An Introduction to Plant Immunity

The diversity of plant aggressors is impressive since it includes cellular or sub-cellular pathogens (fungi, bacteria, viruses, mycoplasmas), weeds, animals (rodents, snails), and insects. Before starting a fight against plant disease, it is necessary to identify the pathogen responsible and to know its ecology, its life cycle and its mode of dissemination in the environment. The constant identification of new taxa is continuously accompanied by a revision of the classifications thanks to the new tools brought by molecular biology. In this chapter, the most recent knowledge on classes of plant pathogens and plant pests in relation with their plant hosts is presented.

Broadly defined, disease is any physiological abnormality or significant disruption in the normal health of a plant that changes its appearance or function. Due to viruses, bacteria or fungi and favored by certain environmental conditions (nutrient deficiency, soil degradation, water problems, climate change, etc.) and certain pests (sometimes playing a role of vector), plant diseases are sources of considerable economic losses for agriculture and forestry, and as such studied by plant pathology or phytopathology.

Plants are called upon to defend themselves against a variety of organisms (bacteria, protists, fungi, insects and vertebrates) that use them as a source of nutrients. Plant immunity is the innate or induced ability of plants to detect and counteract invasive species before they can inflict serious harm. Molecules emitted by pathogens are perceived by receptors at the surface of or inside plant cells. This perception induces complex signaling cascades leading to a defensive response to pathogen attack. This chapter gives an overview of the most important defense strategies in higher plants.

Plants shield against microbes using structural defenses, antimicrobial compounds and secondary metabolites. Most plants have impermeable obstacles, such as waxy cuticles, or morphological adaptive transformations like thorns, which retard the pathogen's progression into plant tissues and prevent the release of deleterious substances such as enzymes for the degradation of walls or toxins. If a pest crosses the barriers of a plant, it is usually confronted with biochemical weapons including, but not limited to, secondary metabolites with antimicrobial ability.

Non-specific defense against plant pathogens can be passive (constitutive) or active (induced by microbes). The activation of general resistance follows the perception of the pathogenic threat. The first class of plant receptors recognizes molecular patterns associated with pathogens / microbes (PAMPs / MAMPs) in a nonspecific way. These are resident membrane receptors, also called pattern recognition receptors, PRRs. Plant PRRs are the source of extremely complex molecular signaling immune machinery. A transmembrane receptor that binds to a ligand then triggers the signalling would be the most simplistic scenario. Yet, in many cases, the recognition scheme would also include co-receptors, as well as regulatory proteins, which activate PRRs leading to the signal trasduction intiation. It is, therefore, reasonable that our current knowledge is only touching the surface of a remarkably intricate immune strategy.

As part of a host-pathogen coevolution, plants have developed very specific resistance proteins (R proteins), which directly or indirectly recognize Avr proteins and thus activate host resistance, or effector-triggered immunity (ETI). ETI can be thought of as an enhanced version of PTI and is often described as leading to localized programmed cell death in infected tissue: the hypersensitive response (HR). This chapter aims to clarify what we know and to identify areas that require further investigation.

Unlike innate resistance, acquired resistance is a defense system activated mainly by an earlier infection and allowing plants to resist later attacks by harmful organisms. Its mode of action does not depend on the direct destruction or inhibition of the invading pathogen, but rather on physiological changes which lead to the increase of the physical or chemical barrier of the host plant. The idea of using this ability of plants to defend themselves, to the aim of protecting them from their bio-aggressors is a completely realistic strategy that can be reached by using certain molecules, which have eliciting properties. These molecules, called natural defense stimulators (NDSs), can be of natural or synthetic origin and are capable of putting the plant on a state of alert in order to respond quickly and effectively in subsequent attacks. This innovative strategy greatly contributes to reducing the risks associated with pesticides, and also has great promises for the future, in terms of both socio-economic impact and technology transfer. This chapter provides a summary of the remarkable progress made in recent years in understanding the mechanisms involved in the acquired resistance of plants to various pathogens.

If breeders use a limited number of genes in their new resistant varieties, the adaptive capacity of pathogenic populations will ultimately lead to more or less rapid overcoming of these resistances, thus limiting the sustainability of their effectiveness. Qualitative resistance is considered less durable than quantitative resistance since the latter oppose less selection pressure on the pathogen and they are often governed by several resistance genes. Quantitative disease resistance has been observed within many crop plants but is not as well understood as qualitative (monogenic) disease resistance and has not been used as extensively in breeding. Mapping quantitative trait loci (QTLs) is a powerful tool for genetic dissection of quantitative disease resistance.

Although some of the resistance strategies rely on simple physical or chemical barriers, modern concepts of plant immunity emphasize the role and evolution of protein receptors in the plant cell. These immune receptors, made up of multidomain proteins, are the key elements in the recognition of pathogen elicitors / effectors, leading to the susceptibility or resistance of plants. Numerous pairs of plant R proteins and corresponding pathogenic Avr proteins have been identified as well as cellular proteins which mediate R/Avr interactions, and the molecular analysis of these interactions has led to the formulation of models on how R gene products recognize pathogens. Data from several R/Avr systems indicate that specific domains within R proteins determine recognition specificity. However, recent evidence suggests that R proteins have recruited cell recognition cofactors that mediate interactions between Avr proteins and R proteins. Overall, to explain this direct or indirect interaction, at least four models are currently widely approved. This chapter highlights the current trends in understanding host–pathogen interactions through a variety of models.

The perception of environmental signals and the ability to react accordingly are essential for the survival of organisms. In plants, extracellular recognition of microbe- and host damage-associated molecular patterns leads to the first layer of inducible defenses, termed pattern-triggered immunity (PTI). Pattern recognition receptors (PRRs) can perceive pathogen/microbe-associated molecular patterns (P/MAMP) from different microbes such as bacteria, fungi, oomycetes or viruses. Danger-associated molecular patterns (DAMPs) correspond to cell wall fragments that can be released by the plant after wounding or pathogen attack. An important group of PRRs is the family of wall associated kinases (WAK) that perceives pathogens indirectly, via DAMPs, and activates oligogalacturonide-dependent defense responses. The present chapter will address the most important perception systems used by plants to perceive pathogen attack and initiate efficient defense responses.

Defense response by NBS-LRR proteins (NLRs) is a sophisticated strategy that induces effector-triggered immunity (ETI). The NBS-LRR proteins are encoded by one of the largest and most important gene families involved in disease resistance in plants. These NBS-LRR proteins are mainly intracellular, and they can specifically recognize effectors secreted by pathogens either directly or indirectly. This will trigger downstream signaling pathways leading to implementation of plant defense response against various classes of pathogens including bacterial, fungal, viral, nematode and insect. In the present chapter we discuss about the present knowledge pertaining to NBS-LRR class of proteins; their structural organization, genomic ditribution and evolution.

Plant resistance (R) genes exhibit conserved domains, each of which performs discrete functions in the resistance to pathogens. The most abundant R genes belong to the classes of nucleotide binding site leucine rich repeats (NBS-LRR), receptor-like kinases (RLK), and receptor-like proteins (RLP). The list also includes genes encoding proteins with a unique transmembrane domain, genes encoding toxin reductases, genes encoding CC and transmembrane proteins and genes encoding an intracytoplasmic protein kinase. This chapter sheds light on recent advances in the classification of R genes, based on their conserved structural characteristics. Knowledge about the R proteins cellular localization and advances in the molecular cloning of R genes are also treated.

Given the current constraints to sustainable agricultural production, with increasing crop losses due to plant pests and diseases and climate change, considerable advances are required in crop improvement approaches for enabling durable disease resistance. Interestingly, advances in fundamental understanding of the plant immune system will have far reaching implications for genetic resistance development, appropriate for effective and durable disease control and global sustainable agriculture. In particular, a deeper understanding of the molecular and functional mechanisms of resistance (R) genes would make it possible to engineer new resistances for future agriculture. In general, there are currently two main strategies, which include nine recognized molecular mechanisms for R genes, most of them (all but one, mechanism 6: executor genes) have been used against various types of biotic stress and tend to be widely applicable among plants.

The signaling pathways play an indispensable role and act as a connecting link between recognizing the stress molecules and generating an appropriate physiological and biochemical response. Recent studies using genomics and proteomics approach enabled decoding and understanding these signaling networks, which increased our knowledge regarding signaling pathways. This chapter offers a review of the most important bases of plant signaling pathways during various stresses.

In order to set up an optimal response to the invading pathogen, the host plant uses transcriptional reprogramming. This phenomenon, involving both DNAbinding transcription factors (TFs) and their regulatory molecules, occurs at several levels of resistance, such as the expression of resistance components (e.g. intracellular and membrane receptor proteins), and downstream defense signalling. In this chapter, we address the structure and function of main TF families associated with plant defense against biotic stress, as well as the role played by MAPK cascades and Ca2+ signaling in regulating transcriptional complexes during plant-pathogen interactions.

Plants are masters of epigenetic regulation. All of the major epigenetic mechanisms known to occur in eukaryotes are used by plants, with the responsible pathways elaborated to a degree that is unsurpassed in other taxa. DNA methylation occurs in plant genomes, in patterns that reflect a balance between enzyme activities that install, maintain, or remove methylation. Histone-modifying enzymes influence epigenetic states in plants and these enzymes are encoded by comparatively large gene families, allowing for diversified as well as overlapping functions. RNA-mediated gene silencing is accomplished using multiple distinct pathways to combat viruses, orchestrate development, and help organize the genome. The interplay between DNA methylation, histone modification, and noncoding RNAs provides plants with a multilayered and robust epigenetic circuitry that has a tangible impact on the control of plant genes conferring resistance to different biotic and abiotic stresses, either directly or indirectly. Eventually, plants with the most suitable epigenome may be subject to selection.

The perception of the pathogen signal by the host specific receptors and its transduction by various signaling pathways culminate in the synthesis and synchronized accumulation of defensive molecules some of which play a structural role while others exercise a direct antimicrobial function. Biochemical mechanisms include, among others, the synthesis of peptides and antimicrobial proteins, hydrolytic enzymes as well as the production of phytoalexins and secondary metabolites with high antimicrobial potential. This chapter provides a synthesis of the remarkable progress made in recent years in terms of understanding the mechanisms applied in the molecular and physiological alterations that occur during the defense response of plants.

Nowadays, agricultural genomics, or agrigenomics (the application of genomics in agriculture), continues to drive sustainable productivity and offer solutions to the mounting challenges of feeding the global population. Omic sciences (genomics, transcriptomics, proteomics, metabolomics) open today opportunities to create plants with high yields, independently of biotic and abiotic stresses. Plant genomic research, genome-wide computational tools and association analyses can assist in the identification of Resistance gene analogs (RGAs) from strategic plant species, and the detection of disease resistance QTLs. This chapter summarizes some of the large-scale genomic tools and studies that have clarified the plant – pathogen interactions.

The improvement of plants, in order to give them better resistance to diseases, relies on the existence of diverse natural populations. Traditionally, the breeder’s role has been to crossbreed populations to obtain varieties possessing the desired traits. Modern advances in genetic engineering, in association with omic sciences, allow breeders to increase the genetic diversity of the populations on which selection operates, and to introgress new traits using various molecular methods, such as chemical or irradiation-based mutagenesis, genetic transformation or genome editing. It is most often a question of modifying existing varieties in order to obtain new ones which have the properties desired by researchers, according to the needs expressed by the various actors concerned. Here, we review the increasing usefulness and applicability of biotechnology and genetic engineering approaches for accelerating variety development and crop improvement.

The methods of management of pathogens and pests have been changing during these years, under the pressure of current societal and political demands. To overcome the drawbacks of chemical control, it is possible to mobilize genetic (i.e. varieties resistant to diseases) and agronomic controlling methods (cultural practices favoring these resistances or reducing the risks of pressure or development of pests). However, the low durability of genetic resistance, which is linked to the adaptation of pathogens, imposes the need to propose solutions in order to improve the durability of genetic resistance. Resistance is said to be durable when its effectiveness lasts for many years in a large spatial environment, at high pressure from the pathogen, favoring, a priori, the selection of virulent variants. The combination of quantitative and qualitative resistance is among the best solutions, but the strategy for deploying the R genes is an interesting track to follow.