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It is increasingly recognized for its regulatory roles in plant signalling. However, the functions of squalene in cotton remain unexplored. Here, we show that exogenous squalene can promote cotton developmental traits (root elongation and ovule development), and identify GhSQS1 as the predominant functional gene encoding squalene synthase. Overexpression of GhSQS1 (GhSQS1-OE) promotes root development, along with metabolic and hormonal reprogramming, including the activation of brassinosteroid (BR)-associated signalling. Furthermore, stable overexpression of GhSQS1 markedly elevates endogenous squalene accumulation, predominantly in leaves. This metabolic enhancement is accompanied by coordinated improvements in root architecture, leaf expansion, fibre elongation, and overall plant vigour. Notably, GhSQS1-OE lines exhibited elevated lignin-associated enzyme activities and increased total lignin content. These changes were correlated with improved tolerance to drought and alkaline stress. Importantly, similar development-promoting phenotypes were reproduced by heterologous expression of a high-activity fungal SQS (sharing only 39.2% amino acid identity with GhSQS1), confirming that enhanced squalene biosynthesis underlies these effects. Collectively, this study establishes squalene biosynthesis as a central metabolic axis coordinating hormonal reprogramming, cotton-specific development and stress adaptation, while concurrently generating squalene-enriched biomass. These findings provide a new paradigm for crop genetic improvement and tolerance enhancement.<\/jats:p>","DOI":"10.1093\/jxb\/erag424","type":"journal-article","created":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T08:16:27Z","timestamp":1789028187000},"source":"Crossref","is-referenced-by-count":0,"title":["<i>GhSQS1<\/i>\n                    \u2013mediated squalene accumulation coordinates cotton development and stress resilience"],"prefix":"10.1093","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7999-222X","authenticated-orcid":false,"given":"Yameng","family":"Xu","sequence":"first","affiliation":[{"name":"State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences , Anyang, Henan 455000 ,","place":["China"]},{"name":"Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural and Biomanufacturing, Zhengzhou University , Zhengzhou, 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Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences , Anyang, Henan 455000 ,","place":["China"]},{"name":"Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural and Biomanufacturing, Zhengzhou University , Zhengzhou, Henan 450001 ,","place":["China"]},{"name":"Xinjiang Key Laboratory of Crop Gene Editing and Germplasm Innovation, Institute of Western Agricultural of CAAS , Changji, Xinjiang 831100 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jicheng","family":"Wei","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences , Anyang, Henan 455000 ,","place":["China"]},{"name":"Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural and Biomanufacturing, Zhengzhou University , Zhengzhou, Henan 450001 ,","place":["China"]},{"name":"Xinjiang Key Laboratory of Crop Gene Editing and Germplasm Innovation, Institute of Western Agricultural of CAAS , Changji, Xinjiang 831100 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4541-2554","authenticated-orcid":false,"given":"Lili","family":"Lu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences , Anyang, Henan 455000 ,","place":["China"]},{"name":"Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural and Biomanufacturing, Zhengzhou University , Zhengzhou, Henan 450001 ,","place":["China"]},{"name":"Xinjiang Key Laboratory of Crop Gene Editing and Germplasm Innovation, Institute of Western Agricultural of CAAS , Changji, Xinjiang 831100 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuya","family":"Ma","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences , Anyang, Henan 455000 ,","place":["China"]},{"name":"Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural and Biomanufacturing, Zhengzhou University , Zhengzhou, Henan 450001 ,","place":["China"]},{"name":"Xinjiang Key Laboratory of Crop Gene Editing and Germplasm Innovation, Institute of Western Agricultural of CAAS , Changji, Xinjiang 831100 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yadi","family":"Xing","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese 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