Pigmented rice grains are important resources for health and nutritional perspectives. Thus, a thorough dissection of the variation of nutrients and bioactive metabolites in different colored rice is of global interest. This study applied LC–MS-based widely targeted metabolite profiling and unraveled the variability of metabolites and nutraceuticals in long grain/non-glutinous black (BR), red (RR), green (GR), and white rice (WR) grains. We identified and classified 1292 metabolites, including five flavonoid compounds specific to BR. The metabolite profiles of the four rice grains showed significant variation, with 275–543 differentially accumulated metabolites identified. Flavonoid (flavone, flavonol, and anthocyanin) and cofactor biosynthesis were the most differentially regulated pathways among the four rice types. Most bioactive flavonoids, anthocyanidins (glycosylated cyanidins and peonidins), phenolic acids, and lignans had the highest relative content in BR, followed by RR. Most alkaloids, amino acids and derivatives, lipids, and vitamins (B6, B3, B1, nicotinamide, and isonicotinic acid) had higher relative contents in GR than others. Procyanidins (B1, B2, and B3) had the highest relative content in RR. In addition, we identified 25 potential discriminatory biomarkers, including fagomine, which could be used to authenticate GR. Our results show that BR and RR are important materials for medicinal use, while GR is an excellent source of nutrients (amino acids and vitamins) and bioactive alkaloids. Moreover, they provide data resources for the science-based use of different colored rice varieties in diverse industries.

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.

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.