Metabolite characteristics and molecular mechanism of different fruit color formation in hybrids from two <i>Lycium</i> species

Hybridization could result in genetic diversity and provide abundant germplasm resources for cross-breeding. Moreover, the diversity of fruit color is a typical phenotypic characteristic of hybrid varieties. In this study, metabolism and transcriptome were combined to uncover the major metabolites and molecular mechanism that result in four different fruit color formations in hybrids from two <italic>Lycium</italic> species. Most differential accumulated metabolites (DAMs) were detected in the black vs dark red comparison. The components that impact fruit sweetness were more abundant in dark red and yellow_spot fruit, and most of the DAMs in flavonoids were highly accumulated in yellow fruit. Some functional oligosaccharide were highly accumulated in yellow_spot and yellow fruit. Dihydroflavonol-4-reductase (DFR) and Lba06g02831 are the key genes in the formation of spots in yellow fruit. The different content of some key metabolites is related to various oxidative reactions and gene modification. This study provides a fresh viewpoint on uncovering the mechanisms in fruit color formation of wolfberry, and lays the foundation for the synthesis and metabolic pathways of substances related to fruit quality and color in wolfberry.