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In-field detection

Work Package 2.1 - Crop and grassland production and disease control

Research Deliverable 
2.1.5 In-field detection
Leading Ideas 
Agriculture
Plant and Animal Health

Introduction

High value crops grown in Scotland (barley, potatoes and soft fruit) are susceptible to damage caused by a wide range of endemic diseases. In the future, these crops are likely to face additional disease challenges from new pests and pathogens due to factors including: the loss of key pesticides through legislation or reduced efficacy; increased global movement of diseased plant material and a changing climate. Integrated Pest Management (IPM) strategies aim to control diseases of particular crops or cropping systems using a combination of tools and approaches. Our research underpins IPM by delivering improved methods of detecting, identifying and quantifying the key pests, pathogens and diseases in a timely manner in ‘the field’. Using both current and emerging technologies we aim to develop diagnostics that are both relevant to stakeholder needs and fit for the future.

Aim of Research

The overall aim is to improve detection of economically important pests/pathogens/diseases affecting key Scottish crops. This will improve decision making for growers and control recommendations and inform policy and statutory recommendations, leading to improved disease control. Much of the research capitalises on outputs from the previous RESAS programme and externally funded research. The initial focus is primarily on developing/improving the necessary assays, tools and techniques. Subsequently, new detection methods will either be validated and incorporated directly into relevant IPM toolboxes or be deployed to develop disease risk assessments and/or forecasting to inform IPM strategies.

Progress

2019
2019

New or improved diagnostics have been developed for key pests and pathogens for which in field detection is an essential component of an Integrated Pest Management (IPM) approach to controlling disease. For potatoes, a diagnostic test for pathogenic Streptomyces spp., which cause common scab on potatoes, has been validated for detection on seed and in soil which complements the range of tests already available.  For soft-fruit, diagnostics have been developed and deployed in monitoring for both a blueberry virus and the Spotted Winged Drosophila (SWD) pest. For cereals, diagnostic developments have improved detection of both aerial and seed-borne cereal pathogens. Improved diagnostic assays for two important fungal pathogens Rhynchosporium and Ramularia are now deployed to facilitate disease risk forecasting using spore samplers. Furthermore, improved DNA extraction methods for large scale seed batches are being developed with industry partners, enhancing ability to detect cereal pathogens in high throughput systems. To ensure diagnostic developments continue to remain fit for the future; new sensor technologies are being evaluated; new software developed for improved design of pathogen specific diagnostic assays; and the potential for new threats for which diagnostics could be required were monitored. Notably, in response to outbreaks of the newly emerging pathogen P. tritici-repentis causing tan spot in cereal crops, diagnostics for the pathogen have been developed.   

Highlights:

  • Improvements were incorporated into the Primer design software package which is freely available and has been used to develop specific primers for both Pectobacterium spp. and Phytopthora spp.  This software will facilitate primer design and therefore diagnostics for plant pathogens world-wide.
  • Diagnostic developments have improved detection of aerially dispersed cereal pathogens and assays for Rhynchosporium and Ramularia spores are now deployed to facilitate disease risk forecasting using spore samplers.
2018
2018

New or improved diagnostics have been developed for key pests and pathogens for which in-field detection is an essential component of an IPM approach to controlling disease. For example, an assay to detect pathogenic Streptomyces spp. on seed and in soil was assessed for potential inclusion in a potato soil-pathogen testing package. A more efficient test for the detection of Spotted winged drosophila (SWD) was developed. SWD poses a threat to soft fruit production and awareness of its potential impacts and how to do the test have been demonstrated widely to stakeholders within the soft-fruit industry. An SWD testing clinic was made available to growers. In response to potential /suspected outbreaks of blueberry virus infections, a strategy to produce blueberry scorch control material has been developed which is expected to improve our ability to do antibody testing of suspected infected blueberry material. Ramularia collo-cygni is the pathogen responsible for the barley disease Ramularia leaf spot (RLS). New tests have been designed for the detection of Ramularia and are undergoing validation. This new assay will be used to test samples for seed infection. Additionally, to ensure diagnostic developments continue to remain fit for the future: new sensor technologies were evaluated; new software was developed for improved design of pathogen specific diagnostic assays; and the potential for new threats for which diagnostics could be required were evaluated.

Highlights:

  • Spotted Winged Drosophila (SWD) is an emerging pest in Scotland potentially affecting the soft fruit industry. A more efficient test for the detection of SWD in fruit was developed. Stakeholder events were held, where attendees were reminded to remain vigilant for the presence of SWD and given advice on identification and testing methods they could use on their farms to look for the pest in traps and fruit to help the fruit industry with early detection of the pest in the crop. A free SWD clinic was also offered to growers.
  • Blueberry production has recently emerged as a new and rapidly growing industry in Scotland. As part of the development of a toolkit of diagnostic virus tests for new and emerging blueberry diseases a nucleic acid-based test for the detection of Blueberry scorch virus was produced and a novel approach to produce positive control material to ensure that ELISA-based virus detection tests was developed.
2017
2017

Work against this aim has resulted in improved diagnostics for the detection and quantification of crop pests and pathogens. For example, four species-specific diagnostic assays targeting nematode vectors of Tobacco Rattle Virus (the cause of potato spraing disease) have been launched as a commercial service with uptake by practitioners across the UK. A new test was designed for the detection of air-borne potato pathogens to support disease risk forecasting using spore trap systems. Club root is an important disease of oil seed rape; club root assays were evaluated and a robust test was identified and is being offered as a service to growers in the SRUC Crop Clinic. Additionally, to ensure diagnostic developments continue to remain fit for the future: new sensor technologies underwent initial testing; new software was developed for improved design of pathogen specific diagnostic assays: and the potential for new threats for which diagnostics could be required were monitored.

Highlights:

  • Molecular diagnostic assays have been developed for the 4 main TRV-vectoring Trichodorid species of free-living nematodes (FLNs). These new molecular diagnostic tests for target FLN species are being offered to growers through Diagnostic Testing and were communicated through numerous stakeholder events, for example, Potatoes in Practice.
  • Club root is an important disease of oil seed rape: an existing club root assay was validated and used to evaluate alternative club-root control treatments and is being used in an AHDB funded project on clubroot spread and is now being offered as a commercial diagnostic assay.

Future Activities

We shall continue the development and validation of diagnostic tools for important crop pests and pathogens affecting or posing a threat to Scottish crops. Assays developed will continue to either be validated and incorporated directly into relevant IPM toolboxes or be deployed to develop disease risk assessments and/or forecasting to inform IPM strategies. The dynamic nature of the soft-fruit industry necessitates the potential for new diagnostics to be developed if necessary. Research using various sensor technologies will progress along a number of threads in this emerging area, ensuring that new diagnostic techniques can be deployed in the near future.

Selected Outputs

The Relative Importance of seed- and soil-borne inoculum of Rhizoctonia solani AG-3 in causing black scurf on potato.

The effect of post-harvest storage conditions on the development of black dot (Colletotrichum coccodes) on potato in crops grown for different durations.

Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens

PHYLIS: A Low-Cost Portable Visible Range Spectrometer for Soil and Plants

The Scottish way-getting results in soil spectroscopy without spending money

Estimating soil properties with a mobile phone

Hydrolysis probe-based PCR for detection of Pratylenchus crenatus, P. neglectus and P. penetrans.

In a Different Class? Whole genome classification of bacterial potato pathogen.

The introduction, persistence and impact of seed and soil-borne pathogens on potato crops within a rotation

Free living Nematodes - Diagnostic Testing. Presentation and discussion at Potatoes in Practice Aug 2016 and industry workshops.

Rapid Diagnostic for Detection of Aphelenchoides besseyi and A. fujianensis Based on Real-Time PCR.

New live screening of plant-nematode interactions in the rhizosphere.

Viral Diagnostics in Plants Using Next Generation Sequencing: Computational Analysis in Practice.

Predictive Diagnostics for soil-borne diseases of potato: an essential component of IPM

My Life In Sequences

On using the precise sensor

A method for automatic segmentation and splitting of hyperspectral images of raspberry plants collected in field conditions

Use of imaging technologies for high throughput phenotyping. In Raspberries: Breeding, Growth and Challenges

Pathogen Testing Requirements for Raspberry Material Entering the EU Certification Scheme

Kodoja: A workflow for virus detection in plants using k-mer analysis of RNA-sequencing data

Pathogens in Raspberry and Other Rubus spp.

The complete sequences of two divergent variants of the rhabdovirus raspberry vein chlorosis virus and the design of improved primers for virus detection

Real-time PCR and LAMP assays for the detection of spores of Alternaria solani and sporangia of Phytophthora infestans to inform disease risk forecasting