Biological networks for citrus metabolism under different cultivation conditions (reuse of omics data and generation of new knowledge)

• Grant number: 25/10318-5
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• Start date: August 01, 2025
• End date: July 31, 2027
• Field of knowledge: Agronomical Sciences - Agronomy - Plant Health
• Principal Investigator: Claudia Barros Monteiro Vitorello
• Grantee: Matheus Henrique Pimenta Zanon
• Host Institution: Escola Superior de Agricultura Luiz de Queiroz (ESALQ). Universidade de São Paulo (USP). Piracicaba , SP, Brazil
• Associated research grant: 24/00985-1 - Smart B100 Advanced Research Center (CCD-SB100), AP.CCD

Abstract

This postdoctoral project is part of a research initiative funded by FAPESP (CCD-SB100, sMART BOLETIM 100) and focuses on deepening our understanding of the molecular mechanisms that regulate citrus responses under different cultivation conditions. The project is based on the premise that interactions between plant genotype, microbiome, and the physical, chemical, and biological characteristics of the soil play a critical role in agricultural productivity and resilience to biotic and abiotic stresses. This approach is supported by recent studies highlighting the importance of integrating molecular, environmental, and agronomic data to develop more sustainable and efficient agricultural practices (Lehmann et al., 2020).Unlike sugarcane, for which a functional biological network has already been developed based on Arabidopsis thaliana data (Rody et al., 2021), there is currently no comparable network available for citrus. Therefore, the first step of this work plan will be the construction of a reference biological network for citrus, integrating functional and omics data available in public databases and the scientific literature. Building this network is essential for the success of subsequent steps in the project.Once the network is established, the proposal aims to: (1) identify and curate relevant experiments based on quality criteria and alignment with the SB100 project context; (2) reuse public data, such as transcriptomes and metagenomes, in in silico experiments using graph-based models and databases such as KEGG, STRING, and BIOGRID; (3) incorporate attributes derived from the metabolic reconstruction of microbiomes associated with agricultural soils; and (4) conduct comparative gene expression analyses integrated with the constructed network to identify molecular patterns associated with cultivation conditions and plant health.The methodology will include a systematic search of repositories such as NCBI BioProjects, focusing on experiments involving citrus under various stress conditions, management practices, and pathogen interactions. The proposed computational approach will enable the construction of functional networks and the identification of relevant patterns linking edaphoclimatic variables, microbiome composition, and plant molecular responses. Furthermore, critical analysis of available data will help identify knowledge gaps and inform new experimental designs to validate hypotheses generated in silico.Ultimately, this project aims to establish a reference biological network for citrus that can be used to interpret gene expression and microbiome data under diverse cultivation scenarios, extending the analytical power of the Boletim 100 initiative to this crop. By integrating metataxonomic, metabolomic, and transcriptomic data, the project will provide new functional layers related to soil quality and plant performance. Alignment with the goals of the SB100 project will be ensured through rigorous curation of datasets and methodologies.This work plan embraces an interdisciplinary approach that combines bioinformatics, systems biology, and agronomy, with strong potential to generate actionable insights for improved citrus management and productivity. Expected outcomes include the unprecedented construction of a citrus biological network, identification of relevant molecular patterns, and the proposal of new hypotheses regarding plant-soil-microbiome interactions across diverse environments. (AU)