Genome-wide identification of GhEDS1 gene family members in cotton and expression analysis in response to biotic and abiotic stresses

Background: Enhanced Disease Susceptibility 1 (EDS1) genes are central regulators of plant immunity and abiotic stress responses. Although well studied in model species, their genome-wide characterisation in cotton (Gossypium spp.) remains lacking. Results: We identified 268 putative EDS1 genes across four Gossypium species (G. hirsutum, G. barbadense, G. arboreum, and G. raimondii) using HMMER-based domain searches. Phylogenetic analysis grouped the genes into five subfamilies, reflecting both conserved ancestry and subgenome-specific diversification. Chromosomal mapping, collinearity, and Ka/Ks analyses revealed that segmental and whole-genome duplications were the primary drivers of expansion, with most duplicates under purifying selection. Promoter analysis using PlantCARE uncovered cis-regulatory elements responsive to abscisic acid, jasmonic acid, drought (MBS), and light signals (G-box). miRNA target prediction via psRNATarget revealed ghr-miR414 as a key regulator targeting multiple GhEDS1 transcripts. Functional enrichment indicated roles in lipid metabolism and ubiquitin-mediated proteolysis. Finally, RNA-seq data and qRT-PCR confirmed that GhEDS1A-13, GhEDS1D-57, and GhEDS1D-48 were significantly upregulated under PEG-induced drought stress, implicating them in ABA-linked stress adaptation. Conclusions: This study provides the first comprehensive characterisation of the EDS1 gene family in cotton, highlighting its evolutionary dynamics, regulatory complexity, and potential in improving drought tolerance through molecular breeding.