Endogenous Phytohormone and Transcriptome Analysis Provided Insights into Seedling Height Growth of Pinus yunnanensis

Plant height plays a crucial role in both the structure and quality of plants. Pinus yunnanensis is a distinctive species of the forest found in Southwest China, where the height of the plants significantly influences both yield performance and plant architecture. Although the phenotypes of P. yunnanensis seedlings with different plant heights were quite different at their seedling stage, the molecular mechanisms controlling the seedling differentiation remain poorly understood. This study is aimed to investigate the underlying mechanisms of P. yunnanensis seedling differentiation using phenotypic, transcriptomic, and endogenous phytohormone analyses. The P. yunnanensis seedlings were categorized into three grades, i.e., Grades A, B, and C, by mean ± 1/2 standard deviation method (H ± 1/2σ), and the seedling height and ground diameter were measured. We conducted the measurements of endogenous hormone levels in the young shoot apexes of seedlings at different grades during the fast-growth period (March). The DEGs were identified through transcriptome sequencing and analyzed by qRT-PCR validation. Significant differences were observed in the content and ratio of endogenous phytohormones among various grades of P. yunnanensis seedlings (p < 0.05). The ABA content in Grade A was prominently more than that in Grades B and C, and the order of the content of auxins was Grade B > C > A. Furthermore, when compared to Grade A, the ratios of auxins/CTKs, auxins/ABA, CTKs/ABA, and (auxins + CTKs)/ABA exhibited significant increases in Grades B and C. Moreover, GO functional annotation analysis indicated the more pronounced enrichment of DEGs in molecular functions. KEGG metabolic pathway analysis revealed notable differences in enrichment pathways between the pairwise comparisons. The “plant hormone signal transduction” pathway exhibited enrichment in the two groups, followed by “plant–pathogen interaction” pathway in the organism system that was enriched in the three groups. In addition, the results for endogenous phytohormone metabolism pathways indicate a significant up-regulation in the expression of AUX1, while AHP and PP2C exhibited significant down-regulation. To sum up, we aimed at investigating the underlying mechanisms of P. yunnanensis seedling differentiation using phenotypic, transcriptomic, and endogenous phytohormone analyses. The results suggested that individual phytohormones have a limited capacity to regulate gene expression, and seedling differentiation results from the combined regulation of multiple hormones. In addition, several candidate genes associated with phytohormone biosynthesis and signal transduction pathways were identified, including AUX1, GH3, AHP, B-ARR, PP2C, etc., which provided candidate genes for the following hormone-related gene overexpression and knockout experiments. These findings provide insights into the molecular genetic control of seedling height growth of P. yunnanensis.