Identifying genomic resources against pests and pathogens in tree genera: a case study in Fraxinus

Lead Research Organisation: University of Oxford
Department Name: Geography - SoGE

Abstract

British ash trees are threatened by the fungal disease ash dieback, which has already arrived in the UK, and by the emerald ash borer (EAB), a beetle found in the USA and Russia. Scientists are currently seeking to develop ash trees resistant to ash dieback, using genetic information already present in European ash trees. In the longer term, Britain and the World need ash trees that are resistant to both ash dieback and EAB. To achieve this, we may need to study not just in Fraxinus excelsior -- the ash species most common in Britain -- but in the whole ash genus, which consists of about 50 species worldwide. Preliminary studies suggest that some of these species are resistant to one or both of these problems, due to co-evolution. Looking in the whole genus may help us (i) to identify genes in Fraxinus excelsior that can give resistance to these threats, which would otherwise have been hard to find, and (ii) reveal genes in other ash species that give resistance but are not found in Fraxinus excelsior.

This consortium is an international team of leaders in research on ash trees, ash dieback, the EAB, ash taxonomy and phylogenetics, ash genomics, tree breeding, phylogenomics and social framings of nature. It is led by Dr Richard Buggs (Queen Mary, University of London) who is currently sequencing a Fraxinus excelsior genome funded by NERC. It will pioneer the application of a new method for finding genes responsible for traits developed by Dr Steve Rossiter's group (Queen Mary, University of London), funded by BBSRC, that has not been used before in tree health contexts. This works by building evolutionary trees for thousands of genes in the ash genus, and examining how the patterns of evolution seen in them fit with patterns of susceptibility/resistance to ash dieback and EAB. This evolutionary approach allows us to identify genes or gene variants that may be involved in resistance.

For this method to work, we need accurate information about the susceptibility of different ash species to ash dieback and the EAB. Our current knowledge of this is patchy and largely anecdotal, so we need to fill this gap. At the moment we do not even have good data on how susceptible the British ash species, Fraxinus excelsior, is to the EAB. We therefore propose an experiment on susceptibility of ash species to the EAB to be carried out in the USA, in an area where this pest is killing thousands of trees. This will be conducted by Dr Jennifer Koch (US Forest Service), who has years of experience and well developed protocols in testing ash trees for EAB susceptibility, but has not carried out a systematic study of the whole genus. This experiment will be carried out on clones of all ash species currently available in American living collections.

A similar experiment will be carried out in the UK, testing the susceptibility of all ash species currently available in British and Irish living collections to ash dieback. This experiment will be led by Dr Steve Lee (Forest Research) who is currently leading a project screening thousands of F. excelsior genotypes for resistance to ash dieback, funded by Defra. This proposal provides a logical extension to that project to include other ash species.

Whilst we carry out experimental work to identify genes for pest and pathogen resistance, a social science study will be conducted by Dr Paul Jepson (Oxford University) about how they might be used in a tree health context in a manner that is socially and politically acceptable. Could we develop ash populations resistant to EAB and ash dieback by planting other ash species? By hybrid breeding programes? By genetic modification? This study will seek answers to these questions in a social and political sense.

This project will pioneer new methods and approaches to tackling both a fungal pathogen and an invertebrate pest in a widespread tree genus. If successful these approaches can be used to tackle tree health issues in other tree genera.

Technical Summary

This consortium will develop a new approach for identifying genes conferring resistance to tree pests and pathogens, using phylogenomic information derived from the genus of a tree species that is at threat. This approach exploits new DNA sequencing technologies and apply the latest methods in phylogenomics, pioneered by co-PI Rossiter in his work on mammals. We will use Fraxinus as a model, as it faces two major threats and preliminary data suggest that resistance to both threats has evolved in parallel more than once in the genus. It is economically and ecologically valuable and some genomic data already exist. The genome of every available species in the genus Fraxinus will be sequenced and aligned, and phylogenies built for up to 10000 shared regions. Data on the susceptibility of each species to ash dieback and the emerald ash borer (EAB) will be generated in experiments in the UK (on ash dieback) and USA (on EAB). Candidate genes and alleles for low susceptibility will be sought by identifying those gene trees that are incongruent with the consensus species tree of Fraxinus, but congruent with patterns of low susceptibility in the genus. Signatures of selection will be analysed in these genes. Identification of these gene candidates will inform future breeding programmes. This complements other approaches currently seeking resistance to ash dieback in F. excelsior, by broadening the net to include over 30 related species; this is analogous to studies of wild relatives of crop species in agricultural pre-breeding programmes. As with crops, there is a danger that the possibilities made available by science may be mis-perceived by the public, causing sociological hindrance to their implementation. Thus, the proposal includes a social study to understand how new possibilities can be communicated to the public, and what possibilities are politically acceptable. The project will show us what solutions to tree health issues are feasible scientifically and politically

Planned Impact

Genomic scientists.-This project tackles a central issues in genome science: associating phenotypes to specific gene regions. We are using an approach that has only recently been developed and proved successful in identifying genes for echolocation in mammals. Demonstration of its usefulness in finding genes for low susceptibility to both an invertebrate pest and a fungal pathogen in trees will be a major step forwards in international genome science.

Tree geneticists.-New methods for discovering candidate genes for traits relating to tree health are of great international interest, because many of the methods used in crop genetics are difficult to carry out in trees due to their long lifespans

Tree breeders.-We aim to find candidate genes for low susceptibility to ash dieback and the emerald ash borer in the ash genus (Fraxinus), and recommend strategies by which tree breeders could implement these to produce ash trees resistant to both threats. Forest Research, the Future Trees Trust and the Earth Trust are the two main UK organisations involved in such research.

Biosecurity policy makers.-Our findings will inform policies for tree biosecurity throughout the northern hemisphere. Ash dieback is currently in Europe but not N. America. EAB is currently in the N. America but not in Europe, though it is near Moscow and spreading westwards. Our research will inform governments on both continents about the susceptibility of their local species of ash to these threats. We do not yet have rigorous data on the susceptibility of British ash trees to EAB, though anecdotal evidence suggests that it is susceptible. This project will provide rigorous data on this, allowing us to better parameterize the risks associated with EAB, with immediate impacts for biosecurity policy.

Biotechnology policy makers.-Our proposal includes a social science study of what genomic solutions to tree health issues would be acceptable to the public, interest and stakeholder groups, and the media. It will make recommendations about how these issues are framed in public discourse.

Plant health experts.-This project will exchange knowledge about EAB and ash dieback among experts in Europe and N. America, allowing efficient early warning of their spread to new continents. In the UK, the ObservaTREE network provides tree health training materials and volunteer networks to deliver a tree health early warning system.

Foresters.-Ash are one of only about six broad-leaved species that are planted commercially in Britain. They can tolerate moist conditions and squirrels. Death or reduced growth of ash due to ash dieback or EAB is a major challenge to the forestry industry. This is represented in the UK by Confor, Institute of Chartered Foresters, and other organisations. The forestry industry is very interested in increasing the resilience and species base of UK forestry.

Biodiversity.-Ash is one of the last trees in the UK to flush in the spring, allowing a rich assemblage of spring-flowering plants on forest floors. It's bark has an unusual pH, giving a niche for rare lichens. Organisations in the UK such as Earth Trust, Woodland Trust and National Trust seek to conserve this biodiversity.

Public health.-A 2013 American study has shown an increase in human mortality related to cardiovascular and lower-respiratory-tract illness in counties where ash trees have died due to the EAB (Am. J. Prev. Med. 44:139-145).

Quality of life.- There are 80 million ash trees the UK alone. If future generations can grow and enjoy ash trees in the UK, this will enhance quality of life and health. The British public is clearly very interested in, and concerned about, this issue. The success of this project will reassure them that ash trees are not lost forever from the landscape, and that there is also hope for other tree species that are currently threatened by pests.

Botanic Gardens/Arboreta.-We will demonstrate the benefits of living collections
 
Title Infographic on tree breeding solutions 
Description The project commissioned creation of an infographic on various tree breeding solutions with the main aim of it being used during public survey, to facilitate and improve understanding of various scientific concepts used in the questionnaire, via easy to understand images. 
Type Of Art Image 
Year Produced 2015 
Impact The infographic facilitated and improved the understanding of scientific concepts by members of public interviewed during the survey, hence improving the quality of the results. 
 
Description We conducted two surveys of public attitudes to different tree breeding solutions to ash dieback.

The first was among 'interested UK publics' ie those who attend countryside events in England and are likely to engage discursively and politically (through letter writing, petitions etc.) This survey population was found to a a) care about the issue, b) want an active response, c) do not really distinguish between ash trees in forestry or ecological settings, and d) prefer traditional breeding solutions. Further that e) younger people and gardeners are open to GM breeding techniques, but f) the more policy-empowered naturalists are more likely to be anti-GM.
A second survey was conducted via YouGov and sampled the 'general population' We found that whilst there was a firm anti-GM and 'we shouldn't tamper with nature' attitude among UK publics, there was an equally firm and perhaps slightly larger pragmatic attitude that GM (science and technology) should be used if there is a good reason to do so, for example if it can help protect trees from disease and help feed the world. The latter view was significantly stronger among younger age groups (Millennials), those living in urban areas and when the (GM)modified trees were destined for urban and plantation, rather than countryside settings.
Exploitation Route We suggest that these findings provide three 'steers' for science and policy: 1) policy needs to include an active intervention component involving the breeding of disease-tolerant trees, 2) that could consider genomic solutions to tree breeding with more confidence in the future as large and influential publics appear to be relaxed about the use of genomic techniques to increase tolerance of trees to disease, and c) there is a need for a dialogue with publics to manage expectations on the extent to which science and policy can control tree disease
Sectors Agriculture, Food and Drink,Environment

 
Description We conducted three focus groups with different types of stakeholders with interests in tree-breeding solutions to ash-dieback. The head of tree policy attended these focus groups and reported that she found them a neutral space to listen to views and reflect on approaches to this complex policy problem - she comments that they were neither and advisory group which can become a bit 'insider' nor a meeting with groups lobbying for their perspective to be taken into account. In addition, we brought new stakeholders into the policy dialogue on this issue. We will reflect more on this science-policy-practice dynamic in our final report.
First Year Of Impact 2015
Sector Environment,Leisure Activities, including Sports, Recreation and Tourism,Other
Impact Types Policy & public services

 
Title Public perceptions to tree breeding solutions to Ash dieback: Interested publics (countryside events) questionnaire survey database 
Description The team carried out a large scale public survey of interested publics on their attitude to various tree breeding solutions to deal with ash dieback. The survey generated significant amount of data which was entered into an SPSS (Statistical Programme for Social Sciences) database and analysed. At the end of the project, the database will be put into the Oxford university research archive. 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact The survey of 1200 respondents carried out last summer was the first of its kind in the UK, and the database contains unique information on public acceptability of various options to deal with ash dieback, including genetic modification solutions. The Survey found that: a) Breeding disease tolerance within native ash using traditional methods was the most acceptable option among these publics, with other natural options such as accelerated breeding and cross-breeding receiving high levels of support. b) Substantial levels of support for cis-genetic breeding solutions, but less for trans-GM. Support for GM approaches was higher among gardeners and younger respondents and increased when information on timescales was provided. Findings suggests that tree health policy in the UK should retain an active intervention component involving the development of tree-breeding solutions, moreover that support for development of disease tolerance using cis-GM technologies may build over time and/or following a wider public dialogue and therefore has a role in a future-looking policy. The study is in press (2017) in Forest Policy and Economics Data deposited on Oxford Research Archive - will become public when above paper published 
 
Title Public perceptions to tree breeding solutions to Ash dieback: Omnibus questionnaire survey database 
Description The online omnibus survey was carried out in March-April 2016 targeting wider UK public. The main aim was to identify public acceptability of various tree breeding solutions to ash dieback. The survey will have a strong focus on public acceptability of GM options to ash dieback. 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact This survey was and extension to the survey of public perceptions of tree-breeding solutions to ash dieback among interested public in the UK carried out at countryside events in summer 2015, but targeting the wider UK population, and with a stronger focus on the acceptability of GM solutions. Similar research has previously not been carried out in the UK. The study: a) confirmed the findings of other surveys that UK publics do not support a 'no-action' option even though this may be the most realistic approach. There is a strong attitude that the government should 'do something'. b) found that a large proportion of respondents expressed the view that GM tree-breeding solutions are unacceptable and we shouldn't 'tamper with nature'. However, a slightly larger proportion answered that GM (science and technology) should be used if there is a good reason to do so e.g. if it can help protect trees from disease and help feed the world. c) That this pragmatic view was significantly stronger among younger age groups (Millennials), those living in urban areas and when the modified trees were destined for urban and plantation, rather than countryside settings. d) That anti- GM attitudes correlated with the view that humans should not interfere with nature: this view was held by 40% of respondents and is consistent with the balance of nature metaphor that has long been rejected by ecologists. This suggests that more effort is need to bring public constituencies up to speed with modern conceptions of nature. e) Overall, our finds suggest that the UK government could include genomic solutions in tree healthy with more confidence if they so wished. In the case of trees at least the opposition between GM-science and public opinion is not what it was and large and influential publics appear to be relaxed about the use of genomic techniques to increase tolerance of trees to disease. Data deposited on Oxford Research Archive - will become public when above paper published 
 
Description Collaborations established during focus groups 
Organisation Department For Environment, Food And Rural Affairs (DEFRA)
Country United Kingdom 
Sector Public 
PI Contribution Defra representative Nicola Spence was present at our focus group discussion in November 2016. The discussions initiated during focus groups will likely influence future policy making.
Collaborator Contribution Nicola Spence's presence added an increased profile and weight to the discussions, and generated a significant media interest.
Impact Defra representative Nicola Spence was present at our focus group discussion in November 2016. The discussions initiated during focus groups will likely influence future policy making. Nicola Spence's presence added an increased profile and weight to the discussions, and generated a significant media interest.
Start Year 2015
 
Description Major stakeholder focus groups 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Media (as a channel to the public)
Results and Impact The project team organised 3 focus groups with key stakeholders in November in 2015. The main aim of the focus group was to discuss the potential solutions to ash dieback and to present findings from the public survey carried out in summer 2015. The first focus group involved the representatives of the media (the Guardian, BBC, Horticulture week etc). The second focus group involved invited members of industry (nurseries, arboriculture association, London tree officers association, Institute of Chartered foresters, Tree council, timber industry representatives etc). The third and final focus group involved representatives of major trusts with a stake in countryside, e.g. Forestry Commission, Forest Research, Woodland Trust, Earth Trust etc. Nicola Spence, Defra chief plant health officer, was present during all 3 focus groups, which added an extra weight and a high profile to the discussions. The first focus group with media representatives resulted in several press articles on our research in some of the major newspapers (e.g. The Observer, The Times etc), which apart from serving as a dissemination tool has helped in putting ash dieback awareness back on public agenda. Overall, the discussion groups were very successful for both dissemination of our research findings, but also for the likely influence they will have on future public opinion (via media articles), and policy making.
Year(s) Of Engagement Activity 2015
 
Description Mid-term THAPBI grantholders workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact The main aim of the workshop was to report on mid-term findings from various THAPBI projects. Richard Buggs presented findings from our research, which included both the scientific component and the social science component run by Oxford.
Year(s) Of Engagement Activity 2015
 
Description Social Science Workshop on Tree Health and Plant Biosecurity 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact The primary aim of the workshop was to communicated findings from any social science research conducted in the are of tree health and tree diseases. Paul Jepson and Irina Arakelyan presented findings from the public survey conducted in summer 2015, and raised awareness of the project. Nicola Spence (Defra chief plant health officer) was present at the workshop, following which she agreed to take part in the focus group discussions planned in London in November 2016.
Year(s) Of Engagement Activity 2015