Joint transcriptomic and metabolomic analyses reveal the mechanism of flesh transcoloration and orange flesh formation in melon

Flesh color is a critical commodity trait of melon, directly influencing consumer preference and the fruit's market value. This study investigates the crucial role of carotenoids in determining melon flesh coloration by examining color transitions and carotenoid profiles during fruit development in 'TianYu' (white flesh) and 'TianJu' (orange flesh) melons. Research has demonstrated that the color change in melon flesh results from carotenoid accumulation, with <italic>β</italic>-carotene being the primary compound responsible for the formation of orange flesh. Transcriptome analysis revealed that 2,459 and 947 differentially expressed genes (DEGs) were involved in melon pulp color change and orange pulp formation, respectively. Among these DEGs, the study identified and analyzed those related to carotenoid synthesis and metabolism. The results indicated that genes encoding key enzymes for pyruvate synthesis, phytoene synthase (PSY), phytoene desaturase (PDS), and lycopene <italic>β</italic>-cyclase (LCYB) play significant roles in fruit pulp color change and carotenoid accumulation. Notably, the genes encoding PDS (<italic>MELO3C017772.2</italic>) and LCYB (<italic>MELO3C020744.2</italic>) were found to be potentially critical genes for <italic>β</italic>-carotene synthesis and orange flesh formation. Moreover, functional enrichment analysis of DEGs emphasized the importance of transcriptional regulation and transcription factors such as MYB, WRKY, ERF, and bHLH, whose differential expression during color change suggests their potential to regulate carotenoid pathway genes. This study not only elucidates the molecular mechanisms underlying melon flesh color variation but also reveals the potential regulatory roles of key genes and transcription factors, providing valuable insights for enhancing melon quality, informing breeding strategies, and exploring potential genetic engineering approaches for color manipulation.