Genomic reconstruction of upland cotton domestication uncovers staged selection, gene flow, and flowering-time adaptation

Abstract

Upland cotton (Gossypium hirsutum L.) underpins the global cotton industry, yet the genetic mechanisms driving its domestication remain poorly resolved. Here, we integrate a large-scale pan-genome of 2,910 accessions to clarify G. hirsutum’s single domestication origin and delineate three previously uncharacterized key stages of its evolutionary domestication. We innovatively pinpoint two pivotal genes: GhTOFD06, a regulator of photoperiod sensitivity, and GhSID05, an asparaginase-encoding gene as a controller of seed yield. Notably, our analysis also uncovers natural gene flow between G. hirsutum and G. barbadense. These findings provide a high-resolution framework for cotton domestication and deliver actionable molecular targets to accelerate breeding for addressing critical needs of the global textile and agricultural sectors.