Mulberry (Morus alba) is an economically important forest tree species, yet cutting propagation is constrained by low adventitious rooting efficiency. Although ABT, a composite rooting promoter, can improve cutting survival, its molecular basis remains unclear. Here, cuttings of the cultivar Qiangsang 1 were treated with ABT, NAA, or IAA (200–1000 mg/L) and subjected to transcriptome profiling to elucidate how ABT enhances rooting. Hormone-related analyses showed that ABT upregulated GH3 (auxin-amido synthetase) at days 0 and 20, implicating auxin homeostasis. ERF1/2 (ethylene response factors) exhibited a temporal oscillation, with induction at day 10 followed by repression from days 20 to 30, consistent with a shift from developmental programs to defense-related processes. In parallel, JAZ (jasmonate ZIM-domain) genes were downregulated at day 0 and subsequently upregulated; together with CYP94C1, these changes may attenuate jasmonate-associated defense signaling. For cell remodeling and defense coordination, ABT reduced the expression of genes associated with cell-wall rigidity while inducing EXPA11 (expansin) at day 20, potentially facilitating root primordium emergence. Meanwhile, PR-1 (pathogenesis-related protein 1) was transiently upregulated at days 0, 20, and 30, and the concomitant modulation of WRKY transcription factors and RPM1 suggests enhanced defense readiness. Integrative network analysis further indicated that a GH3–ERF1/2–PR-1 module links hormonal and defense cues and may activate BAT1 (energy metabolism) and RBOHB (ROS production) to support adventitious root elongation. Collectively, these results suggest that ABT improves rooting efficiency by reshaping hormonal homeostasis and coordinating cell-wall reconstruction with a pre-activated defense state, thereby providing a conceptual framework for balancing root induction and defense responses during vegetative propagation in forest trees.

Quercus variabilis (Q. variabilis), a significant broadleaf species used in afforestation across high, sandy, and mountainous regions, presents unique challenges for transplantation. This species is characterized by its slow above-ground growth and rapid taproot development, which suppresses the proliferation of lateral and fibrous roots, negatively impacting post-transplant survival. Research indicates that targeted root pruning—specifically, the removal of one-third of the roots—promotes the development of lateral roots in these seedlings. This study involved pruning the root systems of Q. variabilis and assessing the subsequent root development in comparison to an unpruned control group. Our analysis, which included transcriptome sequencing and plant hormone metabolism assays conducted at 2, 12, and 25 days post-pruning, yielded 126.02 Gb of clean data and identified 7662 differentially expressed genes (DEGs). These genes were primarily enriched in the plant hormone signal transduction pathway. Further investigation of this pathway, along with hormone content measurements, elucidated the mechanisms that contribute to enhanced root growth following pruning. Additionally, through a weighted correlation network analysis (WGCNA), we identified 20 key genes that are instrumental in promoting root development in Q. variabilis saplings. This research advances the theoretical framework for forestry seedling production and afforestation, laying the groundwork for scientifically informed vegetation restoration techniques.