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Plant Science Today (PST)

Research Articles

Vol. 13 No. 2 (2026)

Anatomic study, comprehensive meta-analysis and co-expression network analysis utilised in identifying candidate genes that play a role in abiotic stress response in tomatoes (Solanum lycopersicum L.)

DOI
https://doi.org/10.14719/pst.9907
Submitted
8 June 2025
Published
04-05-2026 — Updated on 13-05-2026
Versions

Abstract

Solanum lycopersicum L. (tomato) is an economically important crop worldwide. However, its productivity is frequently constrained by abiotic stresses such as salinity, heat and drought, which negatively impact plant growth and yield. This study aimed to identify candidate genes and associated anatomical traits that contribute to abiotic stress tolerance in tomato, using a combination of physiological, anatomical and transcriptomic approaches. Two tomato varieties were subjected to varying NaCl concentrations. Morphological and anatomical traits were recorded and analysed. Simultaneously, a meta-analysis of microarray data was performed to identify genes involved in salinity, heat and drought responses. Gene co-expression network analysis was used to identify hub genes linked to stress tolerance. Salinity significantly reduced germination rates in both varieties. Stress induced structural changes such as increased cell layer numbers, thicker cell walls and fewer vascular bundles. Meta-analysis revealed that the Universal Stress Protein (USP) gene family plays a central role in abiotic stress responses, showing tissue-specific differential expression. Activation of amino acid metabolism and calcium channels helped maintain cytoplasmic calcium homeostasis in tolerant plants. Overall, 2092 differentially expressed genes were identified, with key hub genes involved in calcium signalling, carrier proteins, the Salt Overly Sensitive (SOS) pathway, vesicle trafficking and redox regulation. Integrating anatomical, physiological and transcriptomic data, this study enhances understanding of tomato's stress tolerance mechanisms. It highlights the significance of USPs and calcium signalling in stress adaptation, providing targets for breeding. This work uniquely links anatomical traits with gene expression, offering new insights into multi-stress responses."

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