Huijian Wang

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.

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.

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.