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Genosilva : European Forest Genomics Network

Objective

A.BACKGROUND

It is difficult to overstate the importance of trees. Trees are essential components of the natural landscape, and play a crucial role in global carbon budgeting. Trees also form the foundation of multibillion Euro forest products industries, including the conversion of biomass to energy. Despite their importance from both environmental and economic perspectives, little is know about the mechanisms that underpin the growth and survival of trees. This is surprising, given that an understanding of these mechanisms will guide efforts aimed at ensuring the long-term maintenance of forest health, and the enhancement of forest productivity.

Recently, remarkable progress has been made in the understanding of the mechanisms that control the growth and survival in annual plants. Much of this progress has been made through the application of what it known as functional genomics. Functional genomics entails the analysis of all of the genetic material (the genome) of an organism, and then relating it to the form and function of that organism. The Human Genome Project is perhaps the best known of all genomics projects.

Through the application of the cutting-edge tools of genome analysis, a comprehensive picture of the genes and cellular processes involved in many aspects of plant growth and development is emerging. This includes seed germination, biomass production, flower formation, disease resistance and stress responses. The knowledge obtained in these studies points the way forward for strategies aimed at enhancing the quantity and quality of wood for desired end-uses; or to enhance the ability of trees to adapt to environmental stresses such as pollution and climate change. What is required to realise these goals is a link between this basic plant biology and forest biology. This link is currently being forged.

In Europe, several large programs have recently been initiated that are aimed at the large-scale analysis of tree genomes. These efforts include the functional genomics of wood formation, tree growth, flowering, disease resistance and adaptation to environmental change. These efforts will create invaluable publicly accessible databases on model tree genomes, such as poplar, birch, eucalyptus, and pine. These databases will constitute a platform for tree biologists for the transfer of basic knowledge created in annual model plants, to an understanding of forest trees. The tools that are now available through the analysis of tree genes and proteins could have a profound effect on the capacity to improve forest productivity and monitor forest health. Due to the substantial lag time between seed germination and sexual maturity, trees have not been as amenable to the traditional breeding approaches that have been so useful in the improvement of short-lived crops like maize. The availability of the tools of molecular and cellular biology, coupled with genetics, will enhance the opportunities for and the rate of tree improvement. This can be achieved both by using molecular markers as early selection criteria in traditional breeding, and through genetic engineering if this becomes more accepted by the public in the future. Beyond this, these same tools can be used as precise diagnostics to monitor forest productivity and health.

The challenge is to ensure that the investment that has been made in basic research truly adds value to economically important tree species. It is imperative that forest biologists are able to make the connection between gene sequence and gene function, so as to capitalise on all of the genome data that has been generated. It is for this reason that forest scientists are poised to take advantage of the incredible genome databases, to enhance our understanding of tree productivity and survival.

B.OBJECTIVES AND BENEFITS

The main objective of the Action is to transfer knowledge and technology from basic plant functional genomics to the forestry sector, so as to benefit forest productivity and forest health.

The specific objectives of this COST Action are as follows:

1) To capitalise on the substantial genome resource that has been developed for model tree species, particularly poplar, pine, and birch.

2) To provide a link between gene sequence and gene function and thereby enhance our understanding of the genetic and cellular processes affecting tree growth and survival.

3) To use this understanding to develop new tools and biotechnology to enhance forest productivity and durable forest health.

4) To engage in an active dialogue with forestry practitioners, including tree breeders, silviculturalists, forest owners, forest managers, forest product manufacturers, and policy makers. This dialogue will focus on the needs and requirements for new tools and biotechnology to enhance forest productivity and forest health, and on the use, deployment, and benefits of such new tools and biotechnology.

5) To inform the public of the means through which these new genetic and cellular new tools and technologies can be developed, and the benefits of such tools and biotechnology.

The means to achieve these objectives are:

1) To provide a platform for scientists working on the large-scale genome analysis of model tree species, particularly poplar, birch, eucalyptus and pine, to interact with anatomists, physiologists, biochemists, and ecologists to ascribe gene function. In particular, this platform will focus on the identification and characterisation of genes important in three key areas:

- wood production, including wood quantity and quality
- tree maturation and reproduction, and
- tree health, including disease resistance, adaptation to environmental change, and responses to biotic and abiotic stimuli.

2) To provide forums (symposia) to bring together researchers operating at the interface between forestry and basic plant science, with researchers working on model plant species. Each symposium will focus on specific aspects of plant growth, development and health. These will provide a forum where research 'push' from basic plant science, and from those working on model species, can be used to focus on specific aspects of plant growth, development and health. Each of several symposia may consider a specific topic, for example (i) the control of flowering and maturation, (ii) understanding and manipulating the genetic basis of wood quality, (iii) marker assisted selection in tree improvement or several workshops / symposia may be held concurrently, as one large event unified by the general theme of Functional Genomics of Forest Trees.

3) To provide a platform for dialogue between developers of new genomics-based tools and technologies with forest practitioners. This will provide a forum where research 'pull', from forest practitioners will interact with scientists, to determine current and future research needs and how they may be incorporated into current programmes.

4) To provide a platform for the public understanding of new genomics-based tools and technologies related to forestry. To provide a mechanism to engage the public and to improve the public understanding of the potential of new genetic tools and biotechnology, in developing sustainable forest resources across Europe.

The outputs of the Action are:

1) Establishment of a concerted network of European scientists operating at the cutting edge of Functional Genomics of Forest Trees. To date, no such formal network exists. This network would exchange information and scientists. It would function as a cohesive unit to direct research in the area of Functional Genomics of Forest Trees, identifying funding sources and engaging in collaborative research to derive maximum benefit from this important new area of science.

2) Minimally one Action-supported symposium per year, per Scientific Area (see below).

3) An annual workshop aimed at providing forestry practitioners with information on how Functional Genomics of Forest Trees data can be incorporated into an operational context. This may be part of the larger symposia.

4) Provision of travel funds to allow the exchange of researchers between laboratories of Action participants, or to support forestry practitioners or laypersons an opportunity to visit facilities to learn about Functional Genomics of Forest Trees.

5) Establishment of "virtual centre" for the dissemination of information in the area of Functional Genomics of Forest Trees. This will be accomplished through a website established for the Action. This website will contain information on the following:

a. Aims, Objectives and Strategy of the Action - information contained within this document.
b. Participants in the Action
c. Action publications (see 2 below) - this will be the largest portion of the site.
d. Directory of potential collaborators, indicating research interests, and links to detailed information.
e. Links to other sites of interest in the area of Functional Genomics of Forest Trees.

6) Publications on the state-of-the art of Functional Genomics of Forest Trees. These publications will take three forms:

a. Proceedings of symposia that have been supported by the Action. These will be oriented towards scientists operating in the area of Functional Genomics of Forest Trees.
b. Publications aimed at forest practitioners. Such publications will outline the current state-of-the-art and how it might be applied to practical forestry.
c. Publications aimed at the general public. These "lay" publications will explain the technology of Functional Genomics of Forest Trees and its uses.

In all instances these publications will be electronic and available through the Action website. Under exceptional circumstances, it may be desirable to generate print copies of these publications for distribution. For example, there may be enough interest in one of the Action-supported symposia to generate a textbook, based on the proceedings, and in collaboration with a commercial publisher. In addition, it is envisaged that scientific publications will arise due to collaboration between Action participants (see 4 below).

7) Identification of research priorities in the area of Functional Genomics of Forest Trees. Every Action-supported forum will have a special "working party" session, which will identify research priorities and suggest mechanisms by which these research priorities can be addressed. As an example, it might be decided that a research priority is to establish DNA microarrays for a particular tree. Action participants would then determine a means by which this could be accomplished, then facilitate collaboration, and identification of research funds, for research groups to allow this to occur.

8) Collaboration and cooperation between European researchers working at the cutting edge of Functional Genomics of Forest Trees. The Action will function in a "pump-priming" capacity to bring together researchers from throughout Europe, to determine research priorities and identify strategies to address these research priorities. Thus, the Action would foster and enhance tangible collaborative research between European research groups. Such

collaborations should result in enhanced research funding for Action participants, add value to regional investment in science through pan-European collaboration, and generate scientific results and publications.

The benefits of the Action are as follows:

1) An enhanced knowledge base, founded on the substantial investment that has already been made in model plant species, particularly poplar and birch.

2) The Action will help Europe to maintain a position at the forefront of knowledge in this field and thereby retain the competitiveness of European forest industries.

3) Value added to European forest productivity and health

4) The Action will improve the co-operation between research groups in Europe and increase the exchange of methodologies, ideas, genetic resources, graduate students and researchers between these groups.

5) The Action will enhance co-operation between forest practitioners and lab-based researchers, allowing each to be more responsive to the other.

6) The Action will keep the public abreast of developments in this important area of research, using the latest technology and more traditional routes for information dissemination.

C.SCIENTIFIC PROGRAMME

To achieve the objectives, the Action will :

1) Bring together scientists at symposia, from a wide range of disciplines including:

- Molecular genetics
-
Molecular biology
- Tree and cell physiology and biochemistry
- Tree Breeders
- Forest Practitioners
- Industrial end users
- Policy makers across Europe.
They will share experiences in methodology and this will encourage multi- and interdisciplinary co-operation to increase our knowledge of tree growth and health.

2) Stimulate the exchange of researchers and research students among participating partners, through the provision of travel funds. This will encourage a vertical interaction from scientist to policy makers and practitioners, and also a horizontal interaction between scientists working on similar problems using different approaches.

3) Disseminate information related to the state-of-the-art for Forest Functional Genomics through the establishment of a centralised website for Forest Functional Genomics. Information will be provided on three levels: scientific; forestry practitioner; and layperson.

The Action serves as an important complement to three other COST Actions namely E10 (Wood properties for industrial use), E11 (Characterisation methods for fibres and paper) and E20 (Wood fibre cell wall structure). Action E10 is directed towards the analysis of wood structure at the macroscopic level; whereas, E11 is involved in the analysis of wood fibre specifically for the pulp and paper industry. The objective of Action E20 is focused on the ultrastructure of wood fibre cell walls at the microscopic (i.e. cellular) level. The Action outlined in this proposal extends these foci to the sub-cellular and genetic levels.

It is proposed that the Action is divided into three Scientific Areas:
-
Area 1:Functional Genomics of Wood Formation
- Area 2:Functional Genomics of Tree Maturation and Reproduction
- Area 3:Functional Genomics of Forest Health

The focus of the Scientific Programme Areas: Functional Genomics

In the context of this Action, the definition of functional genomics is as inclusive as possible. That is, in the broadest sense of the word, functional genomics aims at understanding genome function as it relates to any process - be it developmental, cellular, or biochemical. Functional genomics uses a variety of tools, including those of the geneticist, biochemist, cell biologist, anatomist, physiologist, and ecologist to determine genome function. Genome function is ascribed by analysing genetic variation using this variety of tools, and correlating this variation with differences in the functioning of the organisms in question. Thus, functional genomics as we define it encompasses a wide variety of activities, including, but not limited to:

- large-scale gene sequencing
- microarray analysis of gene expression
- proteomics
- genome mapping/QTL analysis
- analysis of wood structure as it relates to the genetic constitution of trees (including both intra- and inter-species comparisons)
- tissue culture of different genotypes/species

The "interwoven nature" of the Scientific Areas

The Scientific Areas are meant to provide participants with an opportunity to refine the focus of the Action, if desired. The overall focus of the Action is on the functional genomics of forest trees, as outlined above. Nevertheless, it is envisaged that it is desirable, within the context of this overall focus, to provide Action participants with a mechanism to address specific scientific issues that are

central themes in forest biology. Therefore, the three Scientific Areas are viewed as logical groupings within the context of the Action, but should in no way be viewed as being exclusionary. That is, it is anticipated that participants in Area 1 will also participate in Area 2 and vice versa. Moreover, functional genomics provides a unifying focal point that brings scientists from sometimes disparate areas of forest biology together. Functional genomics provides an umbrella of commonality in approach that will unify biological understanding between the three Scientific Programme Areas. Furthermore, it is likely that the common functional genomics approach will allow researcher to ratchet off of each other's experiences, regardless of the specific biological questions that they are addressing. Thus, the functional genomics umbrella provides a way of enhancing overall biological knowledge in a synergistic fashion.

The processes that we are interested in understanding will involve the coordinated regulation of tens of thousands of genes in any given tree species. The central aim of the project is to define the identity of the genes and to understand the function of gene products that control wood production, maturation and environmental responses in trees. Studies of such fundamental problems will be greatly facilitated by current development in genomic technologies. The EST (expressed sequence tag) projects of birch and poplar will provide a wealth of information and gene sequences to be used
as tools for the questions we are addressing. The data generated in such projects, coupled with the tools of forward and reverse genetics, and bioinformatics will illuminate areas our understanding of tree growth and development in hitherto unimaginable ways. This COST Action aims to be at the forefront in this area of discovery.

The remit of each of the scientific programme areas is as follows:

Scientific programme Area 1: Functional Genomics of Wood Formation

Wood properties are highly variable between species and even between trees of the same species. This variability arises partly because of differences in the anatomy of the wood and cell wall structure in the former case, and of genetic and environmentally induced variability of these factors

in the latter. One of the aims of this action is to consider ways of improving both productivity of forest trees while maintaining and improving quality. Present attitudes among the public to genetically modified organisms (GMOs) means that at present the best hope for improvement lies in selecting and propagating trees with desired wood characters. Generation times for trees are, however, long, and conventional breeding methods are slow. It is therefore essential to develop methods for vegetative propagation of high quality mature trees, and predicting the quality of mature trees based on seedling characters, using for example, molecular marker-aided selection.

It is essential for the success of this work that those involved in improvement by whatever means, understand fully the features of wood that affect its quality. This means bringing together experts in wood formation and properties with molecular biologists. The former can provide information to the latter about desirable wood properties, while the latter have the means to produce trees in which they occur. In other words, pooling of expertise in this way will provide a foundation for genomics work in which effort can be directed towards the improvement of both tree productivity and the quality of the wood they produce.

Wood, also known as secondary xylem, is formed in trees by the activity of the tissue known as the cambium. Wood properties are, therefore, ultimately derived from the activity of the cambium. In practice, the key to improvement is an understanding of the vascular cambium and the way in which genes, growth regulators, and the environment control of the differentiation of its derivative cells. The study of the molecular biology of the cambium is in its infancy, but is acquiring increasing importance as it is becoming realised that this tissue is the world's major biomass producer. The Edinburgh meeting of COST Action E10, held in 1999 and dedicated to the formation of wood, demonstrated that the number of scientists throughout the world working on this tissue has increased dramatically from only a handful in the 1970s.

Understanding the function of the cambium in the production of wood is a major challenge for forest practitioners aiming at improving wood quality or yield. This understanding will allow foresters to orient tree growth and selection towards specific industrial uses. Silviculturalists and tree breeders are now turning to genomic science to acquire tools to meet this challenge.

Silviculturalists hope to incorporate knowledge of the molecular mechanisms that underpin the activity of the vascular cambium, in order to devise strategies to optimise tree growth at the stand level. Tree breeders are already using the data from gene sequencing projects to better dissect the basis of complex traits, such as wood quality and quantity. It is clear that a platform is needed for scientists to develop and transfer this knowledge base for industrially important tree species. The proposed action will bring together molecular biologists and experts in wood formation and properties. The pooling of expertise in this way will provide a foundation for genomics work in which effort can be directed towards the improvement of both tree productivity and the quality of the wood they produce.

This Action will build on the foundation produced by Action E10, bringing together scientists working on wood formation to set up joint projects. This will accelerate progress in this area in a way that could not be achieved otherwise.

Scientific programme Area 2: Functional Genomics of Tree Maturation and Reproduction

As is the case with many organisms, trees pass from a juvenile phase to a mature phase. This transition may involve numerous physiological and anatomical changes. Sometimes these are very apparent. For example, the change in leaf shape that one observes along the length of the stem of some eucalyptus species. The most obvious visible change in the maturation state of a tree is competency to reproduce; where the stem now has the capacity to produce flowers and bear seeds and fruit. At other times, the changes associated with the transition from the juvenile to the mature phase are hidden from view but may be quite significant. From a forestry perspective, perhaps the most significant of these "invisible" changes is the change that occurs in wood anatomy and chemistry. The wood laid down by the juvenile cambium may have substantially different fibre characteristics than that produced by a mature cambium. Beyond this, many other traits that are
important for forestry are related to maturation state. This includes growth habit, leaf retention, photosynthetic efficiency, adventitious root production, and the capacity to be propagated vegetatively.

Knowledge of the factors that control the transition from the juvenile to mature state is an important foundation for developing approaches to improve the capacity to grow and propagate forests. For example, the length of the juvenile period is inversely related to breeding efficiency of woody perennials and to the selection and production of genetically improved trees; whereas, the length of the juvenile period is directly related to the production of biomass from conifer forests. Furthermore, the ease of cutting propagation, in vitro morphogenesis or somatic embryogenesis for all types of woody perennials is strongly affected by maturation. The ability to reverse maturation is important for the propagation of selected mature trees via either rooted cuttings or tissue culture. Thus, the quantity and quality of productivity of a forest tree species is related to its degree of maturity.

One of the most important traits related to maturation of trees is the competency to reproduce sexually, that is, the ability to produce flowers. There are a number of reasons why this is important, not the least of which is that this process is, of course, essential for continued sexual propagation of tree species. Beyond this, flowering is important as it establishes the genetic structure of plant populations. That is, the extent and timing of flowering has a strong effect on whether a particular species is inbred or outbred, whether it disperses over a wide geographical range or a narrow range, and whether it persists through times of environmental stress or not. Thus, the processes that control flowering have a profound effect on forest biodiversity. In addition, flowering has a significant effect on forest productivity. Trees invest a significant amount of resources into the generation of flowers. This investment detracts from the capacity of the tree to invest those same resources into wood production. Thus, depending on the interplay between resource availability and the timing of flowering, this important component of maturation could have a significant effect on the extent of forest productivity. Therefore, it is useful to have a good understanding of the mechanisms that control the capacity to flower so as to devise strategies to maintain forest reproduction while maximising forest productivity.

In summary, the possibility of effectively controlling maturation has enormous practical significance. Tree breeders find it desirable to accelerate flowering and to rapidly induce the adult condition so as to hasten the production of flower, fruit and seed crops. At other times, it is more important to retain the juvenile condition for a long time for biomass production or to retain desirable characteristics such as the capability of vegetative propagation.

The events that may regulate maturation are not known. The understanding of the molecular mechanisms that underpin tree maturation and reproduction is still in its infancy. The tools of functional genomics are allowing tree biologists to make significant headway towards developing a better picture on the control of these processes. In particular, the understanding of flowering in trees has benefited greatly from the burgeoning knowledge base that is being developed for model annual plants. Maturation specific markers or genes would offer the possibility to easily identify genotypes with desirable mature yield traits at juvenile state, to evaluate material for propagation, to develop and evaluate any method applied for propagation of physiologically adult material or to identify early or late flowering genotypes for seed production. These and other traits may be transferred within classical breeding programs or via genetic transformation when possible. In this way, powerful tools for tree selection, propagation and breeding will become available. A greater degree of interface is needed between basic plant biologist and forest biologists to ensure that this continues to happen.

This COST Action will bring together scientists operating at this interface, and will allow them to develop tools to understand the basis of maturation. Thus, one of the main objectives for participants in this project will be to identify genes and their function that control maturation and reproduction. The results of this research could be exploited in the selection of mature trees with high quality during seedling stage. In addition, they will be useful in developing new vegetative propagation procedures for mature trees as well as to manipulate the length of the juvenile or mature phases. In doing so, participants in this COST Action will generate knowledge that will undoubtedly impact the ability to propagate tree species, and enhance stand productivity.

Scientific programme Area 3: Functional Genomics of Forest Health

Unlike animals, plants cannot avoid unfavourable habitats or sudden changes in the climate or insect attack, by moving over long distances to more suitable environments, and so if they are to survive, they have to be able to adapt rapidly to new conditions. Perennial plants such as trees are even more confronted to environment changes through their life span. Growth, development and productivity of healthy trees are continuously challenged by environmental stresses such as freezing, drought, pollutants, pathogens or wounding (herbivores). In addition, trees must allocate their resources appropriately in response to different light intensities and daylength. Finally, interactions with mutualistic organisms, such as mycorrhizal fungi, can have a profound effect on the nutritional status and overall health of trees.

The optimal growth and development of trees is far from that realised in the forest. One way of increasing productivity is through breeding for trees that are more tolerant to environmental stresses and respond to the insult in an efficient but transient manner not to waste unnecessary energy for the process. Optimisation of stress responses in woody plants with long life spans is of particular interest. Improving tree growth or productivity requires understanding the molecular mechanisms governing growth characteristics and involved in stress adaptation and stress responses in plants. This requires identification of the genes controlling growth, dormancy and stress/defence responses.

Environment changes encountered in complex organisms like trees can involve the modification of hundreds of gene products. The research will be focused on elucidation of signal pathways and components required for expression of specific genes involved in plant response to environmental stimuli, as well as ascribe the function of the corresponding response proteins. The responses to environmental stimuli, such as sub-optimal temperatures, light conditions, drought, pollution, pathogens, mutualistic organisms (e.g. mycorrhizae) and herbivores (wounding) will all trigger a number of signalling events in the plant cell. It is becoming clear that many of the pathways involved in environmental signalling and growth control interact.

To elucidate the nature of these signal pathways we will first define the array of genes controlled by environmental responses. This will be achieved by transcriptional profiling using microarrays of the genes identified through large scale automated sequencing of expressed genes. The "signatures" for these expressed genes will be used to generate tree gene chips, which will allow simultaneous characterisation of the temporal and spatial expression pattern of the genes in response to different biotic and abiotic stimuli. The expression data together with sequence information will define the involvement and likely function of the genes in environment-dependent growth control. Functional assignment of selected genes will be accomplished by a number of techniques using both trees and when applicable the model plant Arabidopsis. Transgenic trees that ectopically express or silence the genes to be tested will help to assign a phenotype to a particular gene. As a complementary approach we will employ QTL mapping. This will allow assignment of particular candidate genes to specific QTLs for stress response and growth control.

The work will result in understanding the cellular and molecular characteristics of environmental responsiveness and growth control in trees. We will be able to identify the key components in these responses and characterise their function. This will lead to understanding of the processes governing growth and hardiness development in trees. Understanding the underlying mechanisms of environmental responses and tolerance development will in turn facilitate breeding of these properties. The isolated genes will be exploited for breeding purposes as molecular markers in marker assisted breeding programs in development of trees with improved control of growth and hardiness properties.

D.ORGANISATION AND TIMETABLE

Organisation

The Action will be led by a Management Committee (MC), headed by an elected Chairperson,

Coordinator

N/A