Physiological and molecular insights into peel thickness variation between mutant and cultivated type apples

The apple peel plays a vital role in determining fruit quality and postharvest performance. In this study, the morphological, physiological, and transcriptomic differences between a thin-peel mutant and a thick-peel cultivated apple were comprehensively investigated. Morphological analysis, including scanning electron microscopy (SEM), revealed that mutant-type apple peels were significantly thinner (18.0–20.2 µm) and more porous than those of the cultivated type (31.3–33.7 µm), with reduced cell layering and fewer cuticular microcracks. Physiologically, mutant-type apples exhibited significantly lower firmness and reduced deposition of key structural components (cellulose, acid-insoluble lignin, and hemicellulose), features that are directly associated with a softer texture and altered postharvest potential. Transcriptomic profiling identified 467 differentially expressed genes (DEGs), comprising 368 upregulated, and 99 downregulated. Functional enrichment analyses highlighted the activation of multiple hormone signaling pathways, including auxin, gibberellin, abscisic acid, jasmonic acid, and salicylic acid, suggesting hormonal modulation of peel development. Additionally, key metabolic and transport pathways were enriched with upregulated DEGs in mutant-type apple peels, including the biosynthesis of secondary metabolites, glutathione and galactose metabolism, ABC transporters, glycosphingolipid biosynthesis, and terpenoid backbone biosynthesis. These transcriptional changes point to enhanced metabolic activity and membrane transport functions in the mutant-type apple peels. Together, these findings offer novel insights into the structural and molecular basis of peel thickness variation in apples and provide a foundation for breeding programs aimed at improving peel-related fruit quality traits.