Transcriptional Interactions of Single B-Subgenome Chromosome with C-Subgenome in <i>B. oleracea-nigra</i> Additional Lines

Serial monosomic alien addition lines (MAALs) provide an ideal system to elucidate the transcriptomic interactions between the alien chromosomes and recipient genome under aneuploidy. Herein, five available <i>Brassica oleracea-nigra</i> MAALs (CCB1, CCB4, CCB5, CCB6, CCB8), their derived <i>B. oleracea</i> plants (non-MAALs), and two parents were analyzed for their gene expressions by using high-throughput technology. Compared to parental <i>B. oleracea</i>, all MAALs showed various numbers of DEGs, but CCB8 gave much higher DEGs; the number of downregulated DEGs was slightly higher than the number of upregulated ones, except for in relation to CCB8. All derived <i>B. oleracea</i> plants also gave certain numbers of DEGs, despite these being much lower than in the respective MAALs. Compared to <i>B. nigra</i>, in all five MAALs more DEGs were downregulated than upregulated. <i>Trans</i>-effects were likely more prevailing than <i>cis</i>-effects, and these DEGs were predominantly associated with material transport by dysregulating the cellular component. Meanwhile, the orthologous genes on alien chromosomes could only play a feeble compensatory role for those gene pairs in C-subgenome, and different levels of the expressed genes had a greater tendency towards downregulation. These results revealed transcriptional aneuploidy response patterns between two genomes and suggested that <i>cis</i>- and <i>trans</i>-mechanisms synergistically regulated alien gene transcriptions after distant hybridization.