Reconstruction of Gene and Protein Networks in Response to Salt Stress in Sunflower (Helianthus annus L.) Using RNA-seq Data

Document Type : Research Paper

Authors

1 Department of Agronomy & Plant Breeding, Faculty of Agronomy Sciences, College of Agriculture & Natural Resources, University of Tehran, Karaj, Iran.

2 Department of Agronomy & Plant breeding, Faculty of Agronomy Sciences, College of Agriculture & Natural Resources, University of Tehran, Karaj, Iran.

3 Professor, Department of Plant Breeding and Biotechnology, Urmia University, Urmia, Iran and Institute of Biotechnology, Urmia University, Urmia, Iran

4 Department of Plant Production and Genetics, Faculty of Agriculture, Urmia University, Urmia, Iran.

Abstract

Objective
Sunflower is one of the most important oilseed products in the world, providing 12% of vegetable oils. Due to the molecular complexity involved in salt stress and its role to physiological and morphological changes in plants, as well as the moderate sensitivity of sunflower to this problem, the purpose of this work is elucidating with priority what affect on the proteins level has a cause-and-effect relationship with tolerance mechanisms.
Materials and methods
FastQC and Trimmomatic were used to process RNA-seq data that was taken from the study by Sharifi et al., (2022). RNA-seq analysis was then carried out using genome-based and de novo assembly techniques. Bowtie2 and Hisat2 were used to map the reads to the reference transcriptome and genome, respectively. RSEM and HT-seq were used to quantify the reads, and edgeR and DE-seq2 were used to identify differentially expressed genes (DEGs). Using the STRING and GeneMANIA databases, DEGs in Arabidopsis were found and incorporated into the Gene Regulatory Networks (GRN) and Protein-Protein Interaction (PPI) networks. Topological analysis of these networks was conducted using 11 algorithms in Cytohubba on Cytoscape, and hub genes were identified. The promoter sequences of these genes were analyzed using Plantcare. Finally, the expression of COP1 gene was evaluated using Real-time PCR.
 
Results
RNA-seq analysis using de novo assembly-based and reference genome-based methods identified 1602 transcripts and 272 genes with distinct expression patterns. Study on GRN and PPI networks led to the discovery of 29 hub genes, including BAK1, ETR1, GER3, HSP70, CDKB2;2, CAS, GRDP1, BSL3, CPN20, AOR, MCM7, DXS, AdoMet-MTases, RCA, CYP90C1, C3H37, CDPK6, Lac1, WRKY50, COP1, PP2C76, CaM-7, Histone H1-3, PPR, LRR-RLK, LACS, LUT5, and Clp5, which play roles in key cellular processes such as plant hormone regulation (ABA, BR, ethylene), MAPK signaling, RNA processing, photosynthesis, stomatal control, protein structure maintenance, and cell cycle. Promoter analysis revealed the existence of important motifs including W-box, TGA-box, ERE, ABRE, MYC, MYB and MBSI and MBS GT-1 motif which led to the co-regulatory role in salt stress response. The real time PCR results of the COP1 gene, which is one of the ABA-activated genes, were consistent with its expression profile from RNA-seq analysis.
Conclusion
The current study through systems biology approach revealed that sunflower directs gene functions in central biological activities, such as plant hormone signaling pathways (ABA, BR and ethylene), MAPK pathway RNA transport, photosynthesis, stomatal function control protein structure stabilization, the cell cycle etc., under salt stress.These results enhance our understanding of the molecular basis of salinity tolerance and can be used to genetically engineer sunflowers for enhanced salinity resistance.

Keywords

References

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Agricultural Biotechnology Journal
Volume 18, Issue 2
February 2026
Pages 69-114

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