Integrated Morphological, Physicochemical, Metabolomic, and Transcriptomic Analyses Elucidate the Mechanism Underlying Melon (Cucumis melo L.) Peel Cracking

Fruit peel cracking significantly reduces the commercial value of melons (Cucumis melo). To elucidate the underlying mechanisms of peel cracking, we conducted integrated investigations including morphological, physiological, metabolomic and transcriptomic analyses of cracked and non-cracked peels from the crack-resistant ‘Xizhoumi 17’ and crack-susceptible ‘Xizhoumi 25’ cultivars. The parenchyma cells in ‘Xizhoumi 17’ exhibited a compact and well-organized arrangement, whereas those in ‘Xizhoumi 25’ displayed a loosely packed and disordered structure. Notably, cracked peels exhibited significantly higher levels of water-soluble pectin and lignin, along with increased cellulase, polygalacturonase, catalase, superoxide dismutase, and peroxidase activities. In contrast, protopectin, cellulose, and hemicellulose contents, as well as polyphenol oxidase activity, were markedly reduced compared to non-cracked peels. Metabolomic analysis revealed that the phenylpropanoid biosynthesis pathway is positively correlated with the progression of peel cracking. RNA-seq analysis revealed 119 and 82 differentially expressed genes associated with cell wall metabolism and lignin biosynthesis pathways, respectively. Collectively, these findings underscore the involvement of genes related to cell wall synthesis and degradation, as well as lignin synthesis, in modulating peel cracking through alterations in cell wall composition and structural stability, thereby offering practical implications for reducing melon peel cracking incidence via targeted molecular breeding of key genes regulating cell wall composition and the phenylpropanoid pathway.