Numerous reviews and reports have documented the global challenges to feeding the growing human population . More people living longer, healthier, more affluent lives will put increased pressure on food production systems. Climate change is predicted to further exacerbate challenges to food production. Furthermore, insufficient food is a major causal factor inciting civil strife. The large investments being made in human health will be of little benefit if people are undernourished. Sustainable increased food production requires both technical and organizational advances. Major, sustained investments in foundational and translational agricultural research are needed. Pathogens, pests, and weeds cause large pre- and post-harvest losses, while beneficial symbionts provide the opportunity to improve yield stability, quantity, and quality . Support for this area of agricultural research is therefore both justified and urgent. Forty researchers from the United States and United Kingdom gathered at the British Embassy in Washington, D.C. for two days in September, 2016, to explore research opportunities focused on the understanding of interactions of plants with pathogens, pests, and weeds as well as with symbionts and other beneficial organisms in the phytobiome. Participants discussed the potential of foundational knowledge generated by such research to enhance the health of plants economically important for agriculture, pipp horticulture racks cost horticulture or forestry in the United Kingdom, United States, and globally.
Research to understand and ameliorate the emergence and spread of resistance of pathogens, pests or weeds to control measures was discussed. In addition, the workshop considered the potential transformative impacts of new technologies, such as high throughput sequencing, synthetic biology, genome editing, and cryo-electron microscopy , on plant health research. This white paper describes the product of these deliberations. Breeding crops for resistance to pests and diseases has tended to be a lower priority than breeding for yield and quality when control chemicals have been available. However, the availability such chemical interventions as well as their efficacies are now becoming limited due to changes in legislation and the evolution of pathogen/pest resistance to control chemicals. Consequently, established cropping systems are highly vulnerable to disruption by adapted pests, weeds, and diseases and there is a pressing need for new interventions . For example, management of insect pests has become much more challenging after recent restrictions on neonicotinoid and organophosphate insecticides in the UK. There are significant problems with herbicide resistant weeds such as black grass and fungicide resistant pathogens such as Septoria leaf blotch. Roundup resistant weeds have emerged in the United States, challenging soil-conservation measures dependent on minimum tillage. Similarly, new strategies for nematode control become essential as soilacting nematicides are phased out.
Durable disease resistance to pests or pathogens can be defined as “resistance that has remained effective over long periods of widespread agricultural use” . This has been a continual and often elusive goal in many disease control programs for decades; however, we now have opportunities to provide more durable resistance based on foundational knowledge and recent technological advances. Long-standing questions as to the molecular and genetic basis of specificity between hosts and pathogens/pests are being answered in increasing detail . There is still much more to be discovered as to how the plant immune system functions and how it can be predictably deployed with minimal side effects on yield and other important agronomic traits. Nevertheless, there is now sufficient foundational knowledge to develop and implement strategies that are likely to provide durable control of pathogens, pests, and weeds as well as to improve yields and yield stability . Although less is known, advances are also being made in the understanding of beneficial biotic interactions, with concomitant opportunities for improving plant health . Many of the recent advances have been enabled by technological innovations and further high impact developments are imminent. In particular, the ever-decreasing cost and increasing output of DNA 5 / Molecular Plant-Microbe Interactions sequencing technologies now enables the genome sequencing of multiple genotypes of many model and non-model plants as well as microbes, pests, weeds and whole communities associated with plants or in soils. Combined with increasing computational resources, these sequences are allowing the characterization of genomic variation, gene expression patterns, the identification of candidate genes for resistance, and pathogen population genetics.
Proteomics, functional screens, ultra-high resolution light microscopy, and cryo-EM are revealing the molecular events involved in resistance and susceptibility . Synthetic biology provides multiple opportunities and approaches for redesigning plant responses, which may allow for more precise control of the plant’s ability to sense and respond to pathogens . Genome editing technologies are greatly enhancing functional investigations and deployment of useful genes . Both synthetic biology and genome editing also provide the opportunity for generating useful genetic variation in numerous crop plants . This workshop report considers the opportunities for advances in foundational research and then the issues involved in translating this knowledge to enhance plant health, particularly in less developed countries.As defined above, durable resistance is an empirical, retrospective attribute that has no single inherent basis. Pathogen and pest populations are highly variable and are evolutionarily driven to overcome plant resistance. Consequently, predicting which new disease resistance genes may be durable is challenging. While some resistance genes are rapidly rendered ineffective by changes in the pathogen, others have proved to be durable. for example, Rps1k in soybean , Xa21 in rice , and H1 in potato for resistance to cyst nematode . Knowledge is needed to implement strategies that maximize evolutionary hurdles for the pathogen to become virulent. Therefore, identification of resistance genes that may prove to be durable requires a comprehensive understanding of pathogen biology, population structure, epidemiology, mechanisms of genetic and epigenetic variation as well as knowledge of plant immune system recognition and signaling to provide predictive outcomes upon manipulation. While it is difficult to predict durability of disease resistance, it is easier to predict, and therefore avoid or minimize, a likely lack of durability based on analyses of pathogen populations. Breeding programs would benefit from avoiding or minimizing the use of narrow-spectrum R genes that are already ineffective against local pathogen races. It is therefore important to define the pathogen/pest component recognized by any to-be-deployed R gene to avoid “pathogen-blind” resistance breeding . Analyzing the durability of resistance genes, including those incorporated into elite germplasm, at the center of pathogen diversity can help predict durability. For R genes that target effectors and for other classes of potential resistance genes that may target other aspects of pathogen biology, it is essential to determine the extent to which the pathogen population is able to evade the targeting of pathogen component and to suppress the defense mechanisms associated with R genes. Even if an R gene is identified that the pathogen cannot be observed to evade or suppress, it is desirable to examine the ability of the pathogen to acquire new genetic or epigenetic variations that enable the pathogen to overcome resistance. R genes that recognize the most conserved and presumably indispensable effectors should be prioritized if it can be ascertained that recognition of such effectors is not masked by other effectors or abrogated by second site genetic variation in the pathogen. Once effective disease R genes have been identified, they should not be deployed individually because widespread plantings will select for variants capable of overcoming single R genes. One approach is to pyramid different R genes; if possible representing different classes , should be pyramided together. This is beginning to occur e.g. soybean–Phytophthora sojae , rice-bacterial blight , pipp racking system and potato-P. infestans interactions. Challenges to implementing this obvious strategy include the efficient identification of sufficient numbers of R genes and ensuring preservation of gene pyramids during breeding that involves crosses. Ideally, pyramids comprised of different combinations of R genes should be deployed in order to diversify selection on the pathogen population in space and time. Furthermore, it is necessary to monitor for any breakdown of individual R genes so that new stacks can be assembled for effective disease control. The use of genome editing to generate stacks of R genes at single chromosomal locations will greatly facilitate the stable deployment of multiple R genes; however, while generating loss of function alleles is now facile, techniques for allele replacements and gene insertions using genome editing need improvement .
Additional layers of disease resistance can also be combined with stacks of PRR and NLR genes. For example, endogenous chemistries may be used to boost signaling, promote the association of beneficial microbes that confer induced systemic resistance, and restrict invading pathogens/pests . There may also be opportunities to amplify responses to help create more durable resistance. Plants employ positive amplification loops mediated in part by membrane proteins that associate with PRRs and endogenous ligand/receptor complexes . The extent to which these associated proteins are limiting and could be manipulated to boost resistance signaling outputs is not known. However, lab experiments with model plants overexpressing some of these components have yielded promising results in priming for stronger immune responses . Both mechanistic studies with tractable model pathosystems and translational trials with crops are needed to determine how well this approach will work. It will also be informative to test whether disease resistance responses mediated by PRR and NLR genes can be reprogramed or amplified using synthetic transcription factors based on engineered TAL effectors or CRISPR/Cas9-based transcriptional activators. Conversely, engineering suppressors of negative immune regulators could also be beneficial for tipping the balance towards plant resistance .Plant defense against pathogens is activated upon pathogen/pest recognition, most commonly via cell-surface PRRs that recognize apoplastic pathogen-derived PAMPs or via intracellular NLR receptors that directly or indirectly recognize pathogen/pest effectors delivered into host cells . Plant breeders have long recruited diverse R genes, which typically encode NLRs, although some encode PRRs or other types of proteins. Elevating disease resistance of crops requires the identification and recruitment of large numbers of diverse resistance genes. This diversity can have multiple sources. Wild relatives of crops are potentially abundant sources of R genes. Most plants carry 100s of NLR-encoding genes that exhibit extensive diversity . Using sequence capture to enrich for NLR genes prior to genome sequencing enables cost-effective interrogation of sequence diversity . Combined with genetic analysis, this can greatly accelerate discovery and recruitment of new recognition specificities . Species outside the primary and secondary gene pools are also potential sources of NLR genes. The discovery of widespread NLR gene pairs, one member of which carries an integrated domain that mimics a host component targeted by pathogen/pest effectors, and the observation that such gene pairs often work when transformed into another plant family, suggests that many such pairs may provide resistance when transferred between distantly related taxa . For example, rice is famously resistant to all rusts; perhaps some of its gene pairs with integrated domains would confer rust resistance if transferred into wheat. The presence of paired NLRs, one with an integrated effector decoy domain , has raised the prospect of replacing one integrated domain with another. For example, removing the Arabidopsis RRS1 WRKY domain and replacing it with another domain targeted by other effectors may be fruitful. However, since such domains are likely to have a role in maintaining the receptor complex in the inactive state prior to interaction with an effector, substitution may perturb intramolecular interactions and result in constitutive activation of defense. It is therefore necessary to better understand the functioning of a diverse set of such NLR pairs and to screen to find pairs that are amenable to substitution of integrated effector decoy domains while retaining function.Engineered R genes have been a long-standing aspiration of researchers in the field and could be a useful source of additional variation. We have not currently reached the point where novel NLRs can be designed to recognize any effector. To be able to design novel recognition capabilities, we need better understanding of the basic mechanisms of NLR protein function. This will be facilitated by structural insights gained by recent advances in biophysical techniques such as cryo-EM . NLRs have two important functions: they must remain “off” and only turn “on” in the presence of a cognate effector. One challenge is that modifications often result in constitutive activity of an engineered NLR; so it is crucial to understand intra-protein domain interactions that inhibit NLR activation prior to effector recognition.