Genomic reconstruction of upland cotton domestication uncovers staged selection, gene flow, and flowering-time adaptation
Xu Y, Cai X, Zhou Z, Lopez-Arredondo D, Hou Y, Zheng J, Li H, Sun G, Jin D, Dai P, Wei Y, Liu Y, Li P, Liu Q, Wang H, Sun R, Li L, Pan X, Wang K, Du X, Song G, Zhang B, Herrera-Estrella LR, He S, Liu F, Peng R.
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.
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