As a result of rapid biotechnological developments in the past century, genetically modified (GM) crops were developed and introduced for field application. Despite the advantages of these crops and the professional marketing policies, people also started questioning the safety of GM products for humans and the environment. In response to that, scientific advisory bodies (such as COGEM, The Netherlands Commission on Genetic Modification) suggested that, among other measurements, an environmental risk assessment (ERA) of a GM crop should be done before introduction into the field. Ecological knowledge about the possible effects was considered a vital component of that assessment. In 2007, the Dutch Government initiated the ERGO (Ecology Regarding Gene-modified Organisms) research programme to generate a scientific basis for a sound ecological risk analysis. The main objective of the ERGO-programme was to develop ecology-based guidelines for how to best assess the possible ecological side-effects of new GM crops. Also the European Food Safety Authority (EFSA) recognised the interaction of a GM crop with non-target organisms as a potential environmental risk and therefore they provided guidelines for selection of a range of non-target organisms and phenotypes to be studied under laboratory conditions as part of a GM crop risk assessment study. These guidelines formed the basis for the ERGO research themes.

Parallel to the new biotechnological developments leading to the introduction of GM plants into the environment, new analytical techniques were also introduced that revolutionized the field of analytical biology. High throughput analytical platforms, collectively called omics technologies, created opportunities for untargeted analysis of cellular components with biological and ecological functions including mRNAs (transcriptomics), proteins (proteomics) and metabolites (metabolomics).  These analytical platforms were recommended by several researchers in the field of GM food/feed safety for the analysis and comparison of a GM product with its safe counterpart. However, EFSA failed to formulate concrete rules about the application of the omics platforms in GM risk assessment perhaps due to a lack of consensus about where and how to employ these technologies in the whole ERA of GM plants. In the ERGO programme, exploration of the potential to apply omics platforms for ERA of GM crops was therefore one of the objectives.

This PhD thesis originates from one of the ERGO themes, assessment of the effect of genetic modification on non-target organisms. Under this theme with three PhD students a multidisciplinary approach was pursued to provide guidelines for how to evaluate non-target effects of GM crops altered in insect resistance using ecological methods as well as omics platforms. In this PhD thesis, I set out to find solutions for some of the limitations in the application of omics platforms such as the lack of a statistical method to evaluate the differences between GM vs. wild type plants at the omics level and the question what would be a fair reference for the judgement about the effect of genetic modification. As a model for the evaluation of the impact of genetic modification on the omics phenotype we used three insect defence traits that we introduced using genetic modification into several different Arabidopsis thaliana accessions. The first trait, indirect defence, was the production of the volatile (E)-nerolidol which has been shown to attract predatory mites that can control spider mites. The other two traits were direct defence traits and consisted of overexpression of the transcription factor (MYB28) to boost aliphatic glucosinolate biosynthesis and the introduction of Cry1from Bacillus thuringiensis encoding the Bt toxin that is effective against lepidopteran insects (caterpillars). As a reference for comparison of the effects of the genetic modification, we used a panel of wild type A. thaliana accessions that were selected in this study and publically available data of different accessions and individuals of a RIL population that together constitute the baseline, the variation present in the non-GM background germplasm.