Integrated Omics Reveal Genetic and Environmental Regulation of Texture and Aroma in Melon Fruit

Abstract

Fruit quality in melon (Cucumis melo L.) is determined by complex traits such as texture and aroma, which are shaped by both genetic factors and environmental conditions. In this study, we applied an integrated physiology–metabolomics–transcriptomics approach to examine the genetic and seasonal regulation of these traits in the near-isogenic line SC10-2, carrying a defined introgression on linkage group X (LG X), in comparison with its recurrent parent ‘Piel de Sapo’ (PS). Fruit firmness, juiciness, respiration, ethylene production, and volatile organic compounds (VOCs) were evaluated over postharvest ripening across two growing seasons. SC10-2 consistently exhibited firmer flesh, reduced juiciness, and distinct VOC profiles relative to PS, although the magnitude of these differences varied between seasons. Transcriptomic analysis identified 2954 differentially expressed genes genome-wide, including 909 genes located within the LG X introgression, among which candidate genes such as CmTrpD, CmHK4-like, and CmNAC18 showed expression patterns associated with texture- and aroma-related traits. Seasonal comparisons indicated that VOC composition was particularly sensitive to environmental variation, underscoring the contribution of genotype × season interactions to fruit quality expression. Together, these results refine the phenotypic and molecular characterization of the LG X introgression in SC10-2 and provide testable candidate genes and hypotheses for understanding the genetic basis of melon texture and aroma under the studied conditions.