Transcriptome Analysis Reveals the Molecular Basis of Peel Protrusion Traits in Ponkan Mandarin and Its Bud Sport Mutant

Bud sport mutations are valuable sources of citrus germplasm innovation and provide an ideal system to dissect genetic regulation of specific traits. The Ponkan mandarin (Citrus reticulata Blanco cv. Ponkan) bud sport mutant “Pumpkin mandarin” displays a Pumpkin-shaped, ribbed peel protrusion phenotype with elevated soluble sugars, but its molecular basis remains unclear. Here, wild-type Ponkan (PG) and Pumpkin mandarin (NG) were compared across six developmental stages (90–240 days after flowering, DAF) for fruit appearance and internal quality, peel firmness, and tissue morphology; RNA-seq was performed on mature peel at 240 DAF. Peel protrusion was detectable as early as flowering. NG showed significantly lower mature fruit weight and consistently higher soluble sugar content throughout development. Peel firmness exhibited a stage-dependent reversal: NG exceeded PG before 180 DAF, PG exceeded NG at 180–210 DAF, and NG again exceeded PG at 240 DAF. RNA-seq generated 41.38 Gb of high-quality data and identified 580 differentially expressed genes (DEGs; 411 upregulated, 169 downregulated). DEGs were enriched in cell wall organization/modification, phenylpropanoid biosynthesis, starch and sucrose metabolism, cutin/wax biosynthesis, and photosynthesis. Expansin (EXP) and GH18 genes were upregulated, while NAM genes encoding NAC transcription factors were downregulated, suggesting an imbalance between cell wall loosening and structural maintenance in protrusion formation. Peel DEGs also included upregulated sucrose synthase (SUS) and sugar transporter (SUT) genes, indicating carbohydrate-related reprogramming in mutant peel. We propose a preliminary network in which NAM may function upstream, cell wall remodeling represents a principal effector module, and the peel carbohydrate metabolism acts as an accompanying module.