Multi-omics analysis reveals the dynamic adaptive mechanisms of rice seedlings in response to cadmium stress

Cadmium (Cd) is a highly toxic heavy metal pollutant that poses a serious threat to rice production and human health. Current research predominantly focuses on physiological or molecular responses at single time points, leaving the dynamic response mechanisms and physiological-molecular synergistic regulatory relationships in rice during different periods of continuous Cd stress largely unclear. In this study, rice roots were treated with Cd for 0, 1, 5, and 9 days. Morphological structures and physiological indices were systematically measured and integrated transcriptomic and metabolomic analyses were performed. The results indicated that in the early stage (1 d), carbohydrate metabolism and the MAPK signaling pathway were rapidly activated, with genes such as ERF15 , FAR7 , and APX3 being significantly upregulated, synergistically mediating signal transduction and oxidative stress defense. At the mid-stage (5 d), pathways for phenylpropanoid, suberin, and wax biosynthesis were significantly enriched, driving lignin deposition and cell wall remodeling to construct a physical barrier. In the late stage (9 d), glutathione metabolism and ABC transporter pathways remained enriched, dominating Cd^{2 +} chelation and compartmentalization. Concurrently, genes such as POD27 and BKI1 were highly expressed, promoting biochemical detoxification and cell protection. Corresponding physiological indicators aligned with these molecular events, manifesting as growth inhibition, structural damage, and significant increases in antioxidant enzyme activities, osmoregulatory substances, and lignin content, along with cell wall thickening. This study dynamically characterizes the sequential activation of these three defense layers across time, revealing the temporal transition and synergistic regulation among signal response, physical barrier construction, and biochemical detoxification. Although each individual defense strategy has been reported, their coordinated temporal dynamics have not been systematically delineated. This provides a theoretical basis and experimental support for in-depth analysis of the rice Cd tolerance molecular network and for breeding rice varieties with low Cd accumulation.