Host plant resistance is an ecologically sound way to manage crop diseases. Approaches to genetic crop improvement span an ever-expanding range of techniques, from simple phenotypic selection through techniques of genome editing (discussed below). Conventional breeding can often produce adequate levels of disease control, and we can expect that all breeding techniques will continue to play important roles indefinitely. However, when conventional breeding and other management options are inadequate, or when linkage drag limits the usefulness of conventionally derived traits, GE offers alternatives. As examples of diseases for which GE presently appears to represent the only acceptable disease management in culturally or economically important crops, consider papaya ring spot in Hawaii [ 21 ], cassava brown streak disease in Africa [ 22 ], and citrus greening in Florida [ 23 25 ]. The loss of important crops to infectious diseases is completely contrary to the principles of sustainability. Thus GE can make it possible to save crops in the face of virulent disease epidemics, crops that may be integral to food security, sources of farmer income, or culturally important dietary components. In addition, GE can make it possible to reduce farmers’ dependence on pest-control products, with undeniable benefits for sustainability. The deployment of Cry proteins for insect control serves as an excellent example of how a GE approach can contribute to sustainability through reduced application of pesticides, resulting in fewer pesticide poisonings, increased biodiversity, and increased biocontrol services [ 26 35 ]. Certainly other examples seem eminently possible as we employ additional GE traits for pest and disease control. One must also acknowledge that Cry proteins serve as an example of how overreliance on single genetic traits can allow for pest evolution to overcome such a trait [ 36 39 ]. In fact, this presents another justification for taking full advantage of the opportunities offered by GE. Selection pressure towards virulence is a “given” whenever managing pests and diseases. Breeders therefore need a wide array of genetic options in order to diversify the arsenal of resistance traits deployed in crops, thereby reducing this selection pressure. As will be apparent in this review, GE is greatly expanding the genetic options for disease control available to breeders.

Practices for managing crop diseases fall into four general categories: host plant resistance, cultural practices, biological control, and chemical control. If pesticide use is to be reduced, it will be necessary to depend more on the remaining three approaches. Cultural practices (examples include crop rotation, polyculture, manipulation of planting date,) certainly play a central role in disease management [ 20 ]. However, control achieved via cultural practices is sometimes inadequate, impractical, or economically nonviable. Natural biological control of plant pathogens is a fact of life, as it undoubtedly occurs at some level in all agricultural soils. However, there are many destructive diseases for which years of research have failed to lead to practical, commercially viable biocontrol options. Thus, in order to reduce the need for pesticides while still attaining acceptable yields, it will be critical to judiciously take full advantage of plant genetics. After all, if farmers are to reduce pesticide use, they must have viable alternatives for controlling diseases.

While pesticides have done much to contribute to food security and food sovereignty for many millions of people worldwide, pest and disease control through the regular use of pesticides is neither desirable nor sustainable over the long term. Pesticide use raises significant concerns over impacts on health [ 2 7 ] and the environment [ 8 12 ]. Furthermore, we cannot address the challenges to sustainability posed by synthetic pesticides by simply switching to the application of natural pesticides, because the same concerns apply to them [ 12 19 ].

Disease management practices can contribute to sustainability by protecting crop yields, maintaining and improving profitability for crop producers, reducing losses along the distribution chain, and reducing the negative environmental impacts of diseases and their management. Crop disease management supports sustainability goals through contributions to food security, food safety, and food sovereignty for producers and consumers alike [ 1 ].

2. Strategies for Engineering Resistance

There is a wide variety of published GE strategies for engineering disease resistance, and ongoing research and expanding genetic resources [ 40 ] are likely to lead to additional strategies. Furthermore, within most of those strategies, diverse applications are conceivable. Taken together, these suggest that GE presents a vast pool of genetic possibilities for future generations. This will allow breeding for disease resistance to remain highly dynamic in the face of pathogen adaptation towards virulence on resistant cultivars.

In contrast to typical pesticides, GE mechanisms are often designed to have selective efficacy against particular target pathogens. High target selectivity is advantageous, in that it minimizes health concerns for consumers as well as risks to non-target biota in and around agroecosystems. However, the drawback is that one GE trait is unlikely to protect against the full spectrum of damaging pathogens on a given crop—which is also true of many conventional genes for disease resistance.

While it is difficult to foretell which GE strategies will have the greatest impact on crop disease control in the coming decades, all those described below hold promise and, in the author’s opinion, merit continued research attention. Some have demonstrated proof-of-concept, while others have been evaluated in the field and, in certain cases, introgressed into commercially viable varieties. All strategies described below take advantage of—and in most cases, mimic—processes that occur in Nature.

2.1. Boosting Plant Recognition of Infection 42,45,46, Plants have evolved to trigger basal defenses upon recognition of certain conserved molecules of an invading pathogen. These molecules, which are highly conserved evolutionarily and are metabolically important for the pathogen, are referred to as pathogen-associated molecular patterns (PAMPs) [ 41 43 ]. Receptor molecules in the host membrane recognize PAMPs and elicit a natural defense response called PAMP-tiggered immunity (PTI). PAMP receptor molecules differ among plant species. Thus, genes encoding PAMP receptors from crops and other plants can be transformed into other crops, expanding the range of pathogen molecules that trigger PTI in the latter [ 43 ]. A gene encoding a PAMP receptor does not introduce a novel defense mechanism into the plant. The transferred PAMP receptor merely allows the receiving plant to recognize infection, so it can respond with its own, natural immune system. Increased resistance has been obtained using this strategy against a range of bacterial diseases in both monocots and dicots [ 44 47 ]. An important question is whether the transfer of PAMP receptors among plant species would increase the risk of selection towards wider pathogen host ranges. Since PAMPs are highly conserved molecules that are metabolically important for the pathogen [ 44 ], rapid evolution of these molecules is unlikely. Rational deployment strategies, such as those described in Section 3 , can also reduce this risk.

2.2. Mining R Genes 48, R protein) which detects the presence or activity of particular pathogen effectors, restoring a resistance response called effector-triggered immunity or effector-triggered defense [42,48, R protein. This coevolutionary, gene-for-gene, “molecular arms race” [ R proteins has yielded pools of R genes (resistance genes) useful in breeding crops for disease resistance [ PTI places strong selection pressure on pathogens to restore a virulent host-parasite interaction. According to the prevailing model of disease resistance, pathogens produce one or more effector molecules which enhance virulence, resulting in effector-triggered susceptibility (ETS) [ 42 49 ]. Over evolutionary time scales, plants respond to ETS by producing an intracellular receptor (protein) which detects the presence or activity of particular pathogen effectors, restoring a resistance response called effector-triggered immunity or effector-triggered defense [ 41 50 ]. In the face of a renewed defense response in the host, a pathogen may eventually evolve to produce a new effector to restore compatibility. In turn, the plant may evolve a newprotein. This coevolutionary, gene-for-gene, “molecular arms race” [ 48 50 ] between pathogen effectors and their correspondingproteins has yielded pools ofgenes (resistance genes) useful in breeding crops for disease resistance [ 42 ]. : engineering only with genetics obtained from a crop’s sexually compatible gene pool [51, One way GE can contribute to resistance breeding is through cisgenicsengineering only with genetics obtained from a crop’s sexually compatible gene pool [ 51 ]. Conventional breeding techniques are often suitable for introgressing cisgenes into new varieties, in which case GE is unnecessary. However, in some crops, such as potato, grape, banana, apple, and strawberry, conventional breeding is exceptionally difficult or time-consuming. For crops such as these, cisgenes can be transferred via GE [ 43 52 ], resulting in a genetic outcome that would be conceivable—although perhaps impractical—by conventional means. A major advantage of cisgenics over conventional breeding is that it circumvents linkage drag [ 43 51 ]. R genes, even from plants that are not part of a crop’s normal breeding pool. For example, in tomato, bacterial leaf spot, a highly destructive disease, was controlled in the field with a single R gene obtained from pepper [ R gene is expected to provide an alternative to the repeated use of foliar copper applications, benefiting both field workers and the environment [ R genes from related as well as unrelated plant species have been published for both monocots and dicots [55, R genes could be enhanced by engineering resistance based on recognition of effectors critical to pathogenicity [ For some plants, hybridization is difficult or impossible using current techniques. In such cases, GE offers an alternative for introgressinggenes, even from plants that are not part of a crop’s normal breeding pool. For example, in tomato, bacterial leaf spot, a highly destructive disease, was controlled in the field with a singlegene obtained from pepper [ 53 54 ]. Indeed, the level of control obtained was higher than that obtained by any conventional breeding approach. Thisgene is expected to provide an alternative to the repeated use of foliar copper applications, benefiting both field workers and the environment [ 54 ]. Other examples of “mining” ofgenes from related as well as unrelated plant species have been published for both monocots and dicots [ 47 56 ]. Recent research has also shown that it is possible to enhance disease resistance by modifying the target of a pathogen effector so that it recognizes other pathogen effectors [ 57 ]. For example, the target molecule of pathogen effector “A” can be modified (with modest edits) so that its product is activated (and thereby triggers a defense reaction) by another pathogen’s effector “B.” This creative approach provides new disease resistance traits while avoiding any transfer of genetic material. Durability ofgenes could be enhanced by engineering resistance based on recognition of effectors critical to pathogenicity [ 57 ]. It is worth recalling that R genes do not code for new biochemical pathways; they merely code for receptor molecules. This allows the plant to recognize the presence of an invading pathogen, thereby taking advantage of their native, natural mechanisms of disease resistance. R genes is often not durable, because widespread deployment of an R genes selects for pathogen strains capable of overcoming it [58,59, R genes from plants outside of a crop’s breeding pool may be especially important for sustainability, in that it opens a vast pool of R genes potentially useful for breeding. Resistance conferred by individualgenes is often not durable, because widespread deployment of angenes selects for pathogen strains capable of overcoming it [ 42 60 ]. The ability to “mine”genes from plants outside of a crop’s breeding pool may be especially important for sustainability, in that it opens a vast pool ofgenes potentially useful for breeding.

2.3. Upregulating Defense Pathways 63, Rhizoctonia solani (the cause of many diseases) and Magnaporthe oryzae (the cause of rice blast) [ Molecules involved in defense signaling, defense regulation, or other processes can be upregulated, boosting general defense responses. Such defenses include generation of reactive oxygen species, callose deposition, synthesis of pathogenesis-related (PR) proteins, and increased activation of systemic acquired resistance (SAR) [ 23 61 ]. As with the previously described strategies, this strategy takes advantage of the plant’s own natural immune system and does not introduce new metabolic pathways. This approach has been successful against bacterial pathogens attacking several host species [ 62 64 ], and it offers promising results for enhancing resistance to citrus greening [ 23 ], a disease of urgency for the citrus industry. Upregulation of defense pathways was also successful against destructive fungal pathogens, including(the cause of many diseases) and(the cause of rice blast) [ 61 65 ]. In both cases, resistance was achieved by expressing a native rice gene under the control of a constitutive promotor from maize, introducing neither a novel pathway nor a non-crop gene. It may eventually be possible to upregulate defense responses using native cisgenic promotors, avoiding the use of any DNA outside of the crop’s breeding pool.

2.4. Disarming Host Susceptibility Genes 68,69, Plants possess genes whose products are important in its normal physiology, but in some way also function to facilitate pathogen infection and colonization. These can be considered susceptibility genes [ 66 ]. (See the Supplemental Table 1 in [ 66 ] for a long list of examples.) Changes in such genes by natural means can result in increased disease resistance [ 47 67 ]. The same is true for GE-induced changes [ 66 70 ]. While we must remain aware that susceptibility genes may have pleiotropic effects, disarming susceptibility genes may hold promise for durable resistance for two reasons: first, in some pathosystems, many host factors contribute to host-parasite compatibility, offering many potential targets to disarm through very modest changes in DNA sequence; and second, overcoming a disarmed susceptibility gene requires the pathogen to gain a new function to replace the lost host factor it was exploiting. Gaining a new function is not likely to be easily accomplished [ 66 ]. Disarming susceptibility genes can be achieved without introducing a novel metabolic pathway or leaving exogenous DNA in the final product.

2.5. Producing Antimicrobial Compounds 72, Genes encoding antimicrobial compounds can be expressed in crop plants, resulting in restricted pathogen activity and, consequently, increased disease resistance. As a result of citrus greening, a highly destructive bacterial disease, the economic health and even survival of the Florida orange juice industry is uncertain [ 25 71 ]. Thus far, the only potentially viable, environmentally acceptable solution may be citrus trees that express antimicrobial peptides called defensins, produced by genes obtained from spinach [ 25 73 ]. Trichoderma species, fungal parasites of other fungi. Plants may be engineered to deliver pest-control substances that act in particular tissues or organs of multicellular, anatomically complex pathogens [ Resistance to diverse fungal diseases was obtained in grape and cotton when plants were transformed to constitutively produce chitin-degrading enzymes [ 74 75 ]. All of the diseases controlled in these studies were caused by fungi that contain chitin as an important component of their cell walls. The sources of the chitinase genes werespecies, fungal parasites of other fungi. Plants may be engineered to deliver pest-control substances that act in particular tissues or organs of multicellular, anatomically complex pathogens [ 76 ], which may have particular relevance to nematode control. in-vitro techniques of molecular evolution to broaden the range of molecular targets of such antimicrobials [ One advantage of transforming crops with genes for natural antimicrobial substances is that one can employtechniques of molecular evolution to broaden the range of molecular targets of such antimicrobials [ 77 ]. Such techniques potentially can be employed to reverse the buildup of pathogen resistance to the antimicrobial. Microorganisms could potentially serve as a source of many antimicrobial compounds, though public acceptance of transgenes from microorganisms is mixed [ 78 ]. In contrast to several strategies described in this review, this strategy does not take advantage of existing defense mechanisms; rather, it creates a new one.

2.6. Silencing Essential Pathogen Genes The presence of double-stranded RNA (dsRNA) in the cytoplasm of eukaryotic cells triggers the natural and targeted process of post-transcriptional gene silencing (RNA silencing, RNA interference, or RNAi) [ 79 ]. Through the use of genetic constructs with sequence identity to important pathogen genes (and, ideally, with little to no identity to mammalian genes), RNAi can be elicited in plants to silence such genes, resulting in reduced disease. In RNAi, no novel protein or biochemical pathway is created in the crop; the natural process of RNAi is invoked in order to silence a particular target gene in the pathogen. The papaya industry in Hawaii was saved by transforming papaya with the coat protein gene of papaya ringspot virus. This gene elicits RNAi against this highly destructive virus [ 21 80 ]. Such a GE application mimics cross-protection, a phenomenon in which symptoms due to severe strains of a virus can be reduced by prior infection by a mild strain. Cross-protection is a perfectly natural phenomenon. Unfortunately, implementing it for disease management has practical drawbacks [ 81 ], which is why transgenic coat-protein-mediated resistance was utilized against this devastating virus disease. While consumers may be hesitant to eat transgenic papaya containing a viral coat-protein gene, they may be surprised to know that they are eating complete virus particles in fruit harvested from non-transgenic, infected trees, including fruit from cross-protected trees. RNAi provides control of other destructive viruses of crops, including the viral complexes that attack cassava in East Africa [ 22 82 ], soybean [ 83 ], and summer squash [ 84 ], and others [ 47 85 ]. 87,88,89,90,93, Recent research clearly highlights the substantial potential which RNA silencing offers for management of diseases caused by biotrophic fungi, necrotrophic fungi, and oomycetes [ 86 91 ]. These studies report partial to complete control of diseases caused by several of the most important pathogens worldwide. Likewise, gene silencing holds much promise for pesticide-free nematode management [ 92 94 ]. Diverse pathogenicity genes in nematodes present many molecular targets [ 95 ], highlighting the promise RNA silencing holds for sustainable, long-term nematode management. Some success in RNAi-based insect control has been obtained by feeding insects dsRNA constructs that trigger RNAi [ 96 97 ]. Commercial products based on this technology are being pursued. Since foliar applications of small RNAs require no genetic changes in the plant, this technology may appeal to consumers for its “non-GMO” status. Of course, compared to genetic changes, there are sustainability costs (both economic and environmental) to the use of products that must be applied repeatedly and indefinitely.

2.7. Modifying Host Targets of Pathogenicity/Virulence Factors Certain plant pathogens produce molecules (virulence factors) that play a role in virulence by binding to host target molecules [ 98 ]. The molecular targets of these in the crop can be engineered so as to result in reduced binding, thereby increasing disease resistance [ 99 ]. Genetic modification of targets of pathogen virulence factors increases host resistance without introducing an exogenous biochemical pathway into the plant, and also can be achieved without transgene insertion.

2.8. Detoxifying Pathogen Toxins Cryphonectria parasitica , the cause of catastrophic epidemics of chestnut blight [ Pathogen-produced toxins can disrupt important biochemical processes of their hosts, thereby facilitating disease development [ 100 ]. In turn, plant resistance may be conferred by a host enzyme that inactivates a pathogen toxin, whether that enzyme is native [ 101 ] or the result of GE. As an example of the latter, the phytotoxin oxalic acid is central to pathogenicity of, the cause of catastrophic epidemics of chestnut blight [ 102 ]. Significantly less disease development was observed in American chestnut trees transformed with a wheat gene coding for the production of the degradative enzyme, oxalate oxidase [ 103 ]. As another example, a toxin-degrading enzyme encoded by a barley gene was transformed into wheat, resulting in resistance in the wheat to the highly destructive disease, Fusarium head blight [ 104 ]. In both examples, the gene constructs used included a viral promotor and a bacterial selectable marker, so in their present configuration, these GE crops clearly qualify as transgenic. However, these potential concerns may be addressed by employing native promotors derived from the engineered crop and marker-free transformation [ 85 ].

2.9. Engineering CRISPR/Cas Immune System 107,108, CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a prokaryotic defense system that targets the DNA of invading viruses and plasmids [ 105 106 ]. In this system, an endonuclease (commonly CRISPR associated protein 9, abbreviated Cas9) is directed to cut the invading DNA at a particular target, where the DNA sequence matches the sequence of an RNA guide strand (gRNA) associated with Cas9. Plants can be transformed to produce both Cas9 and a target-specific gRNA, in order to cleave a specified target of invading DNA. For example, a Cas9/gRNA complex can be engineered to target the replicating DNA of Geminiviruses, which are highly destructive to crops in tropical and subtropical climates [ 106 109 ]. Such an engineered Cas9/gRNA complex produces a sequence-specific, targeted immune response which can result in significant host resistance against a DNA virus. These laboratory-based results are exciting if they are reproduced in the field, since conventional breeding has not been universally successful against Geminiviruses [ 108 110 ]. A variety of viral genetic elements can be successfully targeted [ 106 108 ], which would confer long-term utility to this strategy. Crops engineered to express a CRISPR/Cas immune system are transgenic, containing DNA sequences which are bacterial and viral in origin (coding for Cas9 and gRNA, respectively), which may hamper public acceptance.