Abstract
BACKGROUND: Lipoxygenases (LOXs) catalyze polyunsaturated fatty acid oxygenation and regulate plant stress responses and oxylipin biosynthesis. This study provides comprehensive genome-wide characterization of the soybean LOX gene family, revealing unprecedented expansion and functional diversification. METHODS: We identified unique GmLOX gene loci through systematic database searches and domain analysis, selecting representative isoforms to avoid transcript redundancy. Phylogenetic analysis compared 43 GmLOX with 6 AtLOX proteins. Protein structures, conserved domains, promoter cis-regulatory elements (2,000 bp upstream), and synteny relationships were characterized. Expression profiling under four abiotic stresses (alkaline, drought, heat, salt) across six time points (0-24 h) was performed using qRT-PCR. RESULTS: Genes distribute unevenly across 10 chromosomes, with highest densities on Gm10 (11 genes), Gm08 (9 genes), and Gm07 (8 genes). Phylogenetic analysis revealed six evolutionary clades with soybean-specific expansion. Structural analysis showed 92% encode full-length proteins (average 887 amino acids) with conserved PLAT/LH2 (97%) and catalytic domains. Promoter analysis identified 23 regulatory element categories, including hormone-responsive (auxin 97%, gibberellin 89%, ABA 94%), stress-responsive (95%), and light-responsive elements (100%). Synteny analysis demonstrated ancient whole-genome duplications and recent tandem duplications drove expansion. Expression profiling revealed five functional categories: alkaline-specific, drought-dominant, heat-specific, salt-responsive, and multi-stress responsive genes. GmLOX16 showed exceptional multi-stress responsiveness (40-fold salt, 38-fold alkaline), GmLOX13 displayed strongest heat response (20-fold), and GmLOX17 exhibited peak drought sensitivity (7-fold). CONCLUSION: Soybean possesses the largest crop LOX family with remarkable functional diversification maintained under strong selective pressure (92% functional retention). Key stress-responsive genes, particularly GmLOX16 and GmLOX13, represent valuable targets for molecular breeding to enhance climate resilience, providing critical genetic resources for sustainable crop improvement.