Gossypium hirsutum Raw sequence reads
Polyploidy has shaped plant evolution by providing duplicated genes that can be retained via subfunctionalization, whereby ancestral functions are partitioned between copies. In allopolyploid crops, how domestication remodels this regulatory balance to optimize traits remains unclear. Here, we integrate population genomics, transcriptomics, eQTL mapping, and co-expression network analysis across semi-wild, and cultivated Gossypium hirsutum to dissect the regulatory consequences of domestication.