Integrated Transcriptome and Protein-Protein Interaction Network Analysis Uncovers Pivotal Ribosomal Proteins and Ion Transporters Involved in Rice Salt Tolerance

Abstract Salinity stress is a major challenge for rice production, especially at seedling stage. To gain a comprehensive insight into the molecular mechanisms and potential candidate genes involved in rice salinity stress response, we integrated RNA-Seq and protein-protein interaction (PPI) network analysis to investigate the transcriptome dynamics of two contrasting genotypes. We collected root and shoot tissue samples at two timepoints (6 hours and 54 hours) after exposure to salinity stress. A total of 15,483 differentially expressed genes (DEGs) were identified across different combinations studied. Salt-specific genes were identified by comparing the genotypes under salinity stress. These salt-specific genes were mainly involved in metabolic processes, response to stimulus, and transporter activity, and were enriched in key metabolic pathways such as, biosynthesis of secondary metabolites, plant hormone signal transduction, and carotenoid biosynthesis. The PPI network analysis revealed 50 and 25 hub genes for salt-specific genes in the salt-tolerant CSR28 and salt-sensitive IR28, respectively. These hub genes were mainly involved in ribosome and encoding of important ribosomal proteins such as, RPL5, RPL18 and RPS9 with a potential role in stress signaling and tolerance enhancement in CSR28. Furthermore, the expression patterns of ion transporter genes in the roots at 54-hour timepoint regulated the Na+/K+ balance in the shoot. We also identified key transcription factors (TFs) that exhibited specific expression patterns based on timepoint, organ, or genotype. Our study provides valuable information for further investigation of the candidate genes associated with salt tolerance and development of salt-tolerant rice varieties.