GhSQS1-mediated squalene accumulation coordinates cotton development and stress resilience.

Squalene is a high-value triterpenoid. It is increasingly recognized for its regulatory roles in plant signaling. 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 squalene synthase. Overexpression of GhSQS1 promotes root development, along with metabolic and hormonal reprogramming, including the activation of brassinosteroid (BR)-associated signaling. 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, fiber elongation, and overall plant vigor. 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 recapitulated 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.