Metabolomics and Transcriptomics Analyses Uncover the Potential of Flavonoids in Response to Saline–Alkali Stress in Codonopsis pilosula

<i>Codonopsis pilosula</i> (Cp) is a traditional medicinal herb whose cultivation is limited by environmental factors like saline-alkali. Flavonoids, found in various plant organs, are involved in plant stress responses, but the specific saline-alkali stress response mechanism of Cp's flavonoids is unknown. This study carried out saline-alkali stress treatments in Cp, collected samples from roots, stems, and leaves, and conducted physiological, biochemical, transcriptomic, and metabolomic tests. Phenotypic observations showed varying degrees of saline-alkali stress effects on different organs of Cp. Physiological tests revealed inconsistent antioxidant indicator changes across organs. Metabolomic and transcriptomic analyses revealed that, compared to roots and stems, leaves contained the highest number of differentially accumulated metabolites (DAMs) related to flavonoids, reaching up to 23, and harbored the most differentially expressed flavonoid-related genes, with up to 54; the roots treated with NaHCO₃ contained up to 14 types of flavonoids, while the leaves treated with NaHCO₃ contained up to 20 types of differentially expressed flavonoid-related genes; additionally, flavonoid pathway genes, including <i>CHS</i>, <i>CHI</i>, and bHLH transcription factors, might have responded to saline-alkali stress by modulating the production of flavonoid compounds such as Cyanidin and Galangin. This study preliminarily elucidated the molecular mechanisms of flavonoid response to saline-alkali stress in Cp, providing a theoretical basis for flavonoid exploitation, molecular breeding, and cultivation area expansion.