Transcriptomic analyses of Pinus koraiensis under different cold stresses

Area of Science:

• Plant Molecular Biology
• Transcriptomics
• Cold Stress Physiology

Background:

• Pinus koraiensis exhibits strong cold resistance, but its transcriptomic response to cold stress remains largely uncharacterized.
• Understanding cold stress response mechanisms is crucial for this economically important evergreen tree species.

Purpose of the Study:

• To comprehensively analyze the global transcriptome profiles of Pinus koraiensis seedlings under cold stress (-20°C) over time.
• To identify differentially expressed genes (DEGs) involved in cold signal perception, regulation, and antioxidant defense.

Main Methods:

• High-throughput sequencing was employed to generate transcriptome profiles of P. koraiensis seedlings exposed to -20°C for 6, 24, and 48 hours.
• Bioinformatic analyses included unigene assembly, gene ontology (GO) and clusters of orthologous groups (COG) categorization.
• Quantitative real-time PCR (qRT-PCR) was used to validate the expression patterns of selected DEGs.

Main Results:

• Over 763 million clean reads were assembled into 123,445 unigenes, with 38,905 showing homology to known genes.
• A significant number of differentially expressed genes (DEGs) were identified across time points, with thousands detected at 6, 24, and 48 hours.
• Key DEGs were found in cold signal perception (34), transcription factor regulation (96), and antioxidant mechanisms (27), including genes like annexin D1, alpha-amylase, calcium-binding protein KIC, ABA, DREB3, SOD, CAT, and GPX.

Conclusions:

• A substantial set of DEGs were identified in P. koraiensis under cold stress, highlighting their roles in cold signal transduction, transcriptional regulation, and reactive oxygen species (ROS) scavenging.
• These findings provide a foundation for understanding the molecular mechanisms underlying cold response in conifers and offer potential targets for molecular breeding to enhance cold tolerance.