Integrated analysis of multi-omics and fine-mapping reveals a candidate gene regulating pericarp color and flavonoids accumulation in wax gourd (Benincasa hispida)

Wax gourd ( Benincasa hispida ), a popular fruit of the Cucurbitaceae (cucurbits) family, contains many nutrients with health benefits and is widely grown in China and other tropical areas. In this study, a wax gourd mutant hfc12 with light-color pericarp was obtained through ethane methylsulfonate (EMS) mutagenesis. Integrative analysis of the metabolome and transcriptome identified 31 differentially accumulated flavonoids (DAFs; flavonoids or flavonoid glycosides) and 828 differentially expressed genes (DEGs) between the hfc12 mutant and wild-type ‘BWT’. Furthermore, BSA-seq and kompetitive allele specific PCR (KASP) analysis suggested that the light-color pericarp and higher flavonoid content was controlled by a single gene BhiPRR6 ( Bhi12M000742 ), a typical two-component system (TCS) pseudo-response regulator (PRR). Genetic analysis detected only one nonsynonymous mutation (C-T) in the second exon region of the BhiPRR6 . Weighted correlation network analysis (WGCNA) identified the downstream target genes of BhiPRR6 , probably regulated by light and were intermediated in the regulatory enzyme reaction of flavonoid biosynthetic pathway. Thus, these results speculated that the transcription factor BhiPRR6 , interacting with multiple genes, regulates the absorption of light signals and thereby changes the pericarp color and synthesis of flavonoids in wax gourd.