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Peer-reviewedCC BY 4.0International Journal of Molecular Sciences

Genome-Wide Identification and In Silico Characterization of the Salt Overly Sensitive 3/Calcineurin B-like (GhSOS3) Gene Family in Upland Cotton (Gossypium hirsutum L.) and Expression Profiling of Two Members Under Drought, Salt and Heat Stress

  • Laraib Iqra1
  • Muhammad Naveed Shahid1
  • Muhammad Nadeem Shah2
  • Umar Akram3
  • Dragana Božić4
  • Imran Haider5,6
  • Yuncai Hu7
  • Muhammad Bilawal Junaid8
  • Salah El-Hendawy8
8 affiliations
  1. 1Department of Botany, Division of Science and Technology, University of Education, Lahore 54000, Pakistan
  2. 2Merrillville Education Center, Indiana Wesleyan University, 8415 Georgia St, Merrillville, IN 46410, USA
  3. 3The Institute of Plant Breeding and Biotechnology (IPBB), MNS-University of Agriculture, Multan 60000, Pakistan
  4. 4Faculty of Agriculture, University of Belgrade, Nemanjina 6, 11080 Belgrade, Serbia
  5. 5National Research Center of Intercropping, The Islamia University of Bahawalpur, Bahawlpur 63100, Pakistan
  6. 6Department of Biology, Nakhchivan State University, Nakhchivan 85354, Azerbaijan
  7. 7Precision Agriculture Laboratory, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
  8. 8Department of Plant Production, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
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Abstract

Upland cotton (Gossypium hirsutum L.) is a global cash crop cultivated extensively for its high-quality fiber and oil-rich seeds. Several gene families are involved in the regulatory pathways that enable plants to acclimate to adverse abiotic stresses. One such gene family is the Calcineurin B-like (CBL)/Salt Overly Sensitive-3 (SOS3) family of calcium-sensor proteins associated with plant signaling. Although GhSOS3 has previously been associated with salt–alkali stress responses in cotton, a family level genomic characterization of SOS3-like genes in the allotetraploid G. hirsutum genome has not been reported. We performed in silico characterization of the GhSOS3 gene family, including gene architecture, phylogenetic relationships, protein characterization, selection pressure, promoter elements, collinearity, chromosomal position, and protein structure modeling. This analysis identified five putative GhSOS3 genes. The encoded proteins showed conserved EF-hand-related motifs, with differences in gene structure, predicted physicochemical properties, and motif composition. Putative abscisic acid-responsive (ABRE), salicylic acid-responsive (SARE), drought stress-responsive (DSRE) and gibberellin-responsive (GRE) elements predicted in the promoters suggest that the GhSOS3 genes may be transcriptionally responsive to abiotic stress-related signals; however, these predictions require experimental validation. Experimentally, qPCR analysis showed stress- and time-dependent changes in the transcript abundance of GhSOS3-2 and GhSOS3-3 under drought, salt, and heat treatments in three cotton genotypes, indicating differential transcriptional responses to these stress conditions. Collectively, these findings establish a genomic and expression framework for future functional studies of GhSOS3 candidates in calcium-mediated stress responses in cotton.

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Cite

BibTeXRIS
BibTeX
@article{iqra2026genomewide,
  title = {{Genome-Wide Identification and In Silico Characterization of the Salt Overly Sensitive 3/Calcineurin B-like (GhSOS3) Gene Family in Upland Cotton (Gossypium hirsutum L.) and Expression Profiling of Two Members Under Drought, Salt and Heat Stress}},
  author = {Laraib Iqra and Muhammad Naveed Shahid and Muhammad Nadeem Shah and Umar Akram and Dragana Božić and Imran Haider and Yuncai Hu and Muhammad Bilawal Junaid and Salah El-Hendawy},
  journal = {International Journal of Molecular Sciences},
  year = {2026},
  month = oct,
  doi = {10.3390/ijms27219561},
  url = {https://www.mdpi.com/1422-0067/27/21/9561},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Genome-Wide Identification and In Silico Characterization of the Salt Overly Sensitive 3/Calcineurin B-like (GhSOS3) Gene Family in Upland Cotton (Gossypium hirsutum L.) and Expression Profiling of Two Members Under Drought, Salt and Heat Stress
AU  - Laraib Iqra
AU  - Muhammad Naveed Shahid
AU  - Muhammad Nadeem Shah
AU  - Umar Akram
AU  - Dragana Božić
AU  - Imran Haider
AU  - Yuncai Hu
AU  - Muhammad Bilawal Junaid
AU  - Salah El-Hendawy
PY  - 2026
DA  - 2026/10/26
JO  - International Journal of Molecular Sciences
DO  - 10.3390/ijms27219561
UR  - https://www.mdpi.com/1422-0067/27/21/9561
AB  - Upland cotton (Gossypium hirsutum L.) is a global cash crop cultivated extensively for its high-quality fiber and oil-rich seeds. Several gene families are involved in the regulatory pathways that enable plants to acclimate to adverse abiotic stresses. One such gene family is the Calcineurin B-like (CBL)/Salt Overly Sensitive-3 (SOS3) family of calcium-sensor proteins associated with plant signaling. Although GhSOS3 has previously been associated with salt–alkali stress responses in cotton, a family level genomic characterization of SOS3-like genes in the allotetraploid G. hirsutum genome has not been reported. We performed in silico characterization of the GhSOS3 gene family, including gene architecture, phylogenetic relationships, protein characterization, selection pressure, promoter elements, collinearity, chromosomal position, and protein structure modeling. This analysis identified five putative GhSOS3 genes. The encoded proteins showed conserved EF-hand-related motifs, with differences in gene structure, predicted physicochemical properties, and motif composition. Putative abscisic acid-responsive (ABRE), salicylic acid-responsive (SARE), drought stress-responsive (DSRE) and gibberellin-responsive (GRE) elements predicted in the promoters suggest that the GhSOS3 genes may be transcriptionally responsive to abiotic stress-related signals; however, these predictions require experimental validation. Experimentally, qPCR analysis showed stress- and time-dependent changes in the transcript abundance of GhSOS3-2 and GhSOS3-3 under drought, salt, and heat treatments in three cotton genotypes, indicating differential transcriptional responses to these stress conditions. Collectively, these findings establish a genomic and expression framework for future functional studies of GhSOS3 candidates in calcium-mediated stress responses in cotton.
SN  - 1422-0067
ER  -