Density-dependent intercropping with Peucedanum praeruptorum enhances Pseudostellaria heterophylla yield and quality via photosynthetic reprogramming and metabolic reallocation

Pseudostellaria heterophylla , a valued shade-loving traditional Chinese medicinal herb, experiences severe yield and quality declines under continuous monocropping, threatening the sustainability of its cultivation. Intercropping, which leverages niche complementarity, represents an eco‑friendly strategy to mitigate these issues; however, the regulatory mechanisms underlying it in P. heterophylla remain largely uncharacterized. Here, we evaluated the influence of intercropping P. heterophylla with Peucedanum praeruptorum in 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 the plant by 202.80%, and increased the yield of tuberous root by 82.67% compared to monoculture (MPh). Despite reduced photosynthetic rate, intercropping maintained chlorophyll content and reduced damping rate by up to 58.33%, thereby 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 among the metabolite classes showing altered accumulation under intercropping. 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 containing potential regulators ( GRAS , GATA , BHLH1 ) putatively associated with growth and metabolites biosynthesis. Collectively, P. praeruptorum intercropping triggers adaptive photosynthetic reprogramming and activates hormone-signaling, secondary metabolism, and nutrient-transport pathways, thereby synergistically improving P. heterophylla growth, yield, and quality. This study reveals the adaptive mechanisms of shade-tolerant medicinal plants in the environment under intercropping conditions and provides theoretical and practical guidance for the ecological cultivation of P. heterophylla .