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Could disease 'tolerance' genes give new life to UK ash trees?

Copyright: BBSRC

News from: Biotechnology and Biological Sciences Research Council

News from: Earlham Institute

News from: University of Exeter

News from: Queen Mary University of London

News from: The University of Warwick

News from: University of York

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.

Copyright: Jonathan Stocks
Copyright: Jonathan Stocks

Results from the latest study published in Nature, a UK collaboration between Queen Mary University, 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 Queen Mary University 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 were analysed by researchers at QMU, JIC and NIAB finding evidence for 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.”

Professor Mario Caccamo, previously at EI, now Head of Crop Bioinformatics at NIAB, added: “This effort is a great example of team-work across several complementary 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 breath-taking 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.

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Notes to editors

The paper: Genome sequence and genetic diversity of European ash trees by E. Sollars et al is published in the journal Nature on Monday 26 December 2016. DOI: 10.1038/nature20786.

Appendix 1

Release by QMUL: Researchers at Queen Mary University of London (QMUL) have successfully decoded the genetic sequence of the ash tree, to help the fight against the fungal disease, ash dieback.

Tens of millions of ash trees across Europe are dying from the Hymenoscyphus fraxinea fungus – the most visible signs that a tree is infected with ash dieback fungus are cankers on the bark and dying leaves.

Project leader Dr Richard Buggs from QMUL’s School of Biological and Chemical Sciences said: “This ash tree genome sequence lays the foundations for accelerated breeding of ash trees with resistance to ash dieback.”

A small percentage of ash trees in Denmark show some resistance to the fungus and the reference genome is the first step towards identifying the genes that confer this resistance.

The ash tree genome also contains some surprises. Up to quarter of its genes are unique to ash. Known as orphan genes, they were not found in ten other plants whose genomes have been sequenced.

Dr Buggs added: “Orphan genes present a fascinating evolutionary conundrum as we have no idea how they evolved.”

This research is published today in the journal Nature. It involved a collaboration between scientists at: QMUL, The Earlham Institute, Royal Botanic Gardens Kew, University of York, University of Exeter, University of Warwick, Earth Trust, University of Oxford, Forest Research, Teagasc, John Innes Centre, and National Institute of Agricultural Botany.

The reference genome from QMUL was used by scientists at York University who discovered genes that are associated with greater resistance to ash dieback. They have used these to predict the occurrence of more resistant trees in parts of the UK not yet affected by the disease, which is spreading rapidly.

The genome sequence will also help efforts to combat the beetle Emerald Ash Borer, which has killed hundreds of millions of ash trees in North America.

Ash trees have a huge significance in culture and society – they are one of the most common trees in Britain and over 1,000 species, from wildflowers to butterflies, rely on its ecosystem for shelter or sustenance. Ash timber has been used for years for making tools and sport handles, for example hammers and hockey sticks, and is used often for furniture.

The work was funded by NERC, BBSRC, Defra, ESRC, the Forestry Commission, the Scottish Government, Marie Sklodowska-Curie Actions, Teagasc – the Agriculture and Food Development Authority.

Appendix 2

Supportive press release from University of York: Could disease ‘tolerance’ genes give new life to UK ash trees?

Researchers at the University of York have identified genetic markers for disease tolerance that suggest UK ash trees may have a fighting chance against a fungal infection, which 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, a collaboration between the University of York and Queen Mary University of London, could contribute to breeding new varieties of ash that are tolerant to the disease. 

The disease is aggressive, spreads quickly through the 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 shape scar on the bark.

Professor Ian Bancroft, plant biologist at the University of York, said: “This disease has spread across Europe in less than 10 years so there is some urgency to understand how we can better support breeding programmes for the species.

“Ash trees can be found in home gardens, parks, and roadsides and are an important woodland species that support a number of insects and fungi. It is not known exactly how the loss of this tree species will impact the eco-system, but from past examples, we know that the extinction of any species can fundamentally alter the environment.”

The York team had previously tested a genetic screening process on Danish trees. Using this data alongside information from the ash tree genome, which was sequenced by researchers at Queen Mary University, 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.

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 their genetic tolerance is yet to be tested.

Dr Andrea Harper, plant biologist at the University of York, said: “Working with DEFRA, the next stage of this work will be to establish a UK panel suitable for identifying additional, UK-specific, markers for tolerance. This will improve our predictions on individual trees, and provide more information about why some trees are tolerant to the disease. It will also support breeding programmes to develop tolerant varieties of ash.”

The research is published in the journal, Nature.

Appendix 3

Supportive press release from University of Exeter and The University of Warwick: Ash dieback – Insect threat to fungus-resistant trees

Ash trees which can resist the killer dieback fungus may be more vulnerable to attacks by insects, according to new research.

Scientists from the universities of Exeter and Warwick examined trees which are resistant to ash dieback and – unexpectedly – found they had very low levels of chemicals which defend against insects.

With efforts under way to protect ash trees from dieback, the scientists warn that selecting trees for fungal resistance could put them at risk from insects.

Aside from ash dieback, the other major threat to European ash trees is the Emerald Ash Borer beetle, which has already devastated vast tracts of ash in the USA and is currently spreading westwards across Europe.

“Our research highlights the danger of selecting trees for resilience to ash dieback at the expense of resistance to insects that threaten this iconic UK tree species,” said joint lead author Dr Christine Sambles, of the University of Exeter.

“Ash dieback, which is caused by a fungus called Hymenoscyphus fraxineus, can kill young trees in a season, while older trees tend to decline and die over several years.”

The research, published in the journal Nature, is part of a study involving several universities and Government institutes which looked at the DNA of ash trees in the hope of identifying ash dieback resistance.

Instead of focussing on DNA, the Exeter and Warwick scientists looked at differences in chemical composition between tolerant and susceptible ash trees.

“Plants use a vast range of chemicals to defend against fungal attack, and the primary objective was to identify differences which could be used to screen young ash trees and choose the best ones for replanting,” said co-author Professor Murray Grant, Elizabeth Creak Chair in Food Security at the University of Warwick.

“Our findings underline the need for further research to ensure that we select ash trees resilient to present and future threats.”

Co-author Dr David Studholme, of the University of Exeter, added: "These findings highlight Exeter’s world-class expertise in high-impact, integrative plant science underpinned by key research infrastructure, such as the Mass Spectrometry facility.”

About QMUL

Queen Mary University of London (QMUL) is one of the UK's leading universities, and one of the largest institutions in the University of London, with 21,187 students from more than 155 countries.

A member of the Russell Group, we work across the humanities and social sciences, medicine and dentistry, and science and engineering, with inspirational teaching directly informed by our research. In the most recent national assessment of the quality of research, we were placed ninth in the UK (REF 2014).

As well as our main site at Mile End – which is home to one of the largest self-contained residential campuses in London – we have campuses at Whitechapel, Charterhouse Square, and West Smithfield dedicated to the study of medicine, and a base for legal studies at Lincoln’s Inn Fields.

We have a rich history in London with roots in Europe’s first public hospital, St Barts; England’s first medical school, The London; one of the first colleges to provide higher education to women, Westfield College; and the Victorian philanthropic project, the People’s Palace at Mile End.

Today, as well as retaining these close connections to our local community, we are known for our international collaborations in both teaching and research.

QMUL has an annual turnover of £350M, a research income worth £125M (2014/15), and generates employment and output worth £700M to the UK economy each year.

About the University of Exeter

The University of Exeter is a Russell Group university that combines world-class research with very high levels of student satisfaction. Exeter has over 21,000 students and is in the top 1% of universities worldwide. Exeter is also ranked 9th in The Times and The Sunday Times Good University Guide 2017 and 11th in the Guardian University Guide 2017. In the 2014 Research Excellence Framework (REF), the University ranked 16th nationally, with 98% of its research rated as being of international quality. Exeter was named The Times and The Sunday Times Sports University of the Year 2015-16, in recognition of excellence in performance, education and research. Exeter was The Sunday Times University of the Year 2012-13.

The University will launch its flagship Living Systems Institute in 2016, a world-class, interdisciplinary research community that will revolutionise the diagnosis and treatment of diseases. This follows recent investments of more than £350M worth of new facilities across its campuses in recent years; including landmark new student services centres – the Forum in Exeter and The Exchange on the Penryn Campus in Cornwall, together with world-class new facilities for Biosciences, the Business School and the Environment and Sustainability Institute. www.exeter.ac.uk

About Earlham Institute

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. www.earlham.ac.uk and @EarlhamInst

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 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 £36.9M from BBSRC.

About NIAB

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

About BBSRC

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 £473M in world-class bioscience, people and research infrastructure in 2015-16. 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: www.bbsrc.ac.uk.
For more information about BBSRC strategically funded institutes see: www.bbsrc.ac.uk/institutes.

External contacts

Neha Okhandiar, Press Office, Queen Mary University of London


+44 7834 039266

Samantha Martin, Press Office, University of York

+44 1904 322029

Press Office, University of Exeter


+44 1392 724828

Contact

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Tags: DNA Earlham Institute genetics genome sequencing JIC plants research press release