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ORIGINAL RESEARCH article
Front. Plant Sci.
Sec. Plant Abiotic Stress
Volume 16 - 2025 | doi: 10.3389/fpls.2025.1547723
This article is part of the Research Topic Mechanisms of Stress Tolerance in Horticultural Crops: Physiological and Molecular Insights View all 14 articles
CLC gene family in Solanum lycopersicum: genome-wide identification, expression, evolutionary analysis of tomato in response to salinity and Cd stress
Provisionally accepted- 1 Jiangsu Vocational College of Finance and Economics, Huaian, China
- 2 School of Tea & Coffee, Pu’er University, Pu’er, China
- 3 College of Horticulture, South China Agricultural University, Guangzhou, China
Chloride channels (CLCs) play critical roles in anion transport, stress adaptation, and ion homeostasis in plants. Whereas their genomic wide indetification and functional divergence in tomato (Solanum lycopersicum) remain largely unexplored. In this study, we identified nine CLC genes in the tomato genome, classifying them into two evolutionarily distinct clades (Group I and II) based on phylogenetic analysis. Structural dissection revealed conserved transmembrane domains (9-12 TMDs) and motif patterns (e.g., motifs 3/7/9 in Group I), with SlCLC02 exhibiting the largest gene size (27,041 bp). Promoter analysis indicated the presence of key abiotic stress-responsive cis-elements (ABRE, MYB, MYC), aligning with the pronounced transcriptional dynamics of SlCLCs under salinity stress. Notably, qRT-PCR analysis demonstrated that most SlCLC genes (particularly SlCLC05, an ortholog to AtCLCg) exhibited rapid upregulation within 1-4 hours followed by downregulation in roots under salinity treatment, suggesting early stress signaling roles. Likewise, preliminary expression profiling under cadmium stress further identified specific induction of SlCLC07, proposing gene-specific roles in heavy metal detoxification. Strikingly, SlCLC09 lacked collinearity with Arabidopsis/potato homologs, implying lineage-specific diversification. These findings elucidate the SlCLC family's structural diversity, evolutionary constraints, and stress-responsive regulation, providing a framework for targeting specific SlCLC genes (e.g., SlCLC05) to enhance chloride homeostasis in crops under combined salinity and cadmium stress. This study will open a new research direction for genetic crop improvement to ensure protected vegetable production.
Keywords: Solanum lycopersicum, Chloride Channels, abiotic stress, alleviation of stress, anion transport, Chloride ions
Received: 18 Dec 2024; Accepted: 24 Mar 2025.
Copyright: © 2025 Ma, Li, Zaman and Anwar. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Shah Zaman, School of Tea & Coffee, Pu’er University, Pu’er, China
Ali Anwar, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
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