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

ReferenceBB/L012596/1
Principal Investigator / Supervisor Dr Paul Jepson
Co-Investigators /
Co-Supervisors
Institution University of Oxford
DepartmentGeography - SoGE
Funding typeResearch
Value (£) 101,742
StatusCompleted
TypeResearch Grant
Start date 30/06/2014
End date 29/06/2017
Duration36 months

Abstract

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

Summary

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.

Impact Summary

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
Committee Not funded via Committee
Research TopicsCrop Science, Microbiology, Plant Science
Research PriorityX – Research Priority information not available
Research Initiative Tree Health and Plant Biosecurity Initiative (THAPBI) [2013-2015]
Funding SchemeX – not Funded via a specific Funding Scheme
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