Integrated Transcriptome–Metabolome Analysis Reveals the Flavonoids Metabolism Mechanism of Maize Radicle in Response to Low Temperature

The Northeast region in China is a major maize-producing area; however, low-temperature stress (TS) limits maize (<i>Zea mays</i> L.) seed germination, affecting population establishment and yield. In order to systematically explore the regulation mechanism of maize radicle which is highly sensitive to low-temperature environment response to TS, seeds of ZD958 and DMY1 were used to investigate germination responses under 15 °C (control) and 5 °C (TS) conditions. Phenotypic, physiological, transcriptomic, and metabolomic analyses were conducted on the radicles after 48 h of TS treatment. TS caused reactive oxygen species (ROS) imbalance and oxidative damage in radicle cells, inhibiting growth and triggering antioxidant defenses. Integrated transcriptomic and metabolomic analyses revealed that flavonoid metabolism may play a pivotal role in radicle responses to TS. Compared with the control treatment, ZD958 and DMY1 under TS treatment significantly increased (<i>p</i> < 0.01) the total flavonoid content, total antioxidant capacity, 4-coumarate-CoA ligase activity, and dihydroflavonol 4-reductase activity by 15.99% and 16.01%, 18.41% and 18.54%, 63.54% and 31.16%, and 5.09% and 7.68%, respectively. Despite genotypic differences, both followed a shared regulatory logic of "low-temperature signal-driven-antioxidant redirection-functional synergy." This enabled ROS scavenging, redox balance, and antioxidant barrier formation, ensuring basal metabolism and radicle development.