Multiomics Identifies Key Regulators in Cabbage Nutrients

We would like to highlight a recent publication discussing the results of combined use of metabolomics and transcriptomics to explain nutritional differences between two types of Chinese cabbage. The results of this study can facilitate genetic modification to improve nutritional and health values. “Identification of key genes controlling soluble sugar and glucosinolate biosynthesis in Chinese cabbage by integrating metabolome and genome-wide transcriptome analysis” is published in Frontiers in Plant Science.

The authors compared six cultivars of Chinese cabbage using untargeted metabolomics and transcriptomic analysis. High glucosinolate and carotene content and a lower soluble sugar content in yellow inner-leaf Chinese cabbage was observed. Aliphatic glucosinolate and two soluble sugars (fructose and glucose) were the key metabolites that caused the difference between two types of cabbage. Main biosynthesis structural genes and transcription factors were indicated.

Though previously the breeders were mainly focused on yield and disease resistance rather than the quality and nutritional value, more and more researchers now are focused on nutrients and characteristic flavors. Soluble sugar, carotenoid and glucosinolates (or thioglycosides) are the most common nutrient compounds affecting the flavor of Chinese cabbage. 

In this study MetwareBio worked with the researchers from Shandong Academy of Agricultural Sciences to reveal the insights to the formation of these nutrients. This study of metabolite and transcript biomarkers could be helpful in an effective marker-assisted breeding strategy.

Six representative Chinese cabbage cultivars with yellow or white inner-leaf color were selected for this study. Authors measured 13 soluble sugars with HPLC-MS/MS. D-fructose and glucose were the major components of soluble sugar in Chinese cabbage, accounting for more than 96% of the total soluble sugar content. Fifty-three glucosinolate metabolites were identified and divided into four classes, including thirty-eight aliphatic glucosinolates, nine aromatic glucosinolates, four indole glucosinolate, and one thiocyanate. Four main differential glucosinolates belong to aliphatic gluconosilates. Although inositol was detected in both types of cabbage, the content in yellow inner-leaf was higher that in white inner-leaf Chinese cabbage. Inositol is not only involved in plant sugar transport and resistance, but also inhibits the growth of tumor cells while having functions similar to vitamin B1.

As a result, a significantly higher total carotenoid and glucosinolate content was higher in yellow inner-leaf Chinese cabbage. In the meantime, soluble sugar content was opposite to carotenoid and glucosinolate content.

Transcriptome – differentially expressed genes analysis (DEGs) between yellow and white inner-leaf cabbage was performed. A total of 1163 DEGs including 571 up-regulated and 592 down-regulated genes were detected between those two groups. KEGG annotation and enrichment analysis were used to test the statistical enrichment of the DEGs in KEGG pathways. A total of 18 co-expression modules between soluble sugars and glucosinolates were identified based on co-expression patterns using WGCNA analysis. According to the correlation analysis, the blue module was positively correlated with yellow inner-leaf cabbage and negatively correlated with white inner-leaf cabbage; more than 60% of DEGs enriched in the metabolic pathway and the secondary metabolite synthesis pathway between yellow and white inner-leaf cabbage were present in the blue module, indicating that the blue module is the key module that regulates the metabolism of these metabolites (see link to the publication for the figure).

Reconstruction of the soluble sugar biosynthetic pathway with the differentially expressed structural genes in shown on the image above. Green ellipses represent essential genes we identified by RNA-Seq, and blue ellipses represent the genes involved in the biosynthesis. In a similar manner authors present a reconstruction of the aliphatic glucosinolate biosynthetic pathway with the differentially expressed structural genes. Green ellipses represent essential genes we identified by RNA-Seq; blue ellipses represent the genes involved in the glucosinolate biosynthesis.

The integration of transcriptome and metabolome information offers unique insights into pathways associated with agronomy traits while identifying potential targets for genetic modification. The authors demonstrated that the conjoint use of multiomics datasets supports identification of key metabolites between cabbage varieties and the key genes involved in their biosynthesis.

If you are interested in setting up a Transcriptomics + Metabolomics study with our Boston-based lab, contact us for details.