A Multi-Omics Perspective on the Environmental and Genetic Regulation of Melon

This review leverages multi-omics approaches to explore the environmental and genetic regulation of melon traits, focusing on a near-isogenic line (NIL) of melon with an introgression in linkage group X (LG X). We examine the effects of this introgression on texture, volatile organic compounds (VOCs), and gene expression, presenting a comprehensive overview of molecular mechanisms that govern melon quality and how these interact with seasonal conditions and genetic factors. In comparing NIL SC10-2 with its parental ‘Piel de Sapo’ (PS) line, significant differences in texture and VOC concentrations at harvest were observed across seasons. SC10-2 showed higher whole-fruit hardness, flesh firmness, and fibrousness but lower juiciness than PS. While environmental conditions had a larger impact on VOCs than on textural traits, specific VOCs and potential quantitative trait loci (QTL) in LG X were pinpointed as key aroma contributors. Transcriptomic analysis during ripening indicated that SC10-2 maintained higher flesh firmness and lower juiciness than PS, alongside decreased respiration and ethylene production rates. Differential gene expression analysis identified 909 genes linked to the introgression that influence ripening and quality traits. Several key genes, including CmTrpD, CmNADH1, CmTCP15, CmGDSL esterase/lipase, CmHK4-like, and CmNAC18, were implicated in controlling these traits. Integrating data from genomics, transcriptomics, metabolomics, and phenomics, this review underscores the complex interactions between genetic and environmental factors in shaping melon quality. These findings offer valuable insights for breeding programs aimed at enhancing melon traits to adapt to diverse climatic conditions.