Genetic and epigenetic characterization of the cry1Ab coding region and its 3′ flanking genomic region in MON810 maize using next-generation sequencing

MON810 maize was first commercialized in 1997 and it is one of the most marketed genetically modified crops worldwide. Although MON810 maize has been studied extensively, its genetic stability and epigenetics have not been studied very well. We used next-generation sequencing to investigate the genetics and epigenetics of the cry1Ab coding region and its 3′ flanking genomic region in three different MON810 maize varieties. Genetic characterization of the cry1Ab coding region allowed us to identify and quantify several sequence variants. Samples from seeds containing a stacked MON810 event had more variants than MON810 single event varieties. Specifically, position 71 of the analyzed region varied in 15 of 600 samples tested and thus appears to be a mutational hotspot. In addition, position 71 varied at very different frequencies in the samples. Epigenetic analysis revealed a low degree of methylation, making it difficult to associate the coding region variants with methylation status. In conclusion, the variation in the coding region is either due to the increased age of the seeds from the tested maize varieties, which is known to increase the mutation rate, or due to the presence of a second (non-functional) cry1Ab fragment in the genome of the MON810 maize variety.