Bivalent chromatin states and epigenetic priming in cotton: the role of H3K4me3 and H3K27me3 in cold stress memory and resilience

Cold stress is a significant challenge to cotton (Gossypium hirsutum L.) production during seed emergence and early seedling establishment, as cotton is native to tropical and subtropical environments. Low temperatures during these sensitive stages impair photosynthetic efficiency, damage cellular structures, and reduce yield. Although cotton responses to cold stress have been extensively investigated at physiological, molecular, and transcriptional levels, increasing evidence suggests that transient gene expression changes alone are insufficient to explain sustained stress performance. This review synthesizes current knowledge on cotton cold-stress responses, emphasizing the regulatory roles of key histone modifications histone H3 lysine 4 trimethylation (H3K4me3) and histone H3 lysine 27 trimethylation (H3K27me3) in transcriptional control and within-generation (somatic) epigenetic priming. Although cotton cold epigenome profiling is beginning to emerge, cotton-specific, time-resolved chromatin datasets that span chilling, recovery, and recurrent chilling (stress-recovery-re-stress) remain limited; therefore, several mechanistic inferences necessarily rely on indirect evidence from cotton studies under other conditions and on well-characterized model plant systems. H3K27me3 is implicated in Polycomb-mediated gene silencing and may regulate gene reactivation during cold stress and recovery, whereas H3K4me3 is proposed to support rapid induction of cold-responsive genes. Bivalent chromatin domains containing H3K4me3 and H3K27me3 may maintain stress-related genes in a poised transcriptional state, enabling swift activation while preserving developmental regulation. We highlight key knowledge gaps and experimental priorities for establishing cotton-specific chromatin mechanisms of cold memory and for translating these insights into epigenome-assisted breeding and biotechnological strategies to develop cotton varieties with improved and stable cold resilience.