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: By integrating 244 RNA-seq datasets from Gossypium hirsutum, we demonstrate 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, our study revealed that the regulatory components involved in regulating HEB remodeling were closely related to stress response. CONCLUSIONS: This study systematically characterizes the HEB features in G. hirsutum and demonstrates that HEB remodeling plays a crucial role in stress response. These findings enhance our understanding of polyploidy adaptation and offer a complementary strategy for identifying stress-responsive genes in polyploids.