{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T23:50:28Z","timestamp":1790380228501,"version":"4.1.0"},"reference-count":43,"publisher":"MDPI AG","issue":"5","license":[{"start":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T00:00:00Z","timestamp":1772064000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Key R&D Program of Henan Province","award":["241111114200"],"award-info":[{"award-number":["241111114200"]}]},{"name":"Independent Fund of State Key Laboratory of Cotton Bio-breeding and Integrated Utilization","award":["CB2025C12"],"award-info":[{"award-number":["CB2025C12"]}]},{"name":"Independent Fund of State Key Laboratory of Cotton Bio-breeding and Integrated Utilization","award":["CB2024C05"],"award-info":[{"award-number":["CB2024C05"]}]},{"DOI":"10.13039\/100009110","name":"Natural Science Foundation of Xinjiang Uygur Autonomous Region","doi-asserted-by":"crossref","award":["2025D01A18"],"award-info":[{"award-number":["2025D01A18"]}],"id":[{"id":"10.13039\/100009110","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Kashgar Regional Science and Technology Plan","award":["KS2024014"],"award-info":[{"award-number":["KS2024014"]}]},{"name":"Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural Sciences","award":["CAAS-ASTIP-2016-ICR"],"award-info":[{"award-number":["CAAS-ASTIP-2016-ICR"]}]},{"name":"China Agriculture Research System\u2014Cotton","award":["CARS-15-02"],"award-info":[{"award-number":["CARS-15-02"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Gibberellins (GAs) play a crucial regulatory role in the growth and development of cotton (Gossypium hirsutum L.). Through bioinformatics analyses, we identified a total of 39 GA2ox genes (encoding gibberellin 2-oxidases) in the cotton genome, designated GhGA2ox1 to GhGA2ox39. Based on phylogenetic analysis, these genes were classified into five groups. We further examined their gene structures, conserved motifs, and chromosomal distributions, revealing that members within the same group shared similar structural and motif organizations. Collinearity and cis-element analyses provided important insights into the evolutionary history and regulatory potential of the GA2ox gene family in cotton. Notably, using nucleotide diversity (\u03c0) and population differentiation (FST) analyses across the entire family, we screened and identified nine candidate genes that underwent strong artificial selection during cotton domestication and improvement. Further haplotype-phenotype association analysis identified GH_D09G0919 (GhGA2ox31) as a key regulator of Plant Height (PH). To validate their regulatory roles, we analyzed the genotype distribution in accessions with extreme phenotypes. The results revealed divergent selection histories for these two loci: the favorable allele of GH_D01G0720 (GhGA2ox23) was already fixed in the tested population, whereas GH_D09G0919 maintained significant natural variation. Specifically, the Hap2 allele of GH_D09G0919 was significantly enriched in the shortest accessions compared to the tallest ones. Importantly, quantitative real-time polymerase chain reaction (qRT-PCR) analysis confirmed that the Hap2 allele drives significantly higher gene expression in leaves, suggesting that enhanced GA catabolism underlies the compact phenotype. Additionally, transcriptomic profiling revealed the tissue-specific expression patterns of candidate genes, implying their functional roles in development. Furthermore, functional validation using the Arabidopsis mutant of the homologous gene (AtGA2ox8) confirmed its conserved role in regulating plant height, as the mutant exhibited a distinct short-stature phenotype. These results uncover valuable genetic resources for molecular breeding to shape compact cotton architecture. Collectively, this study aims to analyze the evolutionary patterns of the cotton GA2ox gene family and to identify key genes that regulate plant height under artificial selection, providing theoretical support for molecular breeding of compact plant types.<\/jats:p>","DOI":"10.3390\/ijms27052219","type":"journal-article","created":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T16:57:13Z","timestamp":1772125033000},"page":"2219","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Artificial Selection on the GA2ox Gene Family Contributes to Plant Architecture Improvement in Upland Cotton"],"prefix":"10.3390","volume":"27","author":[{"given":"Tao","family":"Wang","sequence":"first","affiliation":[{"name":"School of Agriculture and Biomanufacturing, Zhengzhou University, Zhengzhou 450001, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9708-943X","authenticated-orcid":false,"given":"Juwu","family":"Gong","sequence":"additional","affiliation":[{"name":"School of Agriculture and Biomanufacturing, Zhengzhou University, Zhengzhou 450001, China"},{"name":"Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ke","family":"Xu","sequence":"additional","affiliation":[{"name":"School of Agriculture and Biomanufacturing, Zhengzhou University, Zhengzhou 450001, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuqian","family":"Yao","sequence":"additional","affiliation":[{"name":"Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haoliang","family":"Yan","sequence":"additional","affiliation":[{"name":"Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Youlu","family":"Yuan","sequence":"additional","affiliation":[{"name":"Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haihong","family":"Shang","sequence":"additional","affiliation":[{"name":"School of Agriculture and Biomanufacturing, Zhengzhou University, Zhengzhou 450001, China"},{"name":"Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gangling","family":"Li","sequence":"additional","affiliation":[{"name":"School of Agriculture and Biomanufacturing, Zhengzhou University, Zhengzhou 450001, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,2,26]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"256","DOI":"10.1038\/22307","article-title":"\u2018Green revolution\u2019 genes encode mutant gibberellin response modulators","volume":"400","author":"Peng","year":"1999","journal-title":"Nature"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"701","DOI":"10.1038\/416701a","article-title":"A mutant gibberellin-synthesis gene in rice","volume":"416","author":"Sasaki","year":"2002","journal-title":"Nature"},{"key":"ref_3","first-page":"42","article-title":"Sustained release effects of exogenous GA3 on germination and growth of rice seedling under salt stress","volume":"24","author":"Zhang","year":"2018","journal-title":"China Rice"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"147255","DOI":"10.1016\/j.gene.2023.147255","article-title":"Heterologous functional analysis and expression patterns of gibberellin 2-oxidase genes of barley (Hordeum vulgare L.)","volume":"861","author":"Ouellette","year":"2023","journal-title":"Gene"},{"key":"ref_5","first-page":"27","article-title":"Effects of Gibberellin Acid (GA3) on Leaf Characters and Panicle Characters at Different Stages of Lu18S","volume":"4","author":"Wang","year":"2018","journal-title":"Hunan Agric. 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