2+ ions, at rupture of the phosphodiesteric bond. This method was suggested by Wu and Wallace in 1989. A characteristic feature of DNA ligase work is high specific activity in ligation of single-stranded ruptures at the template which constitutes the second complementary strand, and low specific activity in simultaneous ligation of two ruptures in both strands or rupture in single-stranded DNA. Implementation of LCR requires finding two pairs of primers complementary to each other and to the initially chosen fragment of the matrix [for instance, DNA of some causative agent], as head to tail arrangement in direction from 5 to 3 end. As early as after the second LCR cycle, the reaction mix accumulates the product which is a ligated double-stranded DNA fragment, structurally identical to the four primers used. It is characteristic that even a one-nucleotide error in the place of annealing leads to a negative result. Therefore, LCR is promising for enhanced detection of plant pathogens and revealing the point mutations in the wild types of causative agents. The LCR has been adapted in a PCR format and modified to detect the potato viruses A and Y in tubers, identify Erwinia stewartii, and to distinguish Phytophthora infestans, P. mirabilis, and P. phaseoli from other Phytophthora species. In the latter case LCR was combined with ELISA.
Cross-Protection and Systemic Acquired Resistance for Control of Plant Diseases
J. ALLAN DODDS, in Handbook of Biological Control, 1999
INTRODUCTION
An axiom of plant pathology is that most plant species are resistant to most pathogens, leading plant pathologists to focus on those interactions that lead to disease between genetically susceptible hosts and their pathogens. Once the susceptible reaction is known and described, a comparison with related varieties that are genetically resistant to the pathogen then follows. Genetic analysis next occurs in an attempt to define genes for resistance in the resistant host, and genes for avirulence/virulence in the pathogen. A great deal of contemporary research is done with such systems on the assumption that a full understanding of what is commonly known as the gene-for-gene interaction will be needed if we are ever to unravel the host-pathogen interaction [Hammond-Kosack & Jones, 1997; Staskawicz et al., 1995].
One of the more surprising observations in plant pathology is that a fully susceptible host can become resistant to a virulent pathogen without the introduction of a gene for resistance either through conventional breeding or by plant transformation. This is not such a feat of magic in mammalian pathology, where a complex multicomponent immune system can be called on to mount a defense in a susceptible individual on infection by a virulent pathogen. While susceptible plants lack such a system, which depends so much on a circulating blood system, they do possess the ability to respond to pathogen attack with an array of biochemical, physiological, and anatomical changes, all of which appear to be aimed at containing the pathogen. This chapter deals with two such responses, cross-protection and systemic acquired resistance [SAR].
Introduction
Joseph S. Semancik, in Viroids and Satellites, 2017
My interest in plant viruses and pathology was extended to viroids with an introduction to exocortis disease of citrus by my colleague Lewis G. Weathers at the University of California, Riverside. Our reports of infectious RNA existing as free nucleic acid in 196870 was followed by the first association of pathogenic activity with a physically identifiable new RNA species in Nature in 1972, a small pathogenic RNA, a viroid RNA. This finding was made possible when samples from physicochemical experiments in my laboratory at the University of Nebraska were assayed at the University of California, Riverside, to provide evidence supporting biological activity. What might be viewed as a whimsical curiosity is that the causal viroid [citrus exocortis viroid] of a disease of citrus was first seen in a laboratory in Nebraska! From that introduction, citrus was later found to harbor a variety of pathogenic and nonpathogenic viroid species.
Fungi
Thomas J. Volk, in Encyclopedia of Biodiversity [Second Edition], 2013
Fungi as Plant Parasites
About 90% of plant diseases are caused by fungi, resulting in billions of dollars in crop and forest losses each year [Farr et al., 1989]. A parasite is referred to as a pathogen if it elicits a recognizable and persistent disease. The most severe pathogens are those that are imported accidentally from other continents and that cause severe problems with the native populations and cultivated plants. The severity of any plant disease is determined by three factors, known as the disease triangle, consisting of the interaction of the host [conditions favoring susceptibility], pathogens [conditions affecting virulence], and the environment [conditions favoring disease] [Figure 16]. All three factors must work in conjunction to produce a disease and determine its harshness.
Figure 16. The disease triangle, showing the three factors that determine the disease severity.
Fungi in Crop Pathology
The science of plant pathology deals mostly with organisms, especially fungi, that cause plant disease. Plant diseases are generally classified on the basis of what kinds of symptoms occur in which part[s] of the plant [Table 2]. Some important fungal pathogens of crop plants include Puccinia graminis [black stem rust of wheat], Erysiphe graminis [powdery mildew of grasses], Claviceps purpurea [ergot], and Ustilago maydis [corn smut].
Table 2. Types of plant diseases
| Blight | Extensive necrosis and rapid death |
| Dieback | Dead branches protruding from apparently healthy tissue |
| Lesion | Localized cell death |
| Canker | Lesion on a woody stem |
| Rot | Extensive decay of tissue |
| Vascular wilt | Blockage of the vascular transport system, resulting in starvation or desiccation |
| Gall | Localized tumor like growth |
| Stunting | Reduction in overall growth size |
| Rusts | Rust-colored lesions on various parts of the plant |
| Smuts | Drastic malformations, usually of reproductive parts |
Fungi in Forest Pathology
There have been a number of fungal diseases of forest trees that have caused great problems in North America [Table 3]. Forest pathogens often need a longer time to kill their larger, perennial hosts, sometimes living inside the tree for several decades before the host finally succumbs.
Table 3. Some important forest pathogens
| Cryphonectria parasitica | Chestnut blight |
| Ophiostoma ulmi | Dutch elm disease |
| Discula destructiva | Dogwood anthracnose |
| Cronaritum ribicola | White pine blister rust |
| Ceratocystis fagacearum | Oak wilt |
| Armillaria spp., especially A. mellea and A. solidipes | Armillaria root rot |
Cryphonectria parasitica, Ophiostoma ulmi, and Discula destructiva are introduced pathogens that have devastated their hosts in North America. In their native Asia, these pathogens coevolved with their hosts and caused them only minor annoyance. However, when they were accidentally introduced into North America, either on live plants or on logs for sawing, the fungus escaped and subsequently devastated the North American tree species because there was not enough time for the host to develop resistance. Cronartium ribicola, Ceratocystis fagacearum, and Armillaria species are native American fungi, but they cause severe diseases nonetheless. A good pathogen does not kill its host right away, but keeps it alive as long as possible to continue deriving nutrients from it.