Project description:<p>Pseudostellaria heterophylla, a valued shade-loving traditional Chinese medicinal herb, faces severe yield and quality decline under continuous monocropping, threatening industry sustainability. Intercropping, which leverages niche complementarity, offers an eco-friendly mitigation strategy, but its regulatory mechanisms on P. heterophylla remain unclear. Here, we evaluated the influence on P. heterophylla intercropped with Peucedanum praeruptorum via field/hydroponic experiments, integrating phenotypic, photosynthetic, metabolomic, and transcriptomic analyses. Intercropping significantly promoted P. heterophylla growth and yield in a density-dependent manner. High-density intercropping (IS3) increased the fresh weight of plant by 202.80%,and increased the yield of tuberous root by 82.67% compared to monoculture (MPh). Despite reduced photosynthetic rate, intercropping sustained chlorophyll content and reduced damping rate by up to 58.33%, prolonging the effective photosynthetic period to compensate for light limitation. Medicinal quality was concurrently improved. Heterophyllin B, the core bioactive component, rose from 0.0064% (MPh) to 0.0099% (IS1), 0.0093% (IS2), and 0.0096% (IS3), with total saponins and crude polysaccharides also elevated slightly. Additionally, metabolomic analysis identified 1157 differentially accumulated metabolites (DAMs). Peptides, terpenoids, and intermediate products of polysaccharide biosynthesis were enriched under intercropping treatment, promoting quality metabolites biosynthesis. Transcriptomic profiling revealed 141 shared differentially expressed genes (DEGs) across intercropping treatments, with upregulation of light-harvesting complex (LHCA4/LHCB1), chlorophyll metabolism (chlE/chlH), and bioactive component synthesis (PREP/CTSF/SQLE) genes. Weighted gene co-expression network analysis (WGCNA) identified the MEred module correlated with biomass and key transcription factors (GRAS,GATA,BHLH1) regulating growth and metabolites biosynthesis. Collectively,P. praeruptorum intercropping creates a favorable microenvironment, triggering adaptive photosynthetic reprogramming and activating hormone-signaling, secondary metabolism, and nutrient transport pathways to synergistically improve P. heterophylla growth, yield, and quality. This study reveals the adaptive mechanism of shade-tolerant medicinal plants to the environment under intercropping conditions, and has provided theoretical and practical guidance for the ecological cultivation of P. heterophylla.</p>