Decoding the Plant Epigenome: Interactions Between Genomics, Transcription, and Epigenetic Regulation

Dear Colleagues,

Plant genomics denotes the vigorous relationship of genetic, epigenetic, and transcriptional schemes controlling the expression of genes, phenotypic variability, and adaptation. This Special Issue aims to decipher how epigenomic alterations, including methylation of DNA and histone modifications, act as molecular adjustments, modulating the accessibility of gene and transcriptional activity without changing the DNA sequence. This includes analysing the interactions of epigenetic inscriptions with transcription factors and non-coding RNAs to explore genetic pathways through developmental stages, biotic and abiotic stress responses, and environmental resilience. Stress-induced epigenetic variations can activate or de-activate genes. Enhancements in multi-omics, including genomics, epigenomics, and transcriptomics are enabling the regular mapping of these interactions, indicating how genetic variation is linked with epigenetic maintenance, regulating networks of genes. Genomics enhancement further bridges causality, granting pointed manipulation of epigenetic marks to examine their roles in trait regulation. Understanding this is vital for improvements in crops, offering approaches to enhance yield, resilience, and nutrient efficiency via epigenetic breeding. Future innovative research should focus on integrating single-cell epigenomics, genome construction, and machine learning to interpret context-specific regulatory logic. This comprehensive approach will illustrate how plants balance genomics with epigenetic plasticity, revealing novel biological explanations for sustainable agriculture.

In this Special Issue, we welcome (but are not limited to) research articles, timely review perspectives, and step-by-step protocols.

Topics of interest for this Special Issue include, but are not limited to, the following:

• Integration of multi-omics
•  Functional genomics
• Gene mining and expression
• Phenotype prediction
• Plant epigenomics

We look forward to receiving your contributions.

Prof. Dr. Zaifeng Li
Guest Editor

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