Molecular Characterization of Omega-3 Fatty Acid Desaturases Reveals Functional Conservation and Their Pivotal Role in Salt and Temperature Stress Adaptation in Arabidopsis thaliana

Omega-3 fatty acid desaturases (FAD3, FAD7, and FAD8) are key enzymes responsible for the production of α-linolenic acid (ALA), which is an essential polyunsaturated fatty acid regulating membrane stability and serves as a precursor for jasmonic acid. In this study, we performed a comprehensive genome-wide molecular characterization of omega-3 fatty acid desaturase genes across seven plant species. Phylogenetic analysis placed FAD3 and FAD7/FAD8 proteins in distinct clades, indicating functional divergence despite strong sequence conservation. Gene structure analysis revealed conserved exon–intron formation with a few unique features. Multiple sequence alignment and motif analysis revealed high sequence similarity with three histidine-rich boxes responsible for catalytic activity. Cis-regulatory elements revealed the abundance of light-responsive and ABA-responsive elements such as Box4 and ABRE, suggesting environmentally induced responses of omega-3 fatty acid desaturase genes. Moreover, q-RT PCR analysis revealed that the combined stresses of temperature and salt strongly influence the transcript levels of omega-3 fatty acid desaturase (FAD3, FAD7, and FAD8) in Arabidopsis thaliana; among them, the FAD8 gene displayed significantly higher expression levels under salt stress conditions, especially at 22 °C temperature, indicating its possible leading role in stress adaptation. Furthermore, comparative promoter analysis revealed enrichment of stress-responsive motifs in the promoter regions of AtFAD7 and AtFAD8, whereas AtFAD3 contained more ABA-responsive elements. In addition, Pearson correlation analysis revealed a temperature-dependent relationship between promoter motifs and gene expression under salt stress at 31 °C in Arabidopsis thaliana. Overall, these findings suggest that omega-3 fatty acid desaturases are highly conserved yet transcriptionally dynamic under environmental conditions. This study provides a foundation for future genetic and functional studies of omega-3 fatty acid desaturase genes aimed at enhancing stress adaptation by targeting and regulating fatty acid metabolism.