Transcriptomic and Weighted Gene Co-Expression Network Analysis Reveals Molecular Regulatory Mechanisms of Cold Stress in Rice.

Background: Cold stress is a major abiotic factor limiting rice growth and yield. Elucidating the molecular mechanisms underlying cold tolerance is therefore of great significance for variety improvement. This study focused on the cold-tolerant variety QJ10 and the cold-sensitive variety DHX2, systematically comparing their physiological and transcriptomic differences under cold stress and identifying genes and modules associated with the cold stress response. Methods: After 0, 3, 5, and 7 days of treatment at 4 °C, we measured leaf MDA and Pro contents, as well as SOD and POD activities. We performed multi-time-point transcriptome sequencing using RNA-seq, and conducted data mining and validation through differential expression analysis, Mfuzz trend clustering, WGCNA co-expression network analysis, GENIE3 regulatory network prediction, and qRT-PCR. Results: Compared with DHX2, QJ10 exhibited lower MDA levels and higher levels of Pro, SOD, and POD under cold stress. Transcriptome analysis identified a total of 13,599 differentially expressed genes. Trend clustering revealed that QJ10 primarily maintained genes associated with growth, development, and basal metabolism, whereas DHX2 tended to activate defense responses. WGCNA identified the MEturquoise module, which showed significant positive correlations with both cold treatment duration and the activities of SOD and POD. Genes in this module were significantly enriched in pathways such as carbon metabolism, photosynthesis, and ion transport. Twelve key transcription factors were identified, nine of which were highly expressed at the late stage of cold stress in QJ10. GENIE3 further predicted seven key regulatory factors centered on OsNAC2, OsLBD, and OsARF19; the expression patterns of these factors were validated by qRT-PCR and were consistent with the transcriptomic results. Conclusions: This study revealed that the cold tolerance of QJ10 is associated with enhanced antioxidant capacity, upregulation of genes related to carbon metabolism, and the induced expression of specific transcription factors. The key transcription factors identified here provide candidate genes for studying the molecular mechanisms of cold tolerance in rice. However, their regulatory functions require further experimental validation.