Regulatory divergence of homoeologs underlies network optimization for fiber improvement in domesticated cotton.

Polyploidy is prominent in plant evolution and in many of the world's most important crops, yet how domestication reshapes the regulation of duplicated genes (homoeologs) to generate superior agronomic traits remains incompletely understood. Here, we integrate population genomics, stage-resolved transcriptomics, expression quantitative trait locus (eQTL) mapping, and coexpression network analysis across 161 semiwild and 376 cultivated accessions of allotetraploid cotton (Gossypium hirsutum) to dissect the regulatory consequences of domestication. We show that domestication increases both the frequency and magnitude of homoeologous expression bias (HEB), with biased pairs preferentially organized into trait-associated, functionally specialized coexpression network modules. Bias-eQTL mapping identifies HEB-associated cis-regulatory variants that are enriched in open chromatin regions. Bayesian colocalization analysis further reveals that 92 bias-eQTLs colocalize with fiber quality-related genetic loci, where favorable alleles exhibit substantial frequency increases during domestication. Collectively, this work provides a mechanistic framework linking selection-driven regulatory asymmetry to coexpression network optimization in polyploids and highlights expression bias as a promising target for precision breeding in crops.