Integrated transcriptomic and metabolomic analyses of peel yellowing in cucumber cultivars during postharvest storage

• Cucumber peel yellowing was analyzed using transcriptomic and metabolomic analyses. • Baekdadagi showed rapid chlorophyll degradation during postharvest storage. • Ethylene and NAC/ERF factors were induced in yellowing-sensitive Baekdadagi. • Mini cucumber retained green peel by suppressing senescence and pigment breakdown. • Cultivar-specific senescence programs offer targets to improve cucumber shelf life. Peel yellowing during storage at 20 °C reduces cucumber shelf life and marketability, but the underlying molecular mechanisms remain unclear. In this study, we investigated the molecular basis of peel yellowing using two contrasting cucumber cultivars— Baekdadagi (yellowing-sensitive) and Mini (yellowing-resistant)—through integrated transcriptomic, metabolomic, and physiological analyses during storage at 20 °C. Baekdadagi exhibited rapid yellowing, with increased Hunter b* values and hue angle, accompanied by a sharp decline in chlorophyll content. This was associated with upregulation of degradation genes ( STAY-GREEN, PHEOPHYTINASE, Pheophorbide a oxygenase ), and downregulation of chlorophyll biosynthetic genes, chlorophyll-binding proteins, and peel color regulators. In contrast, Mini retained higher chlorophyll levels, showed delayed or minimal expression changes in chlorophyll metabolism genes, and maintained stable peel color throughout storage. Ethylene biosynthetic genes ( 1-aminocyclopropane-1-carboxylic acid oxidase (ACO) 1 and 3 ) and senescence-associated transcription factors ( ORESARA1, NAC1, ERF106 ) were strongly induced in Baekdadagi , indicating early activation of ethylene-mediated senescence pathways. Metabolomic profiling revealed the accumulation of lysophospholipids and methyl pheophorbide a in Baekdadagi , whereas Mini showed increased levels of xanthophylls, abscisic acid, and antioxidant phenolics, consistent with delayed senescence and enhanced stress tolerance. These results suggest that Baekdadagi undergoes early ethylene-driven senescence and pigment loss, whereas Mini maintains peel color through transcriptional repression of senescence pathways and favorable metabolic shifts. This study provides new insights into the molecular regulation of peel yellowing and identifies potential targets for improving postharvest quality in cucumbers.