Conservation and divergence of abiotic stress-responsive gene co-expression networks in diploid and tetraploid cotton

Cotton (Gossypium spp.) is highly susceptible to abiotic stresses, including temperature extremes, drought, and salinity. The diploid species Gossypium arboreum retains stress adaptive traits that are poorly represented in modern tetraploid cultivars, yet the evolutionary and regulatory bases of these ploidy associated differences remain insufficiently understood. Here, we performed a comparative transcriptomic analysis of 54 seedling leaf RNA-seq libraries from Gossypium arboreum, Gossypium hirsutum, and Gossypium barbadense subjected to four abiotic stress treatments. By integrating standardized cross-species normalization with an optimized gene co-expression network framework, we minimized interspecific technical heterogeneity and enabled robust comparison of stress responsive regulatory architectures. Consensus network analysis revealed marked topological divergence between diploid and tetraploid cotton. The G. arboreum A₂ network showed strong structural conservation with the A_t subgenome of G. hirsutum, whereas extensive co-expression rewiring was detected in the A_t subgenome of G. barbadense, which may reflect lineage-specific regulatory remodeling of stress-response programs after allopolyploidization. By integrating conserved multi-species networks with five genome or subgenome specific networks, we identified 54 core cold-repressed candidate genes, including a BBR-BPC transcription factor potentially associated with ethylene related stress signaling. The divergent topology of the cold-responsive subnetwork defined by these candidates suggests extensive transcriptional reprogramming associated with polyploid evolution. Module preservation analysis also uncovered an A₂-specific heat-responsive module centered on an ERF transcription factor. In a distinct drought/heat co-responsive module, another ERF was predicted to coordinate both a heat shock factor (HSF) and an ABA responsive TALE transcription factor, suggesting potential regulatory crosstalk between heat and drought signaling pathways. Collectively, our study resolves conserved and lineage-specific components of cotton abiotic stress regulation and provides candidate regulators for resilience oriented molecular breeding.