Cold resistance identification and transcriptomic responses of rapeseed (Brassica napus L.) seedlings under cold...

Freezing temperatures during winter and abrupt temperature fluctuations in winter and early spring pose significant threats to Brassica napus survival, often resulting in substantial yield losses. In this study, three rapeseed lines with close genetic relationships demonstrating notable differences in cold tolerance, were selected for transcriptome analysis, with SX9 exhibiting superior cold resistance compared to SX7 and SX8. RNA-seq revealed numerous differentially expressed genes (DEGs) associated with cold response across these lines. Specifically, 2390 common DEGs were found in SX7, SX8, and SX9, potentially involved in broad cold stress responses, while 3707 DEGs unique to SX9 may contribute to its enhanced cold tolerance. Functional annotation of upregulated genes indicated involvement in processes such as response to abiotic stimuli, oxygen-containing compounds, and the MAPK signaling pathway, while downregulated genes primarily associated with photosynthesis. Transcription factor (TF) analysis identified 3889 TFs within these DEGs, including basic helix-loop-helix (bHLH), MYB, NAC, ethylene-responsive factor (ERF), and WRKY, encompassing key cold-responsive regulatory factors such as SCREAM/inducer of CBF expression 1 (SCRM/ICE1), NAC29, NAC56, dehydration-responsive element-binding protein 1B (DREB1B), and ERF70. Based on gene expression profiles and functional annotations, 139 DEGs were predicted to play critical roles in cold stress responses in rapeseed seedlings. Protein interaction network analysis of them suggested that rapeseed seedlings respond to low temperatures via the DREB1B-dependent pathways, in coordination with other biological processes. Additionally, the candidate gene BnERF70, an AP2/ERF family member upregulated by cold stress, was shown to enhance cold resistance in transgenic Arabidopsis thaliana when overexpressed. This study provides valuable insights into the molecular mechanisms of cold responsiveness in rapeseed seedlings.