Molecular characterization technology in genetically modified organisms, in addition to how transgenic biotechnologies are developed now require full transparency to assess the risk to genetically modified crops. Next generation sequencing (NGS) methodology have been suggested as an effective means in genome characterization and detection of transgenic insert locations. In this study, we applied high-throughput DNA sequencing to detect the insert transgenic loci and characterize genomic variation of three transgenic rice, SNU-Bt-9, SNU-Bt-30, and SNU-Bt-109. Also, we developed a new method for molecular characterization of GM rice event without need for PCR and southern blot analysis. An average of 26 Gb (~68X coverage) was sequenced with a 2 x 150 bp paired end method by Illumina Hiseq2500, which was consecutively mapped to the rice genome and T-vector sequence. Whole genome mapping strategy were applied for identifying genome-wide variations between transgenic and non-transgenic rice genome. The compatible pairs of sequencing reads were successfully mapped to single loci on rice chromosome. We identified chromosome specific and non-specific SNPs that considered as induced by Agrobacterium-mediated transformation. Interestingly, we found that the number of SNPs in transgenic rice is far lower than the number of SNPs between the local rice varieties. GM-rice specific SNPs were mainly detected on chromosome 3, 4, 7, 9 and 11. Our results showed that NGS technology and bioinformatics approaches can offer comprehensive understanding of GM crops, especially for assessment of molecular safety and genomic stability.
