Identification of Candidate Downstream Genes in the Glucose-TOR Pathway Involved in Root Growth Under Salt Stress in the Halophyte <i>Schrenkiella parvula</i> Using Gene Co-expression Network Analysis

Abstract

Background: Schrenkiella parvula is a halophyte capable of maintaining root growth under salt stress, making it a valuable model for studying stress adaptation. The glucose-TOR signaling pathway regulates root development in Arabidopsis; however, its role in extremophytes such as S. parvula under saline conditions remains poorly understood. This study investigated TOR-related gene regulation in S. parvula using gene co-expression network analysis. Objectives: This study aimed to identify key gene modules and hub genes downstream of the glucose-TOR signaling pathway that contribute to the maintenance of root growth under salt stress in S. parvula. Methods: A set of TOR-regulated genes in Arabidopsis roots was used to identify orthologs in S. parvula. RNA-seq data from salt-stressed S. parvula roots were normalized using DESeq2. Weighted gene co-expression network analysis (WGCNA) was performed on 1,858 genes to identify modules correlated with salt stress. Hub genes were identified based on high module membership (kME) values and visualized using Cytoscape. Results: Seven co-expression modules were identified. The green module showed the strongest correlation with salt stress and contained six hub genes associated with cell division and expansion, cell wall modification, detoxification, and osmotic balance. Conclusions: S. parvula may maintain root growth under salinity through the activation of TOR-regulated genes. The identified green module supports cellular and metabolic adaptation. Key genes, such as MEI2-like and expansin, may sustain root development, whereas other genes may contribute to detoxification and osmotic balance. These results provide potential targets for improving stress tolerance in crops.