Meta-analysis of public RNA-sequencing data of drought and salt stresses in different phenotypes of Oryza sativa

Abstract

Environmental stresses, such as drought and salt, adversely affect plant growth and crop productivity. While many studies have focused on established components of stress signaling pathways, research on unknown elements remains limited. In this study, we collected RNA sequencing (RNA-Seq) data from Oryza sativa subsp. indica and Oryza sativa subsp. japonica registered in public databases and conducted a meta-analysis integrating multiple studies. Focusing on two types of stress conditions (salt and drought), we aimed to identify novel stress-responsive genes in Oryza sativa by comparing RNA-Seq data from stress-resistant and stress-susceptible cultivars. We analyzed 105 paired datasets with different phenotypes under drought and salt stress conditions to identify genes with common expression changes across multiple studies. A meta-analysis identified 10 genes specifically upregulated in resistant cultivars and 12 specifically upregulated in susceptible cultivars under both drought and salt stress conditions. Furthermore, by comparing previously identified stress-responsive genes in Arabidopsis thaliana, we explored genes potentially involved in stress response mechanisms that are conserved across plant species. The genes identified in this data-driven study that potentially determine plant stress resistance or susceptibility phenotypes may serve as research targets for elucidating novel plant stress mechanisms and candidates for genome editing.