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

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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

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