Light quality affects plant growth and the functional component accumulation of fruits. However, there is little knowledge of the effects of light quality based on multiomics profiles. This study combined transcriptomic, ionomic, and metabolomic analyses to elucidate the effects of light quality on metabolism and gene expression in tomato fruit. Micro-Tom plants were grown under blue or red light-emitting diode light for 16 h daily after anthesis. White fluorescent light was used as a reference. The metabolite and element concentrations and the expression of genes markedly changed in response to blue and red light. Based on the metabolomic analysis, amino acid metabolism and secondary metabolite biosynthesis were active in blue light treatment. According to transcriptomic analysis, differentially expressed genes in blue and red light treatments were enriched in the pathways of secondary metabolite biosynthesis, carbon fixation, and glycine, serine, and threonine metabolism, supporting the results of the metabolomic analysis. Ionomic analysis indicated that the element levels in fruits were more susceptible to changes in light quality than in leaves. The concentration of some ions containing Fe in fruits increased under red light compared to under blue light. The altered expression level of genes encoding metal ion-binding proteins, metal tolerance proteins, and metal transporters in response to blue and red light in the transcriptomic analysis contributes to changes in the ionomic profiles of tomato fruit.

The large berry mutant (LBM) of the ‘Delaware’ (V. vinifera × (V. labrusca × V. aestivalis)) is known to produce larger berries than ‘Delaware’ when subjected to traditional double gibberellic acid-3 (GA3) treatment. In this study, we first compared ‘Delaware’ and the LBM in terms of their berry and cluster quality to reevaluate previous findings on LBM. Next, we compared berry size without GA3, histological characteristics of the early developmental berry, and then GA-related gene expression to reveal the characteristics of the LBM. The previous finding that LBM yielded larger berry sizes than ‘Delaware’ with double GA3 treatment was verified, but without GA3 treatment, LBM did not produce larger berries than ‘Delaware’. This highlights the prerequisite of exogenous GA for larger berry size in LBM. Histological analysis revealed an increase in cell numbers of the inner and outer mesocarp walls in the early developmental stage of LBM berries. Gene expression analysis of the flower buds and berries indicated an increased expression of VvGID1A, encoding the GA receptor, in LBM than in ‘Delaware’ 3 h after the first GA3 treatment. Additionally, the expression of VvGID1A and VvGID1B was higher in LBM than that in ‘Delaware’ before and after the second GA3 treatment. The expression of VvGID2A, which interacts with the GA receptor and promotes GA signaling, was also higher in LBM than in ‘Delaware’ before the first GA3 treatment. However, the expression of VvSLR1, VvGAI1, and VvGAI2 that encode DELLA proteins, essential negative regulators for GA reactions, mostly showed no significant changes. These results suggest that LBM berries had higher GA sensitivity than the ‘Delaware’. Based on these results, we believe that the larger berry size in LBM may be due to increased cell numbers resulting from high GA sensitivity.

Gibberellin (GA)-based seedless cultivation is widely used in the skin-edible interspecific table grape (Vitis labruscana × Vitis vinifera) ‘Shine Muscat’, yet when and how GA treatment reshapes fracture-type texture during berry development remains unclear. This study aimed to identify developmental stages and tissue/cell-wall features associated with GA-dependent differences in berry fracture behavior. We integrated intact-berry fracture testing at harvest (DAFB105), quantitative histology of pericarp/mesocarp tissues just before veraison (DAFB39) and at harvest, sequential cell-wall fractionation assays targeting pectin-rich (uronic acid) and hemicellulose/cellulose-related pools at cell division period, cell expansion period and harvest, and stage-resolved RNA-Seq across the same three developmental stages. GA-treated berries had a larger diameter and showed a higher fracture load and a lower fracture strain than non-treated berries at harvest, while toughness did not differ significantly. Histology revealed thicker pericarp tissues and lower mesocarp cell density in GA-treated berries, together with increased cell-size heterogeneity and enhanced radial cell expansion. Cell wall analyses showed stage-dependent decreases in uronic acid contents in water-, EDTA-, and Na₂CO₃-soluble fractions in GA-treated berries. Transcriptome profiling indicated GA-responsive expression of putative cell expansion/primary-wall remodeling genes, EXORDIUM and xyloglucan endotransglucosylase/hydrolases, at DAFB24 and suggested relatively enhanced ethylene-/senescence-associated transcriptional programs together with pectin-modifying related genes, Polygaracturonase/pectate lyase and pectin methylesterase, in non-treated mature berries. Collectively, GA treatment modifies mesocarp cellular architecture and pectin-centered wall status in a stage-dependent manner, providing a tissue- and cell wall–based framework for interpreting fracture-related texture differences under GA-based seedless cultivation in ‘Shine Muscat’.