Structural and metabolic basis of pepper (Capsicum spp.) fruit glossiness formation shown by microstructure and metabolomics analyses

Glossiness is a key appearance trait of pepper fruits, which directly affects their market price and consumer purchasing preference. Elucidating the structural and metabolic basis underlying glossiness formation is of great scientific and economic value. In this study, we quantitatively analyzed the microstructure of pepper fruits with high, medium, and low glossiness, and performed integrated non-targeted metabolomics analysis on five materials with extreme glossiness phenotypes. The results showed that the average cuticle thickness ratio of high-glossiness materials was 45%, which was significantly higher than that of low-glossiness materials. A total of 22 differentially enriched metabolites (DEMs) highly correlated with fruit glossiness were identified via metabolomics detection. Among them, high gloss materials were enriched in structural lipids represented by long-chain fatty alcohols and primary polyols represented by myo-inositol, while specific complex sterol derivatives were significantly accumulated in low gloss materials. Meanwhile, we constructed a Capsicum Glossiness Formation Index (CGFI) model: Glossiness (GU) = 0.64 × CTR + 5.72 × Putative 9-Octadecenoic acid derivative − 7.22 . This model can quantitatively explain the continuous phenotype of natural variation in extreme glossiness with high precision within the training dataset. Collectively, these results not only provide important insights into the potential mechanism of glossiness formation on pepper fruit surface, but also lay a solid data foundation for subsequent multi-omics evaluation and the development of targets for molecular design breeding.