Journal of Horticulture and Agricultural Sciences

Vol. 2 No. 02 (2025): Journal of Horticulture and Agricultural Sciences (JHAS)
Articles

In Silico Analysis of Genes and Promoter regions elements in Brassica napus for Agrobacterium-Mediated Genetic Transformation

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  • Faizan Ali,
  • Allah jurio khaskheli,
  • Shahla Baloch,
  • Muharam Ali,
  • Kaleem Kakar,
  • Muhazzam Anwar,
  • Amir Ali,
  • Ghulam Nabi Lashari
Faizan Ali
Department of Biotechnology, Sindh Agriculture University Tandojam
Allah jurio khaskheli
Department of Biotechnology, Sindh Agriculture University Tandojam
Shahla Baloch
Associate Professor
Muharam Ali
Professor
Kaleem Kakar
Agriculture Extension, Killa Abdullah
Muhazzam Anwar
Department of Horticulture, Balouchistan Agriculture College Quetta
Amir Ali
Institute of Horticultural Sciences, University of Agriculture Faisalabad
Ghulam Nabi Lashari
Department of Horticulture, Sindh Agriculture University Tandojam, Pakistan
DOI: https://doi.org/10.63459/jhas.2025.2.23

Published 2025-12-16

Keywords

  • Agrobacterium-Mediated Genetic Transformation,
  • Brassica napus,
  • cis regulatory elements,
  • In silico-analysis,
  • Promoter

How to Cite

Imtian, F., khaskheli, A. jurio, Baloch, S., Ali, M. A., Kakar, K., Anwar, M., … Lashari, G. N. (2025). In Silico Analysis of Genes and Promoter regions elements in Brassica napus for Agrobacterium-Mediated Genetic Transformation . Journal of Horticulture and Agricultural Sciences , 2(02), 131–141. https://doi.org/10.63459/jhas.2025.2.23

Copyright (c) 2025 Faizan, Allah jurio khaskheli, Shahla, Muharam Ali, Kaleemullah, Muhazzam Anwar, Amir, Ghulam Nabi

Creative Commons License

This work is licensed under a Creative Commons Attribution 4.0 International License.

Abstract

This study employed in-silico tools to analyze gene sequences and promoter regions in Brassica napus for optimizing Agrobacterium-mediated transformation. Candidate genes, particularly Auxin Response Factor (ARF) genes, were identified through transcriptome mining and validated via BLAST and ORF analysis. Promoter regions (−1500 bp) were screened using PlantCARE and MEME Suite to identify cis-regulatory elements related to stress tolerance and transformation efficiency. Conserved motifs such as ABRE, TATA-box, CAAT-box, and hormone-responsive elements (AuxRE, GARE, and MYB) were identified in key ARF genes (e.g., Bra005465, Bra016492), indicating roles in drought and salinity response. Phylogenetic analysis revealed evolutionary conservation of ARFs across Brassica species and Arabidopsis, supporting their regulatory roles. Non-coding regions, especially UTRs and introns, exhibited variability and included alternative splicing sites and miRNA binding motifs, suggesting complex post-transcriptional regulation. Heatmap and cluster analyses showed coregulation patterns among stress-responsive promoters. Additionally, tissue culture trials identified MS medium with optimized growth regulators as most effective for callus induction and regeneration. This integrated bioinformatics and experimental approach highlights key genetic components for improving transformation efficiency and stress resilience in Brassica napus, laying groundwork for targeted crop improvement strategies

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