South Asian Research Journal of Biology and Applied Biosciences (SARJBAB)
Volume-8 | Issue-03
Original Research Article
In Silico Genome-wide Identification of Salt Stress-Responsive Genomic Elements with Special Reference to WRKY Genes in Vitis vinifera L
Bharti Chauhan, Arya Ji, Manoj Kumar Sharma, Manoj Kumar Sharma, Sachin Kumar
Published : June 15, 2026
Abstract
Vitis vinifera (grapevine) is a globally significant fruit crop valued for its economic importance, nutritional properties, and adaptability to diverse agro-climatic conditions. However, abiotic stresses, particularly soil salinization, severely constrain its productivity and fruit quality. Transcription factors of the WRKY superfamily play pivotal roles in regulating plant responses to abiotic stress, including salt tolerance. This study presents an integrated bioinformatics pipeline to identify, characterize, and analyze putative salt stress-responsive WRKY genes in V. vinifera. Using Arabidopsis thaliana WRKY8 (UniProt: Q9FL26) as a reference, we performed homology-based screening against the V. vinifera genome via Ensembl Plants BLAST. Candidate sequences underwent rigorous physicochemical profiling (ProtParam), conserved domain analysis (NCBI-CDD), motif elucidation (MEME Suite), phylogenetic reconstruction (MEGA), gene structure visualization (GSDS), and subcellular localization prediction (WoLF PSORT). Iterative filtering based on domain architecture and motif conservation yielded a high-confidence set of WRKY candidates. Phylogenetic analysis revealed diversification across Groups I, II, and III, with evidence of grapevine-specific expansion in Group III. The majority of candidates exhibited predicted nuclear localization, acidic to mildly basic isoelectric points, and thermostable aliphatic indices consistent with transcriptional regulatory functions. Gene structural analysis revealed intron-exon architectural diversity, suggesting evolutionary divergence and potential alternative splicing regulation. This work establishes a foundational genomic framework for understanding WRKY-mediated salt stress signaling in grapevine and identifies candidate targets for future functional validation and translational breeding toward salinity-tolerant cultivars.