Genome-wide Identification and Characterization of Stress-responsive Genomic Elements with Special Reference to the RD22 Gene Family in Faba Bean (Vicia faba L.

Abstract

Background: Abiotic stresses, particularly drought and osmotic stress, severely constrain the productivity of faba bean (Vicia faba L.), one of the most important cool-season food legumes globally. The RD22 (Responsive to Dehydration 22) gene family encodes hydrophilic proteins that play pivotal roles in abscisic acid (ABA)-dependent stress signaling pathways. Despite the agronomic significance of faba bean, the RD22 gene family remains uncharacterized at the genome-wide level. Objective: To identify, characterize, and comprehensively analyze the RD22 gene family in Vicia faba through an integrated in silico approach. Methods: Using the recently available V. faba cv. Hedin2 reference genome, we conducted a genome-wide survey of RD22-like genes. Forty-four putative VfRD22 genes were identified and subjected to comprehensive bioinformatic analyses including conserved domain identification (Pfam/InterProScan), motif analysis (MEME Suite), physicochemical property prediction (ProtParam), subcellular localization prediction (WoLF PSORT), and phylogenetic reconstruction. Results: The 44 VfRD22 genes were distributed across all six chromosomes and unplaced scaffolds, encoding proteins ranging from 117 to 634 amino acids (mean: 332.9 ± 143.9 aa). All proteins were predicted to be hydrophilic (GRAVY: −0.291 ± 0.206) with 65.1% classified as stable (instability index < 40). Conserved domain analysis revealed that all members harbored the characteristic BURP domain, with six genes additionally containing BURP superfamily signatures. Three highly conserved motifs were identified across all family members. Subcellular localization prediction indicated predominant extracellular and cytoplasmic localization, consistent with secreted stress-responsive proteins. Phylogenetic analysis revealed five distinct clades, with chromosome 1 harboring a notable tandem duplication cluster (VfRD22.7–VfRD22.15). Conclusion: This study provides the first comprehensive genome-wide characterization of the RD22 gene family in faba bean, establishing a foundational genomic resource for understanding ABA-mediated dehydration responses and for the development of stress-resilient faba bean varieties through marker-assisted breeding and transgenic approaches.