Metabolomics and machine learning technique reveals that germination enhances the multi-nutritional properties of pigmented rice

Enhancing the dietary properties of rice is crucial to contribute to alleviating hidden hunger and non-communicable diseases in rice-consuming countries. Germination is a bioprocessing approach to increase the bioavailability of nutrients in the germinated sprouts. However, there is scarce information on how germination impacts the overall nutritional profile of pigmented rice sprouts. Herein, we demonstrated that germination could increase certain dietary compounds, such as free phenolics, GABA, and micronutrients (Ca, Na, Fe, Zn, riboflavin, and biotin. In a) and induce new flavonoid glycosides. Metabolomic analysis revealed the preferential accumulation of flavonoid compounds in the germination process. Genome-wide association studies of the altered metabolites revealed the activation of specific genes responsible for increasing certain flavonoid compounds. Notably, the activation of the CHS1 gene boosted the naringenin and the compounds along this pathway. Likewise, the UGT gene is responsible for the formation of flavonoid glycosides derived from kaempferol, caffeic acid, ferulic acid, and quercetin. Haplotype analyses showed a significant difference (P < 0.05) between alleles associated with this genetic region. Genetic markers associated with these flavonoids were incorporated into the random forest model, improving the accuracy of prediction of multi-nutritional properties from 89.7% to 97.7%. Consistent with this feature, the improved model has a faster prediction speed in a shorter training time. Deploying this knowledge to breed rice with multinutritional properties will be timely to address double burden nutritional challenges.