Multi-Omics Integration to Investigate the Effects of Variety and Origin on Volatile and Non-Volatile Metabolites in Melons

This study investigated the effects of different cultivation environments on melon quality development and the underlying metabolic regulatory mechanisms. Using 'Yangjiaocui' and 'Boyang 9' melons, we systematically compared their physicochemical properties, nutritional components, volatile compounds, and metabolites under saline-alkali versus normal conditions, employing an integrated multi-omics analytical model. The results showed that saline-alkali cultivation significantly increased several nutritional components (e.g., soluble solids, vitamin C, flavonoids, and polyphenols) compared to normal conditions. Gas chromatography-ion mobility spectrometry (GC-IMS) detected 36 volatiles, predominantly esters and ketones, with 13 key markers such as isovaleric acid isovaleryl ester and ethyl butyrate, effectively discriminating cultivars and growth origins. Liquid chromatography-mass spectrometry (LC-MS) detected 702 metabolites, chiefly organic acids and lipids. KEGG pathway enrichment analysis revealed that flavonoid biosynthesis was the most significantly enriched pathway (enrichment factor ~1, extreme significance), with coordinated regulation of tyrosine and phenylalanine metabolism redirecting metabolic flux toward defensive secondary metabolites. In conclusion, our results suggest that saline-alkali cultivation may contribute to improved nutritional profiles, and multi-omics analysis effectively differentiates melon varieties and origins. This study provides a theoretical basis for understanding the quality, flavor, and metabolite profiles of melon under saline-alkali stress, employing a multi-omics approach.