Population genomics and evolution of adaptive traits in Pines

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.

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.