Abstract Genetic engineering is a powerful technology of the present century that has revolutionized the agricultural, health, pharmaceutical and food industries worldwide. It is important to identify changes caused by transgenes that may be attributed to unintended traits in the risk assessment of genetically modified (GM) crops. Rhizomania, which is caused by beet necrotic yellow vein virus (BNYVV) infection, is considered to be a significant constraint in order to produce sugar beet worldwide. The resistance of transgenic sugar beet plants to the BNYVV was previously developed through RNA silencing by expression of hairpin RNA (hpRNA) structures. In the present study, the RNA sequencing (RNA-seq) analysis was performed in order to evaluate the transcriptional changes of an event of transgenic sugar beet plants, named 219-T3:S3-13.2 (S3), with the non-transgenic parental plants grown in virus-infected soil. The results of the present study indicate that there are only 0.9% differentially expressed genes (DEGs) at significant levels. The functional analysis shows alterations of transcription in lipids, amino acids, and carbohydrates metabolisms, cellular processes (autophagy), hormone signal transduction, and biosynthesis of secondary metabolites in the transgenic event, which are related to stress-adaption for which most of the genes were up-regulated. All in all, we conclude that the presence of the transgenes does not have substantial effects on the plant gene expression patterns. This work also indicates that RNA-seq analysis can be useful to evaluate the unintended effects and risk assessment of GM sugar beet plants.

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