Natural Variation in the Promoter of OsMOT1;1 Contributes to Differential Molybdenum Accumulation between Indica and Japonica Rice

Understanding genetic differences in nutrient accumulation between indica and japonica subspecies is crucial for utilizing beneficial alleles to enhance genetic improvement. Molybdenum (Mo) is an essential micronutrient for rice growth and development, playing indispensable roles in physiological processes. However, differences in Mo accumulation between indica and japonica have rarely been reported. In this study, field and hydroponic experiments conducted on 529 rice germplasm accessions revealed significant natural divergence in Mo accumulation between indica and japonica, with japonica generally accumulating higher Mo levels than indica. Genome-wide association studies (GWAS) and quantitative trait locus (QTL) analysis revealed that the divergence in Mo accumulation in both subpopulations was primarily driven by the Mo transporter OsMOT1;1. However, all coding region haplotypes of OsMOT1;1 from both indica and japonica displayed comparable Mo transport capability. By contrast, significant differences in OsMOT1;1 expression levels were observed between high-Mo and low-Mo varieties within each subpopulations. Moreover, the overall expression level of OsMOT1;1 was significantly higher in japonica than in indica. Furthermore, we identified several extremely high-Mo rice varieties, whose high Mo levels largely resulted from high expression levels of OsMOT1;1, thus showing great potential for improving Mo efficiency in breeding. These results suggest that natural variation in Mo accumulation between indica and japonica rice is primarily caused by differential expression of OsMOT1;1, highlighting its potential as a target for improving Mo efficiency in rice breeding programs.