Genome-Wide Identification, Abiotic Stress Responses, and Haplotype Variation of the OsMOT Gene Family in Rice

Background Molybdenum (Mo) is an essential trace element for plants, playing critical roles in nitrogen metabolism, hormone biosynthesis, and stress responses. Molybdate transporters (MOTs) mediate molybdate uptake, translocation, and distribution, and are essential for maintaining cellular molybdenum homeostasis. To date, the functional differentiation, abiotic stress response patterns, and genome-wide allelic variation landscape of the MOT family across global rice ( Oryza sativa ) germplasm collections remain poorly understood. Results Through homologous sequence alignment and conserved domain verification, we identified four MOT genes in the Oryza sativa genome, clustered into two subfamilies, MOT1 and MOT2 . All members harbor a transmembrane domain of the major facilitator superfamily (MFS). Phylogenetic, gene structure, and protein 3D structure prediction analyses revealed segmental duplication as the primary driver of family expansion, with the family evolving under dominant purifying selection. The two subfamilies exhibit pronounced divergence in channel geometry and substrate recognition: MOT1 uses a cooperative hydrogen bond-salt bridge network, while MOT2 forms a hydrogen bond interface with few polar residues. Protein-protein interaction network prediction linked the MOT family to the molybdopterin biosynthesis pathway. Tissue expression profiling and abiotic stress qRT-PCR assays revealed spatiotemporal functional divergence between the two subfamilies: OsMOT1; 2 responded rapidly and specifically to salt stress, while OsMOT2;1 responded broadly to multiple abiotic stresses. Haplotype analysis of global rice germplasm whole-genome resequencing data further showed the highest MOT family diversity in the Southeast Asia-South China rice domestication center, with clear indica-japonica differentiation and reduced diversity after transcontinental introduction. Conclusions This study provides insights into the functional differentiation of the rice MOT family from evolutionary, structural, transcriptional, and population genetic perspectives, characterizes the predicted structural features and stress response patterns of the MOT2 subfamily, and uncovers the haplotype distribution and domestication trajectory of MOT genes across global rice germplasms. These findings provide a theoretical basis and candidate genes for improving molybdenum use efficiency and stress tolerance in rice breeding.