Genome-Wide Characterization of the ABI3 Gene Family in Cotton.

Background: The B3-domain transcription factor ABI3 (ABSCISIC ACID INSENSITIVE 3) is a critical regulator of seed maturation, stress adaptation, and hormonal signaling in plants. However, its evolutionary dynamics and functional roles in cotton (Gossypium spp.) remain poorly characterized. Methods: We conducted a comprehensive genome-wide investigation of the ABI3 gene family across 26 plant species, with a focus on 8 Gossypium species. Analyses included phylogenetics, chromosomal localization, synteny assessment, gene duplication patterns, protein domain characterization, promoter cis-regulatory element identification, and tissue-specific/spatiotemporal expression profiling under different organizations of Gossypium hirsutum. Results: Phylogenetic and chromosomal analyses revealed conserved ABI3 evolutionary patterns between monocots and dicots, alongside lineage-specific expansion events within Gossypium spp. Syntenic relationships and duplication analysis in G. hirsutum (upland cotton) indicated retention of ancestral synteny blocks and functional diversification driven predominantly by segmental duplication. Structural characterization confirmed the presence of conserved B3 domains in all G. hirsutum ABI3 homologs. Promoter analysis identified key stress-responsive cis-elements, including ABA-responsive (ABRE), drought-responsive (MYB), and low-temperature-responsive (LTRE) motifs, suggesting a role in abiotic stress regulation. Expression profiling demonstrated significant tissue-specific transcriptional activity across roots, stems, leaves, and fiber developmental stages. Conclusions: This study addresses a significant knowledge gap by elucidating the evolution, structure, and stress-responsive expression profiles of the ABI3 gene family in cotton. It establishes a foundational framework for future functional validation and targeted genetic engineering strategies aimed at developing stress-resilient cotton cultivars with enhanced fiber quality.