Work Package Crop and grassland production and disease control
Introduction
Crops are under constant threat from pests and diseases. In Scotland, major disease threats to potato include late blight caused by the pathogen Phytophthora infestans, a range of bacterial pathogens (Pectobacterium and Dickeya spp) and the potato cyst nematode Globodera pallida, while on barley two major fungal pathogens, Rhynchosporium commune and Ramularia collo-cygni, are of key importance. Aphids attack a wide range of crops (including barley and potato) and may also carry important virus species such potato virus Y, potato virus A, potato leafroll virus and barley and cereal yellow dwarf viruses. Researchers at the James Hutton Institute, Scotland’s Rural College, and Biomathematics and Statistics Scotland are combining their research efforts to determine how these pathogens and pests cause disease on important crop plants, and how resistance in crops can function to limit crop disease.
Aim of Research
A major constraint on achieving food security is crop loss due to pests and diseases. The main aim of this work is to develop a better understanding of the plant-pest interactions that threaten arable crop production in Scotland and elsewhere. Understanding the mechanisms that pathogens use to invade and colonise host plants, in parallel with the processes by which plants resist infection, will provide key insights to drive long term plant protection strategies. Within the EU, there has been a drive for sustainable agriculture with reduced inputs, a consequence of which has been reduction in the choice of pesticides due to tighter constraints imposed by the EU (initially 91/414/EEC, now EC/1107/2009). In many cases, no replacements for withdrawn pesticides are available and resistance against some pathogens is still lacking in commercially viable cultivars. Further, pathogen resistance to some critical pesticide classes is becoming more prevalent. There is thus an acute obligation on the scientific community to find new, durable and sustainable means to combat crop diseases. The overall outcomes will result in increases in the yield and quality of Scottish crops.
Progress
The interactions between Scottish crops, and their major pathogens and pests, was investigated further in year 6 of this strategic research programme (SRP). Throughout the SRP, the major focus has been on how pathogen effector (virulence) proteins drive disease, how these effectors are delivered to their site(s) of action, how they influence plant immunity, and the molecular events leading to immunity. In year 6, potato cyst nematode (PCN) effector diversity was assessed, informing on how nematodes are recognised by host plants. Bioinformatic tools were used to analyse effector proteins from the late blight pathogen P. infestans and PCN for short linear motifs that may predict interacting host plant target proteins. Late blight RXLR effectors were shown to be taken up plant cells by endocytosis, providing insights into how these effectors are able to enter plant cells and influence immunity. Plant cell wall degrading enzymes were catalogued and compared from different Phytophthora pathogens, showing conservation of critical enzyme families. Links between plant hormone action and resistance to raspberry root rot were investigated, and ‘omics resources were developed to determine its molecular basis. Candidate proteins involved in virus infection were investigated for their potential to increase resistance to Potato Virus Y (PVY). Links between light wavelength and immunity to potato late blight were further investigated, with many candidate genes identified. Application of plant hormones to barley was shown to influence the development of Ramularia leaf spot symptom development, a potentially new avenue for disease management. Outputs from RD2.1.3 across the six year SRP have provided new insights into pathogen/pest infection strategies and host plant immunity that can be exploited to develop more resilient Scottish crops.
Highlights:
- A new class of plant cell wall degradation enzyme from P. infestans, essential for infection, was published in the journal Science. Transcriptome analysis for other Phytophthoras showed that this new enzyme is widely conserved across these pathogens and likely plays a key role in disease.
- Genomes of the tree pathogens Phytophthora pseudosyringae and P. boehmeriae were sequenced and effectors catalogued, revealing components of pathogenicity in common with crop infecting species of Phytophthora.
- PCN effectors under selective pressure have been identified by sequencing effectors from PCN lines showing enhanced virulence on resistance. This enables understanding of diversity in effectors and how this relates to recognition of PCN by plants.
- Bioinformatics tools were used to predict eukaryotic linear motifs (ELMs) in effector proteins from P. infestans and PCN. This work has further developed informatics tools that will facilitate prediction and testing of host plant targets of pathogen effectors.
- RXLR class effectors from P. infestans were shown to be taken up by plant cells by clathrin mediated endocytosis. This is resolving how this class of effector proteins enters plant cells to suppress immunity and potentially be recognised by plant resistance proteins.
- Recently identified virus-required host plant factors (nuclear ALY proteins and synaptotagmins) were tested as potential targets for novel resistance to Potato Virus Y (PVY). Removing the activity of these proteins by gene silencing revealed that these proteins do not impact on PVY resistance, and that PVY infection must exploit different host plant proteins.
- Red and blue light sensing and signalling impact on plant immunity to potato late blight. Gene expression experiments have been used to identify candidate genes involved in the response to different light types.
Research into the relationship between leaf senescence and the barley pathogen R. collo-cygni has shown that foliar applications of cytokinins and pre-cursors of ethylene biosynthesis can have significant effects on fungal growth and visible symptom expression. Understanding the mechanisms of these responses could open up potentially new opportunities for controlling this important pathogen.
The development of disease in Scottish crops is driven by the intricate interactions between secreted pathogen molecules called effectors, and the target molecules of effectors in crop plants. The external environment and stage of plant development can also strongly influence disease outcomes. In year 5, novel secreted effector proteins and other pathogenicity factors from potato late blight and PCN were discovered and found to contribute to disease. Late blight effector diversity was assessed, informing breeding for disease resistance in potato. Effectors from the potato late blight pathogen and an aphid pest were found to target the same plant protein, but in different ways. Bioinformatic tools were used to predict candidate targets of pathogen molecules, potentially providing new avenues for disease control. Insights gained have further reinforced the links between plant development, environmental factors and plant immunity. Outputs from RD2.1.3 are providing novel avenues for managing and controlling diseases of importance to Scottish agriculture.
Highlights:
- A protein was identified on the eggshells of PCN that may be involved in detection of chemicals from potato roots to re-start the nematode lifecycle. This research has attracted UKRI funding for the two partner institutions, The James Hutton Institute and the University of St Andrews.
- SRP funded research, in collaboration with the University of York, uncovered a new class of enzyme used by the potato late blight pathogen to break down plant cell walls during infection. This work has attracted UKRI funding for the project partners at the James Hutton Institute and the University of York.
- Sefari scientists successfully gained funding from BBSRC, NERC, Defra and Scottish Government as part of the Bacterial Plant Diseases Initiative to study of the role of free-living nematodes in potato blackleg infection and the development of a national decision support tool for potato blackleg disease.
- New genome assemblies for two strains of PCN were completed, revealing a large family of potentially new effector proteins that are expressed at infectious stages.
- An amino acid transporter from Phytophthora infestans was found to be essential for late blight disease of potato and localised to an intracellular location, suggesting that amino acid recycling is essential for P. infestans pathogenicity.
- Analysis of the transcriptome and pathogenicity of tree pathogen Phytophthora kernoviae revealed features in common with the distantly related late blight pathogen, P. infestans.
- Bioinformatics strategies were developed and implemented to predict candidate plant proteins that interact with potato virus Y.
- Plant proteins were identified that are targeted by multiple pathogen effectors, suggesting the importance of these plant target proteins in immunity and disease.
- Red and blue light signalling in potato have roles in plant immunity, and are targeted by late blight effectors to promote disease.
- The candidate gene cluster responsible for production of the phytotoxin rubellin in Ramularia collo-cygni was identified and results suggest that the genes are coregulated.
Major pests and pathogens of Scottish crops produce hundreds of molecules (called effector proteins) that potentially promote the development of plant disease. Effectors can act inside or outside of plant cells, targeting and interfering with functions of host plant proteins. The function of individual effectors from pathogens of Scottish crops were determined, ranging from their activity as cell death elicitors, importance to pathogenesis, localisation during infection, and which host plant proteins they target. Host plant target proteins common to effectors from different pathogens were identified. Abiotic stress pathways and plant developmental factors were involved in disease development and resistance; these processes were shown to be targeted by pathogen effectors and secondary metabolites. Novel resistances to scald disease in barley were identified, and a major resistance locus defined within the barley genome. Host plant targets of effectors were assessed for their potential to act as novel sources of resistance in potato.
Outputs from this research have further revealed the complexity of the interactions between major Scottish crops and their major pathogens. These findings serve as starting points for identifying and evaluating new sources of crop disease resistance, or for more precise definition of resistance in existing crop germplasm used in breeding programmes.
Highlights:
- Common plant targets were identified for effectors originating from different pests and pathogens. These targets are candidates for improving resistance against multiple pathogens and pests.
- Links were identified between plant nucleolar activities involved in virus infection and plant responses to abiotic stresses. Stress such as heat can compromise disease resistance, and knowledge of the plant processes involved will allow us to better predict and respond to the potential effects of climate change on disease susceptibility and the durability of resistance.
- Novel scald (Rhynchosporium) resistances were identified from barley landraces and a major resistance locus was defined within the barley genome. This provides new resistances that can be included in barley breeding programmes, and improved markers for an existing scald resistance.
- A process called the unfolded protein response (UPR) is induced in plants by the rubellin toxin produced by Ramularia collo-cygni. Ramularia leaf spot symptoms may be reduced if the plant UPR can be maximised.
- Ramularia leaf spot symptom development on barley seedlings was slowed down by treatments that slowed the rate of leaf senescence.
- Genetic analysis of PCN populations was carried out in order to provide advice on deployment of appropriate resistance. Transferring knowledge of PCN genotypes and effector diversity is helping to manage this crop disease and improve food security.
Our research has shown that the major pests and pathogens of Scottish crops produce hundreds of molecules (called effector proteins) that potentially promote the development of plant disease, and that these effectors are strongly associated with the onset of infection. A method was developed for analysing the diversity in pathogen effectors that will greatly accelerate the understanding of pathogen populations and the plant resistance they can overcome. Evidence was found that some effectors from the potato late blight pathogen Phytophthora infestans are delivered to plant cells by novel pathways, and that multiple types of effector are delivered at a single site during plant infection. Pathogen effectors that are delivered inside plant cells were shown to target different locations inside plant cells where they act to suppress diverse resistance responses. The plant targets of effectors were further investigated, and it was revealed that some are essential to the invading pathogen to cause disease (called susceptibility factors), and these may have value as alternative forms of resistance. Additional plant cellular components linking disease development, abiotic stress (e.g. drought, heat), and plant development factors, were identified in virus and late blight infections of plants. Ramularia leaf spot symptom development was shown to involve pathogen targeting of a conserved plant cellular response. DNA markers for disease resistance to the fungal pathogen R. commune, which can be used in breeding, have been identified from barley.
Outputs from this work have provided a deeper understanding of how crop pathogens and pests of importance to Scotland cause disease and can be exploited through, for example, novel markers for disease resistance breeding, alternative strategies for improving disease resistance, and new tools for pathogen diversity monitoring.
Highlights:
- Virulence factors (effectors) from the potato late blight pathogen Phytophthora infestans work in combinations, and in multiple ways, to enable successful infections.
- Responses to heat stress and potato virus Y infection in potato have common underlying mechanisms which control plant sensitivity to multiple stresses depending on cultivar.
- A virulence factor from the potato late blight pathogen Phytophthora infestans exploits links between plant hormone signalling and disease susceptibility to promote disease. Subtle manipulation of the balance between growth and immunity may provide an indirect strategy for delivering plant protection.
- Diagnostic markers for a barley resistance gene (Rrs1Rh4) against rhynchosporium have been identified.
- A method has been developed for tracking multiple disease resistance genes in plant varieties. Called diagnostic resistance gene enrichment sequencing (dRenSeq), it can be used to improve the speed and efficiency of future disease resistance breeding.
- New insights into mechanisms of infection by Potato Cyst Nematode (PCN): An effector from PCN has been identified that suppresses host defences.
- A new tool referred to as Pathogen enrichment Sequencing (PenSeq) has been developed to study the diversity of key pathogen molecules including targets for resistance genes and chemicals.
- We have characterised how a late blight virulence factor exploits a plant susceptibility factor to cause disease. Susceptibility factors offer potential novel targets for disease control.
Plant cellular targets of pathogen molecules that drive the infection process (called effectors) have been identified in potato, revealing aspects of plant cellular function that are exploited by pathogens to cause disease. Several of the identified effector target proteins in plants are potentially also involved in developmental processes or stress responses. Computational tools to examine the evolutionary processes acting on effectors and their plant targets were developed.
Plants carrying novel resistances to late blight and rhynchosporium were identified in potato and barley, respectively. The biochemical basis for resistance to bacterial soft rot of potato is under investigation. Mature plant resistance to potato virus Y was investigated and found to function only in some potato cultivars and against some strains of virus. Indicators of mature plant resistance were identified that can be utilised in the field. Ongoing research investigated the impact of Ramularia infection on photosynthesis and growth in barley.
Results from deliverables in RD2.1.3 have provided novel targets to improve disease resistance, new disease resistant plant germplasm for breeding, and knowledge of crop physiology that can refine disease management.
Highlights:
- A novel strategy that P. infestans, the cause of potato late blight, uses to suppress the plant immune system has been discovered. The pathogen manipulates plant growth and development to boost its infection process. This reveals a vulnerability that could be targeted for improved crop protection.
- The link between drought tolerance and virus spread in plants has been elucidated, allowing strategies for improved drought tolerance and reduced viral spread to be developed.
- A novel late blight resistance gene has been identified using DNA-capture technology and resources from the Commonwealth Potato Collection. This provides an improved tool for breeding more resilient potatoes.
- A novel Potato virus Y resistance gene has been identified and mapped.
- Potato virus Y (PVY) is evolving to produce more virulent strains, and genetics plays the most important role in determining how resistant a potato cultivar will be against these newer strains. The interplay between cultivar and virus strain is complex and cannot be predicted by our current knowledge of resistance genes.
- Ramularia Leaf spot causes yield losses in barley by producing toxins which damage the leaves and reduce plant photosynthesis. Research identified metabolites produced by the fungus during the infection process and may assist in the design of new anti-fungal agents.
- A protein from the barley pathogen R. commune, was shown to cause non-host resistance in Solanaceous plants (e.g. potato, tomato) but not in other families of plants. This will provide a valuable resource for developing non-host resistance in cereals.
- Delivery of effector molecules inside plant cells was directly visualised for the first time in P. infestans.
Important disease promoting effector proteins from major pathogens of Scottish crops and their targets in plants have been identified for barley scald, potato late blight and cyst nematode and aphids.
Potential novel disease resistances have been identified in barley and potato. Links between plant development and defence against pathogens have been identified for viruses and late blight on potato. One potential mechanism for the mature plant resistance against viruses in potatoes has been studied.
The impact of fungicide treatment on barley leaf physiology revealed little effect on photosynthesis or leaf lifespan. However, when Ramularia leaf spot disease pressure is low, there was an increase in grain number formation.
Results have informed on novel targets for improving disease resistance or management, through breeding or chemical application, and crop plant physiology that influences disease resistance.
Highlights:
- Plant factors required by plant pathogens for infection (susceptibility factors) have been identified, leading to a new hypothesis about plant disease.
- Solute transport pathways in plants do not predict whether mature plant resistance will protect potatoes against Potato Virus Y, which means that another, still unknown, mechanism must drive this type of resistance.
- Collaboration with University of Dundee researchers on a BBSRC funded project to examine the role of susceptibility factors in late blight disease development and guide approaches to achieve disease resistance in potato.
- The genome sequence of the barley pathogen Ramularia collo-cygni has been annotated, offering insights into the biology and infection strategy of this fungus, the potential to examine the interaction between it and barley and informing on effective crop protection programmes.
- We have shown that particular protein components facilitate PVY infection in potato, suggesting that deficiency of these proteins may provide resistance against PVY.
Future Activities
Pathogen and pest effector molecules that facilitate the progression of disease in plants will continue to be a major focus of work beyond this SRP. Specifically, the diversity present among specific effector molecules from key pathogens and pests will be determined through enrichment sequencing, especially those known to trigger disease resistance, informing disease management, discovery of new sources of disease resistance, and crop breeding. This will be coupled with phenotypic and genotypic screening of crop germplasm to identify new sources of resistance to late blight, PCN and viruses.
The plant targets of pathogen effectors can reveal novel mechanisms of plant defence or disease resistance, for example, to elucidate the switch in host biology from growth to defence with implications for identifying resilience mechanisms that could improve tolerance to (a)biotic stresses and mitigate effects of climate change.
Key events in pathogen/pest lifecycles represent opportunities for disease control, for example oospore germination in the raspberry root rot pathogen, egg hatching in PCN, and plant leaf penetration in late blight. ‘Omics resources developed during this SRP will be used as a foundation to understand the cellular signalling events involved in coordinating these processes. Findings will be relevant to diseases caused by pests and pathogens of other Scottish crops and threats to Scotland’s natural biodiversity (e.g. tree diseases) and inform disease management strategies.
Selected Outputs
A Phytophthora infestans RXLR effector targets plant PP1c isoforms that promote late blight disease.
The cell biology of late blight disease
Oomycetes seek help from the plant: Phytophthora infestans effectors target host susceptibility factors.
Genome-based discovery of polyketide-derived secondary metabolism pathways in the barley pathogen Ramularia collo-cygni.
A Phytophthora infestans RXLR effector associates with host Susceptibility factor NRL1 to degrade the positive immune regulator SWAP70.
Cajal bodies and their role in plant stress and disease responses.
Phytaspase-mediated precursor processing and maturation of the wound hormone systemin.
The multiple functions of the nucleolus in plant development, disease and stress responses.
Foundational and translational research opportunities to improve plant health
Potato MAP3K StVIK is required for Phytophthora infestans RXLR effector Pi17316 to promote disease.
The Phytophthora infestans haustorium is a site for secretion of diverse classes of infection-associated proteins.
Pathogen enrichment sequencing (PenSeq) enables population genomic studies in oomycetes
Resistance to Rhynchosporium commune in a collection of European spring barley germplasm.
Characterisation of barley resistance to rhynchosporium on chromosome 6HS.
Selected fungal natural products with antimicrobial properties
eLS chapter on Ramularia collo-cygni – An Enemy in Waiting.
AVR2 targets BSL family members, which act as susceptibility factors to suppress host immunity.
CRISPR applications in plant virology: virus resistance and beyond.
eLS chapter on Rhynchosporium commune.
Bingham IJ, Havis ND, Burnett FJ. (2020). Opportunities for rationalising fungicide inputs in the management of spring barley disease. Proceedings Crop Protection in Northern Britain Dundee, UK, February 2020, pp 81-86. https://www.cpnb.org/
Burrell C, Havis ND, Spoel SH, Bingham IJ. (2020). Quantifying the effects of asymptomatic and symptom expressing phases of Ramularia collo-cygni infection on photosynthesis and yield formation of spring barley. Proceedings Crop Protection in Northern Britain Dundee, UK, February 2020, pp 97-102. https://www.cpnb.org/
Devastating Intimacy: The cell biology of plant-Phytophthora interactions.
Natural resistance to Potato virus Y in Solanum tuberosum Group Phureja.
Infection of the model plant Nicotiana benthamiana by the tree pathogen Phytophthora kernoviae.
Secreted pectin monooxygenases drive plant infection by pathogenic oomycetes.
Draft genome assemblies for tree pathogens Phytophthora pseudosyringae and Phytophthora boehmeriae.
Blue-light receptor phototropin 1 suppresses immunity to promote Phytophthora infestans infection.
Biosynthesis of rubellins in Ramularia collo-cygni—genetic basis and pathway proposition.
Research Deliverable Lead
Dr Stephen Whisson
Research Deliverable Staff
Dr Anna Avrova
Professor Ian Bingham
Dr Petra Boevink
Francois Dussart
Dr Eleanor Gilroy
Dr Ingo Hein
Dr Sonia Humphris
Dr Sue Jones
Professor John Jones
Dr Stuart MacFarlane
Dr Sophie Mantelin
Dr Alison Roberts
Professor Ian Toth