Low-temperature stress inhibits seed germination in rapeseed. Nonetheless, the continuous dynamic changes in seed germination under low-temperature stress, particularly at the transcriptome level, remain poorly understood. In this study, two rapeseed lines with contrasting LTG phenotypes—HY7201 (cold-tolerant) and HY3404 (cold-sensitive)—were subjected to transcriptome analysis. In total, we identified 76,996 DEGs across 18 groups, with a greater number of DEGs detected in HY7201 compared to HY3404. Additionally, genes related to antioxidative metabolism were specifically upregulated in HY7201. Furthermore, WGCNA identified 29 hub candidate genes associated with specific time points. Gene expression changes during LTG were most pronounced between 18 and 96 h. The average fold change relative to the control was 4.74. Among these genes, some exhibited particularly high fold changes, such as LOC106407757 (HERK1) and LOC106437922 (FER), which were upregulated 11.6-fold at 24 h and 35.4-fold at 18 h, respectively. Finally, 17 key candidate genes specifically expressed in the two lines were identified. Among these, BnaRGL2 was of particular interest, as it is predicted to interact with ABI3 to modulate LTG through GA and ABA signaling pathways. The findings provide valuable insights for breeders aiming to utilize rapeseed germplasm resources to advance low-temperature resistance breeding.

Salinity stress progressively restricts rapeseed (Brassica napus L.) growth and productivity. However, the molecular mechanism underlying its tolerance remains poorly understood. This study aims to shed light on differential responses between shoots and roots, and further clarify the regulatory mechanisms of ion homeostasis and oxidative defense under early-and long-term salt stress. Under salt stress, the Na⁺/K⁺ ratio increased by 46.26% and 26.33% in shoots and roots, respectively. Activities of SOD and POD increased in both tissues, while CAT activity declined in shoots. MDA content was significantly higher in roots. Transcriptome PCA clearly separated samples of early-term (3–48 h for shoots, 3–24 h for roots) from long-term (72 h 25 d for shoots, 48 h 25 d for roots) salt stress. SOD2 and UGT72E1 were significantly up-regulated in shoots but down-regulated in roots. CAT2 exhibited strongly up-regulation in roots than shoots, whereas RBOHC was markedly down-regulated in roots relative to shoots. Additionally, CAT1 was mainly up-regulated at the early-term salt stress. Most DEGs involved in phenylpropanoid biosynthesis (CYP73A5, PAL2, CCR1/2, CAD1/5, COMT1 and PER66) were up-regulated in both tissues. Notably, HCT and CSE exhibited a striking tissue-specific antioxidant pattern, down-regulated in shoots but up-regulated in roots. PER34 was specifically induced at early-term, and PER31/63/169 were exclusively activated under long-term salt stress in roots. Moreover, we performed weighted gene co-expression network analysis (WGCNA) to describe tissue- and time-specific transcriptional dynamics that occur in rapeseed under salt stress. Several hub genes, including ABI5, MPK6, CAD5, NADK1 and LFG2, exhibited high correlations with early-term salt stress responses in roots. These genes are mainly enriched in transcription factors and hormone signaling pathways, and function in antioxidant defense and redox homeostasis. This study suggests distinct spatiotemporal salt stress response patterns in rapeseed and identifies key genes for salt-tolerance breeding.