Integrated Transcriptomic and Metabolomic Analysis Reveals Molecular Responses Associated with Foliar Selenium Treatment Under Cold Stress in Rapeseed (Brassica napus L.) Seedlings

Rapeseed (Brassica napus L.) is an important oil crop, but seedling growth is often restricted by low temperatures in late autumn and winter. Selenium (Se) may modulate plant stress responses, but its dose-dependent effects and associated molecular responses in rapeseed under cold stress remain unclear. Seedlings were exposed to 4 °C for 3 d and received foliar applications of 10, 20, or 40 mg L−1 Na2SeO3. Based on physiological responses, the 20 mg L−1 treatment was selected for integrated transcriptomic and metabolomic analyses alongside the normal-temperature control and the cold-stress group without Se. Cold stress reduced whole-seedling fresh weight by approximately 40% and increased O2− production, H2O2 and malondialdehyde (MDA) contents, and superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) activities. Relative to the cold-stress group without Se, the 20 mg L−1 treatment showed partial restoration of fresh weight and lower oxidative-stress indicators and antioxidant enzyme activities. Integrated analyses highlighted cysteine and methionine metabolism and phenylpropanoid biosynthesis. Treatment-associated changes involved sulfur-related and methyl-cycle genes, a metabolite feature tentatively assigned to 3-sulfopyruvic acid, and a feature putatively annotated as coniferaldehyde. These findings provide a multi-omics basis for understanding rapeseed responses to foliar-applied selenite during short-term cold stress.