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Transcriptomic analyses of Pinus koraiensis under different cold stresses.

Fang Wang1, Song Chen1, Deyang Liang1

  • 1State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, People's Republic of China.

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Summary

This study reveals key genes in Korean pine (Pinus koraiensis) responding to cold stress, identifying those involved in signal perception, transcription factor regulation, and antioxidant defense mechanisms for improved cold tolerance.

Keywords:
Cold stressDifferential expressed genesPinus koraiensisRNA-seq

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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.