Sugarcane–Peanut Intercropping Enhances Farmland Productivity: A Multi-Omics Investigation into the Coordination of Zinc Homeostasis and Hormonal Signaling

Intercropping triggers coordinated changes in gene expression and metabolite accumulation across sugarcane roots, stems, and leaves, leading to higher crop yields—an effect that has drawn growing attention. Yet, how this transcriptional and metabolic interplay precisely enhances productivity remains poorly understood, limiting insight into intercropping’s yield-promoting mechanisms. This research explored the relationships between sugarcane, its metabolites, and transcriptomes through field trials integrated with multi-omics analysis. Data from the field showed clear differences in gene expression and metabolite patterns between monoculture and intercropped sugarcane. Plants under intercropping displayed stronger differential gene expression, greater metabolite diversity, and shifts in physiological traits. Metabolite variation was closely linked to gene regulation and network complexity, which in turn affected key agricultural characteristics including plant height, stem thickness, and sugar content. Follow-up experiments confirmed that applying zinc—a element boosted by intercropping—improved growth in monoculture sugarcane and modified its hormonal composition. These results highlight the important role of coordinated transcriptome-metabolite activity in intercropping systems. The study provides valuable perspectives for making intensive farming more economical and sustainable, supporting efforts to raise crop output and improve ecosystem functions.