Annual Review of Phytopathology - Volume 56, 2018

Austropuccinia psidii (myrtle rust) is a globally invasive neotropical rust of the Myrtaceae that came into international prominence following extensive damage to exotic Eucalyptus plantations in Brazil in the 1970s and 1980s. In 2005, myrtle rust established in Hawaii (USA), and over the past 12 years has spread from the Americas into Asia, the Pacific, and South Africa. Myrtle rust was detected in Australia in 2010, and the response and ultimately unsuccessful eradication attempt was a lesson to those concerned about the threat of exotic pests and diseases to Australia's environment. Seven years following establishment, we are already observing the decline of many myrtaceous species and severe impacts to native plant communities. However, the recently developed Myrtle rust in Australia draft action plan identified that there is no nationally coordinated response strategy for the environmental dimensions of this threat. Recent reviews have identified a greater need for involvement from environmental agencies in biosecurity preparedness, response, and resourcing, and we believe this approach needs to extend to the management of invasive environmental pathogens once they establish.

Genome editing by sequence-specific nucleases (SSNs) has revolutionized biology by enabling targeted modifications of genomes. Although routine plant genome editing emerged only a few years ago, we are already witnessing the first applications to improve disease resistance. In particular, CRISPR-Cas9 has democratized the use of genome editing in plants thanks to the ease and robustness of this method. Here, we review the recent developments in plant genome editing and its application to enhancing disease resistance against plant pathogens. In the future, bioedited disease resistant crops will become a standard tool in plant breeding.

The plant cytoskeleton is a dynamic framework of cytoplasmic filaments that rearranges as the needs of the cell change during growth and development. Incessant turnover mechanisms allow these networks to be rapidly redeployed in defense of host cytoplasm against microbial invaders. Both chemical and mechanical stimuli are recognized as danger signals to the plant, and these are perceived and transduced into cytoskeletal dynamics and architecture changes through a collection of well-recognized, previously characterized players. Recent advances in quantitative cell biology approaches, along with the powerful molecular genetics techniques associated with Arabidopsis, have uncovered two actin-binding proteins as key intermediaries in the immune response to phytopathogens and defense signaling. Certain bacterial phytopathogens have adapted to the cytoskeletal-based defense mechanism during the basal immune response and have evolved effector proteins that target actin filaments and microtubules to subvert transcriptional reprogramming, secretion of defense-related proteins, and cell wall–based defenses. In this review, we describe current knowledge about host cytoskeletal dynamics operating at the crossroads of the molecular and cellular arms race between microbes and plants.

Plant disease detection represents a tremendous challenge for research and practical applications. Visual assessment by human raters is time-consuming, expensive, and error prone. Disease rating and plant protection need new and innovative techniques to address forthcoming challenges and trends in agricultural production that require more precision than ever before. Within this context, hyperspectral sensors and imaging techniques—intrinsically tied to efficient data analysis approaches—have shown an enormous potential to provide new insights into plant-pathogen interactions and for the detection of plant diseases. This article provides an overview of hyperspectral sensors and imaging technologies for assessing compatible and incompatible plant-pathogen interactions. Within the progress of digital technologies, the vision, which is increasingly discussed in the society and industry, includes smart and intuitive solutions for assessing plant features in plant phenotyping or for making decisions on plant protection measures in the context of precision agriculture.

Plant pathology must address a number of challenges, most of which are characterized by complexity. Network analysis offers useful tools for addressing complex systems and an opportunity for synthesis within plant pathology and between it and relevant disciplines such as in the social sciences. We discuss applications of network analysis, which ultimately may be integrated together into more synthetic analyses of how to optimize plant disease management systems. The analysis of microbiome networks and tripartite phytobiome networks of host-vector-pathogen interactions offers promise for identifying biocontrol strategies and anticipating disease emergence. Linking epidemic network analysis with social network analysis will support strategies for sustainable agricultural development and for scaling up solutions for disease management. Statistical tools for evaluating networks, such as Bayesian network analysis and exponential random graph models, have been underused in plant pathology and are promising for informing strategies. We conclude with research priorities for network analysis applications in plant pathology.

The origin of RNA interference (RNAi), the cell sentinel system widely shared among eukaryotes that recognizes RNAs and specifically degrades or prevents their translation in cells, is suggested to predate the last eukaryote common ancestor (138). Of particular relevance to plant pathology is that in plants, but also in some fungi, insects, and lower eukaryotes, RNAi is a primary and effective antiviral defense, and recent studies have revealed that small RNAs (sRNAs) involved in RNAi play important roles in other plant diseases, including those caused by cellular plant pathogens. Because of this, and because RNAi can be manipulated to interfere with the expression of endogenous genes in an intra- or interspecific manner, RNAi has been used as a tool in studies of gene function but also for plant protection. Here, we review the discovery of RNAi, canonical mechanisms, experimental and translational applications, and new RNA-based technologies of importance to plant pathology.

Assessment of crop loss due to multiple diseases and pests (D&P) is a necessary step in designing sustainable crop management systems. Understanding the drivers of D&P development and yield loss helps identify leverage points for crop health management. Crop loss assessment is also necessary for the quantification of D&P regulation service to identify promising systems where ecosystem service provision is optimized. In perennial crops, assessment of crop losses due to D&P is difficult, as injuries can affect yield over years. In coffee, one of the first perennials in which crop loss trials were implemented, crop losses concurrent with injuries were found to be approximately 50% lower than lagged losses that originated following the death of productive branches due to D&P. Crop losses can be assessed by field trials and surveys, where yield reduction factors such as the number of productive branches that have died are quantified, and by modeling, where damage mechanisms for each injury are considered over several years.

Management of geminiviruses is a worldwide challenge because of the widespread distribution of economically important diseases caused by these viruses. Regardless of the type of agriculture, management is most effective with an integrated pest management (IPM) approach that involves measures before, during, and after the growing season. This includes starting with resistant cultivars and virus- and vector-free transplants and propagative plants. For high value vegetables, protected culture (e.g., greenhouses and screenhouses) allows for effective management but is limited owing to high cost. Protection of young plants in open fields is provided by row covers, but other measures are typically required. Measures that are used for crops in open fields include roguing infected plants and insect vector management. Application of insecticide to manage vectors (whiteflies and leafhoppers) is the most widely used measure but can cause undesirable environmental and human health issues. For annual crops, these measures can be more effective when combined with host-free periods of two to three months. Finally, given the great diversity of the viruses, their insect vectors, and the crops affected, IPM approaches need to be based on the biology and ecology of the virus and vector and the crop production system. Here, we present the general measures that can be used in an IPM program for geminivirus diseases, specific case studies, and future challenges.