Colored rice (black, purple, red and brown) has been consumed in China for nearly 4000 years. Recent research has focused on exploring its nutritional and metabolomic profiles and associated health benefits. Due to the improvement in detection and quantification techniques for health-promoting compounds and their activities, the number of studies has increased significantly. In this regard, a timely and updated review of research on nutritional composition, phytochemistry, and metabolite content and composition can significantly enhance consumer awareness. Here, we present a detailed and up-to-date understanding and comparison of the nutritional and phytochemical (metabolite) composition of colored rice. While earlier literature reviews focus on either single type of colored rice or briefly present nutritional comparison or bioactivities, here we present more detailed nutrient profile comparison (carbohydrates, fats, proteins, amino acids, minerals, and vitamins), together with the most recent comparative data on phytochemicals/metabolites (flavonoids, anthocyanins, fatty acids, amino acids and derivatives, phenolic acids, organic acids, alkaloids, and others). We discuss how metabolomics has broadened the scope of research by providing an increasing number of detected compounds. Moreover, directions on the improvement in colored rice nutritional quality through breeding are also presented. Finally, we present the health-beneficial activities (antioxidant, anti-inflammatory, antimicrobial, hypoglycemic, neuroprotective, anti-aging, and antitumor activities) of different colored rice varieties, together with examples of the clinical trials, and discuss which bioactive substances are correlated with such activities.

Interest in glutinous rice consumption has been expanding in East Asia. However, the extent of metabolite variation between common and glutinous rice has not been fully explored to identify metabolic targets for rice quality improvement. Thus, the objective of this study was to provide insights into the variation of metabolites and nutraceuticals between common and glutinous rice. Two black rice (common rice, BL-N, and glutinous rice, BL-G) and two white rice (common rice, WH-N, and glutinous rice, WH-G) types were analysed via LC-MS-based widely targeted metabolic profiling. We identified 441 and 343 types, including 160 key overlapping differentially accumulated metabolites between BL-N_vs_BL-G and WH-N_vs_WH-G, respectively. Glutinous rice showed a higher relative content of most categories of metabolites, except for quinones (in BL-N) and tannins (in WH-N). Seven vitamins, including B6, B3, B5, B13, isonicotinic acid, N-(beta-D-glucosyl)nicotinate, and 4-pyridoxic acid-O-glucoside, were significantly up-regulated in BL-G compared to BL-N. The biosynthesis of cofactors, zeatin biosynthesis, citrate cycle, amino acid metabolism, alpha-linolenic acid metabolism, and glyoxylate and dicarboxylate metabolism was the most differentially regulated pathway. Key differential metabolites in citrate cycle include citrate, isocitrate, fumarate, malate, succinate, and 2-oxoglutarate; in amino acid metabolism (L-serine, L-cysteine, L-lysine, L-glutamine, L-methionine, and L-tryptophan); and in glycolysis (UDP-glucose, D-glucose-1P, D-glucose-6P, and D-fructose-6P). The data resources in this study may contribute to a better understanding of the function and nutritional value of glutinous rice.

Bacterial blight (BB), caused by Xanthomonas oryzae pv. Oryzae (Xoo), is one of the most devastating diseases in rice worldwide. Common wild rice (Oryza rufipogon Griff.) inhabiting the high-temperature and high-humidity environments of Hainan Island has evolved strong disease resistance through natural selection, representing a valuable genetic reservoir for resistance breeding. However, large-scale characterization of resistance phenotypes, resistance genes, and their combinations remains limited. In this study, we evaluated BB resistance in 1511 Hainan common wild rice accessions against three Xoo strains (HNX004, PXO99^A, and Z173) and analyzed the distribution of ten major known resistance genes (Xa1, Xa3, Xa4, xa5, Xa7, Xa10, xa13, Xa21, Xa23, and Xa27). Phenotypic evaluation revealed distinct strain-specific resistance patterns. Broad-spectrum resistance analysis (defined as moderate resistance or higher) revealed that 35 accessions (2.32%) were resistant to all strains, and 378 accessions (25.02%) showed resistance to two strains. Genotyping of known resistance genes revealed that, except for one accession, which lacked all tested genes but showed resistance to strain PXO99^A, all other accessions carried every tested gene except Xa21 and xa13. Interestingly, different Xoo strains exhibited distinct requirements for resistance genes, revealing a clear strain-specific resistance pattern. Notably, the number of resistance genes did not correlate with resistance level. Instead, specific complementary combinations, particularly Xa1 + Xa10 + Xa23 + Xa4 + Xa7, conferred the strongest broad-spectrum resistance. Our results demonstrate that gene quality and specific complementary combinations are more important than the absolute number of resistance genes. The identified resistant accessions and favorable gene combinations provide valuable resources for rice breeding programs.

To overcome reproductive barriers and utilize beneficial genes from wild rice, total DNA from blast-resistant Oryza officinalis was introduced into elite restorer line R225 via panicle-neck injection (pollen-tube pathway), and after multi-generation selection, the novel restorer ‘Hai Hui 2011′ was developed and crossed with ‘Long Te Fu A’ to produce the hybrid ‘Te You 2011’. Multi-year field trials in Hainan showed that ‘Te You 2011’ yielded 8.48–8.70 t/ha in early seasons, with increases of 2.23–9.70% over the check ‘Te You 009’, and an 8.36% increase in late season, indicating that it has good yield potential. SSR marker RM154 detected a 183bp specific fragment shared with the wild donor in ‘Hai Hui 2011’ and Oryza officinalis but absent in ‘R225’, providing preliminary evidence of genetic relatedness. Marker alleles associated with four known blast resistance loci (Pib, Pik, Pi54, and Pi33) were detected in both ‘Hai Hui 2011’ and ‘Te You 2011’. Under natural field conditions and artificial inoculation with the predominant Hainan YF race group, both lines showed strong resistance. These findings preliminarily suggest that panicle-neck injection of exogenous total DNA may be a potential approach for introducing wild-rice genetic material, and that ‘Te You 2011’ is a promising high-yielding, blast-resistant hybrid for tropical and subtropical rice regions.

Shanlan upland rice is a unique rice resource of the Li and Miao ethnic group in China and serves as a valuable gene pool adapted to tropical mountainous environments. To explore the genetic relationships of Shanlan upland rice from different geographical origins, 21 SSR markers were used to conduct genetic diversity and population structure analyses on 288 Shanlan upland rice accessions from 10 provinces (regions) in southern China. Results: The study revealed that the mean values of effective allele number (Ne), Shannon’s information index (I), polymorphic information content (PIC), observed heterozygosity (Ho), and expected heterozygosity (He) for Shanlan upland rice were 1.616, 0.491, 0.74, 0.129, and 0.306, respectively. Genetic diversity analysis and molecular variance analysis (AMOVA) showed that the main source of variation between materials was the individual Shanlan upland rice plants. Genetic distance and differentiation results revealed the phylogenetic relationships among Shanlan upland rice populations. Both clustering and population structure analyses divided the materials into five subgroups, suggesting that the Shanlan upland rice from Qiongzhong, Hainan, might be the center of genetic diversity for the Hainan Shanlan upland rice, while rice from Dongfang, Hainan, and the inland populations exhibit genetic isolation. This study provides foundational data for the prioritized conservation and innovative utilization of Shanlan upland rice germplasm resources.