Crosstalk between abscisic acid (ABA) and brassinosteroid (BR) signaling pathways is revealed by competing endogenous RNA (ceRNA) network in Brassica napus

Abstract The antagonistic and synergistic effects between phytohormone abscisic acid (ABA) and brassinosteroid (BR) have been reported in some plants. However, the underlying mechanisms of action in rapeseed have not well characterized. To understand the crosstalk between ABA and BR signaling transduction pathways, we performed the whole transcriptome which was including mRNA-seq, lncRNA-seq and miRNA-seq in rapeseed. Then we further explored differentially expressed lncRNA (DE lncRNA) and differentially expressed miRNA (DE miRNA) in mock/ABA-treated and mock/BR-treated combinations. To explore the functions of lncRNAs and miRNAs, we predicted the target genes of DE lncRNA and DE miRNA. We found that trans regulation was the main way in which lncRNAs regulated gene expression. Compared with BR treatment, ABA treatment could regulate a wide range of gene expression at the lncRNA level. The gene ontology (GO) enrichment analyses suggested that the water deprivation pathway and auxin related pathways were the most important pathways for non-coding RNA (ncRNA) to regulate gene expression during early seedling development under ABA or BR treatment, respectively. Interestingly, we found that the ABA and BR responsive pathways were not completely independent. Through competing endogenous RNA (ceRNA) network analyses, we uncovered that there was a local regulatory network co-expressed under ABA and BR signals. Similarly, the four transcription factors (TF) (MYB, ERF, NAC and bZIP) families associated with plant growth and stress responses also shared similarities both under ABA and BR treatment. Our findings provided insights into the molecular mechanism of phytohormone balance and environmental adaptation at the early seedling development stage in rapeseed.