Insights into flavonoid biosynthesis during cucumber fruit peel coloration based on metabolite profiling and transcriptome analyses

The fruit peel color is a crucial trait of cucumber. To better understand the molecular mechanisms underlying cucumber peel coloration, we compared the UPLC-ESI-MS/MS-based flavonoid metabolomic and RNA sequencing-based transcriptomic profiling of the brown peeled cucumber line ‘PW’ at six developmental stages. A total of 210 flavonoid metabolites were identified. Of which, 117 flavonoid metabolites were differentially accumulated. In this study, weighted gene co-expression network analysis combined with Kyoto Encyclopedia of Gene and Genomes enrichment analysis revealed key genes coding for seven enzymes and eight transcription factors (TFs) associated with flavonoid biosynthesis. Among them, the R2R3MYB CsaV3_4G001130 is the best candidate gene that is responsible for controlling mature fruit colors in cucumber. Sanger sequencing revealed one nonsynonymous SNP in the exon of CsaV3_4G001130 among the selected 11 cucumber lines, which introduced a premature stop codon, generating a truncated protein in pale yellow or creamy peeled fruits. Yeast two-hybrid assays showed a direct interaction of CsaV3_4G001130 with the bHLH TF CsaV3_1G002260 and the WD40 protein CsaV3_5G001800. However, the interactions were influenced by the nonsynonymous SNP we identified. Our finding revealed that the integrated transcriptome and metabolome analysis further demonstrated that the abundance of some pigmented flavonoids (especially anthocyanins and chalcones) contributed to the coloration of ‘PW’ fruits. These findings pave the way for elucidation of flavonoid biosynthesis and improvement of cucumber peel color in the future.