How investment in fundamental scientific research leads to practical outcomes

Published on 8 March 2016 in Food, health and wellbeing

Potatoes (c) James Hutton Institute


The societal benefits of funding applied scientific research – research which addresses a question that is immediately and directly relevant to an end user such as a farmer or policy maker – are clear. It is nearly always relatively straightforward to identify practical outcomes that emerge from such projects, making them highly attractive to funding bodies and industrial collaborations, particularly at a time of financial constraint. However, these applied outcomes frequently rely upon and develop previous fundamental research programmes for which practical outcomes were not immediately or obviously apparent at the time. This article describes how Scottish Government (SG) investment in a number of fundamental scientific areas at Main Research Providers (MRP), through the Strategic Research Programme has underpinned research which is now yielding practical outcomes that are making a difference in Scotland and beyond.

Key Points

  • Important practical outcomes are now emerging from long-term investment in genomics of crops and their pathogens.
  • Investment in fundamental science is the basis for innovation.

Research Undertaken

How the potato genome sequence has revolutionised breeding for disease resistance

The UK potato crop has an estimated value of £600 million each year. Pests and diseases cause significant losses to this crop with control of late blight alone thought to cost over £70 million each year in the UK. On a global basis pests and diseases destroy over 30% of the potato crop. High health and quality Scottish seed and ware potatoes are exported to more than 40 different countries worldwide. Scottish seed potato exports to non-EU countries has increased from less than 50,000 tonnes in 2000 to 90,000 tonnes in 2014 adding significant value to the industry. Breeding for resistance to pathogens therefore has the potential to improve grower income and to make a significant contribution towards achieving food security. Commercially grown potato varieties have tetraploid genomes (containing four copies of each gene), making breeding new varieties of potato with improved agronomic characteristics a long and complex process. Scientists at The James Hutton Institute are part of the consortium that has mapped and sequenced the full genome of this important crop. This process took more than 10 years of investment to complete, but is now making the development of new varieties with traits such as disease resistance more straightforward. The availability of the potato genome has allowed the full complement of resistance genes, which provide protection against pests and diseases, to be identified (Jupe et al., 2013). The way in which these resistance genes are organised in the genome has also been determined, a process that is critical for the development of the marker sequences used in plant breeding. As a result, new resistance genes have been identified and deployed into new cultivars. The emphasis of this work has been on the three major potato diseases, potato cyst nematodes, potato virus Y and late blight as their control relies on frequent application of chemicals.

Knowledge of the potato genome sequence also allows the development of methods, such as microarrays or RNAseq, that allow analysis of how the plant responds to disease or to other environmental stresses. These techniques have recently been used to examine the response of potato to various elicitors that are used in “priming”, which involves exposing plants to compounds that might normally indicate the presence of a pathogen, or that form part of the signalling pathways elicited when plants are diseased or stressed. It is thought that exposure to these compounds may place the plant in a higher state of alertness, enabling it to fight off pathogens more effectively. Gene expression platforms have been used to analyse the signalling pathways induced by exposure to various elicitors and provide information on the most effective combinations of elicitors for use in Integrated Pest Management (IPM) strategies.

Pathogen genomics and the search for durable resistance

Natural resistance is the most environmentally friendly method of controlling pests and diseases. Although resistance genes against pathogens have been identified and are used widely in crop breeding programmes, some sources of resistance are rapidly overcome by pathogens. Identifying long lasting, durable, resistance against important pathogens is therefore a key goal for the SG Strategic Research Programme. Resistance is activated when a plant detects the presence of a pathogen molecule called an effector. Over the past 10 years SG funding has allowed MRP scientists to lead genome sequencing projects for many of the key pests and diseases that affect crops in Scotland. These projects, coupled with studies on how the effectors work, are allowing the identification of conserved and essential effectors from a range of key pathogens. Sources of resistance that recognise these effectors and which, if combined, should therefore be more durable are then sought from germplasm resources such as the Commonwealth Potato Collection which is supported through SG Underpinning Capacity. This work builds on long-term investments in pathogen genomics and effector biology and is now leading to practical outputs in terms of disease resistance. Work in this area has placed MRP scientists at the centre of national and international consortia tackling pests and diseases. In addition, the work has attracted funding from national and international grant agencies including BBSRC, The Royal Society, the EU and USDA as well as investment from companies such as Simplot, Syngenta, Omex, Brandon and Hebridean.


Jupe, F., Witek, K., Verweij, W., Sliwka, J., Pritchard, L., Etherington, G.J., Maclean, D., Cock, P.J.A., Leggett, R.M., Bryan, G., Cardle, L., Hein, I. & Jones J.D.G. (2013). Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations. Plant Journal 76, 530-544.

Policy Implications

New tools for the control of pests and diseases based on development in genomics will form an important part of future IPM strategies.

Investment in fundamental scientific research is of key importance to allow longer term practical outcomes to be developed.


John Jones

Ingo Hein


Food, health and wellbeing

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