Integrated Metabolomic, Proteomic, and Transcriptomic Analyses Reveal the Mechanism Underlying Brightness Differences in Eggplant ( <i>Solanum melongena</i> ) Peels

Eggplant (<i>Solanum melongena</i>) peel brightness, which has crucial commercial value, has unclear regulatory mechanisms. This study used integrated metabolomic, proteomic, and transcriptomic analyses to assess brightness and anatomical traits of peels with varying brightness across developmental stages. Results showed that the brightness of high-brightness eggplants increased by 34% from the young fruit stage (LY) to fruiting stage (LC), whereas that of low-brightness fruits decreased by 50% from the young fruit stage (BLY) to fruiting stage (BLC), revealing an opposite tendency. During this process, scanning electron microscopy showed that the outer peel cells arranged loosely and formed raised folds on the surface. Omics analysis identified 627 differential metabolites, 149 proteins, and 3,557 genes that significantly differed between BLC and BLY. Six differential genes for lignin synthesis in the phenylalanine biosynthesis pathway were upregulated, leading to an increase in the levels of a protein (Sme2.5_04906.1_g00004.1), which in turn increased the synthesis of five metabolites (l-tyrosine, l-phenylalanine, chlorogenic acid, conife rin, and coniferyl aldehyde). In addition, three differential genes in the wax synthesis pathway were down-regulated, resulting in the decreased synthesis of two metabolites (hexadecanoic acid and oleic acid). Three-omics joint analysis of the BLC vs BLY group revealed that the upregulating lignin synthesis enzyme and its associated genes during the development of low-brightness eggplant fruits led to decreased eggplant peel brightness through the promotion of lignin biosynthesis, which altered eggplant peel cytoderm cell morphology. Meanwhile, the down-regulating P450 cytochrome family genes led to reduced eggplant brightness by inhibiting wax synthesis through suppressing long-chain fatty acid biosynthesis. The study enhances the understanding of eggplant color formation and lays a theoretical foundation for improving eggplant brightness quality.