Research Article
Open Access
Genome-Wide Identification and Expression Profiling of the SBP-box Gene Family in Medicago truncatula
1
Department of Biotechnology, University of Okara, Okara 56300, Pakistan
2
Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh 11451, Saudi Arabia
3
Department of Forest Protection, College of Forestry and Grassland, Nanjing Forestry University, Nanjing 210037, China
4
Bahauddin Zakariya University, Multan 60800, Pakistan
5
Shanxi Medical University (Zhongdu Campus), Jinzhong 030600, China
6
State Key Laboratory of Tree Genetics and Breeding, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
* Corresponding Author:
Hadia Hussain,
[email protected]
Volume 1, Issue 2
2026
Received: 28 March 2026
Revised: 26 June 2026
Accepted: 28 June 2026
Published: 10 August 2026
Article Information
Abstract
The Squamosa Promoter Binding Protein (SBP) family comprises plant-specific transcription factors widely distributed across green plant lineages and holds significant value for agricultural improvement by regulating key traits including yield, flowering, and stress tolerance. Here, we performed a genome-wide analysis of Medicago truncatula and identified 22 SBP-box genes (MtSBP). These genes are irregularly distributed across seven chromosomes, with chromosome 6 devoid of any SBP-box gene. Sequence alignment confirmed that all MtSBP proteins share conserved nuclear localization signals and two zinc finger structures essential for transcriptional regulation. Phylogenetic analysis grouped these genes into seven subgroups, supported by conserved domain organization, motif composition, and gene structure. Gene Ontology analysis indicated that most MtSBP genes are involved in biological regulation. Expression profiling using public RNA-seq data revealed variable patterns across different nitrogen sources and symbiotic conditions, suggesting roles in nitrogen metabolism, symbiosis, and growth. Overall, this study provides a comprehensive overview of the SBP-box family in M. truncatula and identifies candidate genes for future functional studies on legume growth and nitrogen-use efficiency.
Graphical Abstract
Keywords
Medicago truncatula
SBP-box gene family
phylogenetic analysis
Gene Ontology
expression analysis
nitrogen utilization
symbiotic interaction
Data Availability Statement
Data will be made available on request.
Funding
This work was supported without any funding.
Conflicts of Interest
Hadia Hussain served as an Editorial Board Member of the Plant Innovation Journal at the time of manuscript submission. To ensure the integrity of the peer-review process, Hadia Hussain was not involved in the editorial handling, peer review, or decision-making process for this manuscript, which was handled independently by another editor. The remaining authors declare no conflicts of interest.
AI Use Statement
The authors declare that no generative AI was used in the preparation of this manuscript.
Ethical Approval and Consent to Participate
Not applicable.
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APA Style
Noor, M., Afzal, M., Dilshad, A., Awais, M., Haris, S., Mehar, I., & Hussain, H. (2026). Genome-Wide Identification and Expression Profiling of the SBP-box Gene Family in Medicago truncatula. Plant Innovation Journal, 1(2), 99-117. https://doi.org/10.62762/PIJ.2026.672525
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TY - JOUR AU - Noor, Maryam AU - Afzal, Muhammad AU - Dilshad, Ameena AU - Awais, Muhammad AU - Haris, Sial AU - Mehar, Iqra AU - Hussain, Hadia PY - 2026 DA - 2026/08/10 TI - Genome-Wide Identification and Expression Profiling of the SBP-box Gene Family in Medicago truncatula JO - Plant Innovation Journal T2 - Plant Innovation Journal JF - Plant Innovation Journal VL - 1 IS - 2 SP - 99 EP - 117 DO - 10.62762/PIJ.2026.672525 UR - https://www.icck.org/article/abs/PIJ.2026.672525 KW - Medicago truncatula KW - SBP-box gene family KW - phylogenetic analysis KW - Gene Ontology KW - expression analysis KW - nitrogen utilization KW - symbiotic interaction AB - The Squamosa Promoter Binding Protein (SBP) family comprises plant-specific transcription factors widely distributed across green plant lineages and holds significant value for agricultural improvement by regulating key traits including yield, flowering, and stress tolerance. Here, we performed a genome-wide analysis of Medicago truncatula and identified 22 SBP-box genes (MtSBP). These genes are irregularly distributed across seven chromosomes, with chromosome 6 devoid of any SBP-box gene. Sequence alignment confirmed that all MtSBP proteins share conserved nuclear localization signals and two zinc finger structures essential for transcriptional regulation. Phylogenetic analysis grouped these genes into seven subgroups, supported by conserved domain organization, motif composition, and gene structure. Gene Ontology analysis indicated that most MtSBP genes are involved in biological regulation. Expression profiling using public RNA-seq data revealed variable patterns across different nitrogen sources and symbiotic conditions, suggesting roles in nitrogen metabolism, symbiosis, and growth. Overall, this study provides a comprehensive overview of the SBP-box family in M. truncatula and identifies candidate genes for future functional studies on legume growth and nitrogen-use efficiency. SN - 3142-7596 PB - Institute of Central Computation and Knowledge LA - English ER -
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@article{Noor2026GenomeWide,
author = {Maryam Noor and Muhammad Afzal and Ameena Dilshad and Muhammad Awais and Sial Haris and Iqra Mehar and Hadia Hussain},
title = {Genome-Wide Identification and Expression Profiling of the SBP-box Gene Family in Medicago truncatula},
journal = {Plant Innovation Journal},
year = {2026},
volume = {1},
number = {2},
pages = {99-117},
doi = {10.62762/PIJ.2026.672525},
url = {https://www.icck.org/article/abs/PIJ.2026.672525},
abstract = {The Squamosa Promoter Binding Protein (SBP) family comprises plant-specific transcription factors widely distributed across green plant lineages and holds significant value for agricultural improvement by regulating key traits including yield, flowering, and stress tolerance. Here, we performed a genome-wide analysis of Medicago truncatula and identified 22 SBP-box genes (MtSBP). These genes are irregularly distributed across seven chromosomes, with chromosome 6 devoid of any SBP-box gene. Sequence alignment confirmed that all MtSBP proteins share conserved nuclear localization signals and two zinc finger structures essential for transcriptional regulation. Phylogenetic analysis grouped these genes into seven subgroups, supported by conserved domain organization, motif composition, and gene structure. Gene Ontology analysis indicated that most MtSBP genes are involved in biological regulation. Expression profiling using public RNA-seq data revealed variable patterns across different nitrogen sources and symbiotic conditions, suggesting roles in nitrogen metabolism, symbiosis, and growth. Overall, this study provides a comprehensive overview of the SBP-box family in M. truncatula and identifies candidate genes for future functional studies on legume growth and nitrogen-use efficiency.},
keywords = {Medicago truncatula, SBP-box gene family, phylogenetic analysis, Gene Ontology, expression analysis, nitrogen utilization, symbiotic interaction},
issn = {3142-7596},
publisher = {Institute of Central Computation and Knowledge}
}
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