Advancements in Understanding Histone Modification Regulation Mechanisms and Their Applications in Breeding for Plant Responses to Abiotic Stress

Abstract

Abiotic stresses such as drought, salinity, extreme temperature, and heavy-metal toxicity are among the principal constraints on global crop productivity, and their impact is intensifying under climate change. Beyond changes in DNA sequence, plants rely heavily on reversible chromatin modifications to rapidly and flexibly adjust gene expression in response to fluctuating environments. Among these, histone acetylation, methylation, phosphorylation, and ubiquitination act as an interconnected regulatory layer, often described as the histone code that governs whether stress-responsive genes are activated, repressed, or kept in a poised state for rapid future induction. This review synthesizes current understanding of the molecular writers, erasers, and readers that establish and interpret histone marks in plants, examines how these marks are dynamically remodeled during drought, salinity, temperature extremes, and heavy-metal exposure, and considers the phenomenon of chromatin-based stress memory mediated by bivalent H3K4me3–H3K27me3 domains. We further evaluate how this mechanistic knowledge is being translated into breeding practice, including epiallele-based selection, genome-wide epigenomic profiling, and CRISPR/dCas9-based epigenome editing that directly installs or removes histone marks at target loci without altering the underlying DNA sequence. Representative case studies in Arabidopsis, rice, wheat, cotton, poplar, soybean, and common bean illustrate measurable gains in stress tolerance achieved through manipulation of histone-modifying enzymes such as HDA6, HDA9, HD2C/D, OsHDT701, GCN5/ADA2, and HUB2. We conclude by outlining remaining challenges, including incomplete understanding of crosstalk between histone marks and other epigenetic layers, the stability and heritability of engineered epialleles, and regulatory pathways for non-transgenic epigenome-edited crops, and we propose priority directions for integrating chromatin biology into climate-resilient breeding pipelines.