Comparative Transcriptomic Meta-Analysis of Salinity Stress Response in Rice and Tomato

Document Type : Original Article

Authors

1 Department of Plant Production and Genetics, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran.

2 Department of Plant Productions, Agricultural Faculty of Bardsir, Shahid Bahonar University of Kerman, Kerman, Iran.

3 Research and Technology Institute of Plant Productions, Afzalipour Research Institute, Shahid Bahonar University of Kerman, Kerman, Iran.

10.22126/cbb.2026.13980.1147

Abstract

Introduction: Soil salinity represents a formidable obstacle to global food security, exerting negative pressure on crop productivity across a wide array of botanical species. Despite the substantial body of research dedicated to deciphering salt tolerance in individual crops, there remains a persistent gap in comparative, cross-species analyses that delineate conserved mechanisms of resilience. This study was specifically designed to bridge the chasm between molecular responses and observed morpho-physiological traits. By conducting a parallel investigation into rice (Oryza sativa) and tomato (Solanum lcopersicum), we aimed to identify both the evolutionarily conserved and species-specific genetic architectures governing salt responsiveness. Our ultimate objective was to prioritize core genes and metabolic pathways, thereby providing reliable, high-value targets for precision breeding programs aimed at developing climate-resilient cultivars.
Materials and methods: To achieve a robust overview, we employed a comprehensive meta-analysis approach utilizing transcriptomic (microarray) data archived in the NCBI Gene Expression Omnibus (GEO). Two high-quality datasets were curated for this study: GSE16401, which contrasts the salt-tolerant tomato genotype PL36 against the sensitive ‘Money Maker’ cultivar, and GSE58603, which compares the salt-tolerant rice genotype PL177 with the sensitive IR64 variety. Differential gene expression (DGE) analysis was rigorously performed using the GEO2R analytical platform, applying strict statistical thresholds of |log2FC| ≥ 1 and a False Discovery Rate (FDR) ≤ 0.05 to ensure the reliability of the identified candidates. Differentially Expressed Genes (DEGs) were categorized into conserved and species-specific sets using Venny 2.1.0. Subsequently, to decipher the complex biological roles and the broader metabolic frameworks involved in salinity adaptation, we conducted functional enrichment analyses, specifically Gene Ontology (GO) and KEGG pathway mapping, using WebGestalt 2024.
Results: Our analysis unveiled distinct transcriptomic signatures that clearly differentiate tolerant genotypes from their sensitive counterparts in both species. In tolerant genotypes, we observed a sophisticated and highly coordinated upregulation of genes involved in critical physiological processes, including cell wall remodeling, osmotic adjustment (notably P5CS and TPS pathways), and the mobilization of secondary metabolites. Critically, key ion transporters, particularly members of the HKT and NHX families, were significantly upregulated, underscoring their pivotal role in maintaining ion homeostasis under osmotic stress. Furthermore, the robust expression of antioxidant defense genes—including various SOD, CAT, and APX isoforms—highlighted a proactive strategy to mitigate salt-induced oxidative damage. We also identified several transcription factor families, such as DREB, NAC, and WRKY, as central hubs regulating the salt-stress response network. Conversely, sensitive genotypes displayed a pronounced downregulation in genes fundamental to photosynthesis, carbon metabolism, and hormonal signaling pathways, suggesting a catastrophic breakdown in physiological coordination and metabolic homeostasis under high-salinity conditions.
Conclusion: The findings of this research provide a comprehensive and integrative landscape of the molecular machinery governing salt tolerance in two evolutionary distinct, yet economically vital, crops. The identification of shared pathways—specifically those related to antioxidant capacity, osmotic regulation, and transcriptional control—suggests a fundamental “toolkit” that plants utilize for salinity adaptation. These results offer a set of validated molecular candidates for enhancing salt tolerance through advanced biotechnological tools, such as genomic selection or targeted genome editing. Ultimately, this study offers a strategic roadmap for breeders and biotechnologists to accelerate the development of resilient crop varieties capable of thriving in increasingly challenging and deteriorating environmental conditions.

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References

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Cereal Biotechnology and Biochemistry
Volume 4, Issue 4 - Serial Number 4
December 2025
Pages 568-588

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