Integrated physiological, metabolomic, and transcriptomic analyses reveal the differential molecular mechanisms underlying cadmium stress responses in two Codonopsis pilosula cultivars

Codonopsis pilosula , a widely cultivated medicinal plant, is frequently contaminated with cadmium (Cd) during growth. To elucidate Cd accumulation and tolerance mechanisms, we simulated Cd stress via hydroponics and analyzed physiological/multi-omics responses in two cultivars: CM ( C. pilosula Nannf.var. modesta (Nannf.) L.T.Shen) and CN ( C. pilosula (Franch.) Nannf.). Morphologically, CM exhibited stronger Cd tolerance, with significant growth inhibition observed in CN under 0.64 mM Cd. Physiologically, low Cd stimulated growth, while high Cd inhibited growth, impaired photosynthesis, induced reactive oxygen species (ROS) accumulation, and damaged microstructures. Transcriptomic analysis revealed that high Cd stress altered the expression of 4982 and 5270 genes in CM roots and leaves, markedly exceeding the 10039 and 9403 in CN. With these differentially expressed genes (DEGs) enriched in starch / sucrose metabolism, fatty acid / alpha-linolenic acid metabolism, where unsaturated fatty acid / cysteine-methionine metabolism genes were upregulated in CM roots but downregulated in CN. Metabolomic analysis showed 689 metabolites with altered abundance in CM under high Cd, compared to 845 in CN. These consistent omics results underscore the higher Cd sensitivity of CM. Critically, integrated multi-omics analysis identified glutathione, sulfur, cysteine-methionine, and alpha-linolenic acid metabolism as core Cd-tolerance pathways, with alpha-linolenic acid metabolism dominant in CM and other pathways predominant in CN. Collectively, these results provide a theoretical foundation for breeding low-Cd cultivars. • Cd stress inhibits growth, disrupts photosynthesis/cell structures, reducing yield and medicinal efficacy. • CM resists via antioxidants; CN accumulates more Cd with oxidative damage. • Both use sulfur-glutathione pathways to scavenge ROS and alleviate Cd-induced oxidative stress. • CM enhances Cd tolerance via alpha-linolenic acid metabolism, modifying membrane fluidity to block Cd²⁺ influx.