Remodeling of Homoeolog Expression Bias Buffers Stress Response in Allotetraploid Cotton

Background Homoeolog expression bias (HEB) is ubiquitous in polyploid plants. However, the drivers of HEB remodeling and its contribution to environmental adaptation remain largely unclear. Results Integrating 244 RNA-seq datasets from Gossypium hirsutum , we show that 3.2-41.4% of homoeologs exhibit expression bias across accessions, tissues, and treatments. Under stress, 6.0‐30.2% of homoeologs remodel the expression bias, primarily involving transitions between biased and unbiased states rather than reversals of bias direction. Over 85% of HEB rewiring came from subtle changes in expression, indicating that HEB dynamics are largely decoupled from canonical differential expression. Despite extensive HEB remodeling, the subgenomes remained functionally robust under stress conditions, suggesting that HEB modulation helps maintain a stable phenotype. Additionally, stress-responsive pathways were enriched in homoeologs undergoing HEB transitions, and transcription factors regulating HEB remodeling under similar stress conditions were shared. Conclusions This study systematically characterizes the HEB features in G. hirsutum and demonstrates that HEB remodeling plays a crucial role in stress response, thereby offering a complementary strategy for identifying stress-responsive genes in polyploids.