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Transcriptome, proteome and metabolome analysis to detect unintended effects in genetically modified potato.
Project Code: G02001;
Chassy, B., Hlywka, G.A., Kleter, G.A., Kok, E.J., Kuiper, H.A., McGloughlin, M., Munro, I.C., Phipps, R.H. & Reid, J.E. (2004). Nutritional and safety assessment of foods and feeds nutritionally improved through biotechnology. Prepared by a task force of the ILSI International Food Biotechnology Committee. Comprehensive Reviews in Food Science and Food Safety 3, 35-104.
Defernez, M. & Colquhoun, I.J. (2003). Factors affecting the robustness of metabolite fingerprinting 1H NMR spectra. Phytochemistry 62 1009-1017.
Defernez, M., Gunning, Y.M., Parr, A.J., Shepherd, L.V.T., Davies, H.V. & Colquhoun, I.J. (2004). NMR and HPLC/UV profiling of potatoes with genetic modifications to metabolic pathways. Journal of Agriculture and Food Chemistry 52 6075-6085.
Kok, E.J. & Kuiper, H.A. (2003). Comparative safety assessment for biotech crops. Trends in Biotechnology 21, 439-444.
Kuiper, H.A., Kok, E.J. & Engel, K.-H. (2003). Exploitation of molecular profiling techniques for GM food safety assessment. Current Opinion in Biotechnology, 14, 238-243.
Scottish Crop Research Institute
One of the key issues in safety evaluation of GM crop plants is whether or not unexpected or
unintended compositional changes have taken place in the organism due to the genetic
modification. These changes have the potential to affect, adversely, human and animal
heath and possibly the environment. Unintended alterations in agronomic traits or
composition may arise from insertion mutagenesis, or as a result of metabolic effects of the
novel gene product(s). Currently, the process of searching for potential unintended effects
concentrates on the analysis of specific compounds using traditional ‘targeted’ analytical
approaches. As unintended effects by their nature might be completely unpredictable, such
targeted approaches may or may not detect such perturbations. Plants contain many
thousands of genes, proteins and metabolites so the development and successful
application of new ‘broad scale’ analytical approaches such as transcriptomics, proteomics
and metabolomics in risk analysis holds significant potential. In this project we have used
GM and non-GM potato lines to assess the capacity of profiling approaches to detect
unintended effects. Specifically, the scientific and technical problems addressed were:
1. The development, assessment and applicability of high throughput protocols for profiling
or ‘omics’ approaches (transcriptomics, proteomics, metabolomics) whilst maintaining
the ability to discriminate as many compounds, proteins and, genes as possible.
2. The application of these protocols in the assessment of ‘substantial equivalency’ in a
range of GM potato lines with modified developmental and metabolic process using
appropriate controls and comparators in a real field environment.
3. Assessment of the added value components of validated ‘omics’ or profiling approaches
compared with targeted analyses which are currently the cornerstone of the risk
4. The application of validated protocols to diverse potato germplasm to provide valuable
information on the extent of genetic diversity using the ‘omics’ approaches. Databases
will be constructed to provide a preliminary knowledge base on ‘natural variation’ which
can be used in risk assessment downstream.
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