Unraveling the Spatial Architecture, RGA and ncRNA Mechanisms in the Sugarcane, Diatraea saccharalis, and Fusarium verticillioides Triad

• Grant number: 25/20343-7
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• Start date: January 01, 2026
• End date: December 31, 2028
• Field of knowledge: Agronomical Sciences - Agronomy - Plant Health
• Principal Investigator: Márcio de Castro Silva Filho
• Grantee: Diego Zanardo Gallan
• Host Institution: Escola Superior de Agricultura Luiz de Queiroz (ESALQ). Universidade de São Paulo (USP). Piracicaba , SP, Brazil
• Associated research grant: 22/09473-8 - Sugarcane multitrophic interactions: integrating microbiota composition and function with herbivorous insects, AP.BIOEN.TEM

Abstract

The transition to a more sustainable global economy demands the resilience of strategic crops like sugarcane (Saccharum spp.), which, despite its vast importance for sugar and bioenergy production, faces continuous threats from multifactorial biotic stresses. In particular, the complex synergistic interaction between herbivory by the sugarcane borer, Diatraea saccharalis, and infection by the pathogenic fungus Fusarium verticillioides, vectored by the insect itself and the causal agent of sugarcane red rot, poses an agricultural challenge of great magnitude, surpassing the simplistic notion of binary interactions and creating a "damage hub" where plant defenses are orchestrated under multiple pressures. In this intricate scenario, the sugarcane immune response, far from being a linear sum of isolated mechanisms, requires a deep understanding of how the plant perceives, integrates, and responds to often conflicting signals-a challenge that transcends traditional research approaches.We therefore propose to elucidate, with unprecedented spatio-temporal resolution, the multitrophic defense mechanisms of sugarcane, starting from the central hypothesis that resistance is modulated by a complex network composed of pathogen recognition receptors (RGAs, including NLRs and RLK/RLPs) that act as primary sensors and signaling hubs, as well as non-coding RNAs (ncRNAs) that fine-tune gene expression and mediate interspecies communication via cross-kingdom RNA trafficking, establishing a molecular battleground. Furthermore, we hypothesize an intrinsically spatially organized defense architecture, where different cell types contribute to local and systemic immunity, challenging the homogenized view of plant responses.To unravel this complexity, we will employ a multi-omic and systems biology approach, where, initially, transcriptomics (RNA-seq) will identify and prioritize crucial RGAs/NLRs for resistance modulation, with validation and quantification of candidates by digital PCR. Concomitantly, the characterization of ncRNAs via sRNA-seq and PARE (degradome) will reveal the dynamics of endogenous and inter-kingdom RNAs as integrators of the multitrophic response. A pioneering application of spatial transcriptomics (Visium, LCM-RNA-seq, and snRNA-seq) will also be performed to map the defense architecture, identifying cellular "hotspots" and transcript patterns that define immunity in the culm. This will culminate in Predictive Causal Modeling, which will integrate all data layers (RGAs, mRNAs, ncRNAs, metabolomics) into co-expression networks (WGCNA) and directed acyclic graphs (DAGs), allowing not only to describe the system but also to effectively predict the outcome of the multitrophic interaction, validating these target nodes and causal pathways through targeted experimental perturbations.The results of this highly innovative project, aligned with the frontiers of knowledge in plant genetics, will not only fill fundamental gaps in the understanding of multitrophic defense but also generate validated molecular markers for breeding programs aiming for multiple resistance and prospect targets for advanced biotechnological strategies, such as the use of RNAi for pest control, solidifying the position of the research groups in the international scientific landscape and training highly qualified human resources for the challenges of modern agriculture.