New technique accelerates isolation of late blight resistance genes from a wild potato relative
A team of scientists from The Sainsbury Laboratory (TSL) and The Genome Analysis Centre (TGAC) have developed a new method to accelerate isolation of plant disease resistance genes. The team have also identified a brand new source of blight resistance genes in Solanum americanum, a wild relative of the potato.
Plant pathogens such as late blight can evolve rapidly to overcome resistance genes, so scientists are constantly on the hunt for new resistance genes. Professor Jonathan Jones and colleagues from his lab at TSL pioneered the new technique, called “SMRT RenSeq”, and believe it will significantly reduce the time it takes to define new resistance genes.
The team plan to stack several resistance genes together in one plant, to make it much harder for pathogens to evolve to overcome the plant’s defences. It is hoped the deployment of this new technique will improve commercial crops and will lead to higher yields, significantly reduced environmental impact and lower costs for the producer and eventually the consumer.
Potato late blight remains a major threat to potato and tomato production, with world-wide crop losses estimated to be in excess of £3.5Bn. Prevention measures and crop losses cost UK potato farmers around £55M a year, and on farm blight management can account for as much as half of the total cost of potato production.
Managing the disease requires frequent application of fungicides, which incurs not only a significant economic cost but also environmental costs. Genetic resistance can be introduced into crop species, which reduces the need for chemical spraying. However, using conventional breeding techniques, deploying genetic resistance is long and laborious.
Sources of new plant resistance genes are difficult to find. The TSL team investigated the wild potato relative, Solanum americanum, which carries several resistance genes, and by using the new technique, rapidly isolated a new resistance gene, Rpi-amr3.
SMRT RenSeq makes the process of finding, defining and introducing genetic resistance far quicker and easier by combining two sequencing techniques: ‘RenSeq’ (Resistance gene ENrichment SEQuencing) and ‘SMRT’ ( Single-Molecule Real Time sequencing).
The technique consists of two main steps:
- A sub-set of DNA sequences are “captured” using a method that selects for long DNA molecules that carry a sequence that is commonly associated with resistance genes
- These DNA molecules are sequenced multiple times to make sure the code is determined as accurately as possible using the novel long-read SMRT technology
This results in a very reliable DNA sequence for each candidate resistance gene. Genetic analysis of the results enabled the team to define which of these candidate genes were linked to blight resistance. Following this, the SMRT RenSeq method also enabled the team to identify and define the parts of the genome which regulate the resistance genes. Several candidates were introduced into a model species, of which one (Rpi-amr3) successfully provided broad-spectrum blight resistance. The Platforms & Pipelines Group at TGAC performed the sequencing, led by David Baker.
Professor Jonathan Jones said: “Engineering disease resistance genes into crops is a continuous battle to stay one step ahead of new strains of disease, and scientists are constantly investigating how to speed up this process. This new technique significantly reduces the time and cost of isolating candidate resistance genes, and has great potential for application to other desirable traits in potato and in other crops.”
TGAC Project lead and Plant & Microbial Genomics Group Leader at TGAC, Dr Matt Clark, said: “Our cultivated potatoes and tomatoes are highly susceptible to potato blight, as thousands of years of selective breeding has brought with it a huge loss in genetic variation. However, within closely-related wild species, it is possible to find natural resistance to such pathogens. Finding and using disease resistance genes from closely related plants is critical in the arms race against crop pathogens. This technique accelerates the process and we hope will help reduce crop losses to disease.”
This work was funded by the Biotechnology and Biological Sciences Research Council (BBSRC) and the Gatsby Charitable Foundation.
This paper is one of three papers which will be published together in Nature Biotechnology on Monday 25 April 2016. The other two papers focus on finding new resistance genes for soybean rust (by Dr Peter Van Esse, The Sainsbury Laboratory) and wheat stem rust (by Dr Brande Wulff, the John Innes Centre).
Notes to editors
A copy of the paper 'Accelerated cloning of a potato late blight–resistance gene using RenSeq and SMRT sequencing' can be found on Nature’s press account. If you do not have a Nature press account please contact Nicola Brown or Geraldine Platten (see external contacts below) to receive a PDF version of the paper.
Images to accompany this press release and copies of the press releases for the other Nature Biotechnology papers can be found at: bit.ly/1plEDcV.
For further information or if you would like to interview Professor Jones please see external contact information below.
About The Sainsbury Laboratory
The Sainsbury Laboratory (TSL) is a world-leading research centre focusing on making fundamental discoveries about plants and how they interact with microbes. TSL not only provides fundamental biological insights into plant-pathogen interactions, but is also delivering novel, genomics-based, solutions which will significantly reduce losses from major diseases of food crops, especially in developing countries. TSL is an independent charitable company and receives strategic funding from the Gatsby Charitable Foundation with the balance coming from competitive grants and contracts from a range of public and private bodies, including the European Union (EU), Biotechnology and Biological Sciences Research Council (BBSRC) and commercial and charitable organisations. For more information visit: www.tsl.ac.uk.
The Genome Analysis Centre (TGAC) is a world-class research institute focusing on the development of genomics and computational biology. TGAC is based within the Norwich Research Park and receives strategic funding from the Biotechnology and Biological Science Research Council (BBSRC) – £7.4M in 2013/14 – as well as support from other research funders. TGAC is one of eight institutes that receive strategic funding from BBSRC. TGAC operates a National Capability to promote the application of genomics and bioinformatics to advance bioscience research and innovation.
TGAC offers state of the art DNA sequencing facility, unique by its operation of multiple complementary technologies for data generation. The Institute is a UK hub for innovative Bioinformatics through research, analysis and interpretation of multiple, complex data sets. It hosts one of the largest computing hardware facilities dedicated to life science research in Europe. It is also actively involved in developing novel platforms to provide access to computational tools and processing capacity for multiple academic and industrial users and promoting applications of computational Bioscience. Additionally, the Institute offers a Training programme through courses and workshops, and an Outreach programme targeting schools, teachers and the general public through dialogue and science communication activities. For more information visit: www.earlham.ac.uk.
For more information about the Gatsby Foundation go to: www.gatsby.org.uk
BBSRC invests in world-class bioscience research and training on behalf of the UK public. Our aim is to further scientific knowledge, to promote economic growth, wealth and job creation and to improve quality of life in the UK and beyond.
Funded by Government, BBSRC invested over £509M in world-class bioscience in 2014-15. We support research and training in universities and strategically funded institutes. BBSRC research and the people we fund are helping society to meet major challenges, including food security, green energy and healthier, longer lives. Our investments underpin important UK economic sectors, such as farming, food, industrial biotechnology and pharmaceuticals.
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