Thirty years of molecular cytogenetics in cotton: from chromosome identification to precision breeding design

Abstract Over the past three decades, molecular cytogenetics has profoundly advanced cotton research, evolving from classical karyotyping to precision breeding design. This review outlines the pivotal role of techniques such as fluorescence in situ hybridization (FISH), genomic in situ hybridization, bacterial artificial chromosome-FISH, and oligo-FISH in enabling accurate chromosome identification, elucidating genome architecture and evolution, and characterizing centromeric organization in Gossypium species. These developments have not only refined our understanding of polyploid cotton genomes but also facilitated the tracing of introgressed chromosomal segments in hybrid breeding programs. By integrating molecular cytogenetics with modern genomic tools, cotton breeding has transitioned toward a precision-oriented approach, allowing for targeted genetic improvements and efficient utilization of wild germplasm. The continued innovation in cytogenetic technologies promises to further enhance the capacity for designing and deploying optimized cotton varieties.