Graft-induced physiological, transcriptional, and DNA methylation alterations in ‘Miguang’ Nanfeng tangerine (Citrus reticulata)

Dwarfing rootstocks enable the cultivation of compact citrus orchards, thereby facilitating cost-effective and high-efficiency orchard management while enhancing fruit yield. However, the molecular mechanisms underlying rootstock-induced dwarfing, particularly the potential regulatory role of DNA methylation remains poorly understood. The present study demonstrated that the ‘Miguang’ (MG) Nanfeng tangerine scions grafted onto dwarfing rootstock trifoliate orange (TO) and ‘Flying dragon’ trifoliate orange (FD) exhibited growth reduce compared to those grafted onto the vigorous ‘Carrizo’ citrange (CC) rootstock. Endogenous hormone quantification revealed that the MG/FD stems accumulated higher levels of indole-3-acetic acid (IAA) and abscisic acid (ABA), but lower concentrations of gibberellin 3 (GA3) and trans-zeatin (tZ) than MG/CC. Likewise, the accumulation of key cell wall components including lignin, cellulose, and hemicellulose, was substantially lower in MG/FD stems. Comparative transcriptomic analysis revealed 934 differentially expressed genes (DEGs) between stems of MG/FD and MG/CC, among which many were functionally associated with hormone metabolism and signal transduction and cell wall synthesis. Whole-genome bisulfite sequencing (WGBS) showed that MG/FD had lower genome-wide DNA methylation levels and reduced methylation rates across various genic regions relative to MG/CC. A total of 2,538 differentially methylated cytosines (DMCs) and 794 differentially methylated regions (DMRs) were detected between the two samples, among which 13 candidate genes displayed significant divergence in both methylation and expression levels. Collectively, these results elucidate the physiological basis, transcriptional regulation and methylation mechanism of rootstock-induced dwarfism in the citrus plants, providing the basis for the development of novel dwarfing breeding strategies.