Regulatory networks underpinning climate resilience in cotton: From molecular mechanisms to precision breeding

Background: Cotton (Gossypium hirsutum L.), the world's leading natural fibre crop, is increasingly challenged by climate change, with drought, salinity, waterlogging, temperature extremes, nutrient limitations, and their frequent co-occurrence substantially reducing yield, fibre quality, and production stability. Although extensive studies have identified numerous stress-responsive genes and pathways, a comprehensive understanding of the integrated regulatory networks governing climate resilience and their translation into breeding strategies remains fragmented. Aim of review: This review aims to provide a comprehensive systems-level synthesis of the regulatory mechanisms underlying cotton stress resilience by integrating advances in stress signalling, molecular regulation, multi-omics, and precision breeding into a unified framework for developing climate-resilient cultivars, explicitly distinguishing field-validated, breeding-ready targets from mechanistically supported but field-untested candidates and from speculative, discovery-stage leads across the major bottlenecks constraining translation. Key scientific concepts of this review: This review systematically integrates the regulatory networks controlling cotton adaptation to major abiotic stresses, encompassing stress perception, signal transduction, transcription factor networks, phytohormone crosstalk, reactive oxygen species homeostasis, ion transport, epigenetic regulation, and downstream physiological responses. Particular emphasis is placed on the emerging biology of combined-stress responses, highlighting regulatory interactions that cannot be explained by single-stress paradigms. Furthermore, the review critically evaluates how functional genomics, multi-omics integration, pan-genomics, genome editing, high-throughput phenotyping, and artificial intelligence-assisted prediction are converging to accelerate precision breeding for climate resilience. By bridging mechanistic understanding with translational breeding strategies, this review provides a forward-looking roadmap for developing climate-resilient cotton cultivars capable of sustaining productivity and fibre quality under increasingly unpredictable environments.