Integrated metabolome and transcriptome analysis unveils novel pathway involved in the fruit coloration of Nitraria tangutorum Bobr

Abstract

Background: The desert shrub Nitraria tangutorum Bobr. is important for its resistance to salt and alkali in Northwest China. It is an ecologically important species in this region and provides edible and medicinal berries. This study showed a mutant of N. tangutorum (named Jincan, JC) that has a strong yellow pericarp vs red in a wild type (represented by NT).

Results: In this study, the secondary metabolic and molecular mechanisms responsible for Nitraria fruit coloration were investigated using LC-MS-based widely targeted metabolomics and transcriptomics data. As a result of our study, 122 and 104 flavonoid metabolites were differentially expressed throughout the mature and transition stages between JC and NT, respectively. Furthermore, two cyanidin derivatives (cyanidin 3-O-glucoside and cyanidin-3-O-(2''-O-glucosyl) glucoside) and one pelargonidin derivative (pelargonidin-3-O-glucoside) were identified only in the NT phenotype. The functional genes F3H (flavanone 3-hydroxylase), F3'H (flavonoid 3'-hydroxylase) and UFGT (flavonoid 3-O-glucosyltransferase) and the transcription factors MYB, bHLH, NAC and bZIP were significantly downregulated in JC. Meanwhile, the activity of UFGT was extremely low in both periods of JC, with a five-fold higher enzymatic activity of UFGT in RT than in YT. In summary, due to the lack of catalysis of UGFT, yellow fruit of JC could not accumulate sufficient cyanidin and pelargonidin derivatives during fruit ripening.

Conclusion: Taken together, our data provide insights into the mechanism for the regulation of anthocyanin synthesis and N. tangutorum fruit coloration and provide a theoretical basis to develop new strategies for developing bioactive compounds from N. tangutorum fruits.

Keywords: Anthocyanin; Halophyte; Multi-omics; Nitraria tangutorum; Regulatory networks.

Fig. 1

Morphological observation of two phenotypes from N. tangutorum Bobr. A Yellow fruit phenotype ‘Jincan’ and red fruit phenotype wild type of N. tangutorum in a natural growing environment. B Phenotype of fruit in YT, YM, RT and RM. Scale bar = 1 cm

Fig. 2

Preliminary analysis of metabolome data. A PCA score map. B Heatmap of metabolites in all samples

Fig. 3

Expression analysis and clustering of metabolites. A and C Volcano plot of differential metabolites in YT vs RT (A) and YM vs RM (C); (B and D) Clustering heatmap of metabolites in YT vs RT (B) and YM vs RM (D)

Fig. 4

Correlations of structural genes with taste attributes based on WGCNA. A Clustering dendrogram of the average network adjacency for the identification of structural gene co-expression modules. B Module-trait relationships between fruit color and genes. C KEGG enrichment of the plum module. D KEGG enrichment of the dark sea-green module

Fig. 5

Anthocyanin biosynthesis pathway in the yellow and red fruits of N. tangutorum. The heatmaps indicate the expression/content of respective structural genes/metabolites in two N. tangutorum phenotypes. The percentile value of FPKM/relative content values of structural genes/metabolites ranging from low to high is represented by blue to red. The key enzymes in the anthocyanin synthesis pathway [–26] are shown below: PAL, phenylalanine ammonia lyase; C4H, cinnamate 4-hydroxylase; 4CL, 4-coumarate: CoA ligase; CHS, chalcone synthase; Ch2’GT, chalcononaringenin 2'-O-glucosyltransferase; CHI, chalcone isomerase; F3H, flavanone 3-hydroxylase; F3′H, flavonoid 3′-hydroxylase; DFR, dihydroflavonol 4-reductase; ANS, anthocyanidin synthase; and UFGT, flavonoid 3-O-glucosyltransferase

Fig. 6

Analysis of critical genes expression and enzyme activity analysis involved in the anthocyanin biosynthesis pathway. A-E Analysis of the expression pattern of critical genes involved in anthocyanin biosynthesis among four different samples and (F) UFGT activity analysis in different fruit samples. Each column shows the average value of three replicated experiments, and bars indicate the standard error of the value. Different letters denote significant differences at P < 0.05