Authors
Zhengyang Qi, Jinglei Yang, Yanchao Xu, Xuehan Tian, Zhiwei Chen, Yawen Wang, Boyang Chen, Yang Meng, Wei Zhang, Zeyu Zhang, Xinhui Nie, Lili Tu, Xianlong Zhang, Jonathan F Wendel, Fang Liu, Maojun Wang
Published in
Proceedings of the National Academy of Sciences of the United States of America. Volume 123. Issue 34. Pages e2523784123. Aug 25, 2026. Epub Aug 20, 2026.
Abstract
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.
PMID:
42623441
Bibliographic data and abstract were imported from PubMed on 21 Aug 2026.
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