New genomics-driven surveillance strategy to tackle emerging and re-emerging crop pathogens that threaten global food security
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.
Image: In this micrograph, Yellow Rust spores can be seen bursting out of a wheat leaf from the inside, tearing their way through the epidermis.
SEM photography by Kim Findlay, John Innes Centre
Notes
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.
Research article
Amelia Hubbard, Clare M Lewis, Kentaro Yoshida, Ricardo H Ramirez-Gonzalez, Claude de Vallavieille-Pope, Jane Thomas, Sophien Kamoun, Rosemary Bayles, Cristobal Uauy and Diane G.O. SaundersField pathogenomics reveals the emergence of a diverse wheat yellow rust population
Genome Biology 2015
DOI: 10.1186/s13059-015-0590-8
http://dx.doi.org/10.1186/s13059-015-0590-8
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. www.tgac.ac.uk
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