EPS Research Introduction
During the last decade molecular biology and molecular genetics have strongly contributed to a better understanding of the functioning of plants and the interaction between plants and their biotic and abiotic environment. Key genes and their regulators that control plant development, plant-attacker interactions and plant metabolism have been cloned. With the rapid developments in genome sequencing and functional genomics in plants and plant-related organisms, biological questions can now be addressed that were not amenable before. Another important development in biology is the use of the living cell as a ‘test tube’ to study requirements for cell functioning. This approach, combined with in vitro experiments on biomolecules like cytoskeletal and cell wall elements, is a next step in understanding plant life. Functional genomics, proteomics, metabolomics, bioinformatics and cell physics will quickly change our way of thinking and solving questions in biological research. Genomics and post-genomics research enable a systematic characterization of genes, their functions, interactions and regulation. The information thus gained through focused studies of selected model plants such as Arabidopsis provides an efficient strategy for the systematic transfer of knowledge to crop plants such as tomato and potato. This will have a major impact on agriculture and food improvement in the next decade and allows the control of quality, safety and quantity of food production. These new developments have positively influenced the research of EPS in recent years, which covers a broad field of disciplines with many possibilities for interdisciplinary research. Molecular biologists, cell biologists, plant physiologists, microbiologists, phytochemists, biophysicists, cytologists, taxonomists, biochemists, geneticists, entomologists, virologists, phytopathologists, phytomycologists, nematologists, plant breeders, and ecologists now collaborate more than ever before. Collaborations are stimulated through strategic programmes within and outside the graduate school EPS. EPS plans to have new calls for proposals every two years on selected research themes of which many require interdisciplinary research. In addition, EPS keeps a close watch on the strategic plans of national (NWO-ALW, NWO-CW and NWO-STW) and international (EU, EMBO, HSFP) grant agencies and stimulates members to apply for grants. At the other hand these grant agencies tend to stimulate large research programmes rather than individual projects. In order to achieve all this, EPS provides a national platform for plant sciences in the Netherlands with international links within and outside Europe. The membership of the European Plant Science Organisation (EPSO) of EPS is an example of such an international platform function. In recent years EPS research has rapidly moved to the international forefront of scientific developments. Thus the rapid developments in the area of genomics and related areas have provided excellent new opportunities for the research in plant sciences. Research on molecular ecology and environmental genomics where functions of genes will be unravelled in the context of complex ecological interactions will be performed in EPS-3. We foresee that these developments in plant sciences will allow significant contributions to fundamental as well as applied issues. In the coming years a major focus in research will be on subjects that all fit in the four general research themes of EPS. Apart from new research foci much attention is given to developing high level infrastructure required for the new research programme. The new research foci are:
In this theme we will concentrate on Biosystems Genomics investigating genes, gene expression and gene functioning at the level of the whole organism. In the Centre for Biosystems Genomics (CBSG; http://www.biosystemsgenomics.nl/) that has been founded, two major research themes, i.e. disease resistance and product quality, will be studied on the model plant Arabidopsis and the crop plants tomato and potato. It encompasses complex interactions at all levels of biological information: DNA, mRNA, proteins, metabolites and how these informational networks are integrated. Biosystems genomics addresses complex sustainability issues at the level of whole plants and their environment. The research on disease resistance is mainly aimed at finding alternatives for pesticides that have deleterious effects on the environment. This provides opportunities for innovative, sustainable improvement of crops and entire agro-food production chains and enables a transition to precision agro-production, minimising use of energy, chemical treatments and waste products while maximising product quality. Our goal is to contribute to sustainable quality improvement of food crops and their derived products for the consumer and the environment. This programme will yield new genetic markers that contribute to sustainable agro-production. The further development of marker-assisted breeding will provide new opportunities for crop improvement with or without genetic modification. The option of genetic modification will be used for research purposes but will not be commercially exploited without close consultation with all stakeholders in society.
Overall, the Biosystems genomics research programme will:
- Identify the complex genetic and biochemical mechanisms in potato and tomato underlying pathogen resistances and consumer and industrial quality traits.
- Develop a research platform for genome-based approaches in the crop species potato and tomato and the model plant Arabidopsis.
- Explore the rich biodiversity of solanaceous species to identify new traits and valuable genetic alleles.
- Fully exploit bioinformatics to integrate genomics data from sequence analysis, transcriptomics, proteomics and metabolomics.
- Conduct multidisciplinary research into the societal implications of genomics.
Recently, a new chair in metabolomics has been filled at WU that gives an additional boost to this area of research.
EPS will establish a genome informatics research programme focussed on assembly and annotation of genomes, EST analysis and databases, analysis of regulatory DNA elements, molecular marker predictions, cluster analysis of DNA micro-array data and integration of genomics, transcriptomics, proteomics and metabolomics data. As mentioned earlier, genomics and bioformatics research and facilities are extremely important for further development of plant sciences within EPS. A chair in Genome Informatics has been filled at Wageningen UR in 2002 which will further strengthen EPS education and the EPS research programme in bioinformatics.
In the Netherlands, particularly within EPS, we will focus on plant development in Arabidopsis and petunia with emphasis on somatic embryo development and organ development (shoot, root, flower). Also the formation of structures like nodules in legumes and syncytia in potato, which are induced by biotic agents, will be examined. Furthermore, cell-cell interactions (e.g. pollen-pistil) and molecular mechanisms controlling cell division, -growth, -wall formation and -shape (e.g. root hairs) are being studied. Several research groups in EPS are at the forefront in this research area. The functional genomics approach, boosted with the availability of the Arabidopsis genome sequence, will give insight in the genes involved in these processes, how they are regulated and how their products communicate in a concerted action in time and space. Although most of this basic research will be carried out with Arabidopsis, this type of research will help us to find major regulatory genes crucial in plant development which could possibly be exploited in designing crop plants for various needs. A new chair in plant development has been filled at KUN, which enlarges the research potential in this area. A chair at WU focuses on the physical aspects of cytoskeletal and cell wall polymers using single cells. In addition, a new chair in theoretical cell physics has been filled at WU that gives an additional boost to this area.
Research on interactions between plants and their biotic environment remains a major research focus within EPS. The biotic agents investigated are: viruses, bacteria, fungi, oomycetes, nematodes, mites and insects. Key genes and their regulators involved in communication between biotic agents and their hosts have been identified in recent years. Expression of these genes within the biotic agents and their host plants has been studied. With the availability of micro-arrays covering complete genomes of either biotic agents or their host plant and by exploiting various types of mutants, overall expression patterns during infection of plants should become available. Such approach will provide a better understanding of the interactions between plants and their biotic agents at the molecular level. This allows comparing gene expression patterns between compatible and incompatible interactions, between induced systemic resistance (ISR) and systemically acquired resistance (SAR), between interactions with pathogens and with insects. Furthermore, it will allow the detailed analysis of cross-talk between different types of organisms and their hosts. Research on communication between attacked plants and carnivorous insects that attack herbivorous insects and on communication between attacked plants and their undamaged neighbours will also be included. We will develop a molecular ecological approach to plant-attacker interactions. Developments in micro-array analysis will also allow investigating complex interactions in natural systems that will lead to important contributions to molecular ecology and environmental genomics. The research in this area will focus on Arabidopsis, tomato and potato, but other host plants will be involved as well. This research will contribute to the development of new strategies of durable crop protection in the field of molecular resistance breeding and biological control of pests and diseases.
Genetic, Physiological and Molecular Basis of Plant Performance
A combined physiological and genetic approach, with Arabidopsis as a model system, will be chosen to analyse the genetic and physiological regulatory mechanisms governing plant performance. In this type of research both mutants and natural variants, the latter requiring QTL approaches for initial characterisation, can be used. Here we will exploit genetic variation governing all aspects (including signal transduction) of nutrient partitioning under various growth conditions, including the performance under various stress conditions (e.g. high and low temperature; drought, flooding and salt stress). This knowledge then can be transferred to other plants (e.g. potato tuberisation; tomato fruit formation/ripening). The assumption is that these genetic and physiological regulatory mechanisms are basically similar in most plants. We will exploit the fact that the Arabidopsis genome is fully sequenced and genetic resources, including recombinant-inbred lines of Arabidopsis, are available or can easily be made. The potato and tomato genome projects will benefit from this type of genome research on Arabidopsis.This research will also enable us to develop new strategies to breed for crop plants with improved stress tolerance, improved quality and improved yields. Especially the genetic potential to increase the nutritional value (vitamins, anti-oxidants, micronutrients) of plants will be fully exploited by genomics approaches in the near future.
Chromosome Structure and Gene Expression
The availability of nucleotide sequences of complete chromosomes/genomes of Arabidopsis in combination with high resolution FISH on pachytene chromosomes and interface nuclei provide exciting new opportunities to determine the molecular properties of chromosomal elements like centromeres, telomeres and heterochromatic regions. It is now possible to determine which sequences correlate with these functional elements and in combination with efficient proteomics approaches the nature of the proteins associated with these elements can be revealed. Such studies provide insight in molecular mechanisms controlling chromosomal behaviour but also in how the higher order organisation of the nucleus contributes to the regulation of gene expression (epigenetics).
Heterochromatin is supposed to affect the transcription of genes that are located in its vicinity. The ease by which plants can be transformed, the availability of sensitive molecular cytogenetic detection methods as well as extensive micro-arrays will make it possible to experimentally approach the relation between chromatin organisation and gene expression. Insight in the mechanisms that control the higher order organisation of the nucleus and how this organisation affects gene expression is of importance to design transgenic plants in which the expression of the transgene is fully controlled.
Genomics Research Facilities
World-class plant research is not feasible without excellent infrastructure. EPS has decided to further develop its genomics infrastructure by participating in the Centre for Biosystems Genomics (CBSG), which has its basis at Wageningen UR but is accessible by all EPS researchers. The centre has been raised by the so-called ‘Regie-Orgaan Genomics’ to a so-called ‘zwaartepunt’. It is the only Genomics centre devoted to plant genomics in the Netherlands. Collaboration and facility sharing leads to more efficient use of equipment and guarantees access to state-of-the-art equipment. Building on each other’s expertise provides a strong stimulus for biological and technological innovation. With CBSG EPS has the ambition to:
- Establish the best genomics-infrastructure available for its research
- Continuously innovate through investments in facilities and expertise
- Serve as a cost-effective infrastructure hotel to all participants, lowering financial barriers
- Build personnel expertise through training and individual skill development
- Establish a platform for training, education and demonstration for students, guests and industrial partners
- Establish a European Network of Excellence in Plant Genomics that collaborates with other national and international initiatives to attune new investments and developments.
The different research themes require well-trained scientists, postdocs and PhD students who are able to incorporate technical advances quickly. It has become increasingly important to inform and to explain to the public at large the many technical advances and new insights acquired by the research and to account for their potential sociatal implications. Researchers are often not aware of the emotions, feelings, attitudes and opinions in society about the achievements and consequences of their work. In an open public discussion with and within the society about the essential acceptance of new technologies and their applications, it is necessary that researchers are active in achieving a better mutual understanding.
For that purpose in the future research plans and in the communications on research progress more attention will be paid to societal aspects notably in the research projects on plant biotechnology and plant genomics.
Based on the new developments described above, the third six-year research programme (2004-2009) of EPS has been revised to accommodate new types of both basic and applied research. As discussed above, genomics-related research is embedded in all research themes. A few subthemes are added or readjusted in the new programme.