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

Area of Science:

• Plant Science
• Genetics
• Molecular Biology

Background:

• Cold stress significantly limits rice (Oryza sativa) growth and yield, necessitating research into cold tolerance mechanisms.
• Understanding the molecular basis of cold tolerance is crucial for developing improved rice varieties resistant to low temperatures.

Purpose of the Study:

• To systematically compare physiological and transcriptomic differences between cold-tolerant (QJ10) and cold-sensitive (DHX2) rice varieties under cold stress.
• To identify genes, gene modules, and regulatory networks associated with the rice cold stress response.

Main Methods:

• Physiological assays (MDA, Pro, SOD, POD) and multi-time-point RNA-sequencing were performed on rice under cold treatment.
• Data analysis included differential expression analysis, Mfuzz trend clustering, WGCNA, GENIE3 regulatory network prediction, and qRT-PCR validation.

Main Results:

• The cold-tolerant QJ10 variety maintained lower MDA and higher Pro, SOD, and POD levels compared to DHX2 under cold stress.
• Transcriptome analysis revealed 13,599 differentially expressed genes, with QJ10 maintaining growth-related genes while DHX2 activated defense responses.
• WGCNA identified a turquoise module positively correlated with cold duration and antioxidant enzyme activity, enriched in carbon metabolism and photosynthesis pathways. Nine key transcription factors showed late-stage upregulation in QJ10.

Conclusions:

• Rice cold tolerance is linked to increased antioxidant capacity, upregulated carbon metabolism genes, and induced transcription factors.
• Identified key transcription factors, including OsNAC2, OsLBD, and OsARF19, serve as candidates for further research into rice cold tolerance mechanisms.