Metabolomics and Transcriptomics Reveal Key Metabolism Pathways of Giant Embryo Development in Rice

Rice embryos are rich in high-quality protein, fat, vitamins and minerals, representing the most important nutritional part of brown rice. However, the molecular mechanism of rice embryo development is poorly understood. In this study, map-based cloning, metabolomics, and transcriptomics were applied to explore the giant embryo rice cultivar Dapeimi grown under natural conditions. The map-based cloning results demonstrated that Dapeimi is a novel allelic mutant of GE, and the functional mutation site is a single cytosine deletion in the exon1, which differed from the findings of previous reports. The identification and analysis of differential metabolites indicated that plants lacking the GE mainly promoted amino acid metabolism, energy metabolism, and lipid metabolism pathways in the rice embryo. Changes of gene expression in related metabolic regulatory networks were analyzed, and substantial changes in the transcriptome supported the metabolomics results. By analyzing rice embryo development through a combination of strategies, this research contributes to a greater understanding of the molecular mechanism of rice embryo development, and provides a theoretical foundation for improving rice nutrition and breeding high-nutrition varieties. Overall design: embryo mRNA profiles of 15-day old NIL-D (EG) and NIL-X (CG) were generated by deep sequencing in triplicates