Grafting is a widely used technique to improve stress tolerance in horticultural plants. However, little is known about how grafting affects citrus growth under low-nitrogen (N) stress. To investigate the responses of different grafting combinations to low N availability, we examined root morphology, photosynthesis, chlorophyll fluorescence and semi-quantitative mineral profiles in grafted and ungrafted citrus plants subjected to two N levels (10 and 0.15 mM NO₃⁻ -N) under potted conditions. Analyses were performed on roots and leaves of six plant combinations: ungrafted Trifoliate orange (Poncitrus trifoliata L. Raf., Pt) and red tangerine (Citrus reticulata Blanco, Cr); self-grafted combinations (Pt/Pt and Cr/Cr); and reciprocal heterografts (Pt/Cr and Cr/Pt). Under low-N stress, plant height decreased by 12.3–36.8%, stem diameter by 2.9–31.8%, leaf area by 18.2–26.3%, and SPAD by 11.6–24.5% across the six combinations, with the Cr/Cr combination showing the largest reductions in all parameters. The highest net photosynthetic rate (P_n), intercellular CO₂ concentration (C_i), stomatal conductance (Gs), electron transport rate (ETR), maximum quantum efficiency of PSII (Fv/Fm) and effective quantum efficiency of PSII (Fv’/Fm’) were observed in the Pt and Pt/Pt plants. Low-N stress reduced chloroplastid pigment contents and limited photosynthetic rates. Under 10 mM N treatment, the Fv/Fm values of Pt, Cr, Pt/Pt, and Cr/Pt were approximately 0.82, whereas those of Pt/Cr and Cr/Cr were below 0.82, suggesting lower maximal PSII efficiency in combinations with Cr rootstock. Regarding mineral elements, under low-N stress, the relative levels of P, K, Ca, Mg, and Fe in leaf and root sap increased, while those of N, Cu, Zn, B, and Mn decreased. Overall, combinations with Pt rootstock (Pt/Pt and Cr/Pt) showed better growth and photosynthetic performance, and more stable mineral profiles under low-N stress than combinations with Cr rootstock (Cr/Cr and Pt/Cr). These findings provide a physiological basis for understanding rootstock-specific responses to low-N stress under controlled conditions.

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.