NEWS: New genomics-driven surveillance to track crop diseases

1 Mar 2015

New genomics driven surveillance strategy to tackle emerging and re-emerging crop pathogens that threaten global food security

UK scientists from The Genome Analysis Centre (TGAC), John Innes Centre (JIC), The Sainsbury Laboratory (TSL) and the National Institute of Agricultural Botany (NIAB) have developed a new robust and rapid genomics strategy to track the devastating wheat yellow rust pathogen.

Despite modern agricultural practices, diseases of the major food crops cause up to 15% pre-harvest yield loss worldwide. Among these crops, wheat is a critical staple providing 20% of the calories and over 25% of the protein consumed by humans. One of the major fungal diseases of wheat that has re-emerged globally in recent years is yellow (stripe) rust caused by the fungus Puccinia striiformis Westend f. sp. tritici Eriks. (PST).

This disease is widespread across the major wheat-producing areas of the world and can cause significant reductions in both grain quality and yield in susceptible cultivars. In the last decade, new PST variants have emerged that are adapted to warmer temperatures, have expanded their ability to infect different wheat varieties and are more aggressive than those previously characterised causing a serious threat to UK and global wheat production.

Improved surveillance and diagnostic systems are essential in responding to the threat of such crop diseases. A team of scientists at TGAC, JIC, TSL and NIAB with funding from BBSRC have joined forces to develop a new pathogen surveillance technique called “field pathogenomics” that can be readily applied to these difficult pathogens. Based on new gene sequencing technologies this method enables scientists to assess the population structure of these pathogens directly from infected field samples, accelerating the response time of scientists and farmers to this disease.

Working closely with the UK Cereal Pathogen Virulence Survey (UKCPVS), funded by the Home Grown Cereals Authority (HGCA) and The Food and Environment Research Agency (fera), the team used this strategy to sequence PST-infected wheat leaves from 17 different counties across the UK in 2013. Their analysis uncovered a marked increase in the diversity of PST and a complete change in the population composition when compared to older archived UK samples collected prior to 2011.

The authors conclude that this is likely due to a recent introduction of a disparate set of exotic PST variants that displaced the previous PST populations. This detailed knowledge directly influences the management of the disease and is helping breeders develop more resistant varieties to these new PST variants. This new methodology can be used to accelerate the genetic analysis of such plant pathogen populations and could potentially be widely applied to a variety of emerging plant and animal diseases.

“Our new field pathogenomics method uses the latest sequencing technologies to rapidly generate high resolution data for describing the diversity in a pathogen population directly from infected field samples. This has been vital for characterising the recent dramatic changes in the wheat yellow rust populations in the UK, ensuring breeders, farmers and agronomists have access to the best possible information about the pathogen population to help them effectively manage disease and in breeding for enhanced resistance,” said Diane Saunders, lead author of the study and Computational Biology Fellow at TGAC and JIC.

Rapid and systematic application of “field pathogenomics” has the potential to transform current disease surveillance systems by generating high-resolution genotypic information that can inform disease incidence models and agronomic practices. The next big challenge is to develop this new method further to reduce its cost so it can be routinely integrated into national surveillance programmes such as the UKCPVS. In the long-term this will provide earlier indications of new pathogen variants and help deploy new wheat varieties with enhanced resistance.

Dr Chris Burt, a cereal molecular geneticist at RAGT Seeds said: “There has been an explosion in the genetic diversity of yellow rust in the UK. This research provides us with a vastly improved understanding of this diversity, and a new method to monitor any future changes that occur. This is essential information to help us to develop varieties that are resistant to the wider range of yellow rust isolates that we now find in the field.”

The scientific paper, titled: “Field pathogenomics reveals the emergence of a diverse wheat yellow rust population ” is published today in Genome Biology. With funding from BBSRC, the study is the result of a European collaboration with partners running the UKCPVS at NIAB in Cambridge, The Sainsbury Laboratory in Norwich, and INRA in France.

Authors Dr Saunders and Dr Cristobal Uauy (JIC) are members of the newly-formed Norwich Rust Group – a team of seven research groups, on the Norwich Research Park, tackling the problem of crop rusts. 

TGAC is strategically funded by BBSRC and operates a National Capability to promote the application of genomics and bioinformatics to advance bioscience research and innovation.

Notes to Editors

Emerging and re-emerging diseases of humans, animals and plants pose a significant hazard to public health and food security. These threats can arise from newly discovered pathogens, such as the Middle East Respiratory Syndrome (MERS) coronavirus in humans, or the adapted disease from animals, zoonotic influenza.

Recent disease outbreaks in plants have been associated with expansions of pathogen geographic distribution and increased spread of known pathogens, such as in the European outbreak of ash dieback and wheat stem rust across Africa and the Middle East. Independent of the host organism, the scale and frequency of emerging diseases has increased with the globalisation and industrialisation of food production systems.

With recent advances in DNA and RNA sequencing, bacteriologists and virologists are capitalising on these technological advances by integrating high-resolution genotypic data into pathogen surveillance activities. However, the application of genomics to emerging complex plant pathogens has fallen behind. Due to such plant pathogens’ large genomes and often necessary parasites that cannot be isolated in the laboratory, the inefficient, standard techniques required to maintain these pathogens’ cells, have set-back the translation of genomics technologies into surveillance and diagnostics methods.

About TGAC
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.

About John Innes Centre

Our mission is to generate knowledge of plants and microbes through innovative research, to train scientists for the future, to apply our knowledge of nature’s diversity to benefit agriculture, the environment, human health and well-being, and engage with policy makers and the public.

To achieve these goals we establish pioneering long-term research objectives in plant and microbial science, with a focus on genetics. These objectives include promoting the translation of research through partnerships to develop improved crops and to make new products from microbes and plants for human health and other applications. We also create new approaches, technologies and resources that enable research advances and help industry to make new products. The knowledge, resources and trained researchers we generate help global societies address important challenges including providing sufficient and affordable food, making new products for human health and industrial applications, and developing sustainable bio-based manufacturing.

This provides a fertile environment for training the next generation of plant and microbial scientists, many of whom go on to careers in industry and academia, around the world.


The Biotechnology and Biological Sciences Research Council (BBSRC) invests in world-class bioscience research and training on behalf of the UK public. Its 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, and with an annual budget of around £467m (2012-2013), it supports research and training in universities and strategically funded institutes. BBSRC research and the people it funds are helping society to meet major challenges, including food security, green energy and healthier, longer lives. Research investments underpin important UK economic sectors, such as farming, food, industrial biotechnology and pharmaceuticals.

For more information about BBSRC, our science and our impact:

For more information about BBSRC strategically funded institutes:

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 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.

NIAB is a major international centre for plant research, crop evaluation and agronomy – a unique national resource, with nearly 100 years of experience and an internationally recognised reputation for independence, innovation and integrity. With headquarters in Cambridge and regional offices across the country, NIAB spans the crop development pipeline, with the specialist knowledge, skills and facilities required to support the improvement of agricultural and horticultural crop varieties, to evaluate their performance and quality, and to ensure these advances are transferred into on-farm practice through efficient agronomy.

The UK Cereal Pathogen Virulence Survey (UKCPVS) is funded by Fera and HGCA and managed by NIAB. It has been monitoring cereal rusts and mildews in the UK for more than 40 years, detecting and warning industry and growers of new races of disease emerging on resistant varieties. The UKCPVS:

  • Monitors changes in virulence of UK cereal pathogen populations
  • Maintains and improves variety disease resistance allowing growers to prioritise other characteristics such as yield and quality when choosing a variety
  • Enables breeders and variety testing authorities to screen out potential new varieties and breeding lines that are too susceptible to new races of disease before they get to the HGCA Recommended List stage or onto farm
  • Provides information and warnings to assist disease risk management on farm; underpinning HGCA RL disease resistance ratings and assessing the threat that each new race poses to the full range of commercial varieties.