Regulating growth and stress responses in Abies beshanzuensis seedlings: integrated impacts of shading on morphology, physiology, and molecular pathways

Introduction Abies beshanzuensis M. H. Wu is a critically endangered conifer species of immense ecological and evolutionary significance, with only three wild adult progenitor trees remaining globally. Due to its extreme vulnerability to environmental stress, poor natural regeneration, and obligate mycorrhizal dependency, identifying optimal microclimatic conditions for artificial cultivation is paramount for its survival. This study investigates how varying shading intensities influence the morpho-architectural, physiological, and transcriptomic responses of A. beshanzuensis seedlings to establish ideal conservation protocols. Methods Seedlings were subjected to multiple shading treatments arrayed along an intensity gradient, culminating in extreme shading at T5. The intermediate treatment, T3, represented moderate shading. The experimental framework evaluated phenotypic morphology (plant height, crown width, and root system architecture), physiological parameters (leaf chlorophyll content, chlorophyll fluorescence, antioxidant enzyme activities, and oxidative stress markers), and osmotic adjustments. Furthermore, global transcriptome profiling utilizing advanced RNA-Seq methodologies coupled with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses was conducted to identify Differentially Expressed Genes (DEGs) and map regulatory molecular pathways. Results Moderate shading (T3) profoundly enhanced plant height, crown width, root system architecture, and leaf chlorophyll content, significantly outperforming all other treatments. Root and shoot growth initially increased with shading intensity but declined sharply under excessive shading (T4 and T5). Chlorophyll fluorescence analysis demonstrated optimized photosynthetic performance under T3, characterized by higher electron transport rates and maximal photochemical efficiency, whereas extreme shading (T5) suppressed these parameters. Physiological assessments revealed that T3 seedlings exhibited the highest antioxidant enzyme activities (Superoxide Dismutase, Peroxidase, Catalase) and the lowest Malondialdehyde content, indicating minimal oxidative membrane damage. Soluble sugar, protein, and proline levels fluctuated, reflecting adaptive metabolic adjustments. Transcriptome analysis identified extensive DEGs across treatments, with significant enrichment in pathways related to photosynthesis, secondary metabolism, stress responses, and hormonal signaling. GO and KEGG analyses confirmed that T3 optimized energy metabolism, enhanced defense mechanisms, and differentially regulated hormone signal transduction. Discussion Moderate shading (T3) establishes highly favorable environmental conditions for A. beshanzuensis by achieving a critical biological equilibrium between photosynthetic efficiency, stress resilience, and molecular regulation. Excessive shading disrupts this balance, precipitating carbon starvation and physiological decline. These findings illuminate the underlying regulatory networks of shade adaptation and provide a vital theoretical and practical foundation for the ex-situ conservation, and artificial cultivation of this critically endangered relict species.