Population genomics and evolution of adaptive traits in Pines

Lead Research Organisation: NERC Centre for Ecology and Hydrology
Department Name: Biodiversity (Penicuik)

Abstract

During their evolution, forest trees have migrated (by seed dispersal) and adapted to new environments. This 'local adaptation' caused changes in the parts of the genome that control a tree's ability to survive and reproduce in different climates. As a result, forest trees often show strong differences between populations in observable characters (phenotype), for example in height or shape, in timing of growth, or in ability to withstand cold temperatures or water deficit. Although a lot of research has been done on differences in tree phenotype and how this is shaped by the environment, very little is known about the mutations, genes and biochemical pathways involved. However, information about the genes that control adaptive traits and how they evolve would be useful for conservation, restoration and forest management, particularly in the face of future climate change. For example, if we know how a particular set of genes (genotype) evolved to fit a certain type of environment, we can make better predictions about how changes in that environment will affect the trees. Similarly, foresters want to plant the best tree for their land, which will grow tall and straight, and stay free from disease. But at the moment it takes many years to grow trees to find out which types are the best. By knowing which genes control these important traits, good seedlings can be chosen very early on to provide the best crop from the forest. As forest tree species make up the majority of biodiversity on land and are very important for the economies of many countries, this work can make a big difference.

The project will study how genes control phenotypes in different environments, in four closely-related pine tree species. These are: Scots pine, which is the most widespread pine tree species of all; Dwarf mountain pine, which comes from the mountains of Central and Eastern Europe; Mountain pine, from the mountains of Spain, France and the Western Alps; and Peat-bog pine from the Central European lowlands. Right now, as a result of several years of work by the scientists in the team, we can look at more genes in these species than ever before. By integrating this knowledge with the very latest genetic techniques and a living collection of plants from each of the species we will look for genomic regions and networks involved in the species divergence and adaptations. We hope this will let us understand the link between genotypes and phenotypes, how the environment drives evolution in these tree species and what this means for how forest will change in the future. Worldwide, it will be one of the largest surveys of the genome ever in natural populations of forest trees and will be the first to use molecular data at the whole genome scale of several closely related species to study how tree species evolve.
To make sure the project makes a difference, we will publish our results in international science journals and make our data freely available. We will spread awareness of what we are doing by taking part in Edinburgh's Science Festival and National Science and Engineering Week, by press releases and other special publications and by visits to local schools. We are also talking to forest tree breeders, who work on growing better trees for forestry, about the best ways to use genetic information available in natural populations. Working with them, we will translate what we find out into new ways to grow better trees, but also into better ways to conserve the genetic diversity in natural forests. If both of these messages get across, to foresters and the public, then our project can have a real impact.

Planned Impact

Primarily, the project will deliver new genomic datasets for four pine species that link single nucleotide polymorphisms (SNPs) and variation in phenotypic traits. The outcomes will provide new tools for marker based selection and for the efficient management of natural genetic resources. A range of interested stakeholders, including forest managers and tree breeders, have been identified, partly through directed workshops held as part of the activities of the European Network of Excellence, EVOLTREE, in which CEH is a partner. In the UK, the principal non-academic beneficiaries of the research will be the Forestry Commission and Forest Research, with whom CEH has strong links through ongoing collaborations and who will be able to use data on the spatial distribution of genetic variation in pine species to improve management of forest ecosystems especially in relation to economically and adaptively important traits.

Project outputs will have direct application in science-based conservation of genetic resources in the remnant Scots Pine forest fragments in Scotland and should lead directly to reform of the current guidelines for management. Knowing the geographical distribution of genetic variation in the focal pine species is valuable for conservation and allows, for example, better targeting of seed sources for plantations for restoration. This would be of broad interest to any groups involved in forest management and restoration, which in the UK includes Scottish Natural Heritage and The Woodland Trust.

By developing a genotyping platform (SNP-chip) the project will also contribute to the development of genomic selection in trees. As there is a great need to meet the human demand for forest tree products (solid wood, paper, food and energy), genomics-based breeding approaches can greatly accelerate traditional approaches that generally use long-term and expensive phenotype tests. The beneficiaries of those outcomes include research, end user and stakeholder communities. The European Forestry Institute, in which CEH is a partner through membership of the EVOLTREE network, provides a channel of communication to all of these groups across Europe, whilst IUFRO (International Union of Forest Research Organization), links forest researchers and stakeholders worldwide. These databases, and the corresponding ecological data, will also be valuable to environmental modellers to parameterise models testing the response of forests to environmental change.

There is a major public interest in forests, as seen in the recent debate in the UK on commercialization of nationalised forest lands. This resulted in a huge public response, and a government u-turn on the policy. Our project will work to inform the public about how genetic and genomic data can be used in forest management for dealing with climate change impacts and related threats to forest ecosystems including spread of pathogens and disease susceptibility. The project will spread awareness of the value of Scottish Scots pine populations, the remnants of the historic Caledonian forest of this iconic species for Scotland, and address the issue of strategies for reforestation in Scotland considering its population and evolutionary history.

The project will build new international collaborations by promoting knowledge exchange and synergies between European Research Institutes (CEH, IDPAS, INIA, Edinburgh University, EFI), two NERC funded projects and the EC-funded project, ProCoGen.

To ensure the project delivers the expected impact, a programme of training (career development and science-into-policy) and internal knowledge exchange will be undertaken by project staff. The project results will be presented to general and specialised audiences to promote the project as widely as possible. Finally, project data will be made publicly available via the CEH Gateway, EMBL and EVOLTREE to facilitate future research projects, in particular on genomic selection.
 
Description We have developed a method for rapidly processing genotyping of large numbers of Scots pine trees. This allows us to examine the links between the genes included in our method and the characteristics of the trees. Within Scots pine, our key outcomes link gene markers with differences in response to disease, in timing of growth in spring and to overall growth. We also find that a subset of the genes that vary within Scots pine for characters that help it adapt to different environments, are also involved in the fixed differences that have arisen during evolution of its close relatives Pinus mugo and P. uncinata.
Exploitation Route Genetic resources developed by the project will be of direct benefit to tree breeders and for future research into the genes underpinning adaptation.
Sectors Agriculture, Food and Drink,Environment

 
Description The development of genome-wide genotyping capability has stimulated new collaboration with Forest Research to initiate testing of genomic selection methods for Scots pine. Thiswould contribute directly to better breeding techniques and ultimately provide new applications for nurseries and commercial foresters.
First Year Of Impact 2015
Sector Agriculture, Food and Drink
Impact Types Economic

 
Description BES Scottish Policy Group response to the Scottish Government's consultation on the Forestry Strategy 2019-2029
Geographic Reach Local/Municipal/Regional 
Policy Influence Type Participation in a national consultation
Impact Highlighted need for genetic diversity to secure resilient trees and forests.
URL https://www.britishecologicalsociety.org/policy/reports-publications/consultation-inquiry-responses/
 
Description Inclusion of Forest Genetic Resources as key part of UK government's Tree Health Resilience Strategy (DEFRA, May 2018)
Geographic Reach National 
Policy Influence Type Citation in other policy documents
Impact Research outputs on genetic diversity in trees and their value for the resilience of species underpinned the development of the UK FGR Strategy, which led to the recognition in national Tree Health Resilience policy that genetic diversity is essential to the long term sustainability of our trees and forests.
URL https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/7107...
 
Description (B4EST) - Adaptive BREEDING for productive, sustainable and resilient FORESTs under climate change
Amount € 6,478,663 (EUR)
Funding ID 773383 
Organisation European Commission 
Sector Public
Country European Union (EU)
Start 05/2018 
End 04/2022
 
Description (GenTree) - Optimising the management and sustainable use of forest genetic resources in Europe
Amount € 8,000,000 (EUR)
Funding ID 676876 
Organisation European Commission 
Sector Public
Country European Union (EU)
Start 03/2016 
End 02/2020
 
Title Candidate Gene sequence data. GeneBank Acc. Nr. KC979156 - KC980906 
Description Genetic variation at candidate genes across four pine species 
Type Of Material Database/Collection of data 
Provided To Others? No  
Impact Evidence for the action of selection acting within and among pine species 
URL http://www.ncbi.nlm.nih.gov/popset?DbFrom=nuccore&Cmd=Link&LinkName=nuccore_popset&IdsFromResult=575...
 
Title Raw transcriptomic dataset European Nucleotide Archive 
Description Raw transcriptomic datasets for 17 samples of pine 
Type Of Material Database/Collection of data 
Provided To Others? No  
Impact New genomic resources for Pine genome 
 
Description Formation of the Steering Group for the UK's Forest Genetic Resources Strategy. 
Organisation Earth Trust
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution Jontly with RBGE Kew, led the formation of the collaboration.
Collaborator Contribution The other partners participated actively in the formation and initiation of the collaboration and have committed to involvement in the future.
Impact Publication of the Strategy for the UK's Forest Genetic Resources
Start Year 2017
 
Description Formation of the Steering Group for the UK's Forest Genetic Resources Strategy. 
Organisation Forest Research
Country United Kingdom 
Sector Public 
PI Contribution Jontly with RBGE Kew, led the formation of the collaboration.
Collaborator Contribution The other partners participated actively in the formation and initiation of the collaboration and have committed to involvement in the future.
Impact Publication of the Strategy for the UK's Forest Genetic Resources
Start Year 2017
 
Description Formation of the Steering Group for the UK's Forest Genetic Resources Strategy. 
Organisation Royal Botanic Gardens, Kew
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution Jontly with RBGE Kew, led the formation of the collaboration.
Collaborator Contribution The other partners participated actively in the formation and initiation of the collaboration and have committed to involvement in the future.
Impact Publication of the Strategy for the UK's Forest Genetic Resources
Start Year 2017
 
Description Formation of the Steering Group for the UK's Forest Genetic Resources Strategy. 
Organisation Woodland Trust
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution Jontly with RBGE Kew, led the formation of the collaboration.
Collaborator Contribution The other partners participated actively in the formation and initiation of the collaboration and have committed to involvement in the future.
Impact Publication of the Strategy for the UK's Forest Genetic Resources
Start Year 2017
 
Description Cavers S, Wachowiak W, et al (2018) Pursuing the genetics of local adaptation in Scots pine, Pinus sylvestris L. Keynote Talk at the conference 'Biology and ecology of woody plants', held in celebration of the 85th anniversary of the Institute of Dendrology, Polish Academy of Sciences, Kórnik, Poland. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Keynote speech at an international conference.
Year(s) Of Engagement Activity 2018
 
Description Cavers et al (2015) Genomics tools and genetic conservation. Invited talk, PROCOGEN final conference, Orleans, France. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited talk to open conference, summarising the outcomes of the international Conifer Genome sequencing project. Cavers presented summary of genomic data applied in the context of conserving forest genetic resources.
Year(s) Of Engagement Activity 2015
URL http://bfw.ac.at/rz/bfwcms2.web?dok=9676
 
Description Development of a Strategy for the UK's Forest Genetic Resources 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact 50 delegates attended a workshop or submitted contributions towards development of a national strategy for Forest Genetic Resources.
Year(s) Of Engagement Activity 2018
URL https://www.ceh.ac.uk/our-science/projects/uk-forest-genetic-resources-strategy
 
Description Membership of the Scientific Advisory and Response Team (SART) of Scotland's Plant Health Centre 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact The Plant Health Centre is a virtual centre of expertise funded by Scottish Government through RESAS (Rural and Environment Science and Analytical Services Division) to help tackle plant health challenges for Scotland.
Year(s) Of Engagement Activity 2018
URL https://www.planthealthcentre.scot/about-us
 
Description POSTER: Kevin Donnelly, Joan Cottrell, Richard Ennos, Guiseppe Giovanni Vendramin, Stuart A'Hara, Sarah King, Annika Perry, Witold Wachowiak, Stephen Cavers (2016) Mitochondrial variants in Pinus sylvestris and the P. mugo complex. IUFRO Genomics and Forest Tree Genetics, Arcachon, 30 May-3 June 2016. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Poster at international conference.
Year(s) Of Engagement Activity 2016
URL https://colloque.inra.fr/iufro2016/Programme
 
Description POSTER: Wachowiak, Perry, Donnelly, Cavers (2016) Quantitative and molecular genetic variation in closely related European pine species. IUFRO Genomics and Forest Tree Genetics, Arcachon, 30 May- 3 June 2016. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Poster at international conference.
Year(s) Of Engagement Activity 2016
URL https://colloque.inra.fr/iufro2016/Programme
 
Description Paper given at IUFRO Forest Tree Breeding conference, Prague, Czech Republic 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact Talk and discussion

Offers for new collaborations
Year(s) Of Engagement Activity 2014
URL http://www.iufrobreeding2014.org/
 
Description Talk at 3rd Research-Teaching Conference of the Faculty of Biology A. Mickiewicz University, Poznan, Poland 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact Talk and discussion

Plans for future work with the University emerged.
Year(s) Of Engagement Activity 2014
 
Description Talk at Ancient Tree Forum annual meeting (Aviemore) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Talk and discussion

Strong discussion about right and wrong ways to deal with tree pests / pathogens.
Year(s) Of Engagement Activity 2014
URL http://www.ancient-tree-forum.org.uk/ancient-tree-forum/atfevents/archive/archive.htm
 
Description Talk at Ecological Genetics Group meeting, Newcastle 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact Talk and questions

Good suggestions for other analytical approaches
Year(s) Of Engagement Activity 2014
 
Description Talk at Procogen Dissemination Workshop, Szombathely, Hungary 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact Talk, discussion and planning

Strong post-talk discussion and numerous requests for presentation after the meeting indicated the level of interest
Year(s) Of Engagement Activity 2014
URL http://www.procogen.eu