RNA-seq and ATAC-seq reveal candidate genes and regulatory networks underlying exogenous ABA-enhanced abiotic stress tolerance in Gossypium hirsutum

Drought, heat, and salinity severely constrain the yield and fiber quality of Gossypium hirsutum. Although abscisic acid (ABA) is a central regulator of plant abiotic stress responses, whether exogenous ABA elicits a core response shared with multiple abiotic stresses in G. hirsutum remains unclear. Here, we identified 200 μM ABA as an effective concentration for mitigating physiological damage under drought, heat, and salt stress, and integrated time-series RNA-seq, hormone profiling, and assay for transposase-accessible chromatin sequencing (ATAC-seq) to characterize ABA-induced responses. Comparative transcriptome analysis identified 3345 core differentially expressed genes (DEGs) shared among ABA, drought, heat, and salt treatments, which were enriched in circadian rhythm, photosynthesis, water homeostasis, and carbon metabolism. Hormone profiling showed rapid accumulation of ABA and ABA-glucose ester after ABA treatment, accompanied by enhanced jasmonate- and ethylene-related signals and reduced salicylic acid and gibberellin levels. ATAC-seq revealed increased promoter chromatin accessibility at 12h after ABA treatment, and accessibility changes were generally positively associated with the expression of nearby genes. Integration of shared DEGs, promoter-associated differentially accessible regions (DARs), and motif enrichment identified a candidate regulatory network consisting of 24 transcription factors (TFs) and 439 putative target genes. Functional analysis further supported Gh_MYB-D as a positive regulator associated with tolerance to multiple abiotic stresses. Together, these results provide a candidate regulatory framework for ABA-enhanced abiotic stress tolerance in G. hirsutum and nominate genes for future functional validation.