{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,20]],"date-time":"2026-08-20T18:26:07Z","timestamp":1787250367424,"version":"build-2736575974"},"reference-count":50,"publisher":"National Academy of Sciences","issue":"34","license":[{"start":{"date-parts":[[2026,8,20]],"date-time":"2026-08-20T00:00:00Z","timestamp":1787184000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"MOST | National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["W2411020 32170645"],"award-info":[{"award-number":["W2411020 32170645"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"MOST | National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2021YFF1000900"],"award-info":[{"award-number":["2021YFF1000900"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.pnas.org"],"crossmark-restriction":true},"short-container-title":["Proc. Natl. Acad. Sci. U.S.A."],"published-print":{"date-parts":[[2026,8,25]]},"abstract":"<jats:p>\n                    Polyploidy is prominent in plant evolution and in many of the world\u2019s 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 (\n                    <jats:italic toggle=\"yes\">Gossypium hirsutum<\/jats:italic>\n                    ) 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\n                    <jats:italic toggle=\"yes\">cis<\/jats:italic>\n                    -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.\n                  <\/jats:p>","DOI":"10.1073\/pnas.2523784123","type":"journal-article","created":{"date-parts":[[2026,8,20]],"date-time":"2026-08-20T17:54:21Z","timestamp":1787248461000},"update-policy":"https:\/\/doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":0,"title":["Regulatory divergence of homoeologs underlies network optimization for fiber improvement in domesticated cotton"],"prefix":"10.1073","volume":"123","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2228-4254","authenticated-orcid":false,"given":"Zhengyang","family":"Qi","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/023b72294","id-type":"ROR","asserted-by":"publisher"}],"name":"National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University","place":["Wuhan, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinglei","family":"Yang","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/023b72294","id-type":"ROR","asserted-by":"publisher"}],"name":"National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University","place":["Wuhan, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2432-3325","authenticated-orcid":false,"given":"Yanchao","family":"Xu","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/0313jb750","id-type":"ROR","asserted-by":"publisher"}],"name":"State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences","place":["Anyang, 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Qi RNA-seq data of Gossypium hirsutum fiber tissues. NCBI BioProject. https:\/\/www.ncbi.nlm.nih.gov\/bioproject\/PRJNA1303984. Deposited 9 August 2025."},{"key":"e_1_3_4_49_2","unstructured":"Y. Xu Gossypium hirsutum raw sequence reads. NCBI BioProject. https:\/\/www.ncbi.nlm.nih.gov\/bioproject?term=PRJNA1155012. Deposited 1 September 2024."},{"key":"e_1_3_4_50_2","unstructured":"Z. Qi J. Yang qizhengyang2017\/cotton-domestication-project. GitHub. https:\/\/github.com\/qizhengyang2017\/cotton-domestication-project. Deposited 23 July 2026."}],"container-title":["Proceedings of the National Academy of Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pnas.org\/doi\/pdf\/10.1073\/pnas.2523784123","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,20]],"date-time":"2026-08-20T17:54:26Z","timestamp":1787248466000},"score":1,"resource":{"primary":{"URL":"https:\/\/pnas.org\/doi\/10.1073\/pnas.2523784123"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,20]]},"references-count":50,"journal-issue":{"issue":"34","published-print":{"date-parts":[[2026,8,25]]}},"alternative-id":["10.1073\/pnas.2523784123"],"URL":"https:\/\/doi.org\/10.1073\/pnas.2523784123","relation":{},"ISSN":["0027-8424","1091-6490"],"issn-type":[{"value":"0027-8424","type":"print"},{"value":"1091-6490","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,20]]},"assertion":[{"value":"2025-08-29","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-07-09","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-08-20","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e2523784123"}}