Combined Transcriptome and Metabolome Analysis Elucidates the Mechanism of Open-field Overwintering in ‘Zezhou’ Celery

doi:10.13560/j.cnki.biotech.bull.1985.2025-1038

Abstract

Abstract:

Objective To elucidate the molecular regulatory mechanisms underlying the overwintering of ‘Zezhou’ celery in open fields, providing theoretical support for utilization of valuable germplasm resource and molecular breeding for cold tolerance in crops. Method Using ‘Duoliwang’ celery (CRY) at the seedling stage as the control, differentially accumulated metabolites and differentially expressed genes in the roots were analyzed between different varieties and different stages (seedling stage ZRY and flowering stage ZR) of ‘Zezhou’ celery. Result Metabolomic analysis revealed 57 significantly differentially accumulated metabolites in ZRY vs. CRY, and 187 in ZR vs. ZRY. Further screening identified 9 cold-tolerance-related differential metabolites, including phenylpropanoids and polyketides, lipids and lipid-like molecules, and organo-oxygen compounds, all of which showed increased accumulation. Transcriptomic analysis identified 2 988 differentially expressed genes in ZRY vs. CRY, with 1 001 upregulated and 1 987 downregulated. In ZR vs. ZRY, 8 869 differentially expressed genes were identified, comprising 4 153 upregulated and 4 716 downregulated genes. These genes were primarily enriched in pathways such as plant hormone signal transduction. Following overwintering in open fields, the content of the differential metabolite salicylic acid increased in ‘Zezhou’ celery. Analysis of the salicylic acid biosynthesis pathway indicated that the gene Ag2G02930 plays a significant role in its synthesis. Conclusion ‘Zezhou Celery’ resists cold stress by accumulating key metabolites such as salicylic acid and activating plant hormone signal transduction pathways. The salicylic acid synthesis-related gene Ag2G02930 plays a core regulatory role in its resistance to cold during overwintering in the open field.

Key words: Zezhou celery, overwintering in open-field, metabolome, transcriptome, salicylic acid

SHEN Rui-xue, GUO Zi-qing, PANG Xing-chen, LI Zhi-yuan, DING Wei, DONG Qi, Li Sen, SONG Hong-xia. Combined Transcriptome and Metabolome Analysis Elucidates the Mechanism of Open-field Overwintering in ‘Zezhou’ Celery[J]. Biotechnology Bulletin, 2026, 42(8): 251-262.

Figures/Tables 10

Table 1 ZRY vs CRY, ZR vs ZRY cold resistance differential metabolites

比较的样品对 The sample pairs for comparison	代谢物名称 Metabolite name	类型 Class	Up/down
ZRY vs CRY	5-乙酰水杨酸 5-Acetylsalicylic acid	苯丙素类和聚酮类 Phenylpropanoids and polyketides	Up
	矢车菊-3-芸香苷 Cyanidin-3-rutinoside	苯丙素类和聚酮类 Phenylpropanoids and polyketides	Up
	γ-亚麻酸 Gamma-linolenic acid	脂质和类脂分子 Lipids and lipid-like molecules	Up
ZR vs ZRY	水杨酸 Salicylic acid	苯环型化合物 Benzenoids	Up
	酪醇 Tyrosol	苯环型化合物 Benzenoids	Up
	反式玉米素9-O-葡萄糖苷 trans-zeatin 9-O-glucoside	/	Up
	景天庚酮糖-7-磷酸 s7p	有机含氧化合物 Organic oxygen compounds	Up
	D-（-）-甘露醇 D-（-）-Mannitol	有机含氧化合物 Organic oxygen compounds	Up
	D-脯氨酸 D-Proline	有机酸及其衍生物 Organic acids and derivatives	Up

Fig. 1 PCA analysis of samples in positive ion (pos) and negative ion (neg) modes

Fig. 2 Cluster heat map of differential metabolites in positive ion (pos) and negative ion (neg) modes

Fig. 3 Correlation heat map between samples

Fig. 4 Differential expression gene Venn diagram (A, B) and volcano map (C, D) of ZRY vs CRY and ZR vs ZRY

Fig. 5 GO enrichment analysis and KEGG pathway analysis of differentially expressed genes in ZRY vs CRY (A, C) and ZR vs ZRY (B, D)The horizontal axis indicates the ratio of the number of differentially expressed genes annotated to the KEGG pathway to the total number of differentially expressed genes. The vertical axis indicates the KEGG pathways. The size of the points indicates the number of genes annotated to the corresponding KEGG pathway, while the color gradient from red to purple reflects increasingly significant enrichment

Fig. 6 Differentially expressed genes and differentially accumulated metabolites in the phenylpropanoid biosynthesis pathway in ZR vs ZRYIn the phenylalanine metabolic pathway, blue indicates down-regulated and red indicates up-regulated. The transcriptome heat map indicates the expressions of the gene in different samples (FPKM), and the metabolome heat map indicates the accumulation of metabolites in different samples

Fig. 7 Correlation analysis between differentially expressed genes and differentially accumulated metabolites in the phenylpropanoid biosynthesis pathway in (A), and salicylic acid synthesis pathway and related differentially expressed gene heat map (B)In correlation analysis, red indicates positive correlation and blue indicates negative correlation. In the heat map, red indicates up-regulated expression and blue indicates down-regulated expression. A: ZR vs ZRY; B: ZRY vs CRY, ZR vs ZRY

Fig. 8 Salicylic acid signal transduction pathway and related differential gene expression heat mapIn the salicylic acid signaling pathway, boxes indicate enzymes, circles indicate metabolites, red indicates up-regulation, green indicates down-regulation, and yellow indicates both up- and down-regulation. In the heatmap of differentially expressed genes, blue indicates down-regulation, and red indicates up-regulation

Fig. 9 RT-qPCR validation of differentially expressed genes in celery (Apium graveolens L.) roots

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