Stem Cell Fate Determination in Plants: Genetic, Epigenetic and Environmental Mechanisms Governing In Vitro Regeneration

Dear Colleagues,

Plant in vitro regeneration, including callus formation, adventitious organogenesis and somatic embryogenesis, is fundamentally driven by somatic cell reprogramming and the establishment of functional stem cell niches. The initiation, self-maintenance and directional differentiation of plant stem cells are coordinately governed by three core regulatory layers: intrinsic genetic networks, multilayered epigenetic modifications, and exogenous environmental signals.

Genetic factors, such as master transcription factors and phytohormone signaling cascades, lay the core developmental framework of stem cell identity. Epigenetic regulators (DNA methylation, histone modifications, chromatin remodelers, and non-coding RNAs) act as reversible molecular switches to reshape chromatin status and lock/unlock cell fate during dedifferentiation and redifferentiation. Meanwhile, culture microenvironmental cues (light, temperature, medium composition, osmotic stress, and plant growth regulators) dynamically remodel epigenetic landscapes and genetic programs to regulate regeneration efficiency and developmental plasticity.

There are prominent lineage-specific differences in stem cell regulatory patterns between herbaceous model plants, agricultural crops and woody forest trees. Woody species often suffer from regeneration recalcitrance, somatic variation and declining embryogenic capacity during long-term subculture, which are tightly linked to aberrant genetic and epigenetic responses to culture environments. Existing reviews and special issues usually focus on a single regulatory layer, while an integrated platform systematically linking genetics, epigenetics and environmental signaling for plant in vitro regeneration is still lacking.

We welcome high-quality original research papers, comprehensive reviews and short communications on model plants, agricultural crops and forest tree species. By integrating genetic, epigenetic and environmental regulatory layers, this Special Issue dissects the core molecular logic underlying stem cell fate transitions throughout all in vitro regeneration pathways, offers theoretical strategies to resolve regeneration recalcitrance, and facilitates industrial optimization of plant micropropagation systems.

We welcome manuscripts related to, but not limited to, the following research directions:

1. Core genetic regulatory networks controlling stem cell origination, self-renewal and fate transition during callus induction and somatic embryogenesis;
2. Identification and functional validation of master transcription factors and stem cell-specific marker genes governing in vitro regeneration;
3. Hormone signal transduction and cross-talk with genetic modules that sustain embryogenic stem cell homeostasis;
4. Dynamic epigenetic reprogramming (DNA methylation, histone acetylation/methylation, and chromatin remodeling) during somatic cell dedifferentiation and redifferentiation;
5. Regulatory functions of miRNAs, lncRNAs and circRNAs in mediating stem cell fate and regeneration competence;
6. Sensing and signal transduction pathways of culture environmental factors (light quality, photoperiod, temperature, nutrients, osmotic pressure, and exogenous PGRs);
7. Environmental signal-triggered epigenetic memory and its effects on long-term subcultured embryogenic tissues;
8. Conserved and species-specific genetic–epigenetic regulatory modules in herbaceous crops, conifers and broad-leaved trees;
9. Single-cell multi-omics, ATAC-seq and epigenomic dissection of stem cell fate trajectories under differential culture environments;
10. Molecular basis of regeneration recalcitrance and somatic variation mediated by abnormal genetic and epigenetic responses to culture conditions;
11. Translational applications of genetic/epigenetic/environmental regulation in building efficient tissue culture and genetic transformation systems for difficult-to-regenerate plants.

Prof. Dr. Ling Yang
Guest Editor

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• plant stem cell
• cell fate determination
• in vitro regeneration
• somatic embryogenesis
• genetic regulation
• epigenetic modification
• environmental signal
• cell reprogramming
• tissue culture
• transcription factor
• chromatin accessibility
• woody plant propagation