Bioinformatics
Jan Peter Nap, cluster leader
Bioinformatics relates to the in silico storage, manipulation, analysis and mining of large omics datasets. It is at the cross-roads between molecular biology, computer science and mathematics and is hugely important in converting (abstract) quantitative data into biologically-relevant knowledge.
CBSG has access to the full gamut of genomics technology platforms - covering all molecular levels from DNA, RNA, protein and metabolite. Furthermore, CBSG scientists generate large amounts of phenotypic information on quantitative / qualitative quality aspects, morphology, yield parameters, gene function data etc. This diversity of data and the size of the datasets produced require dedicated state-of-the-art approaches towards data management and mining. The CBSG Bioinformatics programme aims not only to facilitate this but also will enable us to go beyond this and join all these pieces of information together to see even more of the picture behind the puzzle.
Education
Jaap Bakker, cluster leader
CBSG recognises that it has a significant responsibility to train the scientists of the future to meet the needs of both academia and industry. Educating the general public on the ins and outs of genomics research and the impact it can have on Society as well as training young scientists are two key components of our activities.
In this regard, CBSG functions at two main levels:
By providing PhD positions for recent graduates and by establishing state of the art genomics technology platforms that are available for young postdocs to extend their experise, CBSG ensures that these budding future captains of industry develop the best possible scientific background to meet the future needs of science and commerce. Also, through our direct interaction with commercial companies, CBSG scientsist get a first hand view of not just academic but also applied research.
CBSG also reaches out to young secondary school children. Firstly, through a joint initiative with the other NGI genomics centres, CBSG helps populate the genomics information website www.allesoverDNA.nl which provides school children with articles on the applications of genomics research. Secondly, CSBG initiated and helps coordinate the Mobile DNA labs, which allows school children to perform a DNA-based experiment within their own class at school. Approximately 20,000 visitors use the site each month and ca 15,000 school children participate in the Mobile labs each year.
Potato
Richard Visser, cluster leader
Potato is vegetable crop number one in the world. Like its close relative tomato, it is one of the few food crops to be grown virtually everywhere! Potato production is directed towards three clearly distinct market sectors: fresh (for boiling), crisps and french fries (for deep fat frying) and potato starch (for industrial processing). The Netherlands is global leader in the breeding of potato varieties dedicated to each of these three markets. For example, ca 70% of the seed potatoes annually produced for the consumer potato industry, are of varieties coming from our industrial partners.
- The CBSG potato research programme is focused on two key traits of importance to all three industrial sectors: Resistance to late blight - Phytophthora is still the cause of the most devastating potato disease encurring several billion euro costs in crop losses annually, and this despite several billion Euros which are spent on fungicidal sprays.
- Potato tuber quality - in terms of e.g. cold sweetening, tuber size / appearance etc.
Pathogenomics
Pierre de Wit, cluster leader
Pathogenomics is the field of science which focuses on the molecular interaction between plants and pathogens. Use is made of the latest omics technologies to help identify genes which confer resistance or indeed, susceptibility, of a plant to a particular pathogen. Furthermore, determining the molecular mechanisms behind the plant / pathogen interaction is key to developing new strategies for enhancing resistance to important pathogens in crop plants. An important aspect of pathogenomics is that research is two - sided, where the both the genetics of the plant and the pathogen are targets of investigation.
The CBSG pathogenomics programme covers research on both potato and tomato but due to the advantages of speed and versatility, much research on the molecular basis of plant-pathogen interaction is focused on Arabidopsis. Through work on this model plant we aim to home in more rapidly on genes linked to disease and thus arrive earlier at novel strategies for crop protection.
Society
Bart Gremmen, cluster leader
A socially robust strategy for the implementation of plant genomics strategies is essential if we are to succeed in the field of sustainable food production. CBSG recognises a clear responsibility to directly interact with the wider non-scientific community and listen to and act upon public opinion. Therefore, CBSG, together with the Centre for Society and Genomics (CSG), carries out social science research into the societal aspects of our work - in relation to, for example, how genomics is percieved, is the consumer interested / concerned about genomics research, does societal demand meet our expectations etc. Through our societal aspects programme we carry out research geared to understanding better how to most effectively communicate with the public and to understand other aspects of consumer behavious such as consumer preference and consumer perception of genomics-related issues.
In this way, CBSG aims to maximise our chances of effective translation of top level science into commercially viable and usable results.
Technology
Gerco Angenent, cluster leader
The entire field of genomics research is centred on the application of innovative high throughput technologies dedicated to the analysis of plant materials at different molecular levels. CBSG is dedicated not only to applying the latest technologies but also, to developing these and alternative technologies with the aim of efficient data generation and mining.
Building on existing infrastructure, CBSG has established state-of-the-art functional genomics technology platforms designed to meet the needs of the individual projects. These platforms cover transcriptomics, proteomics and metabolomics. In addition, CBSG is active in full genome sequencing activities for both potato and tomato and actively develops bioinformatics tools for data mining and genome annotation.
Tomato
Arnaud Bovy, cluster leader
Tomato is a fruit with ambition. It is also one of the few vegetables both grown and eaten in every part of the world. The annual global market for fresh tomatoes is ca. 4 billion Euros. The market for tomato seed to achieve this production capacity is worth ca 200 million Euros per year and for 1 € you get just 5 seeds! The Netherlands is still a major centre of the tomato breeding industry and the CBSG consortium partners together, provide the varieties and seed for ca 70% of the entire fresh tomato production worldwide.
Fresh tomato quality, in terms of appearance, aroma and flavour are traits of increasing importance in the market. CSBG has established a track record in applying the latest '-omics' technologies to gain a better insight into the molecular basis (genetic and biochemical) of these key traits.
The CBSG tomato programme is wholly dedicated to continuing our quest for information on the genetic basis of tomato quailty traits. This information will then be used by our commercial breeding partners to produce even tastier tomato varieties.
