Integrative Epigenetic Regulation in Crop Stress Resistance: Multi-Omics-Guided Gene Mining and Molecular Breeding

Dear Colleagues,

Unfavorable environmental stressors—including heat, cold, drought, salinity, heavy metal toxicity, and nutrient deprivation—pose increasing threats to global crop productivity, exacerbating food insecurity amid climate change and population growth. While conventional breeding has advanced stress-resilient crop development, the intricate interplay between genetic, epigenetic, and gene expression regulatory networks in plant stress adaptation remains underexplored. Recent advances highlight the pivotal role of integrative epigenetic regulation—such as DNA methylation, histone modifications, and non-coding RNAs—in dynamically fine-tuning stress-responsive gene expression without altering the underlying DNA sequence. Coupled with multi-omics technologies (genomics, epigenomics, transcriptomics, and metabolomics), these epigenetic insights are revolutionizing the discovery of stress-resistance loci, cis-regulatory elements, and epialleles with breeding potential.

This Special Issue of Genes, entitled “Integrative Epigenetic Regulation in Crop Stress Resistance: Multi-omics-Guided Gene Mining and Molecular Breeding”, seeks to advance our understanding of how epigenetic mechanisms synergize with genetic factors and gene expression dynamics to enhance crop resilience. We invite high-quality research articles, reviews, and methodological breakthroughs addressing, but not limited to, the following topics:

• Multi-omics-driven discovery: Identification of stress-resistance loci, epialleles, and non-coding regulators through integrated epigenomic, transcriptomic (including gene expression profiling), and genome-wide association studies (GWAS).
• Mechanistic insights: Functional characterization of gene expression regulation under stress, including transcriptional control, post-transcriptional modifications, and epigenetic modulation (e.g., DNA methylation-mediated silencing/activation and RNA methylation-mediated RNA stability/translation/transport/splicing).
• Technology integration: Development of epigenome-editing tools (e.g., CRISPR-dCas9 systems) for the high-precision modulation of stress-related epigenetic marks and their downstream gene expression networks.
• Breeding applications: Utilizing epigenetic editing technologies to modify or edit stress-resistance genes/loci in crops for the development or engineering of climate-resilient crops.
• Computational innovations: AI/ML frameworks for modeling gene–environment–epigenetic interactions and predicting stress-adaptive gene expression patterns.

By bridging epigenetic regulation, gene expression dynamics, and molecular breeding, this Special Issue aims at catalyzing the translation of fundamental discoveries into sustainable agricultural solutions.

Dr. Qiutao Xu
Dr. Baoqi Li
Dr. Xuan Ma
Guest Editors

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• epigenetic regulation
• DNA methylation
• histone modifications
• RNA biology
• multi-omics
• abiotic stress resilience
• transgenerational epigenetic inheritance
• transcriptional regulation
• phenotypic plasticity