Transcriptomic Profiling and Discovery of Key Transcription Factors Involved in Adventitious Root Formation from Root Cuttings of Mulberry

Abstract Adventitious rooting is a critical aspect of plant morphogenesis and development, and the challenges associated with the limited and inefficient rooting of scions represent a significant impediment to the rapidity and caliber of clonal propagation of forest trees in silvicultural practices. Building upon the findings of prior investigations conducted by our team, it was determined that the application of indole-3-butyric acid (IBA) at a concentration of 1000 mg/L− 1 had the most profound effect on the promotion of mulberry rooting. To elucidate the underlying molecular mechanisms, this study involved the analysis of RNA sequencing data from mulberry phloem pre- and post-treatment with 1000 mg/L− 1 IBA across time intervals of 10, 20, 30, and 40 days, revealing 5226 differentially expressed genes (DEGs). These DEGs were subsequently categorized into Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, with a pronounced enrichment observed in categories pertinent to hormone signaling processes. Weighted Gene Co-expression Network Analysis (WGCNA) was applied to all identified DEGs, resulting in the delineation of eight co-expression modules. Of these, two modules exhibited significant correlations with the 1000 mg/L− 1 IBA treatment. Furthermore, 18 transcription factors implicated in the facilitation of adventitious root formation in mulberry were identified. An exploratory analysis was also conducted on the cis-regulatory elements associated with these transcription factors. The outcomes of this research not only lay the groundwork for a comprehensive understanding of the mechanism of adventitious rooting in mulberry but also provide theoretical support for the discovery and harnessing of exceptional genetic resources within the species.