【#Tech24H】The Cotton Research Institute of the Chinese Academy of Agricultural Sciences has delineated the evolutionary pathway of upland cotton, constructing the world’s largest and most genetically diverse graphical pan-genome for the species. The research revealed the genetic mechanisms by which large chromosomal variations regulate population genetic diversity and environmental adaptability, deciphered the genetic architecture underlying fiber quality traits, and opened new pathways for creating superior cotton germplasm. It provides new scientific insights into the genetic diversity and phenotypic variation of upland cotton.