Integrated transcriptomic and metabolomic analysis provide new insights into the flesh coloration of Cucumis melo L.

Melon (Cucumis melo L.) has a wide variety of flesh colors, which is an important commercial trait influencing consumer preferences. However, the mechanisms underlying the formation of melon flesh colors during ripening remain largely unexplored. In this study, transcriptomics and carotenoid-targeted metabolomic analyses were performed between green-fleshed (GF) and orange-fleshed (OF) melon cultivars at three different stages, and transcriptome data was verified using RT-qPCR. 4907, 3305, and 3348 differentially expressed genes (DEGs) were identified at 10, 25, and 40 days after anthesis (DAA), respectively. Most DEGs were significantly enriched in carotenoid biosynthesis pathways. In addition, 28 annotated carotenoid metabolites was quantified, and R-carotene, (E/Z)-phytoene, and lutein were the primary differentially accumulated metabolite (DAM) responsible for the flesh color variations between OF and GF melon cultivars. Specifically, increased R-carotene and (E/ Z)-phytoene, and decreased lutein content during riping caused the orange flesh color. Meanwhile, correlation network integrating DAMs and DEGs identified 19 candidate genes associated with R-carotene, (E/Z)-phytoene, and lutein, including phytoene synthase genes (CmPSY), lycopene R-cyclase gene (CmLCYB), phytoene desaturase (CmPDS), zeta-carotene desaturase (CmZDS), Cytochrome P450 (CmCYP450), and Geranylgeranyl reductase family protein (CmGGR). Taken together, our results suggest that the orange flesh phenotype should be the result of increased R-carotene and (E/Z)-phytoene content and decreased lutein content in melon. This study will provides insights into our understanding of color variation and pave the way to improving the nutritive value of melon.