Upon grain development, embryos of the same MON810 varieties had lower ABA contents than their conventional counterparts, as assessed using 50 DAP and physiologically mature embryos. Four additional genes, Dirithromycin related to carbohydrate metabolism and specifically clustering in the glycolysis pathway, were repressed in MON810 embryos. Some maize glycolysis genes have been reported to be up-regulated in the embryo at early and later developmental stages and to have low mRNA levels during intermediate stages. Up to one forth genes differentially expressed in DKC6575 and Tietar 20 DAP embryos clustered in overrepresented categories related to DNA organization and Griseofulvin protein metabolism. In particular, genes in the chromatin organization and protein modification categories were up-regulated in MON810, whereas those in the protein and amino acid biosynthesis and synthesis of ribosomal constituents, as well as those in the transcription regulation clusters, were down-regulated in transgenic samples. This seems to indicate that MON810 embryos would display lower protein biosynthesis processes and increased chromatin restructuration and protein ubiquitination. Young maize embryos are known to highly express a number of genes related to protein degradation ; and embryos at late embryogenesis stages are known to repress transcription of genes related to the synthesis of new proteins. Similarly, there is increased expression of histone core genes at the early embryo developmental stages than in late maturation stages. Overall analysis of these results shows that most genes clustering in overrepresentated functional categories display expression levels that are modulated along the embryo developmental process. Thus, we hypothetised that our 20DAP transgenic and conventional embryos might have slight differences in their precise developmental stage, and these small differences in embryo development could explain these observed transcriptome changes, especially for these genes whose expression is known to rapidly change during embryo mid-development.