Time-resolved transcriptomic analysis reveals key regulatory genes and auxin-responsive networks underlying axillary bud branching in Hippophae rhamnoides

The development of axillary buds into branches fundamentally shapes plant architecture, yet how this process is transcriptionally coordinated across developmental stages in woody perennials remains incompletely understood. Using <i>Hippophae rhamnoides</i> (sea buckthorn) as a woody perennial model, we integrated stage-resolved transcriptomic profiling across three axillary bud developmental stages with co-expression network analysis and experimental validation to characterize the regulatory landscape underlying bud activation and branch elongation. Stage-specific expression clustering revealed distinct transcriptional programs associated with developmental transitions: an early-activation gene cluster (Cluster 8, 2003 genes) was enriched in auxin signaling components and transcriptional regulators, reflecting rapid transcriptional reprogramming during bud release from dormancy. In parallel, weighted gene co-expression network analysis (WGCNA) identified key modules (e.g., blue and turquoise) containing hub genes involved in cell proliferation, metabolic adjustment, and stress-related processes, together forming a coordinated regulatory network supporting sustained bud outgrowth. Several candidate hub genes, including <i>ARF, IAA16</i>, and <i>SAUR36</i>, displayed expression patterns responsive to changes in apical auxin status, consistent with a putative "release-and-rescue" transcriptional pattern associated with axillary bud elongation. Collectively, these results support an integrative framework in which axillary bud activation in a woody perennial is regulated through temporally coordinated functional modules rather than bulk hormonal accumulation alone. This systems-level perspective provides molecular insight into shoot branching regulation and identifies candidate genes with potential utility for improving plant architecture in woody species.