Cryo-EM is providing previously unobtainable, high-resolution structures of plant viruses and it holds promise for resolving intracellular macromolecular virus-associated complexes . Approaches such as RNA-seq, small RNA sequencing, metabolomics, and proteomics should facilitate dissection of molecular signatures that are altered in the vector during virus acquisition and in the host upon infection. Furthermore, understanding of vector and host factors that facilitate virus replication and vector-mediated immune response on the virus is fundamental to engineering resistance to vector-transmitted plant viruses.Post-transcriptional gene silencing or RNAi is fundamental to defense against RNA viruses. RNAi-mediated transgenic resistance strategies are effective against RNA viruses , but not DNA viruses, which present different challenges for control. CRISPR/Cas9 has recently been used to engineer resistance against DNA viruses ; additional editing strategies need to be evaluated, including modification of susceptibility factors as has been used against potyviruses . Since mixed infections by multiple viruses are common in field settings, CRISPR/Cas9-based approaches should be evaluated for the feasibility of engineering broad-spectrum resistance against multiple viruses. The control of weeds is rapidly emerging as a major challenge to sustainable agriculture due to the rapid evolution of herbicide resistance in both conventional and GM production systems .
The problem has been further compounded by both the loss of many types of herbicide through stricter regulation and the lack of research and development of new modes of action for herbicides; this situation is unlikely to improve over the coming decade. Herbicide resistance arises through two mechanisms. 1) Target site resistance , pipp shelving where the protein functions targeted by herbicides become insensitive to chemical disruption. This can arise through selection for genetic changes resulting either in reduced binding or in increased expression of the target. 2) Non-target site resistance , where the activity of herbicides in weed tissues is reduced to sublethal levels either by neutralizing the herbicide, or through metabolic responses that reduce chemical injury. Our understanding of both types of resistance, their plasticity and evolution, is currently constrained by the lack of genome information for major agronomic weeds. In the case of NTSR, we lack fundamental understanding of the multiple mechanisms associated with this complex quantitative trait. The opportunities for counteracting herbicide resistance can be broadly divided into developing strategies for the better use of existing chemical control measures, changing cultural practices, and developing new approaches to weed control based on new crop traits. In reality, durable weed control will likely require integration of all of these approaches.
Immediate opportunities will be built on foundational research in the biology of major weed species, including the application of the technologies now in place for functional genomics of crops such as genome sequencing, transformation, and editing. Studies should be aimed at understanding the mechanisms underpinning the plasticity of resistance and the molecular basis of NTSR. Outcomes would include better diagnostic and predictive tools for the stewardship of existing products and the identification of new targets for intervention such as ‘resistance-busting’ synergists . Changes in cultural practice, such as alterations in rotations and the use of cover crops as well as precision and robotic weed control, offer the most immediate opportunities for counteracting resistance; these will be best implemented through expanding training programs for agronomists and agricultural engineers. Public funding for field research programs to objectively test the efficacy of different approaches to weed control along with their life cycle analysis will be required to ensure rapid adoption. To date, the use of genetic improvement as a route to weed control has relied on developing resistance to specific herbicides in the crop, the most well-known example being Round-Up Ready technology. This approach was initially projected to be durable; however, it has not proven durable due to over-dependence on a single herbicide and the resulting selection on weeds to develop resistance.
Transformation of crops with new herbicide resistance genes still offers useful opportunities if used carefully in the field. For example, glyphosate-resistant wheat would be a very useful tool to counteract NTSR in wild grasses in Europe. In the longer term, the introduction of novel weed control traits into crops has great potential for future integrated management. There are multiple reports of weed-suppressive crop varieties. The underpinning mechanisms such as allelopathy, plant vigor, and nutrient use efficiency require greater foundational understanding prior to effective translation. Our advancing knowledge of plant pathology may also provide new strategies for weed control, including new herbicides based on microbial pathogens or mechanisms used by them, matched with crops bred to be resistant to these biologicals.Control strategies developed for pathogens are also relevant to controlling weeds that directly parasitize other plants. Parasitic weeds including Striga in sub-Saharan Africa and Orobanche spp. in the Mediterranean can significantly limit crop yields both in the tropics and temperate regions. Traditionally, chemical control of parasitic weeds has been difficult because parasitic plant lifecycles are complex and the host and parasite have similar physiologies . In addition, resistant germplasm has been difficult to develop. This makes introgression of R genes to current commercially desirable crop varieties now possible and hence a priority for future research and control efforts. Host-induced gene silencing targeted against vital parasite genes should be explored as a control strategy where transgenic crops will be accepted .The implementation of any control strategy imposes selection pressures to overcome it. Recent disease outbreaks in plants have been associated with expansions of pathogen geographic distribution and increased virulence of known pathogens, such as in the European outbreak of ash dieback and wheat stem rust in Africa and the Middle East . The scale and frequency of emerging diseases have increased with the globalization and industrialization of food production systems . In the past it has been difficult to monitor for breakdowns in control. Current surveillance and diagnostic systems are reliant on lengthy and costly in-lab processes, such as PCR or ELISA based protocols. Genomic-based surveillance and diagnostic tools are still in their infancy; however, advances in remote sensing and sequencing technologies and increases in computational power are allowing unprecedented opportunities for real-time assessment of pathogen, pest, weed, pipp mobile systems and symbiont populations and the rapid implementation of interventions. Following the influenza paradigm of continual adjustment of the intervention, deployment of control measures should be driven by knowledge of the variability and evolution of pathogen/pest populations . High throughput sequencing is revolutionizing population genetics with further advances on the near horizon. This has stimulated the development of genomic-based surveillance techniques. One example is the development of “field pathogenomics” for surveillance of pathogen populations . This can be based on high-resolution transcriptome data acquired directly from field-collected samples of infected plant tissue. This approach was recently employed to determine the identity and origin of a Magnaporthe oryzae lineage that caused the first severe outbreak of wheat blast in Asia within just six weeks of sample collection . Selective sequence capture of virulence and resistance associated genes could also improve the cost-effectiveness and resolution of field pathogenomics.
Monitoring of human pathogens has capitalized on the recent advances in sequencing technologies; the deployment of portable real-time genome sequencing for surveillance of the Ebola virus in Guinea using the MinION platform provided sequence data that could be immediately exploited for guiding control measures . Similarly, genome surveillance for Zika virus using portable genotyping in Brazil enabled tracking of viral spread into new geographical regions. Widespread deployment of such devices will allow real-time monitoring of plant pathogen variation as long as it is accompanied by adequate reference sequence information. Detailed surveillance of pathogens and pests will reveal their population structure and effector repertoires at the individual and pan species levels. Genome analyses can reveal the center of pathogen diversity, which could be the basis a network of phenotyping centers to analyze germplasm resistance. Furthermore, genomic-based surveillance can also be employed to improve the diagnosis and differentiation of pathogens present that are often misdiagnosed or present in mixed infections . There are several challenges to robust monitoring. Sampling is a major problem. Recent work has shown that adaptive sampling can improve the efficiency of management of some diseases ; however, effective control requires detailed, intensive sampling of host populations which may not be showing symptoms . The distinction between severe, explosive invasions and minor outbreaks which require less expensive intervention is challenging . Foundational research on both theoretical and actual population dynamics on a landscape scale is essential. Therefore, new ideas and technologies are needed to detect pathogens and pests at very low frequency. This is critical for plant hygiene and preventing introductions in the context of increasing global trade. Monitoring for volatiles that are either produced by the pathogen/pest or produced as a consequence to the plant defense response may help with the detection of certain diseases. This could enable the capture of latent diseases and would be deployable in shipping-based trade routes. Latent disease could be detected by machines or dogs. This could be an excellent opportunity for international collaborations to lead the development of diagnostic tools and testing their implementation. Sensitivity is another challenge. Resistance to fungicides is hard to combat because much of the evolution has already happened when detected at the currently typical threshold levels of a few percent. Also, some fungicides are still effective even when some level of resistance exists . Loci likely to be involved in development of resistance are often known when a new fungicide class is introduced; it would be desirable to detect very low levels of change at these loci. The challenge is to find efficient, inexpensive, ways of sampling and to tackle the bio-informatics challenge of heterogeneous samples with many loci being sequenced and examined simultaneously. Monitoring generates very large datasets. Research is needed into methods for efficient data gathering from large numbers of locations and integration with meteorological data to allow accurate epidemiological modelling. Remote sensing from drones or satellites is also providing vast amounts of data with increasing resolution and opportunities for monitoring crop health. Initiatives such as the aggregation of information from CABI “Plant clinics” with specialists able to analyze overall patterns are of great value, but require research in both population biology and social science rather than only biological understanding at the molecular level. Weeds, viruses, nematodes, soil fungi that have limited capacity for movement and produce patches observable from a distance are well suited to remote sensing. Research is needed to link image analysis with data on field performance and genotype, including ground observation of suspicious patches. There is the opportunity for integration of remote sensing with grower observation and response; however, this will require strong partnerships with growers and pest control advisors.As we move towards lower input, sustainable agriculture under changing climatic conditions, it is critical that disease and pest control strategies be considered in the context of the environmental variation and uncertainties resulting from climate change. Climate change models project a range of potential scenarios; as climates change, pathogens, pests and vectors will spread into new areas and new diseases may emerge more frequently. While accurate climate modeling is still under development, the opportunity now exists to investigate how temperature, humidity, CO2 levels, light quality, soil quality, and other environmental factors will affect plant health in the context of diseases and pests. Experimental systems have advanced to the point that they can inform the pathogen/pest layer of climate change models. Investigations can be conducted using high-throughput, sophisticated phenomics approaches to track pathogen and pest interaction with hosts in controlled environmental chambers as well as in field settings . Nonetheless, individual pathosystems need foundational studies before impact will be realized because our current predictive ability on decadal scales is severely limited . There is a dearth of funding for studies of relationships determining long- and medium-term dynamics of plant disease; current understanding of host-pathogen-weather relations rarely extends to comprehension of changes in pathogen populations. Complementary to studies on ecosystem and population dynamics, it is possible to study how environmental conditions that affect immune signaling at the molecular level. In cases where existing resistance genes are functional only within specific temperature ranges, approaches facilitating the expansion of this functional range could be explored. Additional molecular and genetic approaches to optimizing responses to biotic and abiotic stresses should also be investigated .