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Figure 1. 

Peel morphology of (a) mutant, and (b) cultivar-type apples. Scale bar = 1 cm.

Figure 2. 

Scanning electron microscopy (SEM) analysis of peel microstructure in mutant and cultivar apples. (a), (c), (e) SEM images of the mutant apple peel, showing both cross-sectional and surface structures at varying magnifications. The mutant type exhibits a thinner epidermal layer with a relatively smooth cuticle and less densely packed cell layers. (b), (d), (f) SEM images of the cultivar apple peel, revealing a thicker epidermal region with more compact cell layers and a more complex cuticular surface. The cultivar peel shows more prominent ridges and cuticle folds compared to the mutant type. Scale bars are indicated in each panel.

Figure 3. 

Transcriptomic analysis of mutant-type (MT) and cultivated-type (CT) apple peels. (a) Principal component analysis (PCA) showing distinct clustering of MT and CT samples. (b) Violin plots displaying the distribution of fragments per kilobase of transcript per million mapped fragments (FPKM) values across all samples. (c) Volcano plot of differentially expressed genes (DEGs) between MT and CT groups. Red represents upregulated, green represents downregulated, and blue represents non-significant genes. (d) Heatmap of the DEGs, showing hierarchical clustering of expression profiles. Red indicates high expression, and green indicates low expression.

Figure 4. 

Transcriptomic analysis of mutant-type (MT) and cultivated-type (CT) apple peels. (a) Gene Ontology (GO) enrichment analysis, and (b) Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of differentially expressed genes (DEGs) between MT and CT peels. The vertical axis displays the names of enriched GO terms or KEGG pathways. The size of each dot represents the number of DEGs involved in the corresponding term or pathway (rich factor), while the color indicates the adjusted p-value (padj).

Figure 5. 

Differential expression of hormone signaling-related genes in mutant-type (MT), and cultivated-type (CT) apple peels. The heatmap shows selected differentially expressed genes (DEGs) involved in major plant hormone signaling pathways, including auxin (AUX), gibberellin (GA), abscisic acid (ABA), jasmonic acid (JA), and salicylic acid (SA). Genes related to hormone receptors and downstream response regulators are included. Expression values are represented as log₂ fold change (log₂FC) between MT and CT. The color gradient indicates the relative expression level of each gene.

Figure 6. 

Differential expression of genes involved in specialized metabolism and transport pathways in mutant-type (MT), and cultivated-type (CT) apple peels. The heatmap illustrates selected differentially expressed genes (DEGs) associated with key KEGG pathways, including the biosynthesis of various plant secondary metabolites, glutathione metabolism, galactose metabolism, ABC transporters, glycosphingolipid biosynthesis, and terpenoid backbone biosynthesis. Expression values are represented as log₂ fold change (log₂FC) between MT and CT. The color gradient indicates relative gene expression levels.