Development and implementation of tools, strategies, and stakeholder engagement to understand threats and improve disease management in practice
Project Lead
Challenges
New, emerging, and endemic pests and pathogens are threatening Scotland’s key crops and industries. Cereals represent 65% of arable production in Scotland, with 800,000 tonnes of malting barley a year being used for whisky distillation. The challenge is to meet the expected 20% increase in demand over the next five years. Scotland produces 1.3 million tonnes of potatoes every year (valued at £250 million), 42% of which are grown for seed, with a £55 million export value. Soft fruit growers produce 30,000 tonnes of berries, which are undergoing an exponential increase in sales, contributing approximately £150 million to the economy. A wide range of pests and diseases negatively affect quality and yield in these key Scottish crops and therefore carry a significant economic and environmental burden.
Prevention and mitigation of pest and disease outbreaks are affected by drivers including travel, globalisation of trade, and the effects of climate change. The exploitation of new markets will bring new export trade rules and an increased risk of importing new pests and diseases into Scotland, with associated implications for plant health resilience. The challenge is to tailor strategies to individual pest, pathogen and crop systems and the local environment, whilst delivering at the field and farm scale. We need robust scientific evidence, tools, and strategies to underpin plant health resilience, policy decisions and the uptake of effective integrated pest management (IPM) strategies.
Questions
Solutions
The project is mitigating threats posed to key crops by new, emerging, and endemic pests and pathogens, to protect Scotland’s industries and to deliver integrated and sustainable crop protection strategies for Scottish growers.
Developing new diagnostic tools
We are developing diagnostic tools and technologies to underpin plant health resilience and IPM strategies. Effective diagnostics and markers are essential to identify and track emerging plant pests and pathogens, to protect against the import of threats, and as the basis for plant health certification.
- Metabarcoding: Identifying key targets and investigating Potato Cyst Nematode (PCN), Pectobacterium atrosepticum and Phytophthora spp.
- Next Generation Sequencing: Establishing proof of concept protocols for rapid detection of pathogens. This technology has huge potential for rapid in-field surveillance.
- Potato Late Blight Diagnostics: Improved diagnostics for virulence and fungicide resistance and combined diagnostic tests for the early detection and genotyping of Phytophthora infestans.
- Virus detection in soft fruit: Developing a robust diagnostic test for blueberry shoestring virus.
Developing and testing disease control measures
We are delivering IPM strategies to control pests and diseases of major concern to Scottish agriculture and reduce the reliance on artificial inputs.
- Potato Late Blight host and fungicide resistance: screening commercial cultivars for resistance to P. infestans genotypes and identifying naturally occurring resistance-breaking strains and informing effective resistance and agrochemicals for use in IPM strategies.
- Alternatives to conventional pesticides: Providing evidence on the impact of biostimulants, elicitors and biologicals on barley and potatoes pests.
- Virus health in seed potatoes: Linking models of aphid prevalence and virus spread in the environment to quantify effects of alternative aphid control measures and test performance of alternative aphid control measures.
- Tools for soft fruit IPM: Gathering and summarising existing surveillance tools and identifying technology gaps for tackling soft fruit pest and disease threats.
Informing practice and policy on Integrated Pest Management
We are working closely with stakeholders identifying the key threats to Scottish sectors and prioritising scenarios and knowledge gaps. This includes analysing future scenarios and co-constructing solutions for safeguarding the cereal, fruit and potato sectors against future pest and disease risks. We are transferring knowledge and insights from our project to plant health experts and developing practical guidance for growers.
Project Partners
Progress
2023 / 2024
The RESAS-funded programme has made substantial progress in Year 2 (2023–2024) toward strengthening the science behind Integrated Pest Management (IPM) through diagnostics, disease control tools, and stakeholder engagement. Below is a summary of key achievements structured by work package and objective.
Work package 1: Diagnostics and Understanding New Threats
Objective 1 – Development of Diagnostic Tools and Markers
• Metabarcoding for Potato Cyst Nematode (PCN):
Primers targeting genome regions associated with virulence in PCN were developed and successfully tested against seven known pathotypes.
• Strain Differentiation in Pectobacterium:
K-mer fingerprinting methods were developed and validated using environmental isolates to improve understanding of blackleg disease in potatoes.
• Improved Taxonomic Resolution in Phytophthora spp.:
Two diagnostic approaches were explored:
1. Mitochondrial primers successfully amplified Phytophthora DNA from environmental samples.
2. A CAS assay effectively discriminated previously undifferentiable Phytophthora species.
Objective 2 – Next Generation Sequencing (NGS) for Diagnostics
• Nanopore MinION sequencing successfully detected bacterial pathogens in inoculated soil samples, showcasing the potential of real-time portable sequencing for in-field diagnostics.
Objective 3 – Potato Late Blight Resistance
• Target genes associated with virulence and fungicide resistance in Phytophthora infestans were catalogued, and selected isolates were sequenced.
Data analysis will continue into 2024–2025 to support future control strategies.
Work package 2: Disease Control Tools and IPM Strategies
Objective 1 – Late Blight Host and Fungicide Resistance
• Experimental work is scheduled to recommence in Year 3.
Objective 2 – Alternatives to Conventional Pesticides
• Two biological products and an elicitor were screened for efficacy against Rhynchosporium commune under controlled and field conditions.
• Localisation experiments at three barley field sites tracked the movement and effectiveness of biologicals.
• A separate potato trial assessed the environmental benefits of biostimulant-based management practices.
Objective 3 – Virus Health in Seed Potatoes
• This workstream is due to commence in Year 3.
Objective 4 – Tools for Soft Fruit IPM
• The IPM@Hutton Soft Fruit toolbox was updated with new tools and strategies for pest management.
• Data on blueberry aphid genetic diversity and varietal differences in aphid infestation were collated, reported, and disseminated to stakeholders.
Work package 3: From Research to Practice and Policy
Objective 1 – Scenario Planning and Knowledge Exchange
• Narrative scenarios addressing resilience to future pest and disease threats were co-developed with arable and horticultural stakeholders. These included recommended mitigation actions and were shared with industry partners.
Objective 2 – Trialling and Demonstrating IPM Strategies
• Cover crops were established before spring barley planting in 2024 as part of ongoing research into their role in managing Free Living Nematodes (FLN) in potato crops.
Objective 3 – IPM into Practice
• The Arable IPM Plan 2.0 was launched on the NFU website and is being used to inform the next iteration of the Scottish Arable IPM Plan, which will be hosted on the Scottish Plant Health Centre website.
• IPM themes were analysed using machine learning, and outcomes from cover cropping trials were communicated to stakeholders via regional roadshows.
Knowledge Exchange (KE)
• An extensive KE programme was delivered, with 56 new engagement activities recorded in Year 2, bringing the total to 159. These activities have ensured the research remains stakeholder-informed and policy-relevant.
Next Year
Several workstreams are poised to expand in Year 3, including renewed efforts on late blight resistance, seed potato virus health, and wider implementation of IPM strategies across arable and soft fruit systems. Collectively, these advances demonstrate strong progress toward delivering effective, environmentally sound, and stakeholder-led pest and disease management approaches for Scottish agriculture.
2022 / 2023
Develop diagnostics and markers to identify and track plant pests and pathogens
Metabarcoding approach for several pests and pathogens: Primers to amplify regions of the PCN genomes associated with virulence has been developed and a genetically distinct group of Globodera pallida has been identified. Methods to improve Pectobacterium strain differentiation has been explored with a whole genome sequence approach to allow separation of strains if a mixed sample is being investigated. Mitochondrial primers designed for improved taxonomic resolution successfully amplified Phytophthora DNA from environmental samples.
Next Generation Sequencing approach: This methodology has been used to establish proof of concept protocols intended for the rapid detection of pathogens.
Potato Late Blight diagnostics: To improve diagnostics for virulence and fungicide resistance, target genes have been catalogued, and selected isolates are undergoing PenSeq analysis.
Detection of viruses in soft fruit: Blueberry shoestring virus (BSSV) has been detected in breeding material by ELISA. We have however screened the plants by means of RNA-seq and could not detect either viruses or fungi - allowing us to have confidence in the health status of the material for future use.
Developing and testing disease control measures for the delivery of IPM
Potato Late Blight host and fungicide resistance: Commercial varieties and fungicides have been tested for efficacy with contemporary P. infestans populations, differences in host resistance relating to genotype have been reported to stakeholders.
Alternatives to conventional pesticides: Commercial and experimental products have been tested in barley and potato trails. A biostimulant affected marketable potato tuber numbers and had a compensatory effect on reduced nitrogen fertiliser inputs, no effect on foliar blight was recorded but lower environmental impact programmes were effective. In barley there was a varietal effect, some treatments reduced Rhynchosporium, particularly when used in combination with reduced fungicide rates.
Virus health in seed potatoes: This research will commence in Year 3.
Tools for soft fruit IPM: Knowledge gaps have been identified through discussion with stakeholders and proposed updates will be reviewed. Aphid samples have been collected from blueberry plantations and barcoded for species identity before screening with microsatellite markers.
Informing practice and policy on IPM
Scenario planning and knowledge exchange: The main threats to arable and horticultural production have been identified and prioritised through extensive stakeholder consultation. An extensive knowledge exchange programme had been undertaken with 87 engagement activities being reported across the project.
Trialling and demonstrating IPM strategies: This work is at an early stage, IPM strategies for fruit, potato and cereals will be tested in Years 3 to 5. Sampling to understand the impact of cover crops on FLN is on track.
IPM into practice: IPM metrics that consider effectiveness, potential for uptake and biodiversity impacts have been developed. A hybrid stakeholder workshop explored sector views on IPM threats, challenges and solutions, and identified barriers and incentives for uptake.
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