Morphological, physiological, hormonal, and transcriptomic analyses elucidate axillary bud development mechanisms in Pinus yunnanensis

Pinus yunnanensis is a timber species endemic to southwestern China, and the development of its lateral branches profoundly affects the efficiency and quality of clonal propagation. Consequently, elucidating the dynamic characteristics of lateral-branch development can accelerate both propagation efficiency and quality. In this study, eight-month-old P. yunnanensis seedlings were selected as the experimental material, and, based on external morphological traits and internal anatomical observations, the axillary-bud developmental process was divided into four stages: pre-initiation, activation, formation, and elongation. To investigate the mechanisms governing axillary-bud germination and elongation, we characterized the biological features, developmental progression, and induction/growth mechanisms of P. yunnanensis axillary buds using nutrient assays, carbohydrate quantification, hormone profiling, and transcriptome sequencing. The results demonstrated that during the developmental process of P. yunnanensis axillary buds, the axillary meristem undergoes continuous changes and differentiation. From a nutrient-content perspective, potassium was identified as a limiting element during the bud-formation stage. As axillary buds progressed through their developmental phases, trehalose and starch facilitated pre-initiation release, total soluble sugars and sucrose promoted bud germination, and glucose and fructose supported subsequent elongation growth. Moreover, the concentrations of various endogenous hormones exhibited distinct trends across the four developmental stages. Finally, Weighted Gene Co-expression Network Analysis revealed three candidate genes ( PyPP2C06 , PyTIR1 , and PyPRR ) whose expression profiles are tightly correlated with axillary-bud formation in P. yunnanensis. These findings provide a crucial theoretical basis for the targeted genetic improvement of P. yunnanensis . • This study provides the first elucidation of the developmental stages of axillary bud growth in Pinus yunnanensis , was divided into four stages: pre-initiation, activation, formation, and elongation. • Nutrient dynamics revealed phosphorus and potassium as limiting elements at different stages, with potassium facilitating bud activation. • Carbohydrate partitioning showed trehalose and starch promote dormancy release, sucrose supports germination, and glucose/fructose drive elongation. • Transcriptome analysis combined with WGCNA identified three hormone-related genes ( PyPP2C06 , PyTIR1 , and PyPRR ) as being critical for axillary bud development. • Findings provide an essential theoretical basis for genetic improvement and to offer scientific guidance for the management of seed orchards of Pinus yunnanensis .