Integration of functional genomics and systems biology in transcriptomic analysis associated with the water deficit tolerance and its inference in rice (Oryza sativa) and sugarcane (Saccharum spp.) through network analysis

• Grant number: 23/10829-4
• Support Opportunities: Scholarships in Brazil - Doctorate
• Start date: August 01, 2024
• End date: February 28, 2027
• Field of knowledge: Biological Sciences - Genetics - Plant Genetics
• Principal Investigator: Antonio Vargas de Oliveira Figueira
• Grantee: Pedro Cristovão Carvalho
• Host Institution: Escola Superior de Agricultura Luiz de Queiroz (ESALQ). Universidade de São Paulo (USP). Piracicaba , SP, Brazil
• Associated scholarship(s): 25/10055-4 - Optimizing Spatial Transcriptomics in Plants: Developing an Analysis Pipeline for STOmics-Based Data in Polyploid Crops, BE.EP.DR

Abstract

Sugarcane (Saccharum spp.) is one of the main agricultural crops in the world for the production of sugar and bioethanol. Water stress represents the most limiting abiotic factor in production, highlighting the need to develop more drought-tolerant cultivars. Facing climate change, breeding programs have redirected their strategies towards the development of drought tolerant cultivars, acting from the classical selection to the prospection of genes related to the drought response through the development of transgenic cultivars. The advances in biotechnology provide subsidies to reduce the time of development of a new cultivar, from pursuing the identification of candidate genes through transcriptome analysis, to evaluating the effect of their expression in complex biological systems. The development of transgenics can explore genes involved in all sugarcane response pathways to water deficit, from signal perception to stress response. Recent work conducted by the team of the Centro de Cana (IAC) identified that overexpression of the ShDJ gene (Saccharum hybrid Dirigent-Jacalin) resulted in rice plants with greater productive performance under water restriction conditions, in addition to modifying the biomass composition. This fact signals that ShDJ has biotechnological potential for generating genetically modified plants that are more tolerant to drought. However, it is necessary to identify the effects that manipulation of ShDJ expression level causes on other genes and pathways in sugarcane, and elucidate its role in tolerance to water deficit. In this context, the present project aims to explore systems biology through network analysis associated with transcriptome data from elite events in transgenic rice overexpressing ShDJ as a model system and similar events in sugarcane investigating the associated changes. The analyzes will allow the expansion and validation of the biological network under development for sugarcane, including aspects related to responses to abiotic stress, incorporating transcriptomic data on associated events and available public data. The results will also serve to investigate changes resulting from transgene expression in view of regulatory demands for the environmental release of transgenic events.