Grafting Rewrites the Epigenetic Script Behind Dwarf Citrus Trees

Grafting a tangerine onto a dwarfing rootstock does more than physically constrain a tree. A new study of the ‘Miguang’ Nanfeng tangerine (Citrus reticulata) shows that the choice of rootstock triggers a coordinated cascade of physiological, transcriptional and epigenetic changes in the scion, offering one of the clearest pictures yet of how rootstocks chemically reprogram the shoots grafted onto them. The findings, published in BMC Plant Biology, could reshape how breeders develop compact, high-yield citrus orchards.

Dwarfing rootstocks are prized in modern horticulture because they allow dense planting, easier harvesting and more efficient orchard management without sacrificing fruit yield. Yet the molecular machinery that makes a vigorous scion grow short has remained frustratingly opaque. Researchers led by Qingjiang Wei and Qiaoli Ma of Jiangxi Agricultural University, working with colleagues at Gannan Normal University and the University of Birmingham, set out to dissect this mechanism by comparing the same tangerine cultivar grafted onto rootstocks with radically different growth habits.

The team grafted ‘Miguang’ (MG) scions onto three rootstocks: vigorous ‘Carrizo’ citrange (CC), standard trifoliate orange (TO) and the dwarfing ‘Flying dragon’ trifoliate orange (FD). As expected, scions on FD and TO grew markedly less than those on CC. But the real story lay in the chemistry of the stems. Hormone profiling revealed that MG/FD stems accumulated higher levels of the auxin indole-3-acetic acid (IAA) and the stress hormone abscisic acid (ABA), while containing significantly less gibberellin 3 (GA3) and trans-zeatin (tZ) than MG/CC stems. Because gibberellins drive stem elongation and cytokinins like tZ promote cell division, this hormonal shift provides a direct biochemical explanation for the stunted phenotype.

The structural consequences were equally striking. Cell wall components, including lignin, cellulose and hemicellulose, accumulated at substantially lower levels in MG/FD stems than in MG/CC stems. Since lignified, thickened walls give stems their rigidity and mechanical strength, the reduced deposition suggests that dwarfing rootstocks do not merely slow cell expansion but fundamentally alter the construction of the stem itself, producing weaker, less rigid tissue that cannot sustain vigorous vertical growth.

To understand what drives these physiological shifts, the researchers performed comparative transcriptomics on the stem tissues. They identified 934 differentially expressed genes (DEGs) between MG/FD and MG/CC stems. Functional enrichment showed that many of these genes participate in hormone metabolism and signal transduction as well as cell wall synthesis, tying the transcriptional changes directly to the hormonal and structural phenotypes observed. In other words, the rootstock appears to rewire the scion’s gene expression program in ways that suppress the very pathways needed for tall growth.

The most provocative layer of the study, however, lies in its epigenetic findings. Using whole-genome bisulfite sequencing (WGBS), the team mapped DNA methylation across the genome in both graft combinations. They discovered that MG/FD had lower genome-wide DNA methylation levels and reduced methylation rates across various genic regions compared with MG/CC. This is significant because DNA methylation, the addition of methyl groups to cytosine bases, is a key epigenetic mark that can silence or fine-tune gene activity without altering the underlying DNA sequence.

Quantitatively, the researchers detected 2,538 differentially methylated cytosines (DMCs) and 794 differentially methylated regions (DMRs) between the two graft combinations. Among these, 13 candidate genes stood out because they showed significant divergence in both methylation and expression levels, suggesting that methylation changes at specific loci may directly influence the transcriptional programs governing dwarfism. This convergence of epigenetic and transcriptomic evidence points to DNA methylation as a potential regulatory layer through which rootstocks impose their growth-altering effects on scions.

What makes this study particularly compelling is the implication that grafting, long treated as a purely horticultural technique, may function as a form of natural epigenetic engineering. Signals travelling from root to shoot, whether hormonal, mobile RNAs or other yet-unidentified molecules, appear capable of reshaping the methylation landscape of the scion genome. If confirmed and refined, this opens the possibility of deliberately selecting or engineering rootstocks that induce beneficial methylation patterns, effectively programming trees to stay compact without genetic modification of the scion itself.

For citrus breeders, the practical implications are substantial. The 13 candidate genes identified at the intersection of methylation and expression divergence represent potential molecular markers for breeding new dwarfing rootstocks or for screening scion-rootstock combinations before lengthy field trials. The hormone and cell wall signatures provide additional phenotypic markers that could accelerate the development of compact cultivars suited to high-density orchard systems, reducing labor costs and improving per-hectare yields.

The study, supported by the National Natural Science Foundation of China and the Natural Science Foundation of Jiangxi Province, does not close the case on rootstock-induced dwarfism, but it decisively widens it. By demonstrating that the phenomenon involves not just hormones and cell walls but also heritable epigenetic marks, the researchers have added a new dimension to how scientists think about grafting. The next step will be to determine whether these methylation changes are stable across seasons and generations, and whether they can be deliberately manipulated, a question that could ultimately transform citrus cultivation worldwide.

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

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

Article References: Wei, Q., Ye, G., Chen, D., Zhou, G., Catoni, M., Gu, Q., & Ma, Q. (2026). Graft-induced physiological, transcriptional, and DNA methylation alterations in ‘Miguang’ Nanfeng tangerine (Citrus reticulata). BMC Plant Biology. https://doi.org/10.1186/s12870-026-10076-w

Image Credits: AI Generated

DOI: 10.1186/s12870-026-10076-w

Keywords: citrus, grafting, DNA methylation, dwarfing rootstock, epigenetics, plant hormones, transcriptomics, cell wall, trifoliate orange, Nanfeng tangerine, Graft-induced, physiological