Metabolome and transcriptome profiling reveals light-induced anthocyanin biosynthesis and anthocyanin-related key transcription factors in Yam (Dioscorea Alata L.)

Abstract

Background: Yam is a globally significant crop with both culinary and medicinal value. Anthocyanin, an important secondary metabolite, plays a key role in determining the nutritional quality of yams. However, the research on the light-induced anthocyanins accumulation in yams remains limited. In this study, we revealed light-induced anthocyanin biosynthesis and identified transcription factors associated with anthocyanin-related pathways in yam. These findings enhance our understanding of the molecular mechanisms underlying light-mediated anthocyanin regulation in yams.

Results: Significant variations in color were observed in the stems, leaves, and tuber roots of the two yam varieties 'Xuwen' and 'Luhe'. Under light conditions, the total anthocyanin content in 'Xuwen' tuber roots was significantly higher than that under dark conditions. The targeted metabolomics analysis of anthocyanins identified that procyanidin and cyanidin glycosides, such as cyanidin-3-O-(sinapoyl)sophoroside, cyanidin-3-O-sophoroside, procyanidin B1, procyanidin B3, and quercetin-3-O-glucoside, were the primary anthocyanin components. These compounds were responsible for the observed differences in anthocyanin content between the two varieties and were significantly influenced by light conditions. The non-targeted metabolomics analysis further revealed that light also induce the biosynthesis of flavonoids. Transcriptome analysis showed significant differences in the expression levels of MYB, ERF, and WRKY transcription factors (TFs) between the two yam varieties, with these expressions being strongly influenced by light conditions. The association analysis of the anthocyanin metabolome, candidate TFs, and structural genes involved in anthocyanin biosynthesis revealed significant correlations. Specifically, MYB (Dioal.09G044700 and Dioal.12G068700) and WRKY (Dioal.20G040900 and Dioal.12G062900) showed strong correlations with procyanidins, anthocyanins, and the structural genes associated with anthocyanin biosynthesis. RT-qPCR confirmed that the expression patterns of these four TFs, strongly induced by light, were consistent with the expression of structural genes involved in anthocyanin biosynthesis.

Conclusions: The results of this study provide useful insights into the regulation of light on anthocyanin accumulation in yam, and will be helpful for yam breeding and cultivation practices.

Keywords: Anthocyanin; Light; Metabolome; Transcription factors; Transcriptom; Yam.

Fig. 1

Phenotype of two yam cultivars. (A, B) Stem and leaf phenotype of ‘Luhe’ /W (A) and ‘Xuwen’/P (B); (C, D) Root tubers colors of the two cultivars under different environments conditions and developmental stages. ‘Xuwen-L’/F denotes the ‘Xuwen’ cultivar exposed to light conditions; (E) Total anthocyanin content. ** and *** represent significance of P < 0.01 and P < 0.001, respectively

Fig. 2

Analysis of differential anthocyanin metabolites among W, P and F. (A) PCA analysis of DM; (B) Pearson correlation analysis of the samples in metabolites content. (C) Number of differential anthocyanin metabolites; (D) Venn diagram showed the overlap of differential anthocyanin metabolites among the three groups; (E) Cluster heat map of twenty-three differential anthocyanin metabolites in the three groups; (F) Correlation analysis for the twenty-three differential anthocyanin metabolites in the three groups; (G) The five key DM out of the twenty-three anthocyanin metabolites identified in the three groups. Different letters denote significant differences (P < 0.05) according to Duncan’s multiple range test. The data in figure G is presented as the mean ± SEM. (n = 3 biologically independent samples)

Fig. 3

Analysis of DM among W, P and F. (A) PCA of all metabolites; (B) Classification map of 199 metabolites identified via LC-MS/MS; (C) Venn diagram showing the overlap of DM identified via LC-MS/MS in the three groups; (D) Scatter plot of the top 20 KEGG-enriched pathways for 68 DM; (E) Pearson correlation analysis between peonodin-3-glucoside and eleven flavonoid metabolites. (F) Cluster heatmap of the 68 DM. Red triangle denotes the eleven flavonoid metabolites

Fig. 4

Transcriptome analysis of W, P and F, as well as correlation analysis between core TFs, anthocyanins, procyanin and structural genes involved in anthocyanin biosynthesis. (A) PCA of all genes; (B) Pearson correlation analysis of the gene expression in each sample; (C) Number of DEGs in the three groups; (D) Venn diagram illustrates the overlap of DEGs among the three groups; (E) Cluster heatmap of 391 DEGs; (F) Identification of twenty-one TFs with consistent expression trends in the comparisons (P_vs_W, F_vs_W, F_vs_P); (G) Association analysis of twenty-one TFs, structural genes involved in anthocyanin biosynthesis and twenty-three differential anthocyanin metabolites

Fig. 5

Transcriptome and RT-qPCR analysis of core TFs and structural genes involved in anthocyanin biosynthesis. (A) Schematic diagram of anthocyanin biosynthesis and the expression levels of structural genes. Phenylalanine (PAL), cinnamic acid 4-hydroxylase (C4H), and 4-coumaric acid CoA ligase (4CL), chalcone synthase (CHS), chalcone isomerase (CHI), flavanone 3’-hydroxylase (F3H), flavonoid 3’,5’-hydroxylase (F3’5’H), dihydroflavonol 4-reductase (DFR), anthocyanidin synthase (ANS), anthocyanidin 3-O-glucosyltransferase (BZ1), anthocyanin 3-O-glucoside-6’’-O-malonyltransferase (3MaT1); (B) The expression levels of UFGTs and UGTs involved in phenylpropanoid biosynthesis, flavonoid biosynthesis, flavone and flavonol biosynthesis in ‘Luhe’ (W), ‘Xuwen’ (P) and and ‘Xuwen-L’ (F). UDP-glycose: flavonoid glycosyltransferase (UFGT), UDP-glycosyltransferase (UGT), isoflavone 2’-hydroxylase (I2’H); (C) RT-qPCR analysis of core TFs; (D) RT-qPCR analysis of structural genes involved in anthocyanin biosynthesis