Transcriptomic and DNA methylation insights into polyploidy-enhanced heat tolerance in rice (Oryza sativa L.)

Extreme heat constrains global rice production. Polyploidy, a central driver of flowering plant evolution, is frequently associated with enhanced resilience to adverse environments. However, the epigenomic and transcriptomic programs that support heat tolerance in autotetraploid rice remain largely unexplored. In this study, we compared a diploid japonica rice line (GFD-2X) and its isogenic autotetraploid counterpart (GFD-4X) under short-term heat stress and subsequent recovery using physiological measurements, transcriptome profiling, and whole-genome DNA methylation analysis. Both cytotypes showed elevated physiological and biochemical indicators after heat treatment, with GFD 4X displaying consistently stronger responses. Transcriptome analysis revealed that heat adaptation relies mainly on hormone-related signaling pathways, heat shock proteins, and antioxidant enzyme systems. Genome-wide DNA methylation profiling revealed a contrasting pattern in which polyploidization promotes widespread DNA hypermethylation, while acute heat stress triggers broad DNA hypomethylation. This bidirectional regulatory shift suggests a dynamic feedback mechanism that contributes to environmental adaptability. Integrated analysis of methylation and gene expression further showed that heat stress reshapes the methylation patterns of stress-responsive genes, thereby altering their transcriptional regulation. Together, these results support a model in which polyploidy-associated epigenomic features and heat-induced methylation dynamics are linked to enhanced physiological and molecular responsiveness under elevated temperature. This study provides a systems-level view of how polyploid rice responds to heat stress and offers insight into the potential epigenetic basis of heat tolerance in a warming climate.