Rothamsted Research in Hertfordshire houses the Molecular Diagnostics laboratory for CHAP. Here, The Centre is able to determine the mechanisms of insect, pathogen and weed resistance to control agents, as well as develop diagnostic techniques that can be used in the field for rapid pest-strain identification.

Why is there a need

This asset will create a national capability for resistance and virulence management utilising facilities and capability located at Rothamsted (lead) and Fera. Rothamsted will undertake early-stage diagnostic development to identify the mutations which underlie resistance and virulence that lead to failure to control pests, weeds and pathogens. Fera will develop and validate existing and newly developed diagnostic methods for high-throughput, real-time laboratory services or in-field monitoring, which will be delivered to the industry to support timely advice to prevent inappropriate pesticide use. Outputs will also be utilised in Asset 1 to extend the in-field surveillance and modelling services to growers.

Latest News

An update on CHAP’s Molecular Diagnostics Laboratory

CHAP’s Molecular Diagnostics laboratory, based at Rothamsted in Hertfordshire, is ready for an influx of crop pest samples from the CHAP field sites and additional donors this winter. These samples will be investigated by Kirsty McInnes, the scientist in charge of the Diagnostics lab, to detect genetic features, or ‘biomarkers,’ that are thought to be indicative of pesticide resistance in weeds, insects and pathogens.

Knowledge of these biomarkers can enable identification of pesticide tolerant and/or susceptible pest populations in the field by CHAP consortium members, using a mixture of lab-based and mobile equipment.

The main pieces of kit used to identify genetic biomarkers in the Diagnostics lab include:

  1. The Life Technologies Quantstudio 6 qPCR machine for medium-high throughput gene expression studies and TaqMan assays. These techniques let us monitor the levels of genes associated with e.g. metabolic-based methods of resistance in individual pests, and track the spread of a biomarker linked to resistance across the UK.
  2. An Illumina MiSeq DNA/RNA sequencer that is capable of determining the order of DNA units (or ‘bases’) in genetic material, to identify any anomalies that could be used as a biomarker for pesticide resistance. The main applications for this machine are amplicon sequencing, targeted RNASeq and metagenomics, the latter technique informing us about the microbial diversity of soil samples, which would be useful for e.g. early-detection of soil-borne plant pathogens.

The knowledge and techniques developed on the machines in the Rothamsted Diagnostics lab can then be exploited by some of the other CHAP partners, who can perform in-field diagnostics with smaller, mobile version of the above equipment, to assess the types of pests and their levels of tolerance/susceptibility to commonly used control agents. The purpose of this work is to assist in the effective control of major pests by farmers and breeders in as environmentally and economically friendly a manner as possible, by assessing how a pest population will respond to a pesticide using genetic diagnostic techniques before the pesticide has been applied.

What is the Asset

Our facilities are stocked with high-tech lab equipment (see Figure 1 for more details) that allows the detection of changes in the genetic profiles of pests that could account for their tolerance to specific control agents.  As such, we are able to track the development and/or migration of resistant pest strains in the UK via field samples sent to us by research institutes, farmers or industrial clients. Through the characterisation of genetic features in a pest that correlate with higher rates of resistance to a pesticide, additional partners in CFACS will be able to perform rapid in-field diagnostic tests to inform clients of the particular pest strains present in their fields, allowing efficient, more cost-effective treatment plans to be formulated before large-scale crop destruction has occurred.

How it can help the agricultural sector

The work conducted in this asset at Rothamsted can provide extremely beneficial information to a wide range of researchers and organisations in the agricultural sector: whether you are an agrichemical company looking to investigate the possible development of pest resistance to your product, an academic institute seeking to incorporate some of our expertise and facilities into your next grant proposal related to agricultural pests, or a plant breeder curious as to why your once tolerant crop has suddenly become susceptible to a particular pest, we can assist you.  By sending us your samples, The Centre can apply its professional expertise and specialised facilities to answer your questions, allowing you to focus on other aspects of your business or research.

Asset 6 is now up-and-running at Rothamsted Research, and we look forward to supporting you and your research or breeding goals in the near future, whether you are an academic, company

More information here

To receive more information on this asset, book a tour of our facilities or discuss a potential collaboration with us, please contact:

Kirsty McInnes (kirsty.mcinnes@rothamsted.ac.uk; +44 (0) 1582 938 176)

Andrew Spencer (andrew.spencer@rothamsted.ac.uk; +44 (0) 1582 938 312)

Linda Field (lin.field@rothamsted.ac.uk; +44 (0) 01582 938 355)

Figure 1: The Molecular Diagnostics lab at Rothamsted Research. The range of equipment in this lab will permit extensive, medium- to high-throughput analysis of the genetic profiles of agricultural pests to elucidate their mechanisms of resistance to control agents. Main pieces of equipment include 1) a Molecular Devices SpectraMax i3x plate reader for kinetic studies, 2) an Illumina MiSeq DNA/RNA sequencer, 3) a Life Technologies QuantStudio 6 qPCR machine that can analyse up to 384 samples at once, and 6) a Qiagen QIAxcel capillary electrophoresis machine for high-resolution detection of PCR amplicons (3-5 bp resolution capabilities; useful for microsatellite detection). In addition, 4) an Eppendorf epMotion robot and 5) a Qiagen QiaAgility robot will assist with accurate sample preparation for high-throughput studies.