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Plant Disease and ResistanceJE Leach, Colorado State University, Fort Collins, CO, USAH Leung, International Rice Research Institute, DAPO, Metro Manila, PhilippinesNA Tisserat, Colorado State University, Fort Collins, CO, USA

r 2014 Elsevier Inc. All rights reserved.

GlossaryDisease The continuous abnormal functioning of anorganism; a disruption in the health of the organism.Effectors Pathogen proteins and small molecules that alterhost–cell structure and function.Effector-triggered immunity Direct or indirect recognitionof pathogen effectors by plant resistance (R) proteins thatleads to the activation of plant defense responses.Evolutionary arms race Evolutionary struggle betweencompeting sets of coevolving genes that developadaptations and counteradaptations against each other.

Encyclopedia of Agricult0

PAMP-triggered immunity First active defense response ofplants, also referred to as activation of basal defenses, afterperception of PAMPs by plant PRRs.Pathogen A disease-producing organism or biotic agent.Pathogen-associated molecular patterns Highlyconserved molecules associated with groups of microbesthat are recognized by pattern recognition receptors (PRRs)on plant cell surfaces to activate the innate immune system.Plant immunity The inherent or induced capacity ofplants to withstand or ward off biological attack bypathogens.

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Figure 1 The plant disease triangle shows the three componentsnecessary for disease to occur: (1) the pathogenic microbe must bevirulent on a particular species and cultivar of plant; (2) the plant hostmust be susceptible to a particular strain/isolate/biotype of apathogen; and (3) environmental conditions including temperature,humidity, and availability of nutrients must be suitable for theinteractions that lead to disease. If a pathogen requires an insectvector for dissemination or inoculation then a fourth dimension isadded (a plant disease pyramid).

Plants Get Sick Too!

The earth accommodates a staggering number of microbes,estimated to be as high as 1030 (Kallmeyer et al., 2012).Among these microbes are as many as 5.1 million differentspecies of fungi (Blackwell, 2011), more than 8000 of whichcause disease on plants. Given the huge variety of plantpathogenic microorganisms, which also include viruses, bac-teria, oomycetes, and nematodes, why are there so few dis-eased plants in nature? The reasons are many. Most microbesdo not have the capacity to cause disease in plants, and thosethat do range from very efficient to very weak pathogens. Somemicrobes are even beneficial to plants, facilitating their growthin nutrient-limiting or adverse environments. Even closely re-lated plants may vary greatly in their exposure or susceptibilityto pathogens, ranging from highly susceptible to completelyimmune (resistant). Furthermore, environmental conditionsincluding temperature, humidity, and availability of nutrientscan influence whether the plant–pathogen interactions lead todisease or resistance. The interactions of susceptible host,virulent pathogen, and conducive environment can be con-ceptualized as a disease triangle (Figure 1).

Agriculturists who are interested in producing healthy cropsfrequently focus on the plant side of the arms race, deter-mining which adaptations make the plant resistant to disease.However, given the complicated relationship between patho-gen virulence and plant immunity, the most effective approachto designing a successful disease control strategy is one thatconsiders both the partners. This article explores attributes ofplant pathogenic microbes that enable them to access hostnutrients and cause disease. Mechanisms by which the plantresists invasion by pathogens, and how the intimate inter-actions between microbes and plants have driven their coe-volution are also discussed. Finally, how knowledge of theseinteractions influences disease control strategies in the field isexplored. Although many common themes are found amongthe interactions between pathogens and plants, there is also

huge diversity; thus, examples used are meant to providecontext to this discussion, and are not meant to be com-prehensive. Furthermore, given the breadth of the topic andlimited space, we rely on citation of excellent reviews, whereavailable, and provide primary references for recent examples.

A Conceptual Basis for the Evolution ofPlant–Microbe Interactions

Plant pathogens form intimate relationships with plants togain access to host resources needed to survive, grow, andreproduce. This process, which involves infection, coloniza-tion, and pathogen reproduction, is called pathogenesis. Tocause disease, plant pathogenic microbes must (1) find and

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gain access to the host plant; (2) avoid, suppress, or overcomethe plant's resistance repertoire; and (3) coerce the plant toprovide nutrients or replication machinery to enable growthand multiplication. However, to avoid disease, the plant must(1) recognize the presence of potential pathogens and (2)mount a defense response that has sufficient strength to restrictpathogenic attack without being too detrimental to the plant'sown physiology. The variation in virulence on the part of thepathogen and susceptibility or resistance on the part of theplant are the result of a coevolutionary arms race (Andersonet al., 2010). Increased virulence of a pathogen places a strongselective pressure on the plant host to increase resistance; inresponse, the pathogen is under selective pressure to overcomeresistance. A simple ‘zigzag model’ (Figure 2) was proposed toillustrate our current understanding of plant–pathogen inter-actions in an evolutionary context (Jones and Dangl, 2006).In this article, a step-by-step walk will be taken through thezigzag model to frame the discussion of the processes inpathogen–plant interactions that culminate in disease orresistance.

How do Pathogens Find and Enter the Plant?

For a microbe to cause disease, it needs to come into directcontact with its host plant, and often with a specific host planttissue. Microbes are passively distributed from plant to plantby wind, splashing rains, or insect vectors (Figure 3). However,nonpathogenic microbes, once deposited, do not have thecapacity to find wounds or natural openings on the plantsurface, or to penetrate preformed surface barriers such as awaxy cuticle and thick cell walls. Pathogens, however, haveevolved diverse mechanisms to find and enter plants to es-tablish the disease.

Once they reach the host plant, a pathogenic microbe mayland on the part of the plant suitable for infection, called theinfection court. In other cases, pathogens need to expend energyto move or grow toward the infection court. Elegant work in the1970s–1980s demonstrated that mycelia of some fungi exhibitsdirectional growth toward the infection court of their host, inthis case the stomata (for a review, see Tucker and Talbot, 2001;Mendgen et al., 1996). For example, mycelial growth of Uro-myces appendiculatus, the causal agent of bean rust, is orientedperpendicular to the ridges surrounding the stomata, a processknown as thigmotropism (Figure 4) (Hoch et al., 1987). Sto-matal ridges of a height specific to bean signal the fungus toform specialized infection structures that penetrate the stomatalopening, a process called thigmodifferentiation.

Some pathogens orient themselves toward an infectioncourt by sensing electrical fields (electrotaxis) or chemicalsignals (chemotaxis). Swimming spores of the oomycetePythium aphanidermatum, which infects roots through wounds,are attracted to the negative charges associated with woundsalong the root surface; Phytophthora palmivora zoospores, whichcan directly penetrate undamaged roots, are attracted to posi-tive charges (van West, 2002). Access to wounds or naturalopenings by plant pathogenic bacteria such as Agrobacteriumspp. tumefaciens (crown gall of most dicots), Erwinia amylovora(fireblight of apple and pear), Pseudomonas syringae pv. glycinea(bacterial blight of soybean), and Pseudomonas lachrymans

(angular leaf spot of cucumber) is facilitated by chemotaxistoward simple plant chemicals such as sugars or phenolics.

Once the pathogen reaches the infection court, it needs toenter the plant (Figure 3). Unless the pathogen can enter theplant through indirect penetration of wounds or naturalopenings or is vectored by an insect, it must create an openingto enter the plant through direct penetration. Plant surfaces arebarriers to pathogens, and surface structure varies widelyamong plants and among tissues on the same plant. Woodystems present a very different set of barriers to pathogens thanleaves or flowers do. A typical leaf surface presents a toughouter cuticle that is composed of an insoluble polyester, cutin,embedded in a complex mixture of waxes. The thickness of thecuticle varies among species, organs, developmental stages,and environmental conditions. Many pathogens have evolvedelaborate mechanisms for breaking through this barrier, whichare usually only employed during the penetration phase of thelife cycle. Fungi can penetrate the cuticle by chemical or en-zymatic degradation or by force. Magnaporthe oryzae, a fungalpathogen causing rice blast disease, uses both the mechanisms.After the fungal spores germinate on the plant surface, themycelia form specialized penetration structures called appres-soria. Each appressorium is held in place on the leaf surface bya fungal-produced mucilage that is so sticky that it sticks toTeflon (Hamer et al., 1988). The appressoria secrete cutinase,an enzyme that degrades and weakens the cuticle (Skamniotiand Gurr, 2007). Then, after building up enormous levels ofturgor pressure, the appressorium forces an appendage calledthe penetration peg through the cuticle and the cell wall(Howard and Valent, 1996).

PAMP-Triggered Immunity: The First Line of ActiveDefense

For those microbes that get beyond the preformed structuralbarriers, the zigzag model proposes that the first line of activeplant defense is PAMP-triggered immunity (PTI). PTI, the setof general defense responses of plants to diverse microbes, is aprocess by which plants actively recognize ‘nonself’ from ‘self’via surface receptor molecules called pattern recognition re-ceptors (PRRs). PRRs are membrane-spanning proteins withextracellular receptor domains. The receptor domains of PRRsrecognize highly conserved pathogen molecules called patho-gen-associated molecular patterns (PAMPs, also called mi-crobe-associated molecular patterns or MAMPs) activating asignal transduction cascade that culminates in the induction ofa suite of defense responses. PTI-associated defenses may in-clude the production of reactive oxygen species, increases inintracellular calcium concentration, callose deposition in cellwall, activation of mitogen-activated protein kinases (MAPKs),production of antimicrobial compounds called phytoalexins,and a complex transcriptional response (Schwessinger andZipfel, 2008). Together, these PTI-activated defense responsesare the chief means by which microbes that get past plantstructural barriers.

Plant-derived peptides or cell wall fragments that are re-leased by pathogen degradation, called damage-associatedmolecular patterns (DAMPs), can also be recognized by PRRand activate signaling of PTI (reviewed by Monaghan and

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Figure 2 The zigzag model to illustrate the coevolution of the plant immune system and pathogen virulence effectors. Plants detect pathogen-associated molecular patterns (PAMPs) via pattern recognitionreceptors (PRRs) to trigger PAMP-triggered immunity (PTI). Pathogens evolve effectors that interfere with PTI or other host processes to result in effector-triggered susceptibility (ETS). In response, plantsevolved NB-LRR proteins to detect effectors and to activate effector-triggered immunity (ETI). ETI has a higher amplitude (stronger and longer lasting response) than the PTI. Within the pathogenpopulations, pathogen isolates are selected that have lost the recognized effector, leading to suppression of ETI and restored ETS. Finally, new plant NB-LRR alleles are selected that can recognize a neweffector, restoring ETI. Hypersensitive response (HR). Image drawn by Samuel Vazquez III adapted from Jones, J.D., Dangl, J.L., 2006. The plant immune system. Nature 444 (7117), 323–329, andChisholm, S.T., Coaker, G., Day, B., Staskawicz, B.J., 2006. Host-microbe interactions: Shaping the evolution of the plant immune response. Cell 124 (4), 803–814.

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WoundsAbscission scarsLateral rootsAbrasionsVector bites

Insect vectored

Direct penetrationCuticleEpidermisVulnerable sites

Natural openingsStomataLenticelsHydathodesNectaries

Figure 3 Methods of penetration and invasion by plant pathogens. Pathogens can enter through wounds (e.g., Tobacco Mosaic Virus,Agrobacterium spp. tumefaciens, and soft rot fungi) or natural openings such as stomata (rust fungi and Pseudomonas syringae), lenticels(Pectobacterium carotovorum), or hydathodes (Xanthomonas oryzae pv. oryzae). Fungi that can directly penetrate are powdery mildews, downymildews, or Magnaporthe oryzae. Pathogens that are delivered by insect vectors include Xylella fastidiosa, Cauliflower Mosaic Virus. Image drawnby Samuel Vazquez III and Tony Campillo.

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Zipfel, 2012). In one example, plants produce proteins thatinhibit the activity of fungal-produced cell wall degradingenzymes called endopolygalacturonases. The plant-producedinhibitors reduce the activity of the endopolygalacturonases,leading to the accumulation of long-chain oligogalacturonidesthat function as DAMPs and trigger PTI (D'Ovidio et al.,2004).

PAMPs tend to be highly conserved, essential componentsof the pathogen, so any mutation that affects their function islikely to be detrimental to the pathogen. Some PAMPS con-served among multiple microbes can be recognized by asingle plant receptor, allowing a high degree of efficiency inthe deployment of plant resources. For these reasons, PAMPreceptors can confer resistance that is stable and broad spec-trum, or effective against diverse pathogens. Not surprisingly,pathogens have evolved adaptations to overcome PTI. Thismay occur through the rare evolution of a PAMP to avoidrecognition, or, more commonly, through the production ofvirulence effectors that enable the pathogen to overcome oravoid PTI and cause disease (reviewed by Pel and Pieterse2013).

Effector-Triggered Susceptibility: The PathogenRetaliates

Bacteria, fungi, oomycetes, and nematodes produce a suite ofvirulence effectors that are broadly defined as pathogen-pro-duced proteins or metabolites that directly interact with thehost and enhance virulence (Hogenhout et al., 2009). Effectorsare used by the pathogen to access nutrients, adversely affecthost physiology, or to block PTI; the zigzag model describesthis as effector-triggered susceptibility (ETS) (Jones and Dangl,2006).

Collectively, effectors contribute to diverse pathogen life-styles ranging from necrotrophy to biotrophy. Necrotrophicpathogens kill plant cells by producing effectors such as toxinsor tissue-degrading enzymes; these effectors induce cell ne-crosis and cause leakage of nutrients that are used as substratesby the pathogen. Necrotrophic pathogens include the bacterialsoft rot pathogen Pectobacterium carotovorum subsp. car-otovorum, the fungal gray mold pathogen, Botrytis cinerea, andthe oomycete root rot pathogen P. aphanidermatum. Biotrophicpathogens require living plant cells, and use complex

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Figure 4 Uromyces appendiculatus, the bean rust pathogen, exhibits growth and differentiation directed by contact stimuli (thigmotropism andthigmodifferentiation, respectively). (a) Symptoms of bean rust. (b) Life cycle of U. appendiculatus on bean (Phaseolus vulgaris) showing the stageat which urediniospores are important. (c) Urediniospore germlings on the leaf surface of a bean leaf. The germling grew oriented to the stomata,and then differentiated into an appressorium (infection structure) over the stomate. (d) Polystyrene replica with 0.5 mm high ridges that are highlyinductive for appressorium differentiation. (e) Polystyrene replica with 0.1 mm high ridges that do not induce appressorium formation. (a) and (b)from Howard F. Schwartz. Available at: http://www.bugwood.org/ (accessed 09.09.13); (c) and (d) adapted from Hoch, H.C., Staples, R.C.,Whitehead, B., Comeau, J., Wolf, E.D., 1987. Signaling for growth orientation and cell differentiation by surface topography in uromyces. Science235 (4796), 1659–1662; and (e) photo provided by Harvey Hoch.

364 Plant Disease and Resistance

mechanisms to derive nutrients from the live host. Biotrophsinclude fungi that cause powdery mildew (Blumeria graminis f.sp. hordei) and downy mildew (Plasmopara viticola), and Xan-thomonas oryzae pv. oryzae, the bacterial blight pathogen ofrice. Hemibiotrophic pathogens exhibit both biotrophic andnecrotrophic life stages, keeping the plant cells alive in theearly stages of infection, and killing them at later stages. Theseinclude the rice blast pathogen M. oryzae and the anthracnosepathogen Colletotrichum lindemuthianum. Although these threebroad infection mechanisms (biotrophy, necrotrophy, andhemibiotrophy) provide a useful way to classify pathogens,there is no consistent agreement on what common features arerelevant to support inclusion of a pathogen within a group.For example, Phytophthora infestans, the important oomycetepathogen that causes late blight of potato, has been classifiedas by various authors as a biotroph, hemibiotroph, and even anecrotroph (Oliver and Ipcho, 2004).

How do Pathogens Deliver Virulence Effectors?

Pathogens may secrete effectors into the plant apoplast (thespace outside of the plasma membrane) or directly into theplant cell. Although effector secretion is a common strategyamong bacteria, fungi, and nematodes, different pathogens

have evolved diverse and elaborate secretion mechanisms.Multiple effectors are delivered by one secretion system, andmutations in secretion systems that block effector transfer canseverely reduce or eliminate pathogenicity.

To get outside of a gram-negative bacterial cell, an effectormust cross the inner plasma membrane, the periplasmic space,and the outer lipopolysaccharide membrane. Plant pathogenicbacteria have evolved at least seven types of secretion systemsto accomplish this, most of which have structural and func-tional counterparts among bacteria pathogenic to plants,humans, and animals (Tseng et al., 2009). Secretion systemsvary widely in their structural complexity, but are grouped aseither one-step systems, which move proteins directly throughthe bacterial cell envelope (type I, III, IV, and VI systems), ortwo-step systems, which deliver the protein first across theplasma membrane to the periplasm and then, in a secondstep, across the outer membrane (type III, IV, and VI) (for areview, see Records, 2011). The simplest of these is the type Isecretion system (T1SS), which spans the inner membrane,periplasmic space, and the outer membrane, and transportsproteins from the bacterial cytosol directly to the outside ofthe bacterium. Bacteria that cause soft rot diseases use thissystem to deliver proteases and lipases to the apoplast ofplant cells.

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Type III, IV, and VI pathways have complex structures thatmove effectors across the bacterial envelope and can deliverthe effectors directly into the host plant cytoplasm. Type IV(TT4S) pathway is notable because it is the only pathwaydescribed so far to transport both protein and nucleic acidsubstrates; A. tumefaciens uses the TT4S to deliver plant-transforming DNA, called T-DNA (transferred DNA), alongwith proteins into the host cytoplasm.

Type III (T3SS) pathway is structurally complex, with morethan 25 proteins, and has evolutionary similarities to bacterialflagella. This system delivers effectors from the bacterial cyto-plasm directly to the host plant cytoplasm using a syringe-likestructure that crosses the plant cell wall. Once at the plantmembrane, secreted proteins form a pore in the host mem-brane enabling translocation of the effector proteins into thehost cell (Galan and Wolf-Watz, 2006). On the basis of ana-lyses of sequenced genomes and subsequent functional ana-lyses, plant pathogenic bacteria in the species of Pseudomonasand Ralstonia secrete large numbers of T3SS effectors, in somecases, more than 40. The T3SS is essential for these pathogensto cause disease.

Large numbers of proteins are secreted from bacteria via thetwo-step type II (T2SS) and V (T5SS) secretion systems. Inthese systems, the first step of protein transfer requires anamino terminal signal peptide, which is removed as the pro-tein crosses from the bacterial cytoplasm to the periplasmicspace. The effector is then transported through the outermembrane by a second complex secreton structure. Manyplant cell-wall degrading enzymes (CWDEs), such as pectinlyases, polygalacturonases, and cellulases, are secreted fromXanthomonas and Erwinia-type pathogens through the T2SSpathway. Dickeya dadantii (Erwinia chrysanthemii) secretesadhesins via the T5SS pathway.

For biotrophic and hemibiotrophic fungi and oomycetes,the process of delivering effectors is less well understood. Ef-fectors secreted to the extracellular environment are likelytransported by the eukaryotic (type II) secretory pathway, aprocess involving exocytosis of Golgi-derived secretory ves-icles. Effectors moving through this pathway carry a canonicalN-terminal type II secretion signal, allowing sequence-basedidentification of putative effectors that function in the apo-plast. The hemibiotrophic fungal rice blast pathogen M. oryzaedelivers apoplastic effectors using type II Golgi-dependentsecretory pathway (Giraldo et al., 2013).

For most fungi and oomycete pathogens, the pathway foreffector transfer into the plant cell cytoplasm is just becomingknown. The hyphae typically differentiate into a haustoriumafter penetration of the host cell. As the haustorium develops,a specialized interface forms around it; this interface consistsof the plasma membranes of the pathogen and the host sep-arated by a modified pathogen cell wall. The interface allowsfor a two-way movement; nutrients move from the host cell tothe pathogen, and effectors are delivered from the pathogen tothe host. Secretion and delivery of effectors from these haus-torium-forming pathogens requires N-terminal motifs (RxLR)(Tyler et al., 2013). It is believed that RxLR effectors move intothe host cell independent of specialized structures from thepathogens, and possibly by exploiting the plant endocyticpathway (for a review, see Panstruga and Dodds, 2009). Notall fungi use haustoria, however; M. oryzae effectors targeted to

the host cytoplasm are delivered from invasive hyphae (thehyphae that invade inside the plant cells) into host cells via anovel plant membrane-rich structure (Giraldo et al., 2013).

Nematodes deliver effector proteins into plant cellsthrough a stylet that pierces the host cell wall. Fluids fromglands that contain effectors are then secreted into the hostcytoplasm through an orifice at the tip of the stylet (reviewedby Haegeman et al., 2012; Torto-Alalibo et al., 2009).

Effectors that are Delivered to the Plant Apoplast

Effectors that are delivered to the apoplast were the focus ofearly studies of host–pathogen interactions because they couldoften be isolated from microbes grown in vitro. Apoplastic ef-fectors, including CWDEs, toxins, hormones, and cysteine-richpeptides, are considered more important for necrotrophicpathogens than for biotrophic or hemibiotrophic pathogens.CWDEs facilitate penetration of plant tissues and releasenutrients from the wall polymers. Bacteria that cause soft rotdiseases produce a wide range of CWDEs, including pectinases,cellulases, proteases, and xylanases. Mutagenesis studies de-termined the relative contribution of CWDE-encoding genesfor disease, showing that pectinase genes are especially im-portant for tissue maceration (Beaulieu et al., 1993; Walton,1994). An analysis of the mutants revealed that producing acombination of different enzyme activities allows pathogens toefficiently degrade cell walls and feed on the byproducts. Somepathogens produce multiple CWDEs with the same type ofactivity; D. dadantii produce up to nine different endopectatelyase genes that vary in activity level, optimum pH, substratepreference, and length of product. The evolution and retentionof multiple CWDEs provides the pathogen with flexibility toattack different host plants under diverse conditions, such aswhen the pH of the tissues being degraded changes during theinfection process. The redundancy of these enzymes and thegenes encoding them may also be important for the survival ofthe pathogen as a saprophyte outside of the host plant.

In addition to making use of redundancy in CWDEs,necrotrophic pathogens usually rely on the collective contri-bution of different types of effectors to promote plant celldeath and nutrient acquisition. For example, the arsenal of B.cinerea, the causal agent of gray mold, includes both CWDEsand toxic low molecular weight metabolites (Choquer et al.,2007). Many fungal and oomycete pathogens secrete small,cysteine-rich proteins that protect the pathogen by inhibitingthe activity of plant-produced hydrolytic enzymes (proteases,glucanases, and chitinases). Avr2, an effector produced by thetomato pathogen Cladosporium fulvum, inhibits the activity oftomato apoplastic cysteine proteases. P. infestans secretes asuite of protein inhibitors of plant cysteine proteases, sub-tilisin-like serine proteases, and an endo-β-1,3 glucanase.

Phytotoxins, microbial products that are poisonous toplants, are produced by many necrotrophic bacteria and fungiresulting in chlorosis and necrosis of the affected host tissues.Phytotoxins are grouped into host-selective toxins (HSTs) andgeneral toxins. HSTs, the essential components of pathogeni-city, are toxic only to susceptible plants. These toxins producevisible disease symptoms of the resulting disease; that is,treatment with HST extracts alone induces the same symptomsas pathogen infection. HSTs were critical virulence factors

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contributing to two devastating crop epidemics. The Southerncorn leaf blight epidemic of 1970, caused by the pathogenCochliobolus carbonum destroyed approximately 15% of the USmaize crop. Symptoms on susceptible maize result from theproduction of a cyclic tetrapeptide called HC-toxin. The Vic-toria blight epidemic of oats in the mid-1940s was caused byCochliobolus victoriae, which elicits symptoms caused by thecyclized peptide phytotoxin victorin.

Although most described HSTs are secondary metabolites, afew are proteins, such as ToxA, produced by Pyrenophora tritici-repentis, during the development of tan spot disease of wheat(Tomas et al., 1990; Ciuffetti et al., 1997). Although thepathogen secretes the toxin into the plant apoplast, ToxA mustbe internalized into susceptible wheat cells to have its toxiceffect (Ciuffetti et al., 2010). Resistant wheat cultivars do notinternalize the toxin. Internalization is directed by a specificmotif in ToxA that comprises Arg-Gly-Asp (RGD); this motif ispredicted to interact with a plant membrane receptor that helpstranslocate the ToxA into the plant cell (Ciuffetti et al., 2010).

General toxins, or nonhost selective toxins, are toxic tomost plants, and have a broader host range than the producingpathogen. Often general toxins affect organisms beyondplants, including bacteria or yeast, a feature that has been ex-ploited to study these toxins in systems simpler than plants.General toxins are not essential virulence factors; mutation ofgenes involved in the biosynthesis of these toxins does notrender the pathogen avirulent. The mutant pathogen can stillcause disease, but may be less aggressive. Coronatine, pha-seolotoxin, and tabtoxin are three general toxins produced bythe bacterial species in the Pseudomonas genus.

Some virulence effectors work as plant growth regulators,also called phytohormones. Phytohormones are moleculesthat regulate plant growth, at extremely low concentrations.Pathogen-produced auxins and cytokinins can induce devel-opmental and morphological changes that can result in galls,epinasty, or a number of other grotesque shapes in the plant.The gram-positive bacterium Rhodococcus fascians synthesizesand secretes cytokinins that are taken up by the plant cellssurrounding the infection site. These cytokinins activate a set ofplant genes that keep the cells in a juvenile state, contributing todisease symptoms such as serrated leaves, stunting, and ab-normal flowers (reviewed by Busch and Benfey, 2010). Besidesinducing chlorosis and other disease symptoms, the generaltoxin coronatine produced by Pseudomonas spp. structurally andfunctionally mimics the plant hormone jasmonic acid iso-leucine. In this role, coronotine promotes the opening of plantstomata, allowing the bacteria to enter the plant and access theapoplast (Melotto et al., 2006; Thilmony et al., 2006).

Effectors that are delivered to the inside of plant cellsGenome searches for signature signal domains has led to thediscovery of large numbers of genes encoding effectors thatcould be translocated into the plant cytoplasm. For most ofthese putative effectors, the exact molecular target or role inthe infection process is not known. The widely studied bac-terial effectors delivered by the TTSS provide examples of thebroad range of host pathways and functions that are targeted.Some TTSS effectors, such as the P. syringae effectors AvrRpt2and AvrB, alter the hormone content of plant cells. AvrRpt2, acysteine protease, stimulates turnover of proteins that

negatively regulate auxin signaling to promote pathogenicity(Cui et al., 2013). AvrB activates mitogen-activated proteinkinase MAP kinase 4 (MPK4), which upregulates the ex-pression of jasmonic acid response, a hormone perturbationthat enhances plant susceptibility (Cui et al., 2010).

Some microbial effectors function to actively suppress PTI,and thereby enhance susceptibility. One mechanism, em-ployed by the P. syringae effector AvrPto, is to bind to andblock the kinase activity of the PTI receptors (PRRs) that rec-ognize several PAMPs. A second P. syringae effector AvrPtoBbinds to and targets PRRs for degradation. Other effectors in-directly affect PRR signaling. Virulence effectors produced bysome fungal pathogens, such as Sip1 produced by M. oryzae,bind the fungal PAMP chitin, thereby reducing the availabilityof the chitin for binding to the plant PRR, and inhibitingactivation of PTI.

Still other effectors directly alter gene expression. The uniquetranscription activator-like (TAL) effectors produced and de-livered to plant cells by Xanthomonas spp. enhance pathogenvirulence by directly activating promoters of target plant genesassociated with disease or susceptibility. These protein effectorscontain a central repeat domain comprising 34–35 amino acidmodules that are repeated in tandem; each repeat contains twohypervariable amino acid residues (for a review, see Scholzeand Boch, 2011). The C-terminus carries signal sequences thatdirect the effector into the nucleus (nuclear localization signals;NLSs) and an acidic activation domain (AAD) characteristic oftranscription factors. Once in the host cell, TAL effectors aretargeted to the plant nucleus by the NLS. In the nucleus, the TALeffectors bind specifically to sequences in target plant genepromoters and induce expression of these plant genes. TheDNA-binding specificity of TALs is determined by centralhypervariable amino acid residues. Although the discovery andvalidation of the function of plant genes targeted by TAL ef-fectors is in its infancy, some are known to activate expressionof genes that enhance susceptibility. The X. campestris pv. vesi-catoria effector AvrBs3 induces the expression of auxin-respon-sive genes in susceptible pepper plants; the resulting increase inauxin causes changes in cell division, cell enlargement, andhypertrophy, which may facilitate release of bacteria to the leafsurface and into the environment (Marois et al., 2002; Kay andBonas, 2009). AvrXa7 and PthXo1 produced by Xanthomonasoryzae pv. oryzae induce the expression of sugar transportersOsSWEET14 and OsSWEET11, respectively. The increased ex-pression of these genes is predicted to enhance transport ofsugar outside of the plant cell for bacterial consumption andthereby increasing the risk of disease (Chen et al., 2010).

The few examples above demonstrate that pathogen ef-fectors target a wide variety of plant functions to cause diseaseor increase pathogen fitness. However, functions are knownfor only a few effectors, mainly because the study of effectorfunction is complicated by the large numbers of diverse ef-fectors that any one pathogen secretes. P. syringae secretes morethan 40 effectors (Chang et al., 2005). Although some effectorsare major contributors to pathogen virulence, most effectorslikely function in concert to cause disease, with inactivation ofmultiple effectors needed to observe any change in virulencefunction (Cunnac et al., 2009). As a better understanding ofthe effector function could reveal new strategies for diseasecontrol, effector biology remains a major research area.

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Effector-Triggered Immunity: Evolution of Plants toEvade ETS

In response to the suppression or evasion of PTI by effectors,plants evolved a second line of defense called effector-triggeredimmunity (ETI). In ETI, plants use intracellular immune re-ceptors that are the products of resistance (R) genes to monitoreffectors or their activity and activate strong defense responses.ETI-associated defense responses frequently, but not always,are characterized by a rapid, localized programmed cell death(PCD) of the host cells called hypersensitive response (HR).Other localized host responses activated by ETI can include theproduction of reactive oxygen species, enhancement of cellwalls, accumulation of toxic metabolites or proteins, andaltered hormone regulation. In some cases, ETI results in asystemic activation of resistance, called systemic acquired re-sistance (SAR) or priming for a more efficient activation ofdefense mechanisms in response to a secondary pathogen at-tack (Conrath, 2011).

Flor (1971) first conceptualized the ‘Gene for Gene Hy-pothesis’ positing that R genes direct the recognition ofpathogen avirulence genes (now called virulence effectors) toculminate in resistance. Many R genes and effector genecombinations have since been characterized, supporting thehypothesis. How the R proteins actually confer recognition,though, is still being discovered and debated (Zipfel andRobatzek, 2010). Most, but not all, R proteins contain nucle-otide-binding (NB) and leucine-rich repeat (LRR) domains.There are two subclasses of these NB-LRR proteins; one with acoiled-coil (CC) domain and the other with a toll, interleukin-1 receptor, resistance protein domain (TIR) at the N-terminus(Bernoux et al., 2011). Initially, R proteins were predicted tointeract directly with their target effectors to activate defense ina ligand–receptor manner (Keen, 1990). Indeed, direct, phys-ical interactions have been shown for some R/effector genecombinations. R proteins in rice (Pi-ta, Pik, and RGA4/RGA5)and flax (L-locus NB-LRR proteins) directly bind to translo-cated effectors produced by the fungal pathogens M. oryzaeand Melampsora lini, respectively, to activate resistance (Jiaet al., 2000; Dodds et al., 2006; Ellis et al., 2007; Kanzaki et al.,2012). For many R/effector gene combinations, however, dir-ect interactions could not be detected.

With the realization that R gene partners were pathogenvirulence effectors, and with the identification of plant viru-lence targets for several effectors, a new model was proposed.This ‘Guard Model,’ predicts that R proteins act by monitoring(guarding) the effector target (guardee), and that modificationof this target by the effector results in the activation of the Rprotein, triggering disease resistance in the host (Jones andDangl, 2006). An evolutionary assumption in this model isthat the effector/guardee modification enhances the pathogen'sfitness. Supporting the Guard Model, the Arabidopsis R-proteinRPM1 directly interacts with and responds to the status of aplant membrane-associated protein RIN4. RIN4 is the target ofmultiple bacterial effectors, including the P. syringae effectorAvrB, and AvrB-mediated phosphorylation of RIN4 activatessignaling by RPM1 (reviewed by Chisholm et al., 2006; Jonesand Dangl, 2006). Thus, RPM1 (the guard) monitors the statusof RIN4, and the change in RIN4 (the guardee) by pathogeneffector activity triggers the defense response pathway.

Not all R/effector gene interactions fit the Guard Model,because fitness benefits could not be found for R-gene inter-actors. Therefore, a second model, the Decoy Model, wasproposed (Zipfel and Robatzek, 2010). The Decoy Modelpredicts that the effector target monitored by the R protein is adecoy that mimics the effector target, but only functions inperception of pathogen effectors without contributing topathogen fitness. An example of an interaction fitting thismodel is AvrPto, a TTSS effector produced by P. syringae.AvrPto is a kinase inhibitor that binds to the cytoplasmicSer/Thr kinase domain of a PAMP receptor, blocking PTI andenhancing virulence of the pathogen. AvrPto also binds to thetomato R protein Pto. Pto confers resistance to P. syringaestrains harboring avrPto, but only if the plant contains Prf, aprotein that physically interacts with Pto. Binding of AvrPto toPto is detected by Prf, and ETI is triggered. Thus, Pto is a decoythat binds AvrPto, and the interaction of Pto with AvrPto isdetected by Prf for signaling of ETI.

Defense Response Pathways are Shared between PTIand ETI

Although the categorization of immunity into PTI and ETI mayimply that these are totally distinct responses, in reality, thereis a great deal of overlap in the molecular events induced byboth PTI and ETI (Tsuda and Katagiri, 2010), and a continuumin the two categories is observed (Thomma et al., 2011). Forexample, the downstream signaling machinery used and thedefense genes activated by ETI and PTI overlap extensively,although the strengths of the responses and their duration varyconsiderably. ETI-activated responses are more prolonged androbust than those activated by PTI, and an interesting currenthypothesis is that ETI is a faster and more robust reactivationof PTI (Tsuda and Katagiri, 2010). This is shown by theamplitude of the responses in the zigzag model (Figure 2).

How Does the Environment Impact Disease in theContext of Climate Change?

Crop production, with its wide geographical range and inten-sity, is clearly affected by climate change (Lobell and Gourdji,2012). Climate change may cause unpredictable changes onpathogen populations in varying effects depending on thespecific pathosystem (Newton et al., 2012; Chakraborty et al.,2000). Increased temperature results in more rust disease inwheat and oats, whereas forage species become more resistantto certain fungi. Temperature effects on disease levels can resultfrom temperature-induced changes in the host, pathogen, or thehost–pathogen interactions (Garrett et al., 2006; Newton et al.,2012). Host plant changes might include (1) the alteration ofplant architecture to create more suitable microclimates forpathogen colonization, (2) changes in the effectiveness of plantdisease resistance, and (3) the increase of stress on plants, all ofwhich would affect disease development. Higher temperaturesare predicted to accelerate the breakdown of plant disease re-sistance in many host–pathogen systems by increasing diseasepressure and/or altering R gene efficacy (Garrett et al., 2006;Coakley et al., 1999; Webb et al., 2010).

368 Plant Disease and Resistance

It has been documented that an increasingly warmer wea-ther provides a first glimpse of the impact on disease distri-bution and changes in severity. A simple scenario is that warmtemperatures will reduce the impact of cool season diseases.However, this assumes that the pathogen remains static. Puc-cinia striiformis causes stripe rust of wheat and barley, and is, ingeneral, a cool season pathogen that does well in the PacificNorthwest of the USA (Chen, 2005; Hovmoller et al., 2011).The pathogen was not a problem in the wheat belt of the USGreat Plains before 2001, because the fungus could not thrivein the warmer weather of this region. Unfortunately, a variantof the pathogen that is more adapted to higher temperaturesappeared in the Great Plains in the early 2000s, and stripe rustis now a serious problem in this region.

Applying Knowledge of Plant–Microbe Interactions toDisease Control Strategies

What is out There?

Diverse groups of organisms are capable of causing plantdiseases, and many management strategies to control thesepathogens vary according to the specific pathogen. Thus, a firststep in controlling plant disease is to accurately identify thecause. Diagnosis is based on the presence of symptoms andsigns in the diseased plant. Symptoms are phenotypic

(a) (b)

(c) (d)

Figure 5 Signs and symptoms of plant disease. (a) Botrytis blight of junipe(symptoms). (b) Symptoms of late blight of potato. (c) and (d) Fruiting strucdowny mildew of grape. Photos provided by Ned Tisserat.

expressions of disease in a plant in response to activities of thepathogen, including pathogen effectors. The symptoms may belocalized to specific plant tissues, or systemic, as in the case ofdiseases caused by viruses and vascular wilt pathogens.Symptoms include those that cause plant death or necrosis(e.g., lesions, cankers, and rots), or those that result inhypertrophy and hyperplasia of tissues as in the case of gallsand witches' brooms (Figure 5). Although symptoms are oftenhelpful in field diagnosis, they may be misleading becausecompletely unrelated pathogens can cause nearly identicalsymptoms. Furthermore, the interaction phenotype resultingfrom infection may vary depending on environmental con-ditions or the age and genetic background of the plant. Thus,diagnosticians often rely on signs, or visual confirmation ofthe pathogen in host tissue, for disease identification. Somesigns, including bacterial ooze or fungal hyphae and fruitingstructures (Figure 5) may be readily seen in the field. However,most pathogen signs are visible only by using a hand lens ormicroscope. In some cases, pathogens must be cultured oridentified by serological and molecular detection methods.

Pathogens Function as Populations

While in the laboratory, the focus of the researchers was oncharacterizing how single ‘model’ pathogen strains cause dis-ease; disease at the field level is not caused by a singlepathogen genotype. To cause disease, the pathogen functions

r; mycelium (sign) of Botrytis cinerea showing brown decaytures (sporangia) and mycelium of Plasmopara viticola, causing

Plant Disease and Resistance 369

as a population that is made up of multiple genotypes orstrains with unique genetic and pathogenic attributes. Thepathogenic attributes of the entire pathogen population col-lectively determine the ability to cause disease, the amount ofdisease on a plant and in a plant population, and the epi-demiological consequence on the plant population. The pri-mary evolutionary forces that shape a pathogen populationinclude mutation, population size, gene/genotype flow, re-production system (asexual vs. sexual), and selection imposedon the pathogen by the host and environmental factors(McDonald and Linde, 2002). The interactions of these evo-lutionary forces shape the genetic structure of the pathogenpopulation.

Pathogens with high mutation rates, large population size,mostly asexually reproducing but with occasional sexual re-combination, high dispersal over distance (gene flow), andunder strong directional selection by the host are considered tohave the highest risk potential. In contrast, pathogens with lowmutation rate, relatively small population size, short dispersal,limited recombination, or gene flow present lesser risk in anagroecosystem. This broad characterization of pathogenpopulations provides a useful framework for disease resistancebreeding and disease management. However, ability to ef-fectively manage a pathogen requires detailed and specificknowledge of the pathosystem, and the strategies employedmust be flexible to adjust to changing agricultural productionsystems and physical environments.

Use of Disease Resistance Gene for Pathogen Control

Genetic resistance has been the mainstay of disease control formany crop species. The two broad categories of host resistanceare major gene resistance and quantitative resistance. As dis-cussed earlier, major gene resistance is primarily involved inETI whereas quantitative resistance involves basal defensestriggered by PTI, recognizing that there are considerable over-laps in the mechanisms triggered by ETI and PTI. Under strongdirectional selection, as in the case of major gene resistance,one or a few adapted pathogen strains will predominate thepathogen population, leading to severe epidemics. However,selection imposed by quantitative resistance is predicted to beless, reducing the pressure on pathogen population to evolvetoward high aggressiveness. In agronomic terms, major generesistance provides a ‘clean’ crop but with uncertainty about itsstability. Quantitative resistance, however, allows some level ofdisease development but offers stability. Unlike major R genesthat can be dramatically overcome by simple mutations ofmajor genes in the pathogen, quantitative resistance is pre-dicted to be ‘eroded’ over time through gradual changes ofpathogenicity genes to counteract the defense mechanismsimposed by the host (McDonald and Linde, 2002; Lannou,2012). Finding the right combination of major and quantita-tive resistance to provide effective and potentially durableresistance is the goal of many plant breeding programs.

Pathogen Fitness Penalty as a Predictor of R Gene Durability

More than 50 years ago, Vanderplank (1963) proposed that apathogen with unnecessary virulence has lower parasitic fitness

on the host without the corresponding resistance. Intuitively,accumulation of mutations in avirulence effector genes toavoid recognition by major resistance genes would reach apoint to reduce the overall fitness of the pathogen population.The fitness penalty concept is useful in that it suggests practicalapplications. In a simple case, if an avirulence gene codes for aproduct with important functions other than being a target ofrecognition by the host, a loss-of-function mutation would bedisadvantageous to the pathogen. It follows that measuringthe fitness penalty of mutation from avirulence to virulencecan provide a predictor of the effectiveness of the corres-ponding R genes, which collectively (as in a gene pyramid)result in durability of resistance (Leach et al., 2001). Althoughthere are pathosystems that seem to follow this general ‘rule,’for example, bacterial blight of rice (Vera Cruz et al., 2000),there are cases where a pathogen carrying unnecessary viru-lence does not exhibit lower parasitic fitness. For example,Chen (2005) studied the virulence spectrum of Pucciniastriiformis f. sp. tritici and Puccinia striiformis f. sp. hordei, twoclosely related pathogens, and noted that races of P. striiformisf. sp. tritici with wide virulence still dominated the population.In contrast, P. striiformis f. sp. hordei races with narrow viru-lence tended to predominate, as predicted by the fitness pen-alty hypothesis.

The long history of coevolution between the pathogen andhost would guarantee that the pathogen has evolved multiplemechanisms to compensate the fitness penalty caused bymutation of a single avirulence effector gene. One scenario isthat the pathogen can have multiple copies of related effectorgenes that provide the necessary functions. Secondary mu-tations at different loci may compensate for the primaryfunction of the first mutated gene. Thus, understanding thebiology of changes from avirulence to virulence is essential toeffectively apply the fitness penalty concept in managingdiseases.

With advances in knowledge of the genetic and molecularbasis of avirulence effector genes (Win et al., 2012), there arenow more tools to test the fitness hypothesis. For example, inthe blast fungus M. oryzae, 15 Avr genes have been identifiedand isolated (reviewed by Liu et al., 2013). By genome se-quencing, a further 851 genes in M. oryzae are predicted toproduce effector proteins (Chen et al., 2013). Similarly, withlarge repertoires of confirmed and predicted effector genes, it isnow possible to genetically inactivate avirulence effector genesindividually or in combinations and measure whether theirfitness attributes, such as reproductive rate (fungal spore pro-duction, bacterial multiplication), latent periods, and infectionefficiency under laboratory or greenhouse settings. A caveat ofthis approach is that these standard fitness attributes may notbe the only ones that are important in the natural environ-ment where the pathogen has to survive and compete in thepresence of the host and under harsh environments.

An alternative and complementary approach would be toconduct field survey studies to test the association of aviru-lence effector genes in natural populations. For known effectorgenes, it is possible to test if avirulence gene combinationsexist in random or significantly deviate from random inthe natural populations. If some combinations occur muchless frequently than expected, it would suggest that thecorresponding R gene combinations are more effective. By

370 Plant Disease and Resistance

monitoring the frequency of avirulence gene combinations, itmay be possible to reveal the R gene combinations that aremore effective.

The approach of testing gene associations for the wholepathogen genome, including genes for effectors as well asquantitative pathogenicity in the pathogen, can be generalizedby applying genome sequencing to characterize pathogenpopulations. By combining sequence and pathogenic attributes,genome-wide association studies (GWAS) can be done com-parable to what has been practiced in humans, animals, andplants. Several pathosystems, such as cereal rusts, rice blast andbacterial blight, and potato late blight are particularly amenablefor applying GWAS, considering their global importance. Thealarming spread of the stem rust strain Ug99 since its detectionin 1999 in Uganda (Singh et al., 2011) would present aninteresting case to examine genome-wide changes of the newstrains spreading over a broad geographic region.

Combining Major R Genes and QTL

Despite the concerns of ‘breakdown’ and ‘erosion’ of diseaseresistance, there are examples where a combination of major Rgenes and QTL provide stability of resistance in a farmer's field.Liu et al. (2009) dissected the genetic basis of resistance in arice variety Shan-Huang-Zhan number 2 (SHZ-2) that has areputation of exhibiting durable resistance to rice blast inSouth China. SHZ-2 has multiple major R genes and QTL.Some of the R genes are in clusters rich in NBS-LRR genes (Liuet al., 2013). SHZ-2-derived lines have been tested in diseasehot spots and continue to show stable resistance for more than10 cropping seasons (Manosalva et al., 2009). Owing to itsperformance and the known underlying genetics, SHZ-2 hasbeen used as a donor of blast resistance in breeding programsin Southeast Asia.

There are also examples of atypical R genes providingeffective disease control. A classic example is the recessive genemlo for barley resistance against powdery mildew (B. graminis f.sp. hordei (Jørgensen, 1992). The wild-type Mlo locus encodesa seven-transmembrane protein, which functions as a negativeregulator of resistance to powdery mildew and could have abroad role in regulating resistance to biotic and abiotic stress(Piffanelli et al., 2002). Since 1979, barley varieties carryingmlo resistance have been shown to be effective over large areas,satisfying the criteria of ‘durable resistance’ (Lyngkjær andOstrergård, 1998). More recently, a recessive gene conferringblast resistance in rice was isolated and characterized. In con-trast to the majority of blast resistance genes (Pi genes), whichencode NB-LRR proteins, pi21 encodes a proline-rich protein(Fukuoka et al., 2009). The pi21 recessive mutation is associ-ated with durable resistance to blast in the upland rice grownin Japan. However, the area planted to varieties carrying pi21 isrelatively small. The effectiveness of pi21 needs to be tested invarieties planted widely in intensive production system. Re-gardless, pi21 is a welcome addition to the pool of resistancegenes that are not NB-LRR types.

Another successful case of achieving durable resistance isthe use of high-temperature adult plant (HTAP) resistance tomanage stripe rust of wheat (Xu et al., 2013). The effectivenessof this type of resistance depends on the age of the plant and

high temperatures. Although used to control stripe rust formore than 60 years in the US, the genetic mechanisms ofHTAP resistance were recently revealed through the character-ization of the HTAP gene Yr36 (Fu et al., 2009). Yr36 isupregulated by high temperature, explaining the phenotypicexpression. In contrast to most NB-LRR genes for strongETI-type resistance, HTAP resistance provides partial butstable resistance against stripe rust over time.

Plant Diversity to Manage Disease

The benefits of using plant diversity to manage diseases orenhance crop performance are generally recognized. However,there is much debate in the approaches of how to effectivelydeploy genetic diversity in modern agricultural systems. Di-versity can be deployed at a single genotype level, or diversitycould be used at the population level in a plant community.

Many major crop breeding programs have introduced moregenetic diversity into the crops. For example, the ‘GreenRevolution’ for rice production began with the release of thefirst semidwarf rice variety IR8 in the mid-1960s. IR8 has onlythree landraces in its pedigree. Though breeding efforts havefocused on improving disease and pest resistance and grainquality, diversity was systematically incorporated into modernrice varieties derived from IR8 (Peng et al., 2008). In contrastto IR8, the pedigree of the modern variety IR64, released in themid-1980s, includes 20 landraces. IR64 is grown over millionsof hectares in tropical Asia, partly because it has shown goodresistance to rice blast for more than two decades since itsrelease. The accumulation of diverse genes contributes to thestability of disease resistance observed in IR64. Thus, using abroad genetic base and practicing appropriate selection canplay a key role in developing disease-resistant varieties.

Multilines and varietal mixturesBesides combining diverse genes in a single genotype, indi-vidual genes can be used separately in time and space. Thebasic principle of having different host genotypes in a field isto reduce the selection pressure toward more virulence in thepathogen populations. Multilines carrying up to 10 individualresistance genes are being used for controlling crown rust inoats, and are currently being used to manage rice blast in someareas of Japan (Abe, 2004). In practical breeding, multilines fita specific niche where resistance genes are added to a singlegenetic background to control disease. A main limitation ofthe multiline strategy is that much time and effort is needed toproduce near-isogenic lines with individual resistance genes.Very often, by the time near-isogenic lines are produced, theirother agronomic attributes are surpassed by other improvedvarieties. Wolfe (1985) advocated the use of varietal mixtures,a strategy that uses a mixture of varieties that are agronomic-ally homogeneous but genetically diverse with respect to dis-ease-resistance genes. The system is expected to stabilize theselection on the pathogen population. This strategy alleviatesthe need to produce isogenic lines and captures the comple-mentary agronomic attributes provided by multiple varieties.

InterplantingInterplanting resistant and susceptible varieties in differentratios is another strategy that capitalizes on diversity to control

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disease. This strategy was deployed to control rice blast diseasein a large-scale experiment in the Yunnan province of China(Zhu et al., 2000). Disease was reduced by 94% in the inter-planted plots compared with the monoculture plots. In thisexperiment, the susceptible was glutinous rice, which is 20 cmtaller than the resistant variety (Figure 6(a)). The height dif-ference may alter the microclimate of the canopy to becomeless conducive to disease development. Owing to the successof the interplanting experiment, and because glutinous rice hasa high market value, the interplanting strategy was adopted inmore than a million hectares of rice production (Figure 6(b)).Although interplanting may not be applicable to all crops andcropping systems, its success raised awareness of the import-ance of plant diversity for managing diseases.

Other Disease Control Strategies

Plant diseases cannot always be controlled by resistance. Re-sistance genes to a specific pathogen may not be availablein certain plants, or the suite of quantitative resistance genes insome plants may not provide a sufficient level of control. Inother cases, resistance genes may be difficult to incorporate (asin many woody perennials) or they may be linked to agro-nomically unsuitable traits. Therefore, other managementstrategies are needed to suppress pathogen populations anddisease development, sometimes even where resistance is theprimary means of controlling disease. Some diseases can beavoided by growing crops in regions that are not conducive todisease development. For example, many vegetable cropsgrown for seed are produced in arid regions of the western US,where low rainfall and a lack of extended leaf wetness neces-sary for infection inhibits foliar and seed pathogens. Plantpathogens may be excluded during a growing season by usingpathogen-free seed or propagative parts. Heat treatment andmeristem tip culturing are used to rid plants of viruses and hotwater treatments can disinfest seeds of surface contaminatingbacterial pathogens.

(a) (b)

Figure 6 Interplanting of glutinous and hybrid rice to avoid rice blast diseais 20 cm shorter than the blast-resistant hybrid rice (back). (b) Alteration ofrice was very effective at reducing blast disease on the glutinous rice. Photo

Once introduced into an area, pathogens (other than bio-trophs) can rarely be eradicated, but their populations can bereduced by certain cultural practices. Crop rotation is an ex-cellent method of reducing inoculum levels of some patho-gens that exhibit host specificity. Plowing pathogen-infestedplant residue into the soil at the end of the season hastens itsdecomposition and may reduce populations of pathogens thatare not good soil inhabitants. Although the practice of reducedtillage has been widely adopted by farmers to prevent soilerosion and to conserve soil moisture, it may have the un-desirable consequence of enhancing pathogen survival in cropdebris. Goss's wilt, a bacterial disease of corn, has recentlyincreased in severity in the Great Plains of the US in partbecause of widespread adoption of reduced tillage practicesand a lack of crop rotation.

Many bacterial, fungal, and oomycete diseases are man-aged by chemical applications. Copper-based products, andto a much lesser extent antibiotics (streptomycin sulfate andtetracycline), are used for bacterial diseases whereas a broadarray of fungicides with varying modes of biochemical actioncontrol oomycetes and fungi (see http://www.frac.info/publication/publication.htm). Fungicides are generally clas-sified as protectants (also called contacts) or systemics. Pro-tectants are not absorbed and redistributed but instead forma protective barrier on the plant surface. They, for the mostpart, affect multiple biochemical pathways in pathogensand are not prone to resistance problems. Some systemicfungicides are absorbed and move only in the leaf on whichthey were applied; others move acropetally in the xylem.Only the phosphonate fungicides are capable of acropetaland basipetal movement. Most systemic fungicides targetspecific enzymes in fungal or oomycete biochemical path-ways and are therefore at a higher risk for fungicide resistancedue to selection pressure in the pathogens. For example,there are numerous cases where mutations in the demethy-lase gene of fungal pathogens render them less sensitiveto demethylation-inhibiting fungicides. Fungicide resistanceis a major concern, and strategies such as avoiding multiple

se in Yunnan, China. (a) Blast-susceptible glutinous rice (foreground)four rows of glutinous (short) rice with one row of the hybrid (tall)s courtesy of the International Rice Research Institute.

372 Plant Disease and Resistance

applications of the same fungicide during the growing seasonor mixing or rotating different classes of fungicides have beenrecommended.

Concluding Perspectives

Much progress has been made in understanding the molecularevolution of plants and pathogens, and the integration of thisinformation into crop improvement programs or for diseasemanagement is ensuring sustainable crop production for theimmediate future. Still, the functions for very few pathogeneffectors are known, and often these are only in model sys-tems. Our knowledge is limited on how plant defense re-sponses are differentially regulated or modulated in thespectrum from PTI to ETI, and how this regulation can bemanipulated for better disease control. As an example, therelevance of epigenetic controls on plant disease and im-munity is only just beginning to be addressed (Alvarez et al.,2010).

Most of our knowledge has been gained by studyingplant–microbe interactions in growth chambers and green-houses, and rarely, in fields under conditions typical fora given disease. As a result, little is known about the inter-actions of environment with disease development, PTI, orETI. The trend toward systems approaches to study howplant and pathogen genomes, metabolomes, and physiologyare affected by interactions with each other and with en-vironmental changes is a promising start, but frequentlythey are limited to growth chamber or greenhouse studies.The design of proactive disease management strategies forglobally important diseases will require new experimentalstrategies. One possibility is to establish ‘biostations’ wheredisease can be assessed using a common set of genetic mate-rials over different geographic areas with a range of climatescenarios.

Evolving new, improved, or cheaper technologies, such asgenomics, proteomics, metabolomics, and high throughputphenotyping capacity at the field level, will provide deeperinsights into plant disease and resistance. The integration ofthe molecular, organismal, and systems-level informationgained from using these approaches will ultimately allowimprovement of disease management strategies to includebroad-spectrum and durable disease resistance.

Acknowledgments

The authors thank Jillian Lang, Lindsay Triplett, and TonyCampillo for reviewing the manuscript, and Samuel VazquezIII and Tony Campillo for developing the illustrations.

See also: Biodiversity: Conserving Biodiversity in Agroecosystems.Biotechnology: Plant Protection. Breeding: Plants, Modern. ClimateChange and Plant Disease. Emerging Plant Diseases. EmergingZoonoses in Domesticated Livestock of Southeast Asia. Genomics:Plant Genetic Improvement

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Relevant Website

http://www.apsnet.org/edcenter/intropp/PathogenGroups/Pages/default.aspxAmerican Phytopathological Society.