Integrated analysis of metabolomics and transcriptomics reveals the metabolites responsible for the antioxidant activity of water caltrop hull

• The flavonoids were significant different of water caltrop varieties in types and abundance. • The flavonoids and antioxidant capacity of different water caltrop hulls were high correlation. • The expression level differences of core genes in the flavonoids biosynthesis were the key reason for the difference of flavonoids in the six water caltrop hulls. The water caltrop ( Trapa genus, Lythraceae family) fruit hulls are used as traditional herb medicines in China, Korea, and India due to their secondary metabolites. Although the hulls of multiple water caltrop varieties are applied as herb in these countries, few studies have assessed the metabolite diversity across water caltrop varieties. Here, six representative water caltrop varieties which were distributed in China and significant phenotypic difference, were chosen as the model to analysis the metabolome variation. The wild water caltrop and cultivated water caltrop have significant differences in size, volume, and weight of the fruit. The hulls of water caltrop had abundant secondary metabolites, including flavonoids, polyphenols, polysaccharides, and terpenoids. The metabolomes of the cultivated water caltrops were quite different from those of the wild ones. The abundance of flavonoids in the cultivated water caltrop hulls was lower than that in the wild hulls based on the UPL-MS analysis. The flavonoid composition also differed significantly among the water caltrop varieties. For instance, kaempferol-4′- O -glucoside was absent in three wild water caltrop varieties (Sijiaoyeling, Sliuling, and Geling). The antioxidant activities of the hull extracts of the cultivated water caltrop, SHL and WL, were similar. On the contrary, the extract of the wild water caltrops showed variation in both DPPH radical-scavenging and ferric reducing/antioxidant power. Subsequent analysis indicated that the flavonoids abundance was strongly correlated with the antioxidant activity. Besides, variations were detected in the expression levels of genes associated with flavonoid biosynthesis among the six water caltrop hulls. Comprehensively analysis of the metabolome and antioxidant activity of wild and cultivated species of water caltrop provide a new perspective for utilizing water caltrop varieties.