Plant cells do not easily abandon their mature identity. In apple, that transformation is especially important because somatic embryogenesis underpins regeneration and genetic improvement. This study reveals that an RNA regulatory module centered on miR3699, MdMAN7, and the endogenous target mimic eTM3699 helps trigger that switch by loosening the cell wall. The researchers show that elevated MdMAN7 activity promotes β-mannanase-driven hemicellulose breakdown, thins the cell wall, and creates conditions that favor the formation of embryogenic cells. By contrast, miR3699 suppresses this process, while eTM3699 protects MdMAN7 by sequestering the microRNA. The work uncovers a new molecular route through which mature apple cells regain developmental plasticity.
Somatic embryogenesis is a powerful route for plant regeneration, transformation, and breeding, but one major question has remained unresolved: how highly differentiated cells regain the capacity to divide and develop like embryos. Previous studies suggested that cell wall remodeling is essential for this transition, because rigid walls help lock cells into their mature state. At the same time, small RNAs and long noncoding RNAs have emerged as important regulators of developmental reprogramming, yet their coordinated control of cell wall change in this process has remained poorly understood. Because ceRNA regulation of somatic embryogenesis is still limited, deeper research is needed on how RNA networks and wall remodeling jointly drive embryogenic cell formation.
Researchers from Northwest A&F University, together with Tarim University, reported (DOI: 10.1093/hr/uhaf315) on November 14, 2025 in Horticulture Research that an eTM3699–miR3699–MdMAN7 regulatory module promotes embryogenic cell formation in apple by stimulating cell wall degradation during the earliest stage of somatic embryogenesis.
Using whole-transcriptome sequencing during the first eight days of auxin induction, the team identified miR3699 as a candidate regulator and MdMAN7 as a standout target gene, with MdMAN7 expression rising 55-fold under induction conditions. They also identified MSTRG.1226.2 as eTM3699, an endogenous target mimic predicted to bind miR3699 and release MdMAN7 from repression. Reporter assays strengthened that model: dual-luciferase and GUS experiments showed that miR3699 suppresses MdMAN7, while eTM3699 counteracts that suppression. Cytological analyses then linked this RNA circuitry to physical changes in the tissue. After eight days of induction, embryogenic cells became more numerous and compact, while cell walls thinned and β-mannanase activity rose. In parallel, D-mannose, hemicellulase activity, and hemicellulose content fell, indicating active wall remodeling. Functional tests confirmed the biological effect. Overexpressing MdMAN7 increased somatic embryo induction from 78% to 95%, doubled the germination coefficient from 6 to 12, and shortened embryo germination from about 68 to 50 days. In contrast, knocking out MdMAN7 abolished regeneration, while overexpressing miR3699 sharply reduced embryo formation and plant recovery.
The authors conclude that this module acts as a molecular gatekeeper for cellular reprogramming in apple. By enhancing β-mannanase activity and weakening hemicellulose-rich walls, MdMAN7 appears to remove a structural barrier that normally prevents mature somatic cells from returning to an embryogenic state. In this model, eTM3699 supports reprogramming by buffering miR3699, while miR3699 itself serves as a brake on the process.
The findings offer more than a mechanistic advance. In practical terms, improving somatic embryogenesis efficiency could strengthen apple regeneration systems used in germplasm improvement, functional genomics, and molecular breeding. The study also suggests a broader principle: that targeted tuning of RNA networks controlling wall plasticity may help unlock regeneration capacity in woody crops that are often difficult to reprogram. Beyond apple, the work provides a useful framework for exploring how ceRNA circuits reshape cellular structure to redirect developmental fate, with possible value for crop improvement, propagation, and stress-related trait engineering.
