Identification and expression analysis of SBP-Box-like (SPL) gene family disclose their contribution to abiotic stress and flower budding in pigeon pea (Cajanus cajan)

Tayyaba Shaheen; Abdul Rehman; Amany H. A. Abeed; Muhammad Waqas; Asad Aslam; Farrukh Azeem; Muhammad Qasim; Muhammad Afzal; Muhammad Farooq Azhar; Kotb A. Attia; Asmaa M. Abushady; Sezai Ercisli; Nazia Nahid

doi:10.1071/FP23237

RESEARCH ARTICLE

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Identification and expression analysis of SBP-Box-like (SPL) gene family disclose their contribution to abiotic stress and flower budding in pigeon pea (Cajanus cajan)

Tayyaba Shaheen ^A , Abdul Rehman

^A , Amany H. A. Abeed ^B , Muhammad Waqas ^A , Asad Aslam ^C , Farrukh Azeem

^A ^* , Muhammad Qasim ^A , Muhammad Afzal ^A , Muhammad Farooq Azhar ^D , Kotb A. Attia

^E , Asmaa M. Abushady ^F ^G , Sezai Ercisli ^H and Nazia Nahid

^A ^*

+ Author Affiliations

- Author Affiliations

^A Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan.

^B Department of Botany and Microbiology, Faculty of Science, Assiut University, Assiut 71516, Egypt.

^C Key Laboratory for Sustainable Forest Ecosystem Management – Ministry of Education, College of Forestry, Northeast Forestry University, Harbin 150040, China.

^D Department of Forestry and Range Management, Faculty of Agricultural Sciences and Technology, Bahauddin Zakaria University, Multan 60800, Pakistan.

^E Department of Biochemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh, Riyadh 11451, Saudi Arabia.

^F Biotechnology School, Nile University, 26th July Corridor, Sheikh Zayed City, Giza 12588, Egypt.

^G Department of Genetics, Agriculture College, Ain Shams University, Cairo, Egypt.

^H Department of Horticulture, Faculty of Agriculture, Ataturk University, Erzurum 25240, Turkey.

^* Correspondence to: farrukh@gcuf.edu.pk, nazianahid@gmail.com

Handling Editor: Sajid Fiaz

Functional Plant Biology 51, FP23237 https://doi.org/10.1071/FP23237

Submitted: 9 October 2023 Accepted: 25 December 2023 Published: 15 February 2024

Abstract

The SPL gene family (for Squamosa Promoter-binding like Proteins) represents specific transcription factors that have significant roles in abiotic stress tolerance, development and the growth processes of different plants, including initiation of the leaf, branching and development of shoot and fruits. The SPL gene family has been studied in different plant species; however, its role is not yet fully explored in pigeon pea (Cajanus cajan). In the present study, 11 members of the CcSPL gene family were identified in C. cajan. The identified SPLs were classified into nine groups based on a phylogenetic analysis involving SPL protein sequences from C. cajan, Arabidopsis thaliana, Cicer arietinum, Glycine max, Phaseolus vulgaris, Vigna unguiculata and Arachis hypogaea. Further, the identification of gene structure, motif analysis, domain analysis and presence of cis-regulatory elements in the SPL family members were studied. Based on RNA-sequencing data, gene expression analysis was performed, revealing that CcSPL2.1, 3 and 13A were significantly upregulated for salt-tolerance and CcSPL14 and 15 were upregulated in a salt-susceptible cultivar. Real-time qPCR validation indicated that CcSPL3, 4, 6 and 13A were upregulated under salt stress conditions. Therefore, molecular docking was performed against the proteins of two highly expressed genes (CcSPL3 and CcSPL14) with three ligands: abscisic acid, gibberellic acid and indole-3-acetic acid. Afterward, their binding affinity was obtained and three-dimensional structures were predicted. In the future, our study may open avenues for harnessing CcSPL genes in pigeon pea for enhanced abiotic stress resistance and developmental traits.

Keywords: bioinformatics, genome-wide analysis, molecular docking, molecular interaction analysis, next-generation sequencing, omics data analysis, plant hormone, salinity stress, structure prediction.

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Identification and expression analysis of SBP-Box-like (SPL) gene family disclose their contribution to abiotic stress and flower budding in pigeon pea (Cajanus cajan)

Abstract

References

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