Histological and transcriptomic insights into rugose fruit surface development in pepper (Capsicum annuum L.)

The rugose surface trait, marked by prominent ridges and depressions on the fruit epidermis, is associated with a crisper and more tender texture in pepper (Capsicum annuum L.). However, the underlying cellular and molecular mechanisms remain poorly understood. In this study, we integrated histological, textural, and transcriptomic analyses of genotypes with contrasting fruit surface morphologies to investigate the regulatory basis of rugosity formation. Histological observations revealed that disorganized epidermal cell layers contribute to the rugose phenotype, with structural divergence becoming apparent around 10 days post-anthesis (DPA). A CAD-based rugosity index (RI) was developed, which showed strong correlation with pectinase activity and texture traits such as rupture force and hardness. Transcriptome profiling identified differentially expressed genes related to microtubule organization (e.g., CA03g18310, CA09g13510) and phytohormone signaling (e.g., CA03g35180, CA08g12070), whose expression patterns were validated across tissues and developmental stages. These findings uncover key regulatory components involved in epidermal patterning and cell wall remodeling during rugose surface development, offering new targets for improving fruit texture through molecular breeding in pepper.