Rice embryos are rich in high-quality protein, lipid, vitamins and minerals, representing the most important nutritional part of brown rice. However, the molecular mechanism of rice embryo development is poorly understood. In this study, two rice cultivars with contrasting embryo size (the giant embryo cultivar Dapeimi and the normal embryo cultivar 187R) were used to explore excellent genes controlling embryo size, and the developed near-isogenic lines (NILs) (NIL-D, which has the giant embryo phenotype, and its matching line, NIL-X) were used to explore transcript and metabolic properties in the earlier maturation stage of giant embryo development under natural conditions. The map-based cloning results demonstrated that Dapeimi is a novel allelic mutant of the rice GIANT EMBRYO (GE) gene, and the functional mutation site is a single cytosine deletion in the exon1. A total of 285 differentially accumulated metabolites (DAMs) and 677 differentially expressed genes (DEGs) were identified between NIL-D and NIL-X. The analysis of DAMs indicated that plants lacking GE mainly promoted energy metabolism, amino acid metabolism, and lipid metabolism pathways in the rice embryo. Pearson correlation coefficient showed that 300 pairs of gene-metabolites were highly correlated. Among them, OsZS_02G0528500 and OsZS_12G0013700 were considered to be key genes regulating L-Aspartic acid and L-Tryptophan content during rice giant embryo development, which are promising to be good candidate genes to improve rice nutrition. By analyzing rice embryo development through a combination of strategies, this research contributes to a greater understanding of the molecular mechanism of rice embryo development, and provides a theoretical foundation for breeding high-nutrition varieties.

As one of the most important staple crops in the world, rice plays a pivotal role in world food security. The creation of doubled haploids based on anther culture is an important technology for rice breeding. However, at present, rice anther culture technology still faces many problems, such as genotype dependency, especially genotypes of indica rice. In this study, fifteen rice genotypes, including twelve japonica rice genotypes and three indica rice genotypes, were randomly selected and used to study anther culture by using a modified M8 medium. The results showed that the total callus induction rates of these different rice genotypes ranged from 0.81 to 13.95%, with an average of 6.64%, while the callus induction rates calculated for the top ten highest callus inductions for each rice genotype ranged from 2.75 to 17.00%, with an average of 10.56%. There were varying gaps between the total callus induction rates and the callus induction rates in these different rice genotypes. The fact that the gaps for some rice genotypes were relatively large indicated that standard tiller or anther collection was not applicable to all rice genotypes and that there was still a lot of room for improvement in the callus induction rate of some rice genotypes through optimization of the sampling method. The plantlet regeneration rates ranged from 12.55 to 456.54%, with an average of 200.10%. Although there were many albinos from anther culture for some rice genotypes, these would still meet the requirement if the rice genotypes had higher callus induction rates or regeneration rates. The percentages of seed setting of regenerated green seedlings ranged from 14% to 84%, with an average of 48.73%. Genetic diversity analysis showed that the genetic background of these different rice genotypes was representative, and the phylogenetic tree and Principal Component Analysis (PCA) divided them into indica and japonica types. Therefore, in this study, an anther culture method suitable for both indica and japonica rice genotypes was established, which could improve doubled haploid breeding in rice.

Introduction: Huruan1212 (HR1212) is well-regarded for its superior eating and cooking quality in the lower reaches of the Yangtze River in China. Still, its high susceptibility to rice panicle blast and lack of fragrance have limited its further spread and utilization. Pigm and Pi-ta are two dominant genes known for their stable broad-spectrum resistance against rice blast fungus Magnaporthe oryzae, while badh2 is the crucial gene that regulates rice aroma.Methods: In this study, we utilized a molecular marker-assisted selection backcrossing strategy to introduce Pigm, Pi-ta, and badh2 into introgressed lines employing re-sequencing for precise genetic background selection.Results: Finally, we selected three introgressed lines, including two that carry Pigm with the highest background recovery rates, showing eating and cooking qualities similar to those of HR1212, and one line that pyramids Pigm, Pi-ta, and badh2, which features a strong aroma. They all displayed significantly enhanced resistance to panicle blast and improved yield compared to HR1212.Discussion: In conclusion, this study expanded the germplasm resources of japonica, providing a material foundation for enhancing breeding programs aimed at developing rice blast-resistant and high-quality fragrant japonica varieties. Additionally, the study demonstrated that integrating molecular markers and re-sequencing can inform breeders’ decision-making more precisely and efficiently.

Introduction: Direct-seeding rice faces the prominent challenge of low seedling emergence vigor, particularly under deep-sowing mechanical resistance and hypoxic conditions. Although some physiological traits are known, the systemic molecular networks determining superior emergence remain elusive. Methods: Here, we integrated metabolomic and transcriptomic analyses to compare the elite direct-seeding variety ChongShang2022 (CS2022) with the control Huxiangruan450 (HXR450). Results and discussion: Weighted gene co-expression network analysis (WGCNA) identified germination-associated metabolic modules. Hub metabolite analysis revealed that the accelerated germination of CS2022 correlates with a higher accumulation of cytokinins (zeatin and cis -zeatin-9-N-glucoside), known for antagonizing abscisic acid (ABA)-induced dormancy, alongside key amino acids (e.g., L-lysine) and structural sphingolipids. Physiological validation confirmed the functional significance of these hubs, demonstrating that exogenous trans -zeatin and L-lysine significantly promoted seed germination in a dose-dependent manner. Notably, CS2022 exhibited heightened sensitivity, achieving maximal promotion at concentrations approximately 10-fold lower than HXR450. Targeted LC-MS/MS assays further demonstrated that CS2022 maintains a significantly higher GA20/ABA ratio during germination by accumulating the key precursor GA ₂₀ and deactivating free ABA into ABA-glucosyl ester. This hormonal homeostasis couples with elevated α-amylase activity, accelerating energy mobilization. At the seedling stage, multi-omics integration suggests an optimized growth-defense trade-off in CS2022. Auxin signaling supports rapid elongation, while the upregulation of jasmonic acid (JA) precursor transcripts contrasts with restricted accumulation of bioactive signals (e.g., JA-Ile). This potential signal buffering mechanism likely mitigates growth arrest. Additionally, lipid remodeling involving sphingolipids and waxes may contribute to hypoxia tolerance. Altogether, this study delineates a correlative regulatory network where dynamic hormone buffering, redirected metabolic flux, and adaptive lipid remodeling synergistically maximize direct-seeding rice emergence vigor, providing mechanistic insights and candidate modules for breeding.