Integrated multi-omics analysis reveals hormonal and nutrient networks regulating sugarcane tillering

Introduction: Sugarcane tillering represents a complex developmental process shaped by multiple interacting molecular networks. To outline a multi-omics regulatory framework linking hormonal, ionomic, and transcriptomic variation to contrasting tillering capacities in sugarcane, we analyzed contrasting genotypes using an integrated multi-omics approach. Methods: Four field-grown sugarcane genotypes at the peak tillering stage were analyzed using integrated transcriptomics, targeted phytohormone metabolomics, and ionomics, with three biological replicates per genotype × tissue combination. Results: High-tillering plants maintained a transcriptional and metabolic state optimized for growth, including enhanced expression of photosynthetic and carbon metabolic pathways, marked accumulation of the auxin-associated metabolite tryptamine (Log2FC = 4.97), elevated auxin- and cytokinin-associated metabolites, and preferential enrichment of micronutrients in tiller tissues. In contrast, low-tillering genotypes adopted a stress-prepared phenotype characterized by activation of defense and protein synthesis pathways, reduced 1-aminocyclopropane-1-carboxylic acid (ACC) levels in high-tillering plants relative to low-tillering plants (Log2FC = -2.26), accumulation of jasmonate-, salicylic acid-, and abscisic acid (ABA)-associated metabolites, and distinct ionomic signatures associated with nutrient imbalance. Weighted Gene Co-expression Network Analysis (WGCNA) further revealed a polarized regulatory structure, with the growth-associated module positively correlated with cis-Zeatin riboside (cZR) (yellow-labelled, r = 0.71), whereas the defense-associated module showed strong negative correlations with cZR/cis-Zeatin (cZ) (brown-labelled, r = -0.74/-0.75), and another defense-associated module showed positive correlations with ACC and Salicylic acid (SA) (turquoise-labelled, r = 0.77 and 0.79, respectively) . Discussion: This study provides an integrated multi-omics framework for understanding sugarcane tillering and highlights a coordinated growth-defense trade-off associated with contrasting tillering strategies.