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Publications

Journal Article Epublish

PubMed: 40725500 DOI: 10.3390/genes16070845

Global Transcriptome and Weighted Gene Co-Expression Network Analyses of Cold Stress Responses in Chinese Cabbage.

Genes (Basel) 16(7)

Authors: Jizong Zhang, Songtao Liu, Huibin Li, Mengmeng Sun, Baoyue Yan, Peng Zhang, Lifeng Zhang

Affiliations

  • College of Agronomy, Hebei Agricultural University, Baoding 071000, China.
  • College of Agriculture and Forestry, Hebei North University, Zhangjiakou 075000, China.

Abstract

BACKGROUND/OBJECTIVES

Chinese cabbage (Brassica rapa ssp. Pekinensis, AA) growth and development is highly sensitive to cold temperatures. Prolonged low-temperature exposure during early growth stages can induce premature bolting, which reduces market quality and yield.

METHODS

Here, using comparative leaf RNA-seq transcriptome analysis of plants grown at 6, 9, 12, and 15 °C, we explored key genes and metabolic pathways regulating Chinese cabbage cold response.

RESULTS

RNA-seq transcriptome analysis identified a total of 1832 differentially expressed genes (DEGs) in the three comparison groups, with 5452, 1861, and 752 DEGs specifically expressed in the A6_vs_A15, A9_vs_A15, and A12_vs_A15 groups, respectively. KEGG enrichment analysis of DEGs showed that sulfur metabolism, secondary metabolites biosynthesis and photosynthesis pathways were mostly affected by cold stress. K-means clustering revealed distinct expression profiles among the DEGs enriched in cold stress response-associated clusters. Subsequently, DEGs were divided into 18 modules by WGCNA, whereupon co-expression genes that clustered into similar modules exhibited diverse expression and were annotated to various GO terms at different temperatures. Module-trait association analysis revealed M1, M2, M3, and M6 modules as key clusters potentially linked to vernalization-related processes. These modules harbored candidate hub genes encoding transcription factors (including MYB, bZIP, and WRKY), protein kinases, and cold-stress-responsive genes. Additionally, phenotypic analysis showed that 12 °C to 15 °C supported optimal growth, whereas <9 °C temperature inhibited growth. Physiological measurements showed increased antioxidant enzyme activity and proline accumulation at 6 °C.

CONCLUSIONS

Overall, our study provides a set of candidate cold-stress-responsive genes and co-expression modules that may support cold stress tolerance breeding in Chinese cabbage.

MeSH

Genes, Genomics, Gene Expression Profiling, Growth, Transcriptome, Cold Temperature, Stress, Physiological, Cold-Shock Response, Temperature