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Genetic modification (GM) by Agrobacterium-mediated transformation is a robust and a most popular method to confer new traits to crops. Although T-DNA is delivered into host genome via Agrobacterium-mediated transformation, it has not been evaluated how extent the genome is damaged by this single event at single base resolution. As a part of the safety assessments of GM crops, we conducted whole genome sequencing and transcriptome analysis using a transgenic rice called OSCR11, the rice seed-based edible vaccine containing two major pollen allergens, Cry j 1 and Cry j 2, against Japanese cedar pollinosis. We revealed that genetic differences between OSCR11 and its host a123 were much less than those between a123 and its precedent cultivar Koshihikari. Base substitution pattern from a123 to OSCR11 was almost equivalent to that of somaclonal variation. Mutations caused by transformation event on OSCR11 may occur during cell culture steps, and Agrobacterium infection itself rarely damaged OSCR11 genome other than T-DNA integration, if any, indistinguishable from mutations induced during cell culture. In addition, transcriptomes of a123 and OSCR11 were quite similar. These results suggest that a123 and OSCR11 are substantially identical at genetic level. High-throughput sequencing based safety assessments of transgenic plants would possibly become standard and promote the development of GM crops. |