Natural variation explains most transcriptomic changes among maize plants of MON810 and comparable non-GM varieties subjected to two N-fertilization farming practices Anna Coll • Anna Nadal • Rosa Collado • Gemma Capellades • Mikael Kubista • Joaquima Messeguer • Maria Pla Received: 28 September 2009 / Accepted: 7 March 2010 / Published online: 27 March 2010 Ó Springer Science+Business Media B.V. 2010 Abstract The introduction of genetically modified organisms (GMO) in many countries follows strict regu- lations to ensure that only safety-tested products are mar- keted. Over the last few years, targeted approaches have been complemented by profiling methods to assess possible unintended effects of transformation. Here we used a commercial (Affymertix) microarray platform (i.e. allow- ing assessing the expression of *1/3 of the genes of maize) to evaluate transcriptional differences between commercial MON810 GM maize and non-transgenic crops in real agricultural conditions, in a region where about 70% of the maize grown was MON810. To consider natural variation in gene expression in relation to biotech plants we took two common MON810/non-GM variety pairs as examples, and two farming practices (conventional and low-nitrogen fertilization). MON810 and comparable non- GM varieties grown in the field have very low numbers of sequences with differential expression, and their identity differs among varieties. Furthermore, we show that the differences between a given MON810 variety and the non- GM counterpart do not appear to depend to any major extent on the assayed cultural conditions, even though these differences may slightly vary between the conditions. In our study, natural variation explained most of the vari- ability in gene expression among the samples. Up to 37.4% was dependent upon the variety (obtained by conventional breeding) and 31.9% a result of the fertilization treatment. In contrast, the MON810 GM character had a very minor effect (9.7%) on gene expression in the analyzed varieties and conditions, even though similar cryIA(b) expression levels were detected in the two MON810 varieties and nitrogen treatments. This indicates that transcriptional differences of conventionally-bred varieties and under different environmental conditions should be taken into account in safety assessment studies of GM plants. Keywords GMO (Genetically Modified Organism) Á MON810 Á Maize Á Nitrogen stress Á Transcriptome Á Unintended effects Á Agricultural field Á Natural variation Abbreviations cDNA Complementary DNA CRM Certified reference material Electronic supplementary material The online version of this article (doi:10.1007/s11103-010-9624-5) contains supplementary material, which is available to authorized users. A. Coll Á R. Collado Á M. Pla (&) Institut de Tecnologia Agroalimenta `ria (INTEA), Universitat de Girona, Campus Montilivi, EPS-I, 17071 Girona, Spain e-mail: maria.pla@udg.edu A. Nadal Departament Gene `tica Molecular, Centre de Recerca en Agrigeno `mica, CSIC-IRTA-UAB, Jordi Girona, 18, 08034 Barcelona, Spain G. Capellades Fundacio ´ Mas Badia, ctra. La Tallada s/n, 17134 La Tallada d’Emporda `, Girona, Spain M. Kubista Institute of Biotechnology, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4 142 20, Czech Republic M. Kubista TATAA Biocenter AB, Odinsgatan 28, 411 03 Goteborg, Sweden J. Messeguer Departament Gene `tica Vegetal, Centre de Recerca en Agrigeno `mica. CSIC-IRTA-UAB, Ctra. Cabrils km2, 08348 Barcelona, Spain 123 Plant Mol Biol (2010) 73:349–362 DOI 10.1007/s11103-010-9624-5