Protecting Scotland’s crops: disease resistance and pathogen biology
Project Lead
Challenges
Scottish agriculture faces significant challenges and opportunities related to changing policy, markets, environment, and technology. More specifically, the agriculture sector needs to maintain and increase profitability by responding to changing market conditions while simultaneously contributing to Scottish Government commitments on greenhouse gas emissions and biodiversity. These objectives must be achieved in an evolving natural environment in which risks, such as increased summer drought, and opportunities, such as increased area of prime agricultural land, are rapidly changing. Underpinning these changes is a need to exploit genetic diversity and accelerate the efficient breeding of crop cultivars adapted to new growing technologies and environments.
The potato and soft fruit industries in Scotland are an economically important part of the agricultural sector. Pathogens and pests, both established and newly emerging, represent major constraints to sustainable crop production. There is a need to develop crops for the future which are more resilient to the changes in climate and require lower high-carbon inputs, such as fertilisers and pesticides. It is important to increase biodiversity by introducing new crops which have increased resilience. Crops with these traits reduce the need for pesticides and thus have a positive environmental impact. Establishing such crops can also extend production seasons, mitigating risk for farmers from sporadic unfavourable growing conditions. Extending the growing season for Scottish soft fruit would also extend the period that fresh locally grown soft fruit would be available for Scottish consumers.
Questions
Solutions
This project cuts across the key Scottish crop (potato and soft fruit), to coordinate approaches aimed at mitigating disease threats. Crucial to this research is a detailed molecular understanding of host and pathogen biology and thus the mechanisms that lead to resistance or susceptibility. It is this understanding that will connect germplasm resources with breeding through the development of markers linked to the resistances. We are considering the interactions between microbes, plants, and pathogens in the environment and how these impact disease. Our priorities are the characterisation and mobilisation of durable resistances effective against Potato cyst nematodes (PCN), late blight, and viruses for potatoes, as well as root rot, insects (aphids and two-spotted spider mites) and fungi (botrytis) in soft fruits.
Identifying disease resistance in potatoes and soft fruits
We are identifying resistance and tolerance in potatoes and soft fruit crops to a range of key pathogens (Potato: Potato Cyst Nematode (PCN), late blight, and viruses; Soft fruit: root rot causing oomycetes, insects, and fungi) that impact this industry to accelerate resistance breeding. The results are future-proofing potatoes against newly emerging pathogen variations that could potentially threaten deployed resistances.
Pathogen biology and effector research in potato and soft fruit
This project is enhancing our understanding of plant resistance mechanisms in potato and soft fruit to develop effective and sustainable control strategies. This covers pathogen biology and effector research. In potatoes, we focus on the penetration of host tissue by late blight and egg hatching in PCN. For raspberries, we are determining the factors that initiate infection from P. Rubi oospores that can be dormant in the soil for many years. This work is relevant to diseases caused by pests and pathogens of other Scottish crops and threats to Scotland’s natural biodiversity and informs disease management strategies.
Understanding and enhancing the plant immune system
Sustainable crop production requires attuning the environment (light and light quality, abiotic stresses, and host life cycle) to promote defence are novel aspects. We are exploring how environmental change influences the plant immune system. This includes the identification of beneficial soil microbes for potato protection and the role of beneficial microbes in protecting soft fruit.
Disease control options that consider the interaction between crops and the soil
Our previous research revealed that crops grown under sustainably managed soil conditions are less prone to disease compared to those under conventionally managed soils. We are phenotypically assessing disease suppression potential against PCN of microbial antagonists. In raspberry, arbuscular mycorrhizas have been shown to potentially reduce root rot severity. We are examining how these fungi impact disease and other above and below-ground traits.
Project Partners
Progress
2023 / 2024
The JHI-B1-1 project is advancing efforts to protect Scotland’s potato and soft fruit sectors from harmful plant pathogens. In 2023–2024 (Year 2), the project made progress across three main work packages, focusing on genetic resistance, pathogen biology, and the role of the environment and beneficial microbes.
Work package 1: Identifying Genetic Resistance
Objective 1 – Resistance to Late Blight and Viral Pathogens in Potatoes
Researchers identified and characterised a new resistance gene to late blight from the Commonwealth Potato Collection, named Rpi-blb4. Using advanced genomic tools such as HISS:Snakemake and SMRT-AgRenSeq-d, the team also identified Rpi-Smira1, further enhancing late blight resistance. In addition, existing potato cultivars carrying Ry(chc) and Ry(sto) resistance genes were identified for PVY control, along with lines showing resistance to PLRV.
Objective 2 – Resistance and Tolerance in Soft Fruit Crops
Tolerance and/or resistance traits were identified in soft fruit germplasm against a wide range of pests and diseases, including:
• Insect and mite pests: aphids, two-spotted spider mites, spotted wing drosophila, raspberry beetle, and vine weevil
• Pathogens: raspberry root rot, powdery mildew, leaf rust, cane spot, spur blight, and cane botrytis.
Work package 2: Understanding Pathogen Biology
Objectives 1 and 2
The team uncovered new insights into how pathogens infect crops, including:
• Elucidating the clathrin-mediated endocytosis mechanism used by potato late blight pathogens
• Developing a novel extracellular vesicle (EV) marker and identifying a family of oligosaccharide oxidases critical to late blight infection
• For Potato Cyst Nematodes (PCN), identifying Annexins involved in recognising root exudates, and observing changes in lipid binding affinity in the presence or absence of host signals
• Manipulating the soft fruit pathogen Phytophthora rubi to express fluorescent proteins, enabling better understanding of root infection dynamics.
Work package 3: Environmental Interactions and Beneficial Microbes
The role of beneficial microbes in disease mitigation was explored:
• Arbuscular mycorrhizal fungi (AMF) were shown to form associations with multiple raspberry cultivars, providing protection against root rot
• Trichoderma strains were isolated and showed potential for direct biocontrol of the root rot pathogen
Project-Wide Highlights
Across all workpackages, Year 2 achievements include:
• 23 peer-reviewed publications
• 8 new research collaborations
• Funding secured for 10 additional projects
• 2 policy-facing outputs
• 6 new diagnostic or research tools developed
• 2 new datasets generated
• Over 100 knowledge exchange activities engaging policymakers, industry, stakeholders, and the public.
The project continues to deliver robust scientific evidence and practical innovations that support resilient, sustainable pest and disease management in key Scottish crops.
2022 / 2023
Identifying disease resistance in potato:
We have screened potato cultivars grown in the UK and have been able to identify the resistance gene complements for several diseases. These findings have already been shared with industry through several stakeholder events. Currently, we are identifying and prioritising novel resistance capacity in the Commonwealth Potato Collection.
Identifying disease resistance in soft fruits:
Ongoing screening of members of a Rubus (more commonly referred to as raspberries and blackberries) association mapping population is taking place to identify members that are tolerant or resistant to naturally occurring pests and diseases. Such a screening is also being undertaken for blueberries with regards to aphids. We have also started to perform hyperspectral imaging on these fruit populations to determine whether there are spectral signatures associated with either resistance or tolerance.
Previous Projects
Related Projects
Novel Crops
Novel Crops: To address opportunities for producing alternative protein and carbohydrate crops in Scottish agriculture for fish and crustacean feed, bioenergy, bio-refining, animal feed and human consumption, and to develop design criteria for integrating suitable alternative legume and non-legume crops as sole and intercrops within rotations whilst also accounting for agronomic and ecosystem services.
There are two main areas of research:
Plant-Pest Epidemiology
Improved risk management and control of plant diseases: to be achieved through an understanding of key epidemiological parameters and optimal ways of manipulating them. These parameters underpin the development of epidemiological models that can be used to predict the effect of management strategies, including crop protection and host resistance. This work aims to define the parameters for problematic and economically important diseases of crops of particular importance to Scotland in order to deliver practical disease control solutions.