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Background <p>Vigna radiata (mungbean) is a nutritionally valuable legume crop with notable stress resilience. However, the molecular basis of its salt tolerance remains poorly understood. The Chloride Channel (CLC) protein family, comprising Cl⁻ channels and Cl⁻/H⁺ antiporters, plays crucial roles in anion transport and salt stress regulation in plants. Despite their significance, the CLC gene family has not been systematically investigated in mungbean.</p> Results <p>We performed a genome-wide identification and characterization of <i>CLC</i> genes in mungbean. Seven putative <i>VrCLC</i> genes were identified through conserved domain searches. Phylogenetic analysis placed VrCLC members in close evolutionary proximity to legume CLCs, particularly from soybean. Motif analysis revealed conserved acidic/basic residues and glutamates essential for Cl⁻/H⁺ antiport, while structural modelling confirmed canonical α-helical pores, ligand-binding sites, and CLC/CBS domains. Promoter analysis identified multiple hormone (ABREs- Abscisic Acid Responsive Elements, AF1- auxin-responsive factor binding site) and stress-responsive (MBS-MYB binding sites, STRE-stress response elements, ARE-anaerobic responsive element) cis-elements. qRT-PCR expression profiling revealed that under 100&#xa0;mM NaCl treatment,&#xa0;<i>VrCLC-b1</i>&#xa0;(in leaf and root) and&#xa0;<i>VrCLC-g</i>&#xa0;(in flower) were upregulated by approximately fourfold, whereas under 200&#xa0;mM NaCl,&#xa0;<i>VrCLC-e</i>&#xa0;showed more than a threefold induction in roots. Chloride accumulation assays showed maximum Cl⁻ accumulation in leaves and stems, while root nodules and seeds exhibited no significant change under salt stress. These findings suggest that tissue-specific expression among <i>VrCLC</i> genes may influence differential chloride distribution patterns in mungbean.</p> Conclusion <p>This study provides the first comprehensive genome-wide analysis of the <i>CLC</i> gene family in mungbean and highlights their potential roles in salt stress adaptation. These findings lay a foundation for future functional validation and provide potential molecular targets for marker-assisted selection and genome editing aimed at improving salinity tolerance in mungbean.</p>

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Genome-wide identification, expression and evolutionary analysis of the CLC gene family in Vigna radiata L. reveals its roles in salt resistance

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年12月9日

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  • Ashwini Talakayala,
  • Dhanasekar Divya,
  • P. B. Kirti,
  • Isha Sharma

摘要

Background

Vigna radiata (mungbean) is a nutritionally valuable legume crop with notable stress resilience. However, the molecular basis of its salt tolerance remains poorly understood. The Chloride Channel (CLC) protein family, comprising Cl⁻ channels and Cl⁻/H⁺ antiporters, plays crucial roles in anion transport and salt stress regulation in plants. Despite their significance, the CLC gene family has not been systematically investigated in mungbean.

Results

We performed a genome-wide identification and characterization of CLC genes in mungbean. Seven putative VrCLC genes were identified through conserved domain searches. Phylogenetic analysis placed VrCLC members in close evolutionary proximity to legume CLCs, particularly from soybean. Motif analysis revealed conserved acidic/basic residues and glutamates essential for Cl⁻/H⁺ antiport, while structural modelling confirmed canonical α-helical pores, ligand-binding sites, and CLC/CBS domains. Promoter analysis identified multiple hormone (ABREs- Abscisic Acid Responsive Elements, AF1- auxin-responsive factor binding site) and stress-responsive (MBS-MYB binding sites, STRE-stress response elements, ARE-anaerobic responsive element) cis-elements. qRT-PCR expression profiling revealed that under 100 mM NaCl treatment, VrCLC-b1 (in leaf and root) and VrCLC-g (in flower) were upregulated by approximately fourfold, whereas under 200 mM NaCl, VrCLC-e showed more than a threefold induction in roots. Chloride accumulation assays showed maximum Cl⁻ accumulation in leaves and stems, while root nodules and seeds exhibited no significant change under salt stress. These findings suggest that tissue-specific expression among VrCLC genes may influence differential chloride distribution patterns in mungbean.

Conclusion

This study provides the first comprehensive genome-wide analysis of the CLC gene family in mungbean and highlights their potential roles in salt stress adaptation. These findings lay a foundation for future functional validation and provide potential molecular targets for marker-assisted selection and genome editing aimed at improving salinity tolerance in mungbean.