Nutritional imbalance has led to many chronic diseases and severely affected people’s quality of life. Developing nutrient-dense crops has emerged as a strategy for improving the current state of human nutritional intake globally. We summarized recent advances in rice biotechnology breeding focusing on increasing micronutrients and active natural products, highlighting the cutting-edge metabolic engineering technologies and strategies employed. We discussed common challenges and potential solutions in metabolic engineering breeding. On this basis, the future development direction of rice nutrient metabolism industrialization was prospected.

Seed plumules comprise multiple developing tissues and are key sites for above-ground plant organ morphogenesis. Here, the spatial expression of genes in developing rice seed plumules was characterized by single-cell transcriptome sequencing in Zhongjiazao 17, a popular Chinese indica rice cultivar. Of 15 cell clusters, 13 were assigned to cell types using marker genes and cluster-specific genes. Marker genes of multiple cell types were expressed in several clusters, suggesting a complex developmental system. Some genes for signaling by phytohormones such as abscisic acid were highly expressed in specific clusters. Various cis-elements in the promoters of genes specifically expressed in cell clusters were calculated, and some key hormone-related motifs were frequent in certain clusters. Spatial expression patterns of genes involved in rapid seed germination, seedling growth, and development were identified. These findings enhanced our understanding of cellular diversity and specialization within plumules of rice, a monocotyledonous model crop.

The mesocotyl, a structure located between the basal part of the seminal root and the coleoptile node of seedlings, contributes to pushing the shoot tip through the soil surface, a function that is essential for the uniform emergence of direct-seeded rice. Its elongation is inhibited by light and induced in darkness. This investigation of an indica rice (P25) with vigorous mesocotyl elongation was aimed at identifying the “omics” basis of its light-induced growth inhibition. A transcriptomic comparison between mesocotyl tissues that had developed in the dark and then been exposed to light identified many differentially expressed genes (DEGs) and differentially abundant microRNAs (miRNAs). Degradome sequencing analysis revealed 27 negative miRNA-target pairs. A co-expression regulatory network was constructed based on the miRNAs, their corresponding targets, and DEGs with a common Gene Ontology term. It suggested that auxin and light, probably antagonistically, affect mesocotyl elongation by regulating polyamine oxidase activity.