Integrated analysis of DNA methylation and transcriptome reveals the mechanism of differences in adventitious root formation ability between juvenile and mature shoots of apricot

The adventitious root formation in fruit trees is crucial for cultivating high-quality rootstocks. It is currently understood that organogenesis varies significantly among tissues of different physiological ages, but the specific mechanisms remain unclear. To uncover the mechanism, this study systematically compared the differences in adventitious root formation ability, genome-wide DNA methylation patterns, and transcriptome expression profiles between rejuvenated apricot materials (basal shoots, BS) and mature materials (annual shoots at the top, AS). The results revealed that BS achieved an adventitious root formation rate of approximately 35%, compared to merely 5% in AS. Furthermore, BS displayed a thinner cortex and reduced lignification in parenchyma tissue. Additionally, lower DNA methylation levels were observed in the promoter and gene coding regions. Transcriptome data revealed that the differentially expressed genes (DEGs) between AS and BS were significantly enriched in pathways related to plant hormone signal transduction and cell wall metabolism. Integrated analysis found that the overlapping genes between differentially methylated regions and DEGs were involved in the biosynthesis and degradation processes of cellulose, pectin, and lignin. The low methylation levels in the promoters of pectin hydrolase-encoding genes and coniferin/sinapyl alcohol synthesis-related genes in BS may be key to releasing transcriptional repression, thereby promoting cell wall softening, enhancing plasticity, and creating a favorable cytological microenvironment for adventitious root formation. This study deepens the understanding of the mechanism of adventitious root formation in apricots from epigenetic and transcriptional perspectives, providing a theoretical basis and candidate targets for improving rootstock rooting ability through genetic engineering. • DNA methylation is a key epigenetic switch responsible for the differences in adventitious root formation capability in apricot trees of different physiological ages. • Hypomethylation of the promoters of pectin hydrolase-encoding genes and lignin monomer biosynthetic genes may be a epigenetic mechanism that relieves their transcriptional repression and enhances cell wall plasticity. • The study integrates "epigenetic regulation–cell wall plasticity–rooting ability" into a complete pathway, proposing that "cell wall softening is the core of the rooting advantage in juvenile plant materials.