Multi‐Omics Analysis Links MYB/bHLH Expression to Cyanidin Accumulation and Antioxidant System in Purple‐Stemmed Codonopsis pilosula

As a medicinal and culinary important species, Codonopsis pilosula requires comprehensive germplasm research and innovation. This study elucidated the molecular mechanisms underlying stem pigmentation in C. pilosula through integrated transcriptomic and metabolomic analyses. Comparative profiling of purple-stemmed (CZ) and green-stemmed (CL) cultivars revealed 8674 differentially expressed genes (DEGs) and 105 differentially expressed metabolites (DEMs). Notably, the CZ cultivar demonstrated elevated levels of procyanidin B2, delphinidin, and four cyanidin derivatives, exhibiting 44.6-fold higher total anthocyanin content compared to the CL cultivar. This phenotype was associated with the coordinated regulation of MYB/bHLH transcription factors and structural genes (including F3'5'H, ANS, and CHS). Multi-omics networks identified flavonoid biosynthesis (enriched with 30 DEMs) and redox regulation (involving 23 antioxidant-related DEGs) as pivotal pathways. Enhanced catalase (CAT) and peroxidase (POD) enzymatic activities, coupled with increased accumulation of proline and raffinose, together with anthocyanin-mediated reactive oxygen species (ROS) scavenging, were associated with enhanced stress tolerance in the CZ cultivar. Key transporters (such as GSTU45 and MATE30), potentially involved in vacuolar anthocyanin deposition, were characterized. These findings provide novel insights into metabolic regulation and molecular breeding strategies for medicinal plant quality improvement, primarily through understanding the mechanisms underlying stem-specific anthocyanin accumulation and associated stress resilience.