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. 2025 Jun 24;47(7):481.
doi: 10.3390/cimb47070481.

Metabolomics and Transcriptome Analysis of Rapeseed Under Salt Stress at Germination Stage

Menglin Zhou  1 , Xi Song  1 , Qingqing Yu  1 , Bingbing Dai  1 , Wei Zhou  1 , Xiaofei Zan  1 , Wuming Deng  1
Affiliations

Metabolomics and Transcriptome Analysis of Rapeseed Under Salt Stress at Germination Stage

Menglin Zhou et al. Curr Issues Mol Biol. .

Abstract

Salt stress is a significant abiotic factor that adversely impacts the yield of rapeseed (Brassica napus L.). Under salt stress conditions, the growth of rapeseed is markedly inhibited. This study integrates transcriptomic and metabolomic analyses to elucidate the molecular and physiological mechanisms underlying the salt stress response during the germination of the rapeseed variety ZS11. Metabolomic analysis revealed 175 differentially expressed metabolites, predominantly comprising amino acids, carbohydrates, and organic acids. Transcriptomic analysis highlighted the crucial roles of plant hormones and phenylpropanoid biosynthesis in enhancing the salt stress resistance of rapeseed. Comprehensive multi-omics analysis identified phenylpropanoid metabolism (p < 0.001), amino acid metabolism (FDR < 0.01), and carbohydrate metabolism (|log2FC| ≥ 2) as the most significantly affected pathways. Crucially, we demonstrate that early-stage phenylpropanoid activation in hypocotyls dominates salt adaptation during germination. These findings provide actionable targets for molecular breeding and novel insights for optimizing crop establishment in salinized agroecosystems.

Keywords: metabolomics; rapeseed; salt stress; transcriptome.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
The effect of NaCl treatment on the growth of the ZS11 seedling. (A) Seedling phenotype. (B) Plant height. (C) Proline content. (D) Catalase activity. Analysis of variance and Tukey test were performed. The significance levels were expressed as * and **, corresponding to p < 0.05 and p < 0.01, respectively. Scale: 2 cm.
Figure 2
Figure 2
The effect of the NaCl treatment on the rapeseed metabolism was assessed through several analytical approaches. (A) PCA was conducted to compare the metabolites in the control samples versus those treated with NaCl. (B) A volcano plot was generated to illustrate the DEMs. (C) A KEGG enrichment plot was created to analyze the pathways associated with the differential metabolites. (D) The number of DEMs. (E) The classification of the DEMs was performed to categorize their variations.
Figure 3
Figure 3
The effect of the NaCl treatment on the rapeseed transcriptome is illustrated in several analyses. (A) A principal component analysis (PCA) was conducted to compare the control and NaCl-treated samples. (B) A scatter plot depicts the KEGG pathway enrichment of differentially expressed genes. (C) A volcano plot illustrates the differential expression of genes. (D) The number of DEGs. (E) The GO annotation classification statistics for the differentially expressed genes are presented.
Figure 4
Figure 4
Correlation analysis of the metabolomics and transcriptomics data is presented. (A) The O2PLS loading plot illustrates the joint changes observed between the transcript and metabolite data sets. (B) A Venn diagram displays the DEGs and DEMs. (C) The analysis of transcriptomics and metabolomics has identified the top 10 KEGG pathways that exhibit the highest number of DEGs and DEMs.
Figure 5
Figure 5
Integration analysis of DEGs and DEMs. (A) Correlation Analysis Nine Quadrant Chart. (B) The loading value maps of the first 15 genes and metabolites. (C) The iPath integrated analysis diagram.
See this image and copyright information in PMC

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