## 2 Results
### KEGG Enrichment Analysis  
The pathway enrichment analysis revealed metabolic or signal transduction pathways that were significantly over-represented, when comparing DEGs to the entire genome. In the M7_5 mutant fruits, the most significantly impacted gene categories involved the fol  
Figure 3: Enriched gene ontology (GO) analysis. **(A,C)** GO enrichment analysis histograms. The most upregulated and downregulated gene categories in the two mutant lines (A: M7_5, C: M29_2) are presented. The abscissa in the figure is the ratio of the number of differential genes linked with the GO term to the total number of differential genes, and the ordinate is the GO term’s level of significance of enrichment, expressed as -log10(padj). The different colors represent different functional categories: BP: biological processes; CC: cellular components; MF: molecular functions. **(B,D)** GO enrichment analysis scatter plots. The most significant 30 terms were selected for display. The size of each point represents the number of genes annotated to a specific GO term, and the color from red to purple represents the significant level of the enrichment; padj: adjusted \(p\)-value.  
lowing: plant-pathogen interaction, plant hormone signal transduction, MAPK signaling, glycolysis/gluconeogenesis, glycerolipid metabolism, arginine and proline metabolism, and the proteasome pathway (Figure 4A). The plant hormone signal transduction, MAPK signaling, and plant-pathogen interaction pathways exhibited the highest number of gene annotations with 113 DEGs, followed by arginine and proline metabolism, as well as the MAPK signaling pathway and glycerolipid metabolism (Figure 4B). Accordingly, in the M29_2 mutant fruits, the most affected KEGG categories included ribosome, plant hormone signal transduction, MAPK signaling, plant-pathogen interaction, photosynthesis, brass-nosteoroid biosynthesis and the biosynthesis of phenylalanine, tyrosine and tryptophan (Figure 4C). The plant-pathogen interaction pathways had the highest number of associated genes (87), followed by MAPK signaling, plant hormone signal transduction, and ribosome (Figure 4D).  
Figure 4: The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the _III4_ mutant fruits. KEGG pathway enrichment scatter plots comparing M7_5 vs. WT (**A**) and M29_2  
vs. WT. (**C**). The _x_-axis represents the ratio of DEGs associated with the KEGG pathway to the total number of DEGs. The _y_-axis represents the KEGG pathway. The point size indicates the number of genes annotated to the KEGG pathway, while the color gradient (red to purple) indicates the enrichment significance level. KEGG pathway enrichment histograms comparing M7_5 vs. WT (**B**) and M29_2 vs. WT (**D**). The abscissa is the KEGG pathway, and the ordinate is the significance level of pathway enrichment.  
Interestingly, both mutant lines exhibited similar affected pathways, including the plant-pathogen interaction, MAPK signaling, and plant hormone signal transduction. However, the fruit of the M7_5 displayed a greater response on resource reallocation, as evidenced by the enriched glycerolipid metabolism, glycolysis/glucoseogenesis, arginine and proline metabolism, which possibly contributed to enhanced stress tolerance responses and modifications in the fruit metabolic profiles, such as the lipid and sugar contents. On the other hand, M29_2 appeared more enriched in the pathways related to photosynthesis, brassinosteroid biosynthesis, and ribosome activity, indicating a stronger need for energy capture, while M7_5 displayed a metabolic energy adaptation strategy.