Ahmad J and Firdous H, 2026. Molecular and genomic ınsights into stress resilience in cotton (Gossypium spp.). Trends in Animal and Plant Sciences 7: 74-91. https://doi.org/10.62324/TAPS/2026.009

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Cotton (Gossypium spp) as a vital fiber crop in the world is being continually limited due to yield losses caused by increasing abiotic and biotic stresses linked with global warming. The review summarizes recent molecular and genomic developments that have changed our concept of stress resilience in cotton fundamentally. The facets of regulatory architecture of responses to drought, heat, salinity, and pathogen inoculations have been unveiled by the emergence of pan-genomics and multi-omics techniques, such as transcriptomics, proteomics, metabolomics and epigenomics. Families of stress-responsive genes, including heat shock proteins (HSPs), late embryogenesis abundant proteins (LEAs) and aquaporins, NAC, WRKY transcription factors have been well-characterized, with promising areas of crop improvement present in novel gene families including CER (cuticular wax) and PsbX (photosystem II). The high precision of editing these candidate genes has been made possible through functional genomics tools, especially CRISPR/Cas9-based genome editing, which would consequently advance the creation of resilient cultivars. Further on, genomic selection, high-throughput phenotyping and marker-assisted selection are all integrated into breeding pipelines making it easier to transfer molecular findings into elite varieties. Still, issues in functional validation, understanding of multi-stress interactions and application on the field remain. The next generation activities should take advantage of the genetic diversity of wild relatives, apply the systems biology methods, and integrate artificial intelligence to design the next-generation, climate-resistant cotton that would guarantee sustainable production despite increasingly unfavorable environmental factors.