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Plant disease resistance protects plants from pathogens in two ways: by pre-formed structures and chemicals, and by infection-induced responses of the immune system. Relative to a susceptible plant, disease resistance is the reduction of pathogen growth on or in the plant (and hence a reduction of disease), while the term disease tolerance describes plants that exhibit little disease damage despite substantial pathogen levels. Disease outcome is determined by the three-way interaction of the pathogen, the plant and the environmental conditions (an interaction known as the disease triangle). Defense-activating compounds can move cell-to-cell and systematically through the plant's vascular system. However, plants do not have circulating
immune cells White blood cells, also called leukocytes or leucocytes, are the cells of the immune system that are involved in protecting the body against both infectious disease and foreign invaders. All white blood cells are produced and derived from multi ...
, so most cell types exhibit a broad suite of
antimicrobial An antimicrobial is an agent that kills microorganisms or stops their growth. Antimicrobial medicines can be grouped according to the microorganisms they act primarily against. For example, antibiotics are used against bacteria, and antifungals ar ...
defenses. Although obvious ''qualitative'' differences in disease resistance can be observed when multiple specimens are compared (allowing classification as “resistant” or “susceptible” after infection by the same pathogen strain at similar inoculum levels in similar environments), a gradation of ''quantitative'' differences in disease resistance is more typically observed between plant strains or
genotype The genotype of an organism is its complete set of genetic material. Genotype can also be used to refer to the alleles or variants an individual carries in a particular gene or genetic location. The number of alleles an individual can have in a ...
s. Plants consistently resist certain pathogens but succumb to others; resistance is usually specific to certain pathogen species or pathogen strains.


Background

Plant disease resistance is crucial to the reliable production of food, and it provides significant reductions in agricultural use of land, water, fuel and other inputs. Plants in both natural and cultivated populations carry inherent disease resistance, but this has not always protected them. The late blight Great Famine of Ireland of the 1840s was caused by the oomycete ''
Phytophthora infestans ''Phytophthora infestans'' is an oomycete or water mold, a fungus-like microorganism that causes the serious potato and tomato disease known as late blight or potato blight. Early blight, caused by ''Alternaria solani'', is also often called " ...
''. The world’s first mass-cultivated banana
cultivar A cultivar is a type of cultivated plant that people have selected for desired traits and when propagated retain those traits. Methods used to propagate cultivars include: division, root and stem cuttings, offsets, grafting, tissue culture, ...
Gros Michel Gros Michel (), often translated and known as "Big Mike", is an export cultivar of banana and was, until the 1950s, the main variety grown. The physical properties of the Gros Michel make it an excellent export produce; its thick peel makes it re ...
was lost in the 1920s to Panama disease caused by the fungus ''
Fusarium oxysporum ''Fusarium oxysporum'' (Schlecht as emended by Snyder and Hansen), an ascomycete fungus, comprises all the species, varieties and forms recognized by Wollenweber and Reinking within an infrageneric grouping called section Elegans. It is part of ...
''. The current wheat
stem rust Stem rust, also known as cereal rust, black rust, red rust or red dust, is caused by the fungus ''Puccinia graminis'', which causes significant disease in cereal crops. Crop species that are affected by the disease include bread wheat, durum wh ...
, leaf rust and yellow stripe rust epidemics spreading from East Africa into the Indian subcontinent are caused by rust fungi ''
Puccinia graminis Stem rust, also known as cereal rust, black rust, red rust or red dust, is caused by the fungus ''Puccinia graminis'', which causes significant disease in cereal crops. Crop species that are affected by the disease include bread wheat, durum whe ...
'' and '' P. striiformis''. Other epidemics include
Chestnut blight The pathogenic fungus ''Cryphonectria parasitica'' (formerly ''Endothia parasitica'') is a member of the Ascomycota (sac fungi). This necrotrophic fungus is native to East Asia and South East Asia and was introduced into Europe and North America ...
, as well as recurrent severe plant diseases such as
Rice blast ''Magnaporthe grisea'', also known as rice blast fungus, rice rotten neck, rice seedling blight, blast of rice, oval leaf spot of graminea, pitting disease, ryegrass blast, Johnson spot, neck blast, wheat blast, and Imochi (Japanese:稲熱) is a ...
,
Soybean cyst nematode The soybean cyst nematode (SCN), ''Heterodera glycines'', is the most devastating pest to soybean crop yields in the U.S., targeting the roots of soybean and other legume plants. When infection is severe SCNs cause stunting, yellowing, impaired c ...
,
Citrus canker Citrus canker is a disease affecting ''Citrus'' species caused by the bacterium '' Xanthomonas'' (''X.axonopodis; X. campestris''). Infection causes lesions on the leaves, stems, and fruit of citrus trees, including lime, oranges, and grapefrui ...
. Plant pathogens can spread rapidly over great distances, vectored by water, wind, insects, and humans. Across large regions and many crop species, it is estimated that diseases typically reduce plant yields by 10% every year in more developed nations or agricultural systems, but yield loss to diseases often exceeds 20% in less developed settings. However, disease control is reasonably successful for most crops. Disease control is achieved by use of plants that have been bred for good resistance to many diseases, and by plant cultivation approaches such as
crop rotation Crop rotation is the practice of growing a series of different types of crops in the same area across a sequence of growing seasons. It reduces reliance on one set of nutrients, pest and weed pressure, and the probability of developing resistant ...
, pathogen-free seed, appropriate planting date and plant density, control of field moisture, and
pesticide Pesticides are substances that are meant to control pests. This includes herbicide, insecticide, nematicide, molluscicide, piscicide, avicide, rodenticide, bactericide, insect repellent, animal repellent, microbicide, fungicide, and lam ...
use.


Common disease resistance mechanisms


Pre-formed structures and compounds

*
Plant cuticle A plant cuticle is a protecting film covering the outermost skin layer (epidermis) of leaves, young shoots and other aerial plant organs (aerial here meaning all plant parts not embedded in soil or other substrate) that have no '' periderm''. The ...
/surface * Plant
cell walls A cell wall is a structural layer surrounding some types of cells, just outside the cell membrane. It can be tough, flexible, and sometimes rigid. It provides the cell with both structural support and protection, and also acts as a filtering mech ...
*
Antimicrobial An antimicrobial is an agent that kills microorganisms or stops their growth. Antimicrobial medicines can be grouped according to the microorganisms they act primarily against. For example, antibiotics are used against bacteria, and antifungals ar ...
chemical A chemical substance is a form of matter having constant chemical composition and characteristic properties. Some references add that chemical substance cannot be separated into its constituent elements by physical separation methods, i.e., wit ...
s (for example:
polyphenol Polyphenols () are a large family of naturally occurring organic compounds characterized by multiples of phenol units. They are abundant in plants and structurally diverse. Polyphenols include flavonoids, tannic acid, and ellagitannin, some of ...
s,
sesquiterpene lactone Sesquiterpene lactones (SLs) are a class of sesquiterpenoids that contain a lactone ring. They are most often found in plants of the family Asteraceae (daisies, asters). Other plant families with SLs are Umbelliferae (celery, parsley, carrots) an ...
s,
saponin Saponins (Latin "sapon", soap + "-in", one of), also selectively referred to as triterpene glycosides, are bitter-tasting usually toxic plant-derived organic chemicals that have a foamy quality when agitated in water. They are widely distributed ...
s) *
Antimicrobial peptides Antimicrobial peptides (AMPs), also called host defence peptides (HDPs) are part of the innate immune response found among all classes of life. Fundamental differences exist between prokaryotic and eukaryotic cells that may represent targets for an ...
*
Enzyme inhibitors An enzyme inhibitor is a molecule that binds to an enzyme and blocks its activity. Enzymes are proteins that speed up chemical reactions necessary for life, in which substrate molecules are converted into products. An enzyme facilitates a s ...
* Detoxifying enzymes that break down pathogen-derived
toxin A toxin is a naturally occurring organic poison produced by metabolic activities of living cells or organisms. Toxins occur especially as a protein or conjugated protein. The term toxin was first used by organic chemist Ludwig Brieger (1849� ...
s * Receptors that perceive pathogen presence and activate inducible plant defencesLutz, Diana (2012)
Key part of plants' rapid response system revealed
Washington University in St. Louis.


Inducible post-infection plant defenses

*
Cell wall A cell wall is a structural layer surrounding some types of cells, just outside the cell membrane. It can be tough, flexible, and sometimes rigid. It provides the cell with both structural support and protection, and also acts as a filtering mec ...
reinforcement (
cellulose Cellulose is an organic compound with the formula , a polysaccharide consisting of a linear chain of several hundred to many thousands of β(1→4) linked D-glucose units. Cellulose is an important structural component of the primary cell w ...
,
lignin Lignin is a class of complex organic polymers that form key structural materials in the support tissues of most plants. Lignins are particularly important in the formation of cell walls, especially in wood and bark, because they lend rigidity ...
,
suberin Suberin, cutin and lignins are complex, higher plant epidermis and periderm cell-wall macromolecules, forming a protective barrier. Suberin, a complex polyester biopolymer, is lipophilic, and composed of long chain fatty acids called suberin acid ...
,
callose Callose is a plant polysaccharide. Its production is due to the glucan synthase-like gene (GLS) in various places within a plant. It is produced to act as a temporary cell wall in response to stimuli such as stress or damage. Callose is composed ...
, cell wall proteins) * Antimicrobial chemicals, including reactive oxygen species such as
hydrogen peroxide Hydrogen peroxide is a chemical compound with the formula . In its pure form, it is a very pale blue liquid that is slightly more viscous than water. It is used as an oxidizer, bleaching agent, and antiseptic, usually as a dilute solution (3 ...
or peroxynitrite, or more complex
phytoalexins Phytoalexins are antimicrobial substances, some of which are antioxidative as well. They are defined, not by their having any particular chemical structure or character, but by the fact that they are defensively synthesized ''de novo'' by plants t ...
such as genistein or camalexin * Antimicrobial proteins such as defensins, thionins, or PR-1 * Antimicrobial enzymes such as chitinases, beta- glucanases, or peroxidases *
Hypersensitive response Hypersensitive response (HR) is a mechanism used by plants to prevent the spread of infection by microbial pathogens. HR is characterized by the rapid death of cells in the local region surrounding an infection and it serves to restrict the growth ...
- a rapid host cell death response associated with defence induction.


Immune system

The plant immune system carries two interconnected tiers of receptors, one most frequently sensing molecules outside the cell and the other most frequently sensing molecules inside the cell. Both systems
sense A sense is a biological system used by an organism for sensation, the process of gathering information about the world through the detection of stimuli. (For example, in the human body, the brain which is part of the central nervous system r ...
the intruder and respond by activating antimicrobial defenses in the infected cell and neighboring cells. In some cases, defense-activating signals spread to the rest of the plant or even to neighboring plants. The two systems detect different types of pathogen molecules and classes of plant receptor proteins. The first tier is primarily governed by
pattern recognition receptor Pattern recognition receptors (PRRs) play a crucial role in the proper function of the innate immune system. PRRs are germline-encoded host sensors, which detect molecules typical for the pathogens. They are proteins expressed, mainly, by cells of ...
s that are activated by recognition of evolutionarily conserved pathogen or microbial–associated molecular patterns (PAMPs or MAMPs). Activation of PRRs leads to intracellular signaling, transcriptional reprogramming, and biosynthesis of a complex output response that limits colonization. The system is known as PAMP-Triggered Immunity or as Pattern-Triggered Immunity (PTI). The second tier, primarily governed by
R gene Resistance genes (R-Genes) are genes in plant genomes that convey plant disease resistance against pathogens by producing R proteins. The main class of R-genes consist of a nucleotide binding domain (NB) and a leucine rich repeat (LRR) dom ...
products, is often termed effector-triggered immunity (ETI). ETI is typically activated by the presence of specific pathogen "effectors" and then triggers strong antimicrobial responses (see R gene section below). In addition to PTI and ETI, plant defenses can be activated by the sensing of damage-associated compounds (DAMP), such as portions of the plant cell wall released during pathogenic infection. Responses activated by PTI and ETI receptors include ion channel gating, oxidative burst, cellular
redox Redox (reduction–oxidation, , ) is a type of chemical reaction in which the oxidation states of substrate change. Oxidation is the loss of electrons or an increase in the oxidation state, while reduction is the gain of electrons or a ...
changes, or protein kinase cascades that directly activate cellular changes (such as cell wall reinforcement or antimicrobial production), or activate changes in
gene expression Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product that enables it to produce end products, protein or non-coding RNA, and ultimately affect a phenotype, as the final effect. T ...
that then elevate other defensive responses Plant immune systems show some mechanistic similarities with the
immune systems The immune system is a network of biological processes that protects an organism from diseases. It detects and responds to a wide variety of pathogens, from viruses to parasitic worms, as well as cancer cells and objects such as wood splinte ...
of insects and mammals, but also exhibit many plant-specific characteristics. The two above-described tiers are central to plant immunity but do not fully describe plant immune systems. In addition, many specific examples of apparent PTI or ETI violate common PTI/ETI definitions, suggesting a need for broadened definitions and/or paradigms.


Pattern-triggered immunity

PAMPs, conserved molecules that inhabit multiple pathogen
genera Genus ( plural genera ) is a taxonomic rank used in the biological classification of living and fossil organisms as well as viruses. In the hierarchy of biological classification, genus comes above species and below family. In binomial nomencla ...
, are referred to as MAMPs by many researchers. The defenses induced by MAMP perception are sufficient to repel most pathogens. However, pathogen effector proteins (see below) are adapted to suppress basal defenses such as PTI. Many receptors for MAMPs (and DAMPs) have been discovered. MAMPs and DAMPs are often detected by transmembrane receptor-kinases that carry LRR or LysM extracellular domains.


Effector triggered immunity

Effector Triggered Immunity (ETI) is activated by the presence of pathogen effectors. The ETI response is reliant on
R gene Resistance genes (R-Genes) are genes in plant genomes that convey plant disease resistance against pathogens by producing R proteins. The main class of R-genes consist of a nucleotide binding domain (NB) and a leucine rich repeat (LRR) dom ...
s, and is activated by specific pathogen strains. Plant ETI often causes an
apoptotic Apoptosis (from grc, ἀπόπτωσις, apóptōsis, 'falling off') is a form of programmed cell death that occurs in multicellular organisms. Biochemical events lead to characteristic cell changes ( morphology) and death. These changes inclu ...
hypersensitive response Hypersensitive response (HR) is a mechanism used by plants to prevent the spread of infection by microbial pathogens. HR is characterized by the rapid death of cells in the local region surrounding an infection and it serves to restrict the growth ...
.


R genes and R proteins

Plants have evolved
R gene Resistance genes (R-Genes) are genes in plant genomes that convey plant disease resistance against pathogens by producing R proteins. The main class of R-genes consist of a nucleotide binding domain (NB) and a leucine rich repeat (LRR) dom ...
s (resistance genes) whose products mediate resistance to specific virus, bacteria, oomycete, fungus, nematode or insect strains. R gene products are proteins that allow recognition of specific pathogen effectors, either through direct binding or by recognition of the effector's alteration of a host protein. Many R genes encode NB-LRR proteins (proteins with nucleotide-binding and leucine-rich repeat domains, also known as NLR proteins or STAND proteins, among other names). Most plant immune systems carry a repertoire of 100-600 different R gene homologs. Individual R genes have been demonstrated to mediate resistance to specific virus, bacteria, oomycete, fungus, nematode or insect strains. R gene products control a broad set of disease resistance responses whose induction is often sufficient to stop further pathogen growth/spread. Studied R genes usually confer specificity for particular strains of a pathogen species (those that express the recognized effector). As first noted by Harold Flor in his mid-20th century formulation of the gene-for-gene relationship, a plant R gene has specificity for a pathogen avirulence gene (Avr gene). Avirulence genes are now known to encode effectors. The pathogen Avr gene must have matched specificity with the R gene for that R gene to confer resistance, suggesting a receptor/
ligand In coordination chemistry, a ligand is an ion or molecule ( functional group) that binds to a central metal atom to form a coordination complex. The bonding with the metal generally involves formal donation of one or more of the ligand's ele ...
interaction for Avr and R genes. Alternatively, an effector can modify its host cellular target (or a molecular decoy of that target), and the R gene product (NLR protein) activates defenses when it detects the modified form of the host target or decoy.


Effector biology

Effectors are central to the pathogenic or symbiotic potential of microbes and microscopic plant-colonizing animals such as nematodes. Effectors typically are proteins that are delivered outside the microbe and into the host cell. These colonist-derived effectors manipulate the host's cell physiology and development. As such, effectors offer examples of co-evolution (example: a fungal protein that functions outside of the fungus but inside of plant cells has evolved to take on plant-specific functions). Pathogen host range is determined, among other things, by the presence of appropriate effectors that allow colonization of a particular host. Pathogen-derived effectors are a powerful tool to identify plant functions that play key roles in disease and in disease resistance. Apparently most effectors function to manipulate host physiology to allow disease to occur. Well-studied bacterial plant pathogens typically express a few dozen effectors, often delivered into the host by a Type III secretion apparatus. Fungal, oomycete and nematode plant pathogens apparently express a few hundred effectors. So-called "core" effectors are defined operationally by their wide distribution across the population of a particular pathogen and their substantial contribution to pathogen virulence. Genomics can be used to identify core effectors, which can then be used to discover new R gene
allele An allele (, ; ; modern formation from Greek ἄλλος ''állos'', "other") is a variation of the same sequence of nucleotides at the same place on a long DNA molecule, as described in leading textbooks on genetics and evolution. ::"The chro ...
s, which can be used in plant breeding for disease resistance.


Small RNAs and RNA interference

Plant sRNA pathways are understood to be important components of pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) and effector-triggered immunity (ETI). Bacteria‐induced microRNAs (miRNAs) in ''
Arabidopsis ''Arabidopsis'' (rockcress) is a genus in the family Brassicaceae. They are small flowering plants related to cabbage and mustard. This genus is of great interest since it contains thale cress (''Arabidopsis thaliana''), one of the model orga ...
'' have been shown to influence hormonal signalling including auxin, abscisic acid (ABA), jasmonic acid (JA) and salicylic acid (SA). Advances in genome‐wide studies revealed a massive adaptation of host miRNA expression patterns after infection by fungal pathogens ''
Fusarium virguliforme Sudden death syndrome (SDS), a disease in soybean plants, quickly spread across the southern United States in the 1970s, eventually reaching most agricultural areas of the US. SDS is caused by a ''Fusarium ''Fusarium'' is a large genus of f ...
'', '' Erysiphe graminis'', ''
Verticillium dahliae ''Verticillium dahliae'' is a fungal plant pathogen. It causes verticillium wilt in many plant species, causing leaves to curl and discolor. It may cause death in some plants. Over 400 plant species are affected by ''Verticillium'' complex. M ...
'', and '' Cronartium quercuum'', and the oomycete ''
Phytophthora sojae ''Phytophthora sojae'' is an oomycete and a soil-borne plant pathogen that causes stem and root rot of soybean. This is a prevalent disease in most soybean growing regions, and a major cause of crop loss. In wet conditions the pathogen produces z ...
''. Changes to sRNA expression in response to fungal pathogens indicate that gene silencing may be involved in this defense pathway. However, there is also evidence that the antifungal defense response to '' Colletotrichum'' spp. infection in maize is not entirely regulated by specific miRNA induction, but may instead act to fine-tune the balance between genetic and metabolic components upon infection. Transport of sRNAs during infection is likely facilitated by extracellular vesicles (EVs) and multivesicular bodies (MVBs). The composition of RNA in plant EVs has not been fully evaluated, but it is likely that they are, in part, responsible for trafficking RNA. Plants can transport viral RNAs,
mRNA In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of synthesizing a protein. mRNA is created during t ...
s, miRNAs and small interfering RNAs (siRNAs) systemically through the phloem. This process is thought to occur through the plasmodesmata and involves RNA-binding proteins that assist RNA localization in mesophyll cells. Although they have been identified in the phloem with mRNA, there is no determinate evidence that they mediate long-distant transport of RNAs. EVs may therefore contribute to an alternate pathway of RNA loading into the phloem, or could possibly transport RNA through the apoplast. There is also evidence that plant EVs can allow for interspecies transfer of sRNAs by RNA interference such as Host-Induced Gene Silencing (HIGS). The transport of RNA between plants and fungi seems to be bidirectional as sRNAs from the fungal pathogen ''
Botrytis cinerea ''Botrytis cinerea'' is a necrotrophic fungus that affects many plant species, although its most notable hosts may be wine grapes. In viticulture, it is commonly known as "botrytis bunch rot"; in horticulture, it is usually called "grey mould" o ...
'' have been shown to target host defense genes in Arabidopsis and tomato.


Species-level resistance

In a small number of cases, plant genes are effective against an entire pathogen species, even though that species that is pathogenic on other genotypes of that host species. Examples include
barley Barley (''Hordeum vulgare''), a member of the grass family, is a major cereal grain grown in temperate climates globally. It was one of the first cultivated grains, particularly in Eurasia as early as 10,000 years ago. Globally 70% of barley ...
MLO against
powdery mildew Powdery mildew is a fungal disease that affects a wide range of plants. Powdery mildew diseases are caused by many different species of ascomycete fungi in the order Erysiphales. Powdery mildew is one of the easier plant diseases to identify, as ...
,
wheat Wheat is a grass widely cultivated for its seed, a cereal grain that is a worldwide staple food. The many species of wheat together make up the genus ''Triticum'' ; the most widely grown is common wheat (''T. aestivum''). The archaeologica ...
Lr34 against leaf rust and wheat Yr36 against wheat stripe rust. An array of mechanisms for this type of resistance may exist depending on the particular gene and plant-pathogen combination. Other reasons for effective plant immunity can include a lack of coadaptation (the pathogen and/or plant lack multiple mechanisms needed for colonization and growth within that host species), or a particularly effective suite of pre-formed defenses.


Signaling mechanisms


Perception of pathogen presence

Plant defense signaling is activated by the pathogen-detecting receptors that are described in an above section. The activated receptors frequently elicit reactive oxygen and nitric oxide production,
calcium Calcium is a chemical element with the symbol Ca and atomic number 20. As an alkaline earth metal, calcium is a reactive metal that forms a dark oxide-nitride layer when exposed to air. Its physical and chemical properties are most similar ...
,
potassium Potassium is the chemical element with the symbol K (from Neo-Latin ''kalium'') and atomic number19. Potassium is a silvery-white metal that is soft enough to be cut with a knife with little force. Potassium metal reacts rapidly with atmosphe ...
and
proton A proton is a stable subatomic particle, symbol , H+, or 1H+ with a positive electric charge of +1 ''e'' elementary charge. Its mass is slightly less than that of a neutron and 1,836 times the mass of an electron (the proton–electron mas ...
ion fluxes, altered levels of
salicylic acid Salicylic acid is an organic compound with the formula HOC6H4CO2H. A colorless, bitter-tasting solid, it is a precursor to and a metabolite of aspirin (acetylsalicylic acid). It is a plant hormone, and has been listed by the EPA Toxic Substa ...
and other hormones and activation of
MAP kinase A mitogen-activated protein kinase (MAPK or MAP kinase) is a type of protein kinase that is specific to the amino acids serine and threonine (i.e., a serine/threonine-specific protein kinase). MAPKs are involved in directing cellular responses t ...
s and other specific protein kinases. These events in turn typically lead to the modification of proteins that control
gene transcription Transcription is the process of copying a segment of DNA into RNA. The segments of DNA transcribed into RNA molecules that can encode proteins are said to produce messenger RNA (mRNA). Other segments of DNA are copied into RNA molecules called ...
, and the activation of defense-associated
gene expression Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product that enables it to produce end products, protein or non-coding RNA, and ultimately affect a phenotype, as the final effect. T ...
.


Transcription factors and the hormone response

Numerous genes and/or proteins as well as other molecules have been identified that mediate plant defense signal transduction.
Cytoskeleton The cytoskeleton is a complex, dynamic network of interlinking protein filaments present in the cytoplasm of all cells, including those of bacteria and archaea. In eukaryotes, it extends from the cell nucleus to the cell membrane and is compose ...
and vesicle trafficking dynamics help to orient plant defense responses toward the point of pathogen attack.


Mechanisms of transcription factors and hormones

Plant immune system activity is regulated in part by signaling hormones such as: *
Salicylic acid Salicylic acid is an organic compound with the formula HOC6H4CO2H. A colorless, bitter-tasting solid, it is a precursor to and a metabolite of aspirin (acetylsalicylic acid). It is a plant hormone, and has been listed by the EPA Toxic Substa ...
*
Jasmonic acid Jasmonic acid (JA) is an organic compound found in several plants including jasmine. The molecule is a member of the jasmonate class of plant hormones. It is biosynthesized from linolenic acid by the octadecanoid pathway. It was first isolate ...
*
Ethylene Ethylene ( IUPAC name: ethene) is a hydrocarbon which has the formula or . It is a colourless, flammable gas with a faint "sweet and musky" odour when pure. It is the simplest alkene (a hydrocarbon with carbon-carbon double bonds). Ethylene ...
There can be substantial cross-talk among these pathways.


Regulation by degradation

As with many signal transduction pathways, plant gene expression during immune responses can be regulated by degradation. This often occurs when hormone binding to hormone receptors stimulates
ubiquitin Ubiquitin is a small (8.6 kDa) regulatory protein found in most tissues of eukaryotic organisms, i.e., it is found ''ubiquitously''. It was discovered in 1975 by Gideon Goldstein and further characterized throughout the late 1970s and 1980s. ...
-associated degradation of repressor proteins that block expression of certain genes. The net result is hormone-activated gene expression. Examples: *
Auxin Auxins (plural of auxin ) are a class of plant hormones (or plant-growth regulators) with some morphogen-like characteristics. Auxins play a cardinal role in coordination of many growth and behavioral processes in plant life cycles and are essenti ...
: binds to receptors that then recruit and degrade repressors of transcriptional activators that stimulate auxin-specific gene expression. * Jasmonic acid: similar to auxin, except with jasmonate receptors impacting jasmonate-response signaling mediators such as JAZ proteins. *
Gibberellic acid Gibberellic acid (also called gibberellin A3, GA, and GA3) is a hormone found in plants and fungi. Its chemical formula is C19H22O6. When purified, it is a white to pale-yellow solid. Plants in their normal state produce large amounts of GA3. It ...
: Gibberellin causes receptor conformational changes and binding and degradation of Della proteins. * Ethylene: Inhibitory phosphorylation of the EIN2 ethylene response activator is blocked by ethylene binding. When this
phosphorylation In chemistry, phosphorylation is the attachment of a phosphate group to a molecule or an ion. This process and its inverse, dephosphorylation, are common in biology and could be driven by natural selection. Text was copied from this source, wh ...
is reduced, EIN2 protein is cleaved and a portion of the protein moves to the nucleus to activate ethylene-response gene expression.


Ubiquitin and E3 signaling

Ubiquitination plays a central role in cell signaling that regulates processes including protein degradation and immunological response. Although one of the main functions of ubiquitin is to target proteins for destruction, it is also useful in signaling pathways, hormone release, apoptosis and translocation of materials throughout the cell. Ubiquitination is a component of several immune responses. Without ubiquitin's proper functioning, the invasion of pathogens and other harmful molecules would increase dramatically due to weakened immune defenses.


= E3 signaling

= The E3 Ubiquitin ligase enzyme is a main component that provides specificity in protein degradation pathways, including immune signaling pathways. The E3 enzyme components can be grouped by which domains they contain and include several types. These include the Ring and U-box single subunit, HECT, and CRLs. Plant signaling pathways including immune responses are controlled by several feedback pathways, which often include negative feedback; and they can be regulated by De-ubiquitination enzymes, degradation of transcription factors and the degradation of negative regulators of transcription.


Timing of immunogenesis


Seedling resistance

Seedling resistance is resistance which begins in the
seedling A seedling is a young sporophyte developing out of a plant embryo from a seed. Seedling development starts with germination of the seed. A typical young seedling consists of three main parts: the radicle (embryonic root), the hypocotyl (embryo ...
stage of plant development and continues throughout its lifetime. It is ''not'' meant to comprehend resistance which ''only'' applies to the seedling stage. Synonymous with ''major gene resistance''.


Adult plant resistance

Adult plant resistance does not appear in the seedling stage but does exist throughout the rest of the plant's lifetime. The difference between seedling resistance and adult-stage resistance is especially important in annual crops. APR and quantitative resistance often go together, although they are not synonymous. Synonymous with ''minor gene resistance''.


Plant breeding for disease resistance

Plant breeders emphasize selection and development of disease-resistant plant lines. Plant diseases can also be partially controlled by use of pesticides and by cultivation practices such as
crop rotation Crop rotation is the practice of growing a series of different types of crops in the same area across a sequence of growing seasons. It reduces reliance on one set of nutrients, pest and weed pressure, and the probability of developing resistant ...
, tillage, planting density, disease-free seeds and cleaning of equipment, but plant varieties with inherent (genetically determined) disease resistance are generally preferred. Breeding for disease resistance began when plants were first domesticated. Breeding efforts continue because pathogen populations are under selection pressure for increased virulence, new pathogens appear, evolving cultivation practices and changing climate can reduce resistance and/or strengthen pathogens, and plant breeding for other traits can disrupt prior resistance. A plant line with acceptable resistance against one pathogen may lack resistance against others. Breeding for resistance typically includes: * Identification of plants that may be less desirable in other ways, but which carry a useful disease resistance trait, including wild plant lines that often express enhanced resistance. * Crossing of a desirable but disease-susceptible variety to a plant that is a source of resistance. * Growth of breeding candidates in a disease-conducive setting, possibly including pathogen inoculation. Attention must be paid to the specific pathogen isolates, to address variability within a single pathogen species. * Selection of disease-resistant individuals that retain other desirable traits such as yield, quality and including other disease resistance traits. Resistance is termed ''durable'' if it continues to be effective over multiple years of widespread use as pathogen populations evolve. " Vertical resistance" is specific to certain races or strains of a pathogen species, is often controlled by single
R gene Resistance genes (R-Genes) are genes in plant genomes that convey plant disease resistance against pathogens by producing R proteins. The main class of R-genes consist of a nucleotide binding domain (NB) and a leucine rich repeat (LRR) dom ...
s and can be less durable. Horizontal or broad-spectrum resistance against an entire pathogen species is often only incompletely effective, but more durable, and is often controlled by many genes that segregate in breeding populations. Durability of resistance is important even when future improved varieties are expected to be on the way: The average time from human recognition of a new fungal disease threat to the release of a resistant crop for that pathogen is at least twelve years. Crops such as potato, apple, banana and sugarcane are often propagated by
vegetative reproduction Vegetative reproduction (also known as vegetative propagation, vegetative multiplication or cloning) is any form of asexual reproduction occurring in plants in which a new plant grows from a fragment or cutting of the parent plant or speci ...
to preserve highly desirable plant varieties, because for these species, outcrossing seriously disrupts the preferred traits. See also
asexual propagation Plant propagation is the process by which new plants grow from a variety of sources: seeds, cuttings, and other plant parts. Plant propagation can also refer to the man-made or natural dispersal of seeds. Propagation typically occurs as a step i ...
. Vegetatively propagated crops may be among the best targets for resistance improvement by the
biotechnology Biotechnology is the integration of natural sciences and engineering sciences in order to achieve the application of organisms, cells, parts thereof and molecular analogues for products and services. The term ''biotechnology'' was first used by ...
method of plant transformation to manage genes that affect disease resistance. Scientific breeding for disease resistance originated with Sir Rowland Biffen, who identified a single recessive gene for resistance to wheat yellow rust. Nearly every crop was then bred to include disease resistance (R) genes, many by introgression from compatible wild relatives.


GM or transgenic engineered disease resistance

The term GM ( "genetically modified") is often used as a synonym of transgenic to refer to plants modified using recombinant DNA technologies. Plants with transgenic/GM disease resistance against insect pests have been extremely successful as commercial products, especially in maize and cotton, and are planted annually on over 20 million hectares in over 20 countries worldwide (see also
genetically modified crops Genetically modified crops (GM crops) are plants used in agriculture, the DNA of which has been modified using genetic engineering methods. Plant genomes can be engineered by physical methods or by use of '' Agrobacterium'' for the delivery of ...
). Transgenic plant disease resistance against microbial pathogens was first demonstrated in 1986. Expression of viral coat protein gene sequences conferred virus resistance via small
RNA Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and deoxyribonucleic acid ( DNA) are nucleic acids. Along with lipids, proteins, and carbohydra ...
s. This proved to be a widely applicable mechanism for inhibiting viral replication. Combining coat protein genes from three different viruses, scientists developed squash hybrids with field-validated, multiviral resistance. Similar levels of resistance to this variety of viruses had not been achieved by conventional breeding. A similar strategy was deployed to combat
papaya ringspot virus ''Papaya ringspot virus'' (PRSV) is a pathogenic plant virus in the genus ''Potyvirus'' and the virus family ''Potyviridae'' which primarily infects the papaya tree. The virus is a non-enveloped, flexuous rod-shaped particle that is between 760& ...
, which by 1994 threatened to destroy
Hawaii Hawaii ( ; haw, Hawaii or ) is a state in the Western United States, located in the Pacific Ocean about from the U.S. mainland. It is the only U.S. state outside North America, the only state that is an archipelago, and the only ...
’s
papaya The papaya (, ), papaw, () or pawpaw () is the plant species ''Carica papaya'', one of the 21 accepted species in the genus '' Carica'' of the family Caricaceae. It was first domesticated in Mesoamerica, within modern-day southern Mexico and ...
industry. Field trials demonstrated excellent efficacy and high fruit quality. By 1998 the first transgenic virus-resistant papaya was approved for sale. Disease resistance has been durable for over 15 years. Transgenic papaya accounts for ~85% of Hawaiian production. The fruit is approved for sale in the U.S., Canada and Japan. Potato lines expressing viral replicase sequences that confer resistance to potato leafroll virus were sold under the trade names NewLeaf Y and NewLeaf Plus, and were widely accepted in commercial production in 1999-2001, until McDonald's Corp. decided not to purchase GM potatoes and Monsanto decided to close their NatureMark potato business. NewLeaf Y and NewLeaf Plus potatoes carried two GM traits, as they also expressed Bt-mediated resistance to Colorado potato beetle. No other crop with engineered disease resistance against microbial pathogens had reached the market by 2013, although more than a dozen were in some state of development and testing.


PRR transfer

Research aimed at engineered resistance follows multiple strategies. One is to transfer useful PRRs into species that lack them. Identification of functional PRRs and their transfer to a recipient species that lacks an orthologous receptor could provide a general pathway to additional broadened PRR repertoires. For example, the ''
Arabidopsis ''Arabidopsis'' (rockcress) is a genus in the family Brassicaceae. They are small flowering plants related to cabbage and mustard. This genus is of great interest since it contains thale cress (''Arabidopsis thaliana''), one of the model orga ...
'' PRR ''EF-Tu'' receptor (EFR) recognizes the bacterial translation elongation factor '' EF-Tu''. Research performed at Sainsbury Laboratory demonstrated that deployment of EFR into either ''
Nicotiana benthamiana ''Nicotiana benthamiana'', colloquially known as benth or benthi, is a species of ''Nicotiana'' indigenous to Australia. It is a close relative of tobacco. A synonym for this species is ''Nicotiana suaveolens'' var. ''cordifolia'', a descrip ...
''or '' Solanum lycopersicum'' (tomato), which cannot recognize ''EF-Tu'', conferred resistance to a wide range of bacterial pathogens. EFR expression in tomato was especially effective against the widespread and devastating soil bacterium
Ralstonia solanacearum ''Ralstonia solanacearum'' is an aerobic non-spore-forming, Gram-negative, plant pathogenic bacterium. ''R. solanacearum'' is soil-borne and motile with a polar flagellar tuft. It colonises the xylem, causing bacterial wilt in a very wide ran ...
. Conversely, the tomato PRR '' Verticillium 1'' (''Ve1'') gene can be transferred from tomato to ''Arabidopsis'', where it confers resistance to race 1 Verticillium isolates.


Stacking

The second strategy attempts to deploy multiple NLR genes simultaneously, a breeding strategy known as stacking. Cultivars generated by either DNA-assisted molecular breeding or
gene transfer Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between unicellular and/or multicellular organisms other than by the ("vertical") transmission of DNA from parent to offspring (reproduction). H ...
will likely display more durable resistance, because pathogens would have to mutate multiple effector genes. DNA sequencing allows researchers to functionally “mine” NLR genes from multiple species/strains. The ''avrBs2'' effector gene from '' Xanthomona perforans'' is the causal agent of bacterial spot disease of pepper and tomato. The first “effector-rationalized” search for a potentially durable R gene followed the finding that ''avrBs2'' is found in most disease-causing '' Xanthomonas'' species and is required for pathogen fitness. The ''Bs2'' NLR gene from the wild pepper, '' Capsicum chacoense'', was moved into tomato, where it inhibited pathogen growth. Field trials demonstrated robust resistance without bactericidal chemicals. However, rare strains of ''Xanthomonas'' overcame ''Bs2''-mediated resistance in pepper by acquisition of ''avrBs2'' mutations that avoid recognition but retain virulence. Stacking R genes that each recognize a different core effector could delay or prevent adaptation. More than 50 loci in wheat strains confer disease resistance against wheat stem, leaf and yellow stripe rust pathogens. The Stem rust 35 (''Sr35'') NLR gene, cloned from a diploid relative of cultivated wheat, '' Triticum monococcum'', provides resistance to wheat rust isolate ''Ug99''. Similarly, ''Sr33'', from the wheat relative '' Aegilops tauschii'', encodes a wheat ortholog to barley ''Mla'' powdery mildew–resistance genes. Both genes are unusual in wheat and its relatives. Combined with the ''Sr2'' gene that acts additively with at least Sr33, they could provide durable disease resistance to ''Ug99'' and its derivatives.


Executor genes

Another class of plant disease resistance genes opens a “trap door” that quickly kills invaded cells, stopping pathogen proliferation. Xanthomonas and
Ralstonia ''Ralstonia'' is a genus of bacteria, previously included in the genus ''Pseudomonas ''Pseudomonas'' is a genus of Gram-negative, Gammaproteobacteria, belonging to the family Pseudomonadaceae and containing 191 described species. The membe ...
transcription activator A transcriptional activator is a protein (transcription factor) that increases transcription of a gene or set of genes. Activators are considered to have ''positive'' control over gene expression, as they function to promote gene transcription and, ...
–like (TAL) effectors are DNA-binding proteins that activate host gene expression to enhance pathogen virulence. Both the rice and pepper lineages independently evolved TAL-effector binding sites that instead act as an executioner that induces hypersensitive host cell death when up-regulated. ''Xa27'' from rice and Bs3 and Bs4c from pepper, are such “executor” (or "executioner") genes that encode non-homologous plant proteins of unknown function. Executor genes are expressed only in the presence of a specific TAL effector. Engineered executor genes were demonstrated by successfully redesigning the pepper ''Bs3'' promoter to contain two additional binding sites for TAL effectors from disparate pathogen strains. Subsequently, an engineered executor gene was deployed in rice by adding five TAL effector binding sites to the ''Xa27'' promoter. The synthetic ''Xa27'' construct conferred resistance against Xanthomonas bacterial blight and bacterial leaf streak species.


Host susceptibility alleles

Most plant pathogens reprogram host gene expression patterns to directly benefit the pathogen. Reprogrammed genes required for pathogen survival and proliferation can be thought of as “disease-susceptibility genes.” Recessive resistance genes are disease-susceptibility candidates. For example, a mutation disabled an ''Arabidopsis'' gene encoding pectate lyase (involved in cell wall degradation), conferring resistance to the powdery mildew pathogen '' Golovinomyces cichoracearum''. Similarly, the Barley ''MLO'' gene and spontaneously mutated pea and tomato ''MLO'' orthologs also confer powdery mildew resistance. ''Lr34'' is a gene that provides partial resistance to leaf and yellow rusts and powdery mildew in wheat. ''Lr34'' encodes an
adenosine triphosphate Adenosine triphosphate (ATP) is an organic compound that provides energy to drive many processes in living cells, such as muscle contraction, nerve impulse propagation, condensate dissolution, and chemical synthesis. Found in all known form ...
(ATP)–binding cassette (ABC) transporter. The dominant allele that provides disease resistance was recently found in cultivated wheat (not in wild strains) and, like ''MLO'' provides broad-spectrum resistance in barley. Natural alleles of host translation elongation initiation factors ''eif4e'' and ''eif4g'' are also recessive viral-resistance genes. Some have been deployed to control
potyvirus ''Potyvirus'' is a genus of positive-strand RNA viruses in the family ''Potyviridae''. Plants serve as natural hosts. The genus is named after member virus ''potato virus Y''. Potyviruses account for about thirty percent of the currently known p ...
es in barley, rice, tomato, pepper, pea, lettuce and melon. The discovery prompted a successful mutant screen for chemically induced ''eif4e'' alleles in tomato. Natural promoter variation can lead to the evolution of recessive disease-resistance alleles. For example, the recessive resistance gene ''xa13'' in rice is an allele of ''Os-8N3''. ''Os-8N3'' is transcriptionally activated by'' Xanthomonas oryzae pv. oryzae'' strains that express the TAL effector ''PthXo1''. The ''xa13'' gene has a mutated effector-binding element in its promoter that eliminates ''PthXo1'' binding and renders these lines resistant to strains that rely on ''PthXo1''. This finding also demonstrated that ''Os-8N3'' is required for susceptibility. Xa13/Os-8N3 is required for pollen development, showing that such mutant alleles can be problematic should the disease-susceptibility phenotype alter function in other processes. However, mutations in the ''Os11N3'' (OsSWEET14) TAL effector–binding element were made by fusing TAL effectors to nucleases (
TALEN Transcription activator-like effector nucleases (TALEN) are restriction enzymes that can be engineered to cut specific sequences of DNA. They are made by fusing a TAL effector DNA-binding domain to a DNA cleavage domain (a nuclease which cuts DNA ...
s). Genome-edited rice plants with altered ''Os11N3'' binding sites remained resistant to ''Xanthomonas oryzae pv. oryzae'', but still provided normal development function.


Gene silencing

RNA silencing RNA silencing or RNA interference refers to a family of gene silencing effects by which gene expression is negatively regulated by non-coding RNAs such as microRNAs. RNA silencing may also be defined as sequence-specific regulation of gene expres ...
-based resistance is a powerful tool for engineering resistant crops. The advantage of RNAi as a novel gene therapy against fungal, viral and bacterial infection in plants lies in the fact that it regulates gene expression via
messenger RNA In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of synthesizing a protein. mRNA is created during the ...
degradation, translation repression and
chromatin Chromatin is a complex of DNA and protein found in eukaryotic cells. The primary function is to package long DNA molecules into more compact, denser structures. This prevents the strands from becoming tangled and also plays important roles in r ...
remodelling through small non-coding RNAs. Mechanistically, the silencing processes are guided by processing products of the double-stranded RNA (
dsRNA Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and deoxyribonucleic acid ( DNA) are nucleic acids. Along with lipids, proteins, and carb ...
) trigger, which are known as small interfering RNAs and microRNAs.


Host range

Among the thousands of species of plant pathogenic microorganisms, only a small minority have the capacity to infect a broad range of plant species. Most pathogens instead exhibit a high degree of host-specificity. Non-host plant species are often said to express ''non-host resistance''. The term ''host resistance'' is used when a pathogen species can be pathogenic on the host species but certain strains of that plant species resist certain strains of the pathogen species. The causes of host resistance and non-host resistance can overlap. Pathogen host range is determined, among other things, by the presence of appropriate effectors that allow colonization of a particular host. Pathogen host range can change quite suddenly if, for example, the pathogen's capacity to synthesize a host-specific toxin or effector is gained by gene shuffling/mutation, or by
horizontal gene transfer Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between unicellular and/or multicellular organisms other than by the ("vertical") transmission of DNA from parent to offspring (reproduction). HG ...
.


Epidemics and population biology

Native populations are often characterized by substantial genotype diversity and dispersed populations (growth in a mixture with many other plant species). They also have undergone of plant-pathogen
coevolution In biology, coevolution occurs when two or more species reciprocally affect each other's evolution through the process of natural selection. The term sometimes is used for two traits in the same species affecting each other's evolution, as well ...
. Hence as long as novel pathogens are not introduced/do not evolve, such populations generally exhibit only a low incidence of severe disease
epidemics An epidemic (from Greek ἐπί ''epi'' "upon or above" and δῆμος ''demos'' "people") is the rapid spread of disease to a large number of patients among a given population within an area in a short period of time. Epidemics of infectious d ...
. Monocrop agricultural systems provide an ideal environment for pathogen evolution, because they offer a high density of target specimens with similar/identical genotypes. The rise in mobility stemming from modern transportation systems provides pathogens with access to more potential targets. Climate change can alter the viable geographic range of pathogen species and cause some diseases to become a problem in areas where the disease was previously less important. These factors make modern agriculture more prone to disease epidemics. Common solutions include constant breeding for disease resistance, use of pesticides, use of border inspections and plant import restrictions, maintenance of significant genetic diversity within the crop gene pool (see
crop diversity Crop diversity or crop biodiversity is the variety and variability of crops, plants used in agriculture, including their genetic and phenotypic characteristics. It is a subset of and a specific element of agricultural biodiversity. Over the past ...
), and constant surveillance to accelerate initiation of appropriate responses. Some pathogen species have much greater capacity to overcome plant disease resistance than others, often because of their ability to evolve rapidly and to disperse broadly.


See also

*
Disease resistance in fruit and vegetables There are a number of lines of defence against pests (that, those animals that cause damage to the plants we grow) and diseases in the orchard, principal among these being the practice of good husbandry, creating healthy soil and ensuring high ...
* Gene-for-gene relationship * Plant defense against herbivory * Plant pathology * Plant use of endophytic fungi in defense *
Systemic acquired resistance Systemic acquired resistance (SAR) is a "whole-plant" resistance response that occurs following an earlier localized exposure to a pathogen. SAR is analogous to the innate immune system found in animals, and although there are many shared aspects be ...
* Induced Systemic Resistance


References

*


Further reading

* Lucas, J.A., "Plant Defence." Chapter 9 in Plant Pathology and Plant Pathogens, 3rd ed. 1998 Blackwell Science. * Hammond-Kosack, K. and Jones, J.D.G. "Responses to plant pathogens." In: Buchanan, Gruissem and Jones, eds. Biochemistry and Molecular Biology of Plants, Second Edition. 2015. Wiley-Blackwell, Hoboken, NJ. * * Schumann, G. Plant Diseases: Their Biology and Social Impact. 1991 APS Press, St. Paul, MN.


External links


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