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Foreword

The advent of genomics technology in the plant sciences in the last decade of the past century has created a wealth of new opportunity in fundamental and applied plant sciences. One of the consequences of the application of genomics technology in biology in general is that the way research has been done is changing.

There is more and more need for multidisciplinary approaches, resource sharing and sharing of facilities, meaning that cooperation and coordination by scientists and national research programmes is an increasingly important issue. For the European plant sciences community this is a challenge in a rapidly changing world. Genomics research in plant sciences is a driving factor in innovation in agriculture and will be important if we are to realise ambitions in areas such as sustainability, consumer demand and world food supply. However although in today€s Europe the plant genomics research is of world class level, the research efforts are still rather fragmented. This is a problem if we subscribe to the notion that we can only be innovative if we remain competitive.

One of the solutions to this is to build a science base which is driven by the ambition to create added value through excellent research, synergy and cooperation. This can only be realised by appropriate funding and integration.

The ERA-NET Plant Genomics, ERA-PG, has its major focus on the development of collaborative activities between European funding organisations in the field of plant genomics. As ERA-PG cannot only by itself realise the ambition of the European Research Area in the field of plant sciences, close collaboration is needed with other initiatives of the European Commission, for example the Technology Platform Plants for the Future.

This report is the result of one of the activities of ERA-PG. It describes the results of several inventories, made by the funding bodies which cooperate in ERA-PG, of public and private research at a national, European and global level in plant genomics. The output from these inventories is summarised in this report and is the basis for a major ERA-PG workshop which is held on the 29-30 June 2005 at the John Innes Centre in Norwich, UK. This workshop was attended by funders and scientists involved in the respective national research programmes and representatives from industry. The workshop serves to provide a common understanding of the overlaps and gaps in national programmes, evaluation and administrative systems and national contractual and IPR strategies and to build a common agreed basis for the implementation of joint strategic activities. Scientists and funders will outline the framework for truly integrative, multilateral plant genomics programmes.

The selected research themes, topics and ideas will be the basis for the development of an ERA-NET research programme in the area of plant genomics. Herewith ERA-PG is one of the first ERA-NET initiatives of the European Commission which will develop and announce a transnational research programme which will serve the ambition of the commission to build a European Research Area which serves both the community and the economy. The overview of the current status of plant genomics in Europe provided by this report will be instrumental in building a good ERA-PG programme which should be the basis for continuity in the joining up of national programmes in European plant genomics research. It is the intention of ERA-PG to announce the call for the programme by the end of 2005.

I would like to thank all partners and others for their contribution to the questionnaires which are the basis for this report and especially the working group that prepared this report.

This programme has been made possible by the European Commission under the flag of the sixth frame work programme.

Bernard de Geus PhD, Coordinator ERA-PG, Netherlands Genomics Initiative, The Hague, May 2005

Summary

This report describes the output of the first Workpackage of ERA-PG, a major information-gathering exercise. It presents a wealth of information about plant genomics programmes in the ERA-PG partner countries, and in some pre-eminent nations worldwide, which, in combination with its annexes and presentations, is a valuable resource in itself. We show that Europe makes important contributions, both to the plant genomics research and more broadly to the global agriculture based economy. European research capability is demonstrated by the large number of high impact scientific papers coming out of the institutions supported by European plant genomics programmes. Additionally, resource generation in Europe has been substantial - much of the initial funding of plant genomics work was directed at providing resource and infrastructure to support this emerging area.

We are beginning to see the fruits of these early investments, and the Workpackage study shows us that there are many opportunities to build on. The inventory of facilities and expertise available in the different programmes will help scientists in their search for partners in advance of the trans-national ERA-PG call. However, we have seen that in spite of substantial investment Europe is slipping in competitiveness when compared with other nations worldwide, and a closer alliance between European partners is needed.

Research efforts can benefit from cooperation between nationally funded public research bodies, but there is also great potential in increasing collaboration between public and industry researchers. Both aspects have already been demonstrated by the transnational programmes, first between France and Germany, and more recently with the participation of Spain. We have seen that there exists a good history of collaboration with plant breeders, and this is an area where we can hope to enjoy increased cooperation in the future. During the information gathering process it was clear that there is currently a climate of willingness to share information in mutually beneficial projects with breeding companies and the first ERA-PG call should be designed to take this into account.

It is clear that latterly there has been less involvement of European biotech companies in collaborative plant genomics research, as many of these multinational companies are undertaking this work out of Europe because of the problems arising from previous experience with genetically modified crops. There are two other sectors at opposite ends of the spectrum, where collaboration in the future might be beneficial. These are SME€s including those involved in biotech activities and smaller breeders focussing on high value fruit and vegetable crops, and large national and multinational agrifood companies. Consideration should be given to how we can welcome these industries as partners in our programmes in Europe.

A study of the focus of the different plant genomics programmes in Europe and beyond has shown some alignment with the primary crops of the regions. In the US, for example, there is a huge research effort in maize, in Japan a large proportion of the funding goes into rice and in Europe there is an emphasis on wheat research.

There are other important crops in Europe such as barley and grapevine that could be considered to have received insufficient investment and may be a focus of the future. Alongside this, all countries have taken advantage of the publishing of the sequences of model organisms, firstly Arabidopsis, and more recently rice. There are a number of challenges now facing us; how do we translate the information (and the investment that was required to produce it) from model organisms into the crops in the field; which crops and traits do we focus on in the future in a European context; how do we work together, with academic and industrial partners, to achieve our goals; how do we assess our progress and continue beyond the current programme?

There are a number of common crops in Europe, and also a dichotomy between northern and southern countries that must be addressed in order for all partners to be satisfied with the investment. Additionally we need to look at the investments by non-European nations and ask ourselves whether there are certain areas where we cannot hope to be competitive, and others where the filling of gaps will give us real advantage.

A vitally important component of the ERA-PG programme is the study of administrative processes used by the different national funding agencies. From this we can see that there are a variety of different methods of Plant Genomics Research in Europe administering national funds which at first sight appear difficult to bring together. However, on key components such as influence in the design of programmes, and the evaluation criteria used in assessment, there are probably enough common elements to allow a robust system to be developed. Above all, there is a desire to succeed in this project which has grown over the last eighteen months.

A consensus between the partners exists which should allow us to overcome the many minor and some major hurdles in the pursuit of the goal of a common programme. This is underpinned by a real expectation of funding commitment depending on the successful outcome of planning stages which will give us a substantial opportunity to make the difference in plant genomics in the next few years in Europe. The challenge in the Norwich workshop is to get the programme design right and put the next phase of the programme into motion. Beyond this, we hope to have a system that will be enduring and will also have the flexibility to incorporate changes; in science and also in the membership of nation states, anticipating and encompassing the changes that we are currently experiencing throughout Europe.

Contents

Foreword
List of Tables and Figures
Summary
1. Introduction
1.1. Plant genomics
1.2. Structuring research programmes in Europe
1.3. Inventory of the state of the art
1.4. Towards joint strategic actions
2. National Plant Genomics Programmes
2.1. Introduction and goal of inventory
2.2. The national programmes
2.3. Funding and participation
3. Programme Implementation Approaches
3.1. Introduction and goal of inventory
3.2. Programme initiation
3.3. Application, proposals, evaluation
5 3.4. Administrative procedures and programme and project management
3.5. Conclusions and outlook
4. The Landscape of Plant Genomics in Europe
4.1. Introduction and goal of inventory
4.2. Relative importance of agriculture, agrochemical industry and agrifood industry
4.3. Priority crops in ERA-PG countries
4.4. Plant genomics in breeding companies
4.5. Plant genomics in agrochemical companies
4.6. Plant genomics in agrifood companies
4.7. Biotech companies providing services in plant genomics
4.8. National public research expenditure in biosciences
4.9. Public institutions involved in plant genomics
4.10. Plant genomics resources centres
4.11. Transnational programmes involving plant genomics activities
4.12. Consumers' attitude towards GM crops & food
4.13. Conclusion
5. The Landscape of Plant Genomics outside Europe
5.1. Introduction and goal of inventory
5.2. Relative importance of agriculture, agrochemical and agrifood industries
5.3. Crops
5.4. Exports and imports
5.5. Major plant science related companies
5.6. Science budget and research focus
5.7. Consumer attitude towards genetically modified crops
5.8. Conclusion
6. Europe's Competitiveness
6.1. Relative importance of agriculture, agrochemical industry and agrifood industry
6.2. Priority crops
6.3. Companies with an interest in plant genomics
6.4. National budgets for plant genomic research
6.5. Public institutions involved in plant genomics
6.6. Plant genomics resources
6.7. Conclusions
Annexes
Annex 1. ERA-PG partners
Annex 2. Questionnaire - National Plant Genomics Programmes
Annex 3. Questionnaire - Programme Implementation Approaches
Annex 4. Questionnaire - RTD Landscape
Annex 5. Fact sheets of national plant genomics programmes
Annex 6. Key elements in programme initiation phases
Annex 7. Elements requested in proposals
Annex 8. Production and economic values of the 4 most important crops in ERA-PG countries
Annex 9. Company information of surveyed countries in Europe
Annex 10. Plant species studied in national plant genomics programmes
Annex 11. Currently running transnational programmes involving plant genomics
Annex 12. Consumers' attitude towards GM crops in ERA-PG countries
Annex 13. The landscape of plant genomics outside Europe
Annex 14. Company information of surveyed countries outside Europe
Annex 15. GM - the view from the rest of the world
Presentations
Presentation 1. National plant genomics programmes
Presentation 2. Programme implementation approaches
Presentation 3. The landscape of plant genomics
Presentation 4. Europe's competitiveness
Databases
Inventory 1. National plant genomics programmes
Inventory 2. Programme implementation approaches
Inventory 3. The landscape of plant genomics in ERA-PG countries
Inventory 4. The landscape of plant genomics outside Europe

Contacts

Contact

• ERA-PG managing office / Netherlands Genomics Initiative NETHERLANDS