The sequence of the 59 junction upstream from the 35S promoter shows 88% identity with the 22 kDa alpha zein gene whereas the host 39 flanking region corresponds to a gene putatively coding for the HECT E3 ubiquitin ligase, in the opposite orientation. Read-through transcription of the MON810 transgene has been described as 39 past the truncation site generating a variety of polyadenylated transcripts of different lengths that extend 1 kb downstream of the truncation site. As a result of a stop codon at position +7 downstream of this site, the Griseofulvin transgenic protein includes two additional amino acids, which is compatible with the reported protein size. We selected 30 differentially expressed genes that clustered in overrepresented GO categories and further confirmed their differential expression in DKC6575 and Tietar embryos using real-time qPCR. This alternative approach additionally validated mRNA-seq and microarray hybridization data. The same experimental approach was used to assess to what extent the observed transcriptome differences in DKC6575 and Tietar embryos were TG100713 conserved in other MON810 and nearisogenic variety pairs. To test if there were differences in the embryo physiology and/ or morphology that could explain the observed transcriptomic differences, we collected some data relevant to embryo development at the 20DAP stage. The hormone ABA controls acquisition of desiccation tolerance, one of the key processes during the late embryogenesis phase. We measured ABA contents in embryos of three MON810-near isogenic variety pairs. Twenty DAP embryos of all three MON810 commercial varieties had similar ABA contents to their corresponding near-isogenic counterparts. However, there were statistically significant differences in the ABA levels of 50 DAP embryos, MON810 embryos displaying lower levels than their near-isogenic conventional counterparts. These differences were slightly reduced in fully mature embryos. We then checked whether ABA differences could have an effect on the germination process and initial plant development. In an in-vitro germination assay we compared DKC6575 and Tietar by measuring the radicle and plumule emergence and growth during nine days upon imbibition.