Black rice, a nutritionally superior yet genetically uncharacterized germplasm, exhibits extreme rarity (∼ 1%) in natural rice populations. Here, we establish a global germplasm collection of 367 black rice accessions and employ integrated multi-omics (genomics, transcriptomics, metabolomics) to dissect its divergence from white rice. Population genomic analyses reveal a two-step domestication trajectory for black rice from the wild progenitor: initial Rc-mediated loss of proanthocyanidin pigmentation, followed by OsKala4/OsMYB3-driven anthocyanin activation under artificial selection. Genome-wide scans identify 238 differentially selected regions between black and white rice that orchestrate extensive transcriptomic reprogramming (up to 22% differentially expressed genes) and metabolomic remodeling (up to 32% differentially accumulated metabolites) in black rice seeds. Multi-omics analysis and a genome-wide association study uncover previously uncharacterized regulators (OsWRKY1, OsBBX13, OsTT12) that synergistically enhance the MYB-bHLH-WD40 (MBW) transcriptional complex to regulate anthocyanin biosynthesis and vacuolar sequestration. Furthermore, we reconstructed a comprehensive biosynthetic pathway network for phenolic acids and flavonoids in black rice through integration of experimental metabolomic and transcriptomic datasets with Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotations. Finally, we evaluated the selection status of 225 quantitative trait genes and compared agronomic traits between black and white rice. Our findings provide a molecular roadmap for precision breeding strategies to develop elite black rice cultivars with optimized nutritional and agronomic performance.

As an important global food crop, rice is damaged by a variety of piercing–sucking pests. Identifying a broad-spectrum promoter induced by the physical signal of sucking pests and applying it to transgenic breeding to mitigate the damage caused by different sucking pests will significantly improve the efficiency of our breeding. This study compared the transcriptome changes in two rice varieties under needle-wounding stress to investigate their differential responses to mechanical damage. The results showed that the insect-susceptible variety TN1 exhibited more differentially expressed genes (DEGs) and greater changes in expression levels after needle treatment, indicating a more active internal gene regulatory network. GO and KEGG enrichment analysis further revealed that TN1 not only exhibited changes in genes related to the extracellular environment, but also mobilized more genes associated with stress response and defense. By screening the differentially expressed genes, we identified two promoters (P1 and P2) with inducible expression characteristics in both the resistant and susceptible rice varieties. These promoters were able to effectively drive the expression of the insect resistance gene OsLecRK1* and enhance the resistance of transgenic plants against the brown planthopper. This study provides promoter resources for the development of insect-resistant transgenic crops.

Insect pests and weeds are the two major biotic factors affecting crop yield in the modern agricultural system. In this study, a brown planthopper (BPH) resistance gene (BPH9) and glufosinate tolerance gene (bar) were stacked into a single T-DNA cassette and transformed into an indica rice (Oryza sativa L.) line H23. The present study employed a gene stacking process that combines more than one gene/trait into an individual transgenic plant to meet the increasing cropping demands under complex conditions. The transgenic rice H23 (H23R) co-expressing bar and BPH9 genes demonstrated both glufosinate tolerance and BPH resistance. We utilized transcriptome data to reveal the mechanism of BPH9-mediated brown planthopper resistance and to analyze the impact of exogenous transgenic fragments on upstream and downstream genes at insertion sites. The evaluation of insect resistance and glufosinate tolerance confirmed H23R as an excellent double-resistant transgenic rice. These findings indicate that H23R can satisfy insect management and weed control in the modern rice agricultural system. However, a deregulation study will help with prospective commercial planting.