Disease tolerant genes renew hope for UK ash trees
Researchers have identified genetic markers for disease tolerance that suggest UK ash trees may have a fighting chance against a fungal infection that has the potential to wipe out 90% of the European ash tree population.
The disease, called ash dieback, was first identified in Poland, where it devastated the native ash tree population. It rapidly spread across northern Europe and was discovered in the UK in 2012.
Results from the latest study published in Nature, a UK collaboration between Queen Mary University of London (QMUL), University of York, Earlham Institute (EI), John Innes Centre (JIC), NIAB and the University of Copenhagen, could contribute to breeding new varieties of ash that are tolerant to the disease.
Much like Dutch elm disease, ash dieback is aggressive, spreads quickly through the ash tree population, and has no cure, other than individual natural tolerance to the infection. It is spread on the wind or via the transfer of infected saplings between areas. Symptoms include loss of leaves and lesions, which are a useful way to diagnose fungal ash dieback, as they leave a characteristic diamond-shaped scar on the bark.
The York team had previously tested a genetic screening process on Danish trees identified by collaborators at the University of Copenhagen as having a range of different levels of disease susceptibility. Using this data alongside information from the ash tree genome, which was sequenced by researchers at QMUL by utilising EI’s reference gene models, they were able to improve the genetic markers for disease tolerance and use them to predict the tolerance of a sample of trees from across the UK.
Leading to these research findings, EI (previously ‘The Genome Analysis Centre’) generated the transcriptome and re-sequencing (together with the Institute’s previous analysis of the resistant ‘Tree 35’ from Denmark released in 2013) data to conduct the bioinformatics analysis of the UK ash tree, in alignment with the Nornex Consortium to combat Ash Dieback, funded by DEFRA and BBSRC. The analysis was carried out on a subset of the tree’s genetic regions, with high coverage across the samples. This increased the number of potential markers that could be used to sustain ash tree diversity for breeding programmes.
EI also sequenced 37 trees originating from across Europe to investigate genomic diversity in ash. The data was analysed by researchers at QMU, JIC and NIAB finding evidence for the apparent long-term decline in effective population size. The EI team generated the most comprehensive annotation of ash genes to date, and this will aid researchers in identifying genetic variants linked to specific traits associated with the killer tree disease. This will help seek out the suspected tolerant genes and support future breeding programmes of ash trees with low susceptibility to the disease.
Dr David Swarbreck, Regulatory Genomics Group Leader at EI, said: “Having a more comprehensive annotation of ash genes has improved the identification of markers for ash dieback and will aid future functional studies into this prevalent disease.”
Professor Mario Caccamo, previously at EI, now Head of Crop Bioinformatics at NIAB, added: “This effort is a great example of teamwork across several leading UK research organisations responding to the devastating threat of ash dieback. The identification of markers for tolerance will be a very important tool in the toolbox that complements other ongoing efforts to manage the threat of this disease. We have also generated important genomic resources that will support other studies and offer the foundations for more research into tackling the epidemic.”
Professor Allan Downie, Emeritus Fellow at JIC and coordinator of the NORNEX programme, commented: “This work represents significant new progress in our understanding of ash dieback disease and the patterns of inheritance of tolerance to this disease. Our success has been built on excellent national and international collaborations. These have brought the strengths of genomics and transcriptomics research in the UK together with the excellent analyses of disease susceptibility done in Denmark, to enhance our research into UK ash trees. This progress has been breathtaking in its speed and as a research coordinator based at JIC; I have been delighted by the spirit of collaboration and determination brought to this project by my Danish and UK collaborators.
Early indications suggest that the proportion of UK trees with tolerance to ash dieback is greater than that of the Danish and Polish trees, but it is still unknown whether the UK trees have previously been infected with the disease and built tolerance or whether this is due to their genetic tolerance, is yet to be tested.
The study, “Genome sequence and genetic diversity of European ash trees” is published in the journal, Nature.
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About Earlham Institute
The Earlham Institute (EI) is a world-leading research institute focusing on the development of genomics and computational biology. EI is based within the Norwich Research Park and is one of eight institutes that receive strategic funding from Biotechnology and Biological Science Research Council (BBSRC) - £6.45M in 2015/2016 - as well as support from other research funders. EI operates a National Capability to promote the application of genomics and bioinformatics to advance bioscience research and innovation.
EI offers a 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 key stakeholders, and wider public audiences through dialogue and science communication activities.
The Biotechnology and Biological Sciences Research Council (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 and is the leading funder of wheat research in the UK (over £100M investment on UK wheat research in the last 10 years). 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.
For more information about BBSRC, our science and our impact see: http://www.bbsrc.ac.uk For more information about BBSRC strategically funded institutes see: http://www.bbsrc.ac.uk/institutes
About the 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 wellbeing, 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 John Innes Centre is strategically funded by the Biotechnology and Biological Sciences Research Council (BBSRC). In 2014-2015 the John Innes Centre received a total of £36.9 million from the BBSRC.
NIAB is the UK’s fastest growing crop science organisation, with rapidly expanding research capabilities in plant genetics, agronomy, farming systems and data science, the largest national field trials capability, and strong research links with industry, Government and academia. With headquarters in Cambridge, and regional offices across the country, employing more than 300 people across the UK, NIAB provides scientific research, technical services and practical advice to improve the yield, efficiency and resilience of crop production across the arable, horticulture and top and soft fruit sectors. (www.niab.com)