Herein, we performed high-throughput technology to detect gene expression alterations of a whole set of nine Brassica rapa-oleracea monosonic alien addition lines (MAALs, C1-C9) in comparison of parental restituted B. rapa (RBR). Both MAALs and RBR obtained previously are in the background of natural B. napus genotype “Oro”. We found that, compared to diploid RBR, all the MAALs showed various degree of dysregulated expression genes resulting from cis-effect and more prevailing trans-effect. And trans-effect on gene expression in MAALs likely was increasing with the homology between recipient A genome and additional C chromosome instead of genes content of extra C chromosome. Totally, 10 trans-effect dysregulated expression genes mainly involved in the function of transporter activity were observed in all pairwise comparisons. Strikingly, highly expressed gene was more prone to down-regulated and opposite situation was observed for low expressed genes in all pairwise comparisons, suggesting this is a common character in transcriptional patterns response to aneuploidy. Overall design: The newly expanded third leaves without petioles from six plants of each genotype were collected and immediately stored in liquid nitrogen for RNA extraction. Three samples with three replicates were sequenced via Illumina HiSeqTM 3000.