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Exploring the genetic potential of Pakistani soybean cultivars through RNA-seq based transcriptome analysis

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Abstract

Background

Soybean is largely grown and considered among the top oilseed crops. Three Pakistani cultivars, NARC-II (N), Swat-84 (S), and Rawal-I (R) were employed for RNA-Seq based transcriptome analysis to explore their genetic potential and performance in our local environment.

Methods and results

We grew the plants in glass house at same conditions and sampled leaves for RNA-Seq analysis in triplicate for each variety. We retrieved 2225 differentially expressed genes (DEGs) between S vs R, 2591 DEGs between S vs N, and 1221 DEGs between R vs N cultvars. These genes consist of transcription factors representing Basic Helix-loop Helix, myeloblastosis, ethylene response factors, and WRKY amino acid motif (WRKY) type major families that were up-regulated. KEGG pathway analysis revealed that MAPK, plant hormone signal transduction, and Phenylpropanoid biosynthesis pathways were the most dominant pathways involved in plant defense and growth. Comparative analysis showed that Swat-84 (S) cultivar had better gene expression among these varieties having higher number of DEGs, where mostly genes related to important phenotypic traits were up regulated.

Conclusions

This is a pilot study to investigate and functionally characterise the DEG involved in the stress response in the cultivars studied.

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Data availability

All RNA-Seq reads have been submitted to the NCBI Sequence Read Archive (SRA) database under accession number PRJNA718712.

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Funding

Higher Education Commission (HEC), Pakistan has provided funds through its NRPU Project No. 7838/Balochistan/NRPU/R&D/HEC/2017.

Author information

Authors and Affiliations

  1. Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan

    Arslan Tariq, Zahra Jabeen, Sumaira Farrakh, Kiran Noreen, Waleed Arshad, Haroon Ahmed & Waseem Haider

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  1. Arslan Tariq
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  2. Zahra Jabeen
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  3. Sumaira Farrakh
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  4. Kiran Noreen
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  5. Waleed Arshad
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  7. Waseem Haider
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Contributions

ZJ and WH designed and executed the experiment. KN grew the plants and did sampling for RNA-Seq, AT and WA did data analysis. HA and SF contributed to manuscript preparation and review.

Corresponding author

Correspondence to Waseem Haider.

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The authors decolor no conflict of interest.

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This article does not contain any studies with human participants or animals performed by any of the authors.

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Supplementary Information

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Supplementary file1 (XLSX 1120 kb)

11033_2021_7104_MOESM2_ESM.pptx

Supplementary Fig. S1 An overview of regulated TFs in three comparisons. a Differentially regulated TFs show that mostly TFs are upregulated. b Venn diagram showing the overall differentially expressed TFs. c The number of TF of different families identified in the DEGs of three comparisons. (PPTX 189 kb)

Supplementary Fig. S2 KEGG pathway enrichment analysis of DEGs of three comparisons. (PPTX 43 kb)

11033_2021_7104_MOESM4_ESM.pptx

Supplementary Fig. S3 a KEGG pathway analysis showing the enrichment of DEGs in “Phenylpropanoid Biosynthesis pathway”. b Heatmap illustrating the expression pattern of DEGs of three comparisons. (PPTX 761 kb)

11033_2021_7104_MOESM5_ESM.pptx

Supplementary Fig. S4 Plant hormone signal transduction pathway showing the expression pattern of three companions. (PPTX 1060 kb)

11033_2021_7104_MOESM6_ESM.pptx

Supplementary Fig. S5 MAPK pathway illustrating the enrichment of DEGs and heatmap showing the expression pattern of all DEGs of three comparisons. (PPTX 974 kb)

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Tariq, A., Jabeen, Z., Farrakh, S. et al. Exploring the genetic potential of Pakistani soybean cultivars through RNA-seq based transcriptome analysis. Mol Biol Rep 49, 2889–2897 (2022). https://doi.org/10.1007/s11033-021-07104-3

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  • DOI: https://doi.org/10.1007/s11033-021-07104-3

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