Comparative transcriptome reveals circadian and hormonal control of adventitious rooting in mulberry hardwood cuttings

Adventitious rooting derived from the parenchyma cells of vascular cambium is a highly efficient rooting type for cutting propagation of woody species. To unravel the molecular mechanisms underlying this distinct rooting process in mulberry stem hardwood cuttings, RNA-seq approach was adopted to perform wide transcriptional expression profiles of three stages characterized by initial excision (stage 1), root primordia induction (stage 2) and emergence of adventitious roots (stage 3). Compared to the former two stages, stage 3 had the most expressed genes (19,987) to establish functionally mature adventitious roots. In contrast, differentially expressed genes (DEGs) identified in stage 1 vs stage 2 comparison group were over threefold higher than stage 2 vs stage 3 comparison group (8930 vs 2739), suggesting a drastic transcriptional activation of genes involved in root primordia induction. GO and KEGG enrichment analysis of the DEGs showed that circadian rhythm-plant pathway was significantly enriched in response to environmental and endogenous changes in stage 2, whereas plant hormones including auxin, ethylene and cytokinin coordinately participated in the formation of adventitious roots in a stage-specific manner via an extensive and delicate regulation of their biosynthesis and signal transduction. Among which, several sets of genes relevant to circadian clock and hormone biosynthesis and signaling are speculated to potentially associated with the induction and differentiation of parenchyma cell initiated adventitious rooting. These findings will enrich our understandings to the mechanisms of adventitious rooting in mulberry, and provide theoretical support for the development of rooting techniques for other woody crops.