Autopolyploidization reshapes transcription factor regulatory networks and enhances MAPK-associated thermotolerance...

Polyploidization is an important evolutionary mechanism that contributes to plant adaptation to environmental stresses; however, the transcriptional regulatory mechanisms underlying enhanced thermotolerance in autopolyploid crops remain poorly understood. In our previous work, we demonstrated that the superior thermotolerance of tetraploid rice compared with diploid rice under heat stress was associated with DNA methylation and accompanied by differential expression of related genes. Nevertheless, the underlying molecular mechanisms remain to be further elucidated. In this study, we compared diploid japonica rice (GFD-2X) and its naturally derived autotetraploid counterpart (GFD-4X) under control, heat stress, and recovery conditions to investigate transcription factor (TF)-centered regulatory networks. Transcriptomic analysis identified 1,141 expressed TF genes across 56 families. Heat stress induced widespread transcriptional repression in both genotypes, with approximately 70% of differentially expressed TF genes (DETFs) downregulated. However, the autotetraploid genotype exhibited nearly threefold more genotype-specific DETFs under stress and demonstrated pronounced transcriptional reactivation during recovery, with upregulated DETFs exceeding downregulated genes by more than twofold. Family-level analysis revealed a regulatory shift from bHLH-dominated regulation during acute heat stress to WRKY- and MYB-associated modulation during recovery. Functional enrichment analysis highlighted hormone-mediated signaling and the mitogen-activated protein kinase (MAPK) signaling pathway as central regulatory components. Weighted gene co-expression network analysis (WGCNA) identified four modules positively associated with the autotetraploid genotype and 67 hub genes, including five MAPK-associated TFs (OsbZIP23, OsbZIP49, OsbZIP84, OsRR26, and OsMYC2) forming a coordinated regulatory core. These findings suggest that autopolyploidization enhances thermotolerance by restructuring TF-centered regulatory networks, reinforcing MAPK-hormone signaling integration, and strengthening recovery-phase transcriptional reprogramming. Our study provides network-level insights into how genome duplication promotes stress resilience in rice.