Global Transcriptome and WGCNA Analysis Uncover Cultivar-Specific Molecular Signatures Associated with Low-Temperature Germination in Brassica napus L.

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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.

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