Integrated physiological, transcriptomic and widely targeted metabolomic analyses reveal the underlying mechanism of cold stress response in the panicle apical abortion line J876 derived from Oryza rufipogon

Cold stress is a major environmental factor that significantly limits rice yield. However, the coordinated systemic responses of rice leaves and roots to cold stress remain poorly understood. In this study, we developed Oryza rufipogon introgression lines (ILs) using the recipient parent Dianjingyou 1 (DJY1). Among these lines, J876 exhibits panicle apical abortion and was selected to investigate cold tolerance at the seedling stage. Phenotypic analysis showed that J876 was significantly more sensitive to cold stress than DJY1. To elucidate the underlying mechanisms, we conducted integrated physiological, biochemical, transcriptomic, and widely targeted metabolomic analyses to compare cold stress responses between DJY1 and J876. Under cold treatment, J876 accumulated higher levels of reactive oxygen species (ROS) in both leaves and roots, while exhibiting lower oxidoreductase activity than DJY1. Furthermore, differentially expressed genes and metabolites were mainly involved in amino acid and carbohydrate metabolism. Integrative analyses revealed that the arginine, proline, and phenylpropanoid metabolism pathways were commonly regulated in both leaves and roots, whereas flavonoid biosynthesis was specifically activated in leaves and galactose metabolism was uniquely modulated in roots under cold stress, highlighting their potentially coordinated roles in rice cold tolerance. These findings provide new insights into the regulation of cold-induced oxidative stress in rice and offer valuable guidance for breeding cold-tolerant rice varieties. • Using the cold-sensitive near-isogenic line J876 developed by us as the research material. • We aimed to investigate the systemic response mechanisms of rice leaves and roots to cold stress. • We found that phenylpropanoid metabolism may be one of the key secondary metabolic pathways involved in the rice response to cold stress.