Epigenetic control of heat stress responses in cotton: Mechanisms and breeding prospects

Global climate change intensifies heat stress, severely threatening cotton production by impairing growth, reproduction, and fiber quality. Recent advances highlight that dynamic epigenetic mechanisms—including DNA methylation, histone modifications, chromatin remodeling, and non-coding RNAs (ncRNAs)—orchestrate stress-responsive gene networks and establish heat stress memory in cotton. These reversible modifications provide a crucial regulatory layer for sensing, responding to, and potentially recalling thermal stress. Multi-omics integration has been pivotal in linking these epigenetic changes to physiological and agronomic outcomes. Translational tools such as epigenome editing and marker-assisted selection demonstrate the potential of harnessing epialleles (allelic variants defined by epigenetic modifications rather than DNA sequence changes) for breeding resilient varieties. However, challenges persist, including understanding epigenetic crosstalk and tissue-specificity. This review synthesizes current knowledge on epigenetic regulation in heat-stressed cotton, explores integrative omics approaches, and discusses their application in crop improvement. We conclude by outlining key research priorities to accelerate the development of epigenetics-informed breeding strategies for climate-resilient cotton.