Integration of Physiological and Transcriptomic Analyses Provides Insights into the Regulatory Mechanisms of Adventitious Root Formation in Phoebe bournei Cuttings

Phoebe bournei is an important economic tree species in China, its large-scale propagation is limited by the difficulty of adventitious root (AR) formation in cuttings. In this study, morphological, physiological, and transcriptomic analyses were conducted to investigate the process of AR formation in P. bournei. The results showed that ARs mainly originated from callus tissue. During AR formation, soluble sugar and soluble protein contents changed significantly. Malondialdehyde (MDA) and oxygen free radicals (OFRs) peaked at first sampling stage (PB0), while the activities of polyphenol oxidase (PPO) and indoleacetic acid oxidase (IAAO) exhibited similar patterns. Lignin content increased during callus induction stage, whereas phenolic content continuously declined throughout rooting. Endogenous hormone levels also changed markedly, and Orthogonal partial least squares discriminant analysis (OPLS-DA) analysis indicated that indole-3-acetic acid (IAA) and abscisic acid (ABA) played dominant roles in this process. KEGG enrichment analysis revealed significant enrichment of the phenylpropanoid biosynthesis pathway in all three comparison groups. A total of 48 differentially expressed genes (DEGs) were enriched in plant hormone signal transduction pathways, with 22 and 14 genes associated with IAA and ABA signaling, respectively. Weighted gene co-expression network analysis (WGCNA) further identified two hub modules related to IAA and ABA contents, including eight hub genes such as D6PKL1 and ISTL1. Correlation analysis revealed that the hub genes D6PKL1 and HSP were significantly positively correlated with IAA4 in the IAA signaling pathway. Overall, this study provides new insights into the mechanisms underlying AR formation in P. bournei cuttings and offers a theoretical basis for optimizing its clonal propagation system.