Cytoplasmic male sterility (CMS), which is governed by mitochondrial-nuclear interactions that disrupt pollen development, is a crucial mechanism for hybrid seed production in rice. The wild abortive CMS system underpins over 95% of commercial hybrid rice, but overreliance on this single cytoplasm increases vulnerability to biotic and abiotic stresses. Limitations such as occasional incomplete fertility restoration, and a narrow restorer gene pool further constrain breeding efficiency. Diversifying CMS systems is therefore essential to enhance genetic resilience and hybrid performance. This review discusses strategies for CMS diversification, including the exploration of novel cytoplasmic sources from wild rice, the development of new CMS lines through backcrossing, and the molecular characterization of mitochondrial and restorer genes. Advances in genomics, proteomics, and CRISPR/Cas9-mediated genome editing have identified key sterility-associated genes such as orf79, orf312, and RMS, enabling precise fertility restoration. Integrating CMS diversification with cropping system innovations can further improve hybrid rice productivity, resource use efficiency, and climate resilience. Genomic insights into adaptive divergence among rice subpopulations provide promising avenues for developing novel CMS types. Coordinated research in mitochondrial biology, molecular breeding, and biosafety policy will be critical to fully harness the potential of diversified CMS systems for sustainable and high-yielding hybrid rice cultivation.

Rice bran oil (RBO) is an emerging cooking oil, known for its high level of bioactive compounds that play an important role in the management of different diseases. The RBO extraction methods directly impact the level of bioactives in RBO, resulting in alterations of therapeutic activities. The green extraction processes, including supercritical CO₂, subcritical CO₂ Soxhlet, subcritical liquefied dimethyl ether, enzyme-assisted aqueous, microwave-assisted, and ultrasound-assisted extraction, were applied to obtain RBO from rice bran. RBO exhibited potential health benefits via upregulation and downregulation of several types of molecular pathways and gene expression. In addition, the unique physicochemical properties of RBO enable its use in cosmetics, novel drug delivery systems, biosurfactant applications, and the development of moisturizing, detoxifying, and anti-aging products. Several novel formulations, such as nanoemulsions, emulgels, self-nanoemulsifying systems, and oleogels, were prepared in which RBO significantly improves solubility, bioavailability, and intestinal absorption of lipophilic drugs. Animal feed, biofuel, and food products are other applications of RBO. Considering all these aspects of RBO, this review was designed to explore the in-depth RBO extraction phenomenon, the molecular mechanism exerted by functional agents in RBO, and the emerging applications in diverse fields.

Rice landraces harbor extensive genetic diversity, and those sustained on-farm are intrinsically embedded within their surrounding ecological and cultural contexts. However, this diversity manifests in multiple ways and is often obscured by a morphologically uniform exterior. This review explores multiple dimensions of diversity in rice landraces, aiming to establish a hierarchy of genetic variations both within and among landrace populations, as well as their patterns of genetic differentiation. The review describes the natural, cultural, and agroecological niches, in which rice landraces have evolved across Asia. It then proceeds to review the structure of genetic diversity, as established through both varietal nomenclature and molecular analyses. Functional diversity within and among landrace populations, particularly that underlying key adaptation traits and grain quality characteristics, is described. The principal finding is that rice landraces are not merely reservoirs of genetic diversity, but rather well-structured genetic systems. These dynamic populations arise from the interplay of natural selection, cultural practices, and farmers’ preferences, carrying both practical and evolutionary significance. Growing evidence from farmers’ fields confirms that genetic diversity in rice landraces underpins their capacity for sustained, dynamic adaptation to environmental change, while also enabling the capture of new economic and other opportunities, a feature that distinctly sets them apart from genetically uniform modern varieties and pure-line cultivars. Molecular analyses and functional trait identification have revealed significant and well-structured genetic variation, often concealed beneath morphological uniformity. The hierarchical structure of this diversity, within fields, among seed lots, and across landscapes, is critical not only for local adaptation and resilience to changing conditions, but also for the design of effective conservation and utilization strategies. Thus, rice landraces represent not merely the legacy of past selection, but a vital resource for securing future economic prospects and navigating an uncertain world.

Successful establishment of direct-seeded rice (DSR) under deep sowing depends on rapid seedling emergence in darkness, mechanical impedance, and hypoxia conditions under which mesocotyl elongation becomes a decisive adaptive trait. Here, we integrated multi-year phenotyping, anatomy, phytohormone profiling, transcriptional analysis, and bulked segregant analysis sequencing (BSA-seq) in near-isogenic lines to dissect the regulatory basis of mesocotyl elongation and early seedling vigor under deep-sown DSR systems. Deep sowing selectively triggered mesocotyl elongation, enhanced aerenchyma formation, and elevated auxin and ethylene accumulation in tolerant genotypes, while susceptible lines failed to activate these responses. Light exposure strongly suppressed mesocotyl elongation, but this inhibition was attenuated under soil-imposed darkness and mechanical constraint. Genomic analyses converged on rice chromosome 7 as a central regulatory hub, with partially distinct loci governing mesocotyl elongation and integrated emergence. Successful emergence was associated with early repression of growth inhibitors (Myb30 and ICL) and depth-induced activation of a basic helix-loop-helix (bHLH) transcription factor (LOC_Os12g08025), linking transcriptional regulation with hormonal signaling and anatomical plasticity. Together, these findings define a narrow early developmental window in which coordinated hormonal, anatomical, and genomic programs enable mesocotyl-driven emergence under deep sowing, providing tractable targets for breeding rice cultivars adapted to mechanized DSR systems.

Direct-seeded rice (DSR) offers a sustainable alternative for climate-resilient agriculture, but it is severely threatened by the root-knot nematode Meloidogyne graminicola. Knockout of susceptibility (S) genes has emerged as a promising strategy to combat such obligate parasites. Among candidate S genes, heavy metal-associated (HMA) domain containing isoprenylated plant proteins (HIPPs) are central regulators of plant stress responses. Here, we show that CRISPR/Cas9-mediated knockout of the nematode-responsive S gene, OsHIPP19, reduces susceptibility to M. graminicola in the DSR cultivar Pusa 2090. Given the variable transformation efficiency among Oryza sativa ssp. indica rice cultivars, we first standardized an immature embryo-derived callus culture method for Pusa 2090. Subsequently, we generated three loss-of-function mutant lines harboring novel alleles. In microplot trials, these lines exhibited a 38.75%‒40.08% reduction in gall counts and a 40.26%‒42.66% reduction in nematode multiplication compared with control plants. Conversely, OsHIPP19 overexpression lines conferred hypersusceptibility to M. graminicola, and reintroducing OsHIPP19 into a resistant knockout line restored susceptibility. The role of OsHIPP19 as an S gene was further confirmed by promoter-GUS reporter assays and expression analysis of defense-related marker genes. Notably, OsHIPP19 knockout did not cause yield penalties in Pusa 2090, highlighting the translational potential of this approach for engineering sustainable nematode resistance in crops.

Leaf senescence is a programmed cell death process that reallocates nutrients from aging leaves to developing parts of the plant, influencing crop yield and stress responses. NAC transcription factors play a crucial role in this transition, but the upstream signals and downstream targets in rice remain largely unclear. In this study, we identified ONAC039 as a positive regulator that connects abscisic acid (ABA) signaling to chlorophyll degradation. Transcripts of ONAC039 increased during age-dependent and dark-induced senescence, as well as following ABA treatment. CRISPR-Cas9-generated lines exhibited delayed yellowing and retained higher chlorophyll levels, whereas ONAC039 activation-tagged and overexpression lines showed accelerated senescence. ONAC039 upregulated key senescence-associated and chlorophyll catabolic genes, along with ABA signaling components. Yeast one-hybrid, chromatin immunoprecipitation, and dual-luciferase reporter assays demonstrated that ONAC039 directly bound to the promoters of three senescence-related genes and one ABA signaling gene, resulting in their transcriptional activation. Collectively, ONAC039 plays a crucial role in linking ABA signaling with senescence-associated genes in rice, providing a foundation for future studies aimed at modulating senescence timing.

Seed storability is a critical factor influencing the long-term viability of seeds in genebanks. However, evaluating seed storability remains challenging, as current methods such as viability loss curves are time-consuming and require substantial seed resources. This study investigated the role of phenotypic and physiological factors in seed storability using 56 japonica rice seed samples with initial germination rates exceeding 90%. Our analysis revealed that phenotypic traits, such as 1000-grain weight, grain width, and length-to-width ratio, did not significantly correlate with seed storability, highlighting the complexity of the relationship between phenotype and storability. Dynamic changes in antioxidant enzyme activities [superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX), peroxidase (POD), and glutathione reductase (GR)] were analyzed, and a significant positive correlation was observed between POD activity and seed storability. POD activity remained relatively high in storage-tolerant seeds, whereas it decreased more sharply in storage-sensitive seeds. Gene expression analysis of 11 highly expressed POD genes in seeds generally reflected the dynamic change in POD activity. A linear regression model constructed using POD activity and initial germination rate showed that POD activity could reliably assess seed storability, with an R² value of 0.919 for storage-tolerant seeds. Cluster analysis of 28 seed samples validated these findings, establishing a POD activity threshold of 12 U/μg protein in unaged seeds imbibed for 48 h as a key indicator for distinguishing storage-tolerant seeds. This study provides valuable insights into the physiological and genetic mechanisms underlying seed storability and offers a promising approach for rapidly assessing japonica rice seed storability in genebanks.

The ubiquitin-proteasome system (UPS) shapes rice (Oryza sativa) development and stress responses through the actions of E3 ubiquitin ligases; however, the functions of most plant E3 ubiquitin ligases remain unresolved, and integrative, rice-focused multi-omics resources to prioritize E3 ligases remain limited. We developed the Rice E3 Ubiquitin Ligase Database (RE3DB; https://re3db.khu.ac.kr/) as a rice-focused platform for exploration and prioritization of E3 ubiquitin-ligase-system genes. RE3DB consolidates 1 602 curated E3 ubiquitin-ligase-system genes with 15 published datasets, including RNA-seq data from 25 tissues and diverse stress conditions, protein-to-transcript ratios (PTRs) from 14 tissues, 6 high-confidence protein-protein interaction resources, and family-level phylogenies. Interactive modules enable (i) classification and functional annotation, (ii) prioritization of candidate E3-substrate relationships based on interaction evidence, co-expression, and coordinated proteolytic turnover, and (iii) assessment of potential functional redundancy using phylogenetic heatmaps. As a resource-use case study, we analyzed tissue- or organ-specific expression profiles of rice E3-system genes, observing strong enrichment of F-box genes in reproductive tissues, including 284 F-box genes preferentially expressed in mature anthers. Comparative transcriptomics across 9 male-sterile rice mutants prioritized 111 F-box candidates that were downregulated in at least one mutant with defects in pollen germination or tube growth, forming distinct co-regulation clusters. Integrating these candidates with a literature-curated regulatory network highlighted previously uncharacterized F-box genes within modules associated with pollen-tube initiation and elongation, consistent with regulation by the RUPO receptor-like kinase and the OsMADS62/63/68 transcription-factor complex. RE3DB provides a rice-focused resource to support hypothesis generation and candidate prioritization for ubiquitin signaling, with potential applications in understanding fertility and yield stability.