Search Results (1,238)

Water deficit severely limits rice productivity. The elite Dian (D1)-type hybrid japonica rice ‘Dianheyou 615 (ZH1)’ exhibits exceptional drought adaptation in high-altitude rainfed uplands of the Yungui Plateau, yet the underlying molecular mechanisms remain unknown. We compared phenotypic and transcriptomic responses of ZH1 and six other japonica cultivars under well-watered and water-deficit conditions. Water-deficit stress significantly impaired agronomic traits across all cultivars; however, ZH1 uniquely maintained relatively stable flag leaf morphology and seed-setting rate, and displayed distinctive stomatal traits, in stark contrast to its parental lines and other cultivars. Transcriptomic profiling at the jointing-to-booting stage defined a core drought response module of 174 conserved genes across all cultivars. Critically, by intersecting 1097 ZH1-specific genes with drought-responsive elements, we pinpointed 15 core, cultivar-specific regulatory genes. These candidates are enriched in functions related to cuticle formation, carbohydrate metabolism, and stress signaling; among them, a DREB transcription factor (LOC4347618) is a prime candidate. qRT-PCR validated their expression. Using CRISPR/Cas9-mediated gene editing, we generated homozygous knockout mutants for LOC4333842, LOC4347618, and LOC4328441. Under 20% PEG-6000-simulated drought stress, all three mutant lines showed significantly increased drought susceptibility relative to wild-type controls, confirming the positive regulatory roles of these genes in drought stress tolerance in japonica rice. These results establish these three genes as promising targets for molecular breeding aimed at enhancing drought resistance in rice. Full article

In Guangxi, China, winter ratoon tissues of perennial rice provide overwintering habitats for the migratory crop pest Mythimna separata (Walker, 1865) (Lepidoptera: Noctuidae). To understand the overwintering potential and fitness of this pest in perennial rice cropping systems, we evaluated the life history, population parameters, and flight performance of M. separata cohorts initiated in November, December, January, and February using group rearing and age-stage, two-sex life tables. The November cohort showed the highest intrinsic rate of increase (r_m = 0.1009 d⁻¹), while the February cohort exhibited the greatest fecundity (752.88 eggs/female) and flight capacity (7.61 h of flight during the 12 h flight period). In contrast, prolonged exposure to deep-winter cold severely suppressed survival, reproduction, population growth, and adult flight performance. These findings demonstrate that overwintering success depends strongly on the timing of cold exposure: gradual autumn cooling and late-winter warming can support population persistence, whereas sustained deep-winter cold is associated with reduced fitness. Perennial rice ratoon tissues may therefore facilitate pest carry-over between cropping cycles, and the overlap between spring ratoon regrowth and reproduction of late-winter cohorts may increase the risk of early-season outbreaks. Monitoring overwintering cohort dynamics together with ratoon phenology could improve early warning and support timely management of M. separata in perennial rice systems. Full article

To investigate photosynthetic physiological response mechanisms of rice (Oryza sativa L.) seedling leaves under drought stress, a pot experiment with controlled watering was conducted. Four treatments were applied—control (CK), mild drought (LD), moderate drought (MD), and severe drought (SD)—to four cultivars (H17B7, HY3015, LH1H, WNSM) at seedling stage. The results showed that, after drought stress, the morphological indicators and chlorophyll content of the four rice cultivars all showed decreased trend, but a compensatory effect appeared in some varieties under the LD treatment. As drought intensified, the chlorophyll fluorescence induction kinetics (OJIP) curves’ polyphasic rise was inhibited, mainly affecting the J-I and I-P phases. Under SD, the P-phase declined by 44.36%, 36.75%, 32.61% and 50.62% compared with CK, and positive L-band, K-band, and J-band. Chlorophyll fluorescence parameters showed dynamic changes. Most chlorophyll fluorescence parameters (e.g., F_v/F_m) decreased, whereas TR_o/CS_o and DI_o/CS_o exhibited cultivar-dependent variations. Principal components of the chlorophyll fluorescence parameters in seedling leaves of the four rice cultivars showed differences and were clearly distinguished. Plant height, chlorophyll content, etc., are highly significantly positively correlated with F_o, DI_o/CS_o, etc., as well as chlorophyll content with DI_o/CS_o. The OJIP/JIP-test responses suggest impairment of the PQ pool and downstream electron transport, with the extent of damage varying among cultivars. Full article

Chlorophyll content is a key determinant of photosynthetic efficiency and grain yield in rice (Oryza sativa L.), while premature chlorophyll degradation during the reproductive stage can markedly reduce crop productivity. However, the genetic basis underlying chlorophyll degradation and its environmental responsiveness remains incompletely understood. In this study, an F₂ population derived from a cross between the japonica cultivar Shennong0530-9 and the indica cultivar Habataki was used to identify quantitative trait loci (QTLs) associated with chlorophyll content at different developmental stages. A total of 22 QTLs were detected; among these, qCD2 consistently showed a major and stable effect on chlorophyll degradation after heading. Fine mapping using residual heterozygous lines delimited qCD2 to a 54.0 kb genomic interval on the short arm of chromosome 2 containing nine predicted genes. Near-isogenic lines (NIL-qCD2) carrying the qCD2 allele exhibited accelerated chlorophyll loss after heading, accompanied by disrupted chloroplast ultrastructure, reduced photosynthetic capacity, and significant decreases in grain yield and grain quality compared with the recurrent parent. Furthermore, the chlorophyll-deficient phenotype became progressively more severe under elevated temperature conditions, indicating that the phenotypic effect associated with qCD2 is temperature sensitive. Consistent with these physiological changes, the expression patterns of genes involved in chloroplast development, photosynthesis, and leaf senescence were significantly altered in NIL-qCD2. Collectively, these results identify qCD2 as a stable QTL associated with chlorophyll degradation during the reproductive stage and provide a foundation for future identification of the causal gene, providing valuable genetic resources for the molecular breeding of rice with improved photosynthetic efficiency, grain yield, and grain quality. Full article

Rising temperatures pose daunting challenges for sustainable yield and nutritional quality of rice (Oryza sativa L.), thus putting food security at risk. Limited information exists regarding cis-acting regulatory elements and candidate genes controlling the heat shock transcription factor (HSF) gene family in rice. Therefore, the present study identified HSF genes in the japonica (Nipponbare) and indica (9311) rice cultivars through in silico repositories. Three candidate genes (HSFC2B, HSFB1, and HSFC2A) were selected for qRT-PCR analysis to validate their expression patterns under heat stress (HS). The present findings reported a total of 25 OsHSF genes through in silico genome-wide identification. Comparative analysis illustrated that the OsHSF genes had structural similarities but different expression and transcriptional regulation between the two cultivars. HSF genes were unevenly distributed across the 12 rice chromosomes, suggesting that tandem duplication and gene repetition may have contributed to the evolution of novel genes. Phylogenetic analysis revealed that all OsHSF gene family members have shared common ancestry, but several genes lack introns, potentially facilitating swift stress responses as indicated by gene structure analysis. Expression analysis revealed that candidate genes were active, with HSFC2A exhibiting the highest level of expression in the japonica cultivar compared to indica under heat-stressed conditions. HSFC2B gene showed a higher statistical difference in its response between cultivars, time points, and cultivar vs. time points interactions compared to HSFC2A and HSFB1. These findings offer valuable insights into the function of OsHSF genes that will contribute to the development of climate-resilient rice cultivars. Full article

Abiotic stresses—drought, salinity, extreme temperature, flooding, and heavy-metal toxicity—constrain rice (Oryza sativa L.) yield worldwide, and the cellular programmes underlying them are unevenly distributed across cell types that bulk-tissue assays average together. This review examines, from a methodological standpoint, what single-cell and spatial omics technologies can and cannot establish about rice abiotic stress biology. We first define the modality space: single-cell omics measures RNA, chromatin accessibility, DNA methylation, protein, or metabolite features at the resolution of individual cells or nuclei, whereas spatial omics measures such features while retaining tissue coordinates; the two are complementary rather than interchangeable. We then treat each platform class—droplet-based scRNA-seq, combinatorial-indexing approaches including SPLiT-seq, nuclei-based snRNA-seq and multiome, sequencing-based and imaging-based spatial transcriptomics—under a common template covering measurement principle, the questions each can answer, applicability to rice tissues, dominant biases, and the inferences each cannot support. To make evidence strength comparable across a heterogeneous literature, we apply a four-tier scheme throughout: Tier A, direct rice cell-resolved or spatial evidence with functional or field validation; Tier B, robust rice functional and localization evidence without single-cell data; Tier C, cell-resolved evidence without causal validation; and Tier D, cross-species analogy or reasoned proposal. Applying this scheme shows that the genes with genuine breeding traction in rice—SUB1A, OsHKT1;5, OsHMA3, OsNRAMP5, DRO1—rest on Tier B evidence from classical genetics and field testing, whereas the most cell-resolved rice evidence concentrates in root outer layers and barrier formation at Tier C, and heat and cold stress, despite dominating yield loss, lack rice cell-resolved data almost entirely. We extend the discussion beyond transcriptomics to single-cell DNA methylome profiling, spatial proteomics and metabolomics, and three-dimensional analysis of thick plant tissues, in each case distinguishing demonstrated plant capability from mammalian-only capability, and we assess the expanding role of artificial intelligence in annotation, segmentation, batch correction, integration, and perturbation prediction alongside its documented failure modes. Rice, maize, and wheat are compared to identify transferable methodology. Cell-resolved omics has to date improved biological interpretation and candidate prioritization; demonstrating an incremental breeding advantage from it remains an unmet requirement. Full article

Flooding during the rice (Oryza sativa L.) jointing stage threatens yield stability in regions with concentrated rainfall and limited drainage. However, the extent to which the water regime before flooding modifies rice growth and yield formation remains poorly understood. A pot experiment was conducted over two years to compare controlled irrigation (CI) with conventional flooding irrigation (CF) across three flooding depths and two durations imposed at the jointing stage. Flooding increased tiller number, plant height, and total leaf area, but reduced net photosynthetic rate and grain yield. Yield loss increased with flooding depth and duration. Under corresponding flooding treatments, CI moderated vegetative expansion and maintained a higher net photosynthetic rate, greater root dry matter, and a higher root-to-shoot ratio than CF. Relative to the corresponding non-flooded controls, yield loss ranged from 4.11% to 39.33% under CI and from 5.63% to 52.50% under CF. The lower yield loss under CI was associated with greater effective panicle number, higher seed setting rate, and better maintenance of photosynthetic activity and root biomass. These findings indicate that the water regime before flooding can influence biomass allocation and yield formation during the jointing stage flooding. Controlled irrigation combined with timely drainage may help reduce yield risk in rice systems exposed to temporary flooding. Full article

Irrigation water management in arid systems requires spatially distributed estimates of crop evapotranspiration (ET) that fixed crop coefficients cannot provide. The actual ET of flood-irrigated rice (Oryza sativa L.) on the arid northern coast of Peru was mapped with the METRIC surface energy balance model (Mapping EvapoTranspiration at high Resolution with Internalized Calibration) on Google Earth Engine (GEE). Ten cloud-free Landsat 8/9 scenes (January–July 2022) were processed over 113 ha at Ferreñafe (Lambayeque) on the 30 m product grid, onto which the 100 m native thermal observation was resampled, with internal calibration based on automatic anchor-pixel selection and hourly ERA5-Land data. Daily field-mean ET ranged from 4.2 to 8.1 mm d⁻¹, peaking during flooding and establishment and declining towards harvest. Because the same reference $E{T}_o$ underlies the METRIC internal calibration and the FAO-56 estimate, this is a comparison between two modelling approaches rather than an independent validation. Against the FAO-56 reference ET, METRIC showed a positive bias of $+0.65$ mm d⁻¹ (percent bias (PBIAS) $=+13\%$; root mean square error (RMSE) $=1.23$ mm d⁻¹; $r^2=0.57$; $n=9$, after excluding one date with anomalous reanalysis forcing), concentrated during flooding and after harvest, whereas at full canopy cover the two estimates converged. Two global ET products that share neither the METRIC formulation nor the ERA5-Land forcing reproduce the same seasonal decline once the canopy closes ($r=0.63$ and $0.91$) but stay far below in magnitude, as expected from their 500 m pixel. ET did not differ between sowing methods and varied only slightly among cultivars (∼0.3 mm d⁻¹), against marked intra-field variability. The METRIC–GEE workflow offers a low-cost, high-resolution tool for monitoring water use in data-scarce arid rice systems. Full article

Cadmium (Cd) is a toxic metal that poses a significant threat to crop production and global food security. Transporters play a critical role in mediating the uptake of metal ions, including Cd. However, a substantial number of Cd transporters in rice remain uncharacterized. In this study, we identify OsMDR4, a member of the multidrug resistance protein family, as a mediator of Cd uptake in rice. Heterologous overexpression of OsMDR4 in yeast increased both Cd sensitivity and intracellular Cd accumulation. Consistent with this, the Cd concentrations in both roots and shoots of the mdr4 mutants were significantly lower than those in wild type. Kinetic analysis further revealed that the maximum Cd uptake rate in mdr4 mutants was markedly reduced compared with wild type. Expression analysis showed that OsMDR4 is primarily expressed in the epidermis and root hairs of rice seedlings and in floral organs during the flowering stage. Notably, OsMDR4 expression in seedling roots was upregulated in response to Cd exposure. Subcellular localization analysis revealed that OsMDR4–EGFP was predominantly localized to the plasma membrane in a heterologous Arabidopsis protoplast system. In summary, we have identified and characterized OsMDR4 as a previously uncharacterized protein that contributes to cadmium accumulation in rice. Full article

Elucidating the evolutionary trajectories and genetic basis of critical agronomic traits in regional rice germplasm is paramount for discovering elite allelic variations for crop improvement. Here, we systematically characterized a panel of 109 rice accessions from Zhejiang Province through whole-genome resequencing (~10× coverage) coupled with two years of rigorous field phenotypic evaluations. A total of 4,753,071 high-quality genomic variants, including 4,147,316 SNPs, were identified across the genome. Population structure and evolutionary analyses revealed sharp genetic differentiation at the subspecies level, partitioning the panel into distinct indica and japonica clusters accompanied by intricate subpopulation stratification and historical gene flow. Through a joint scanning of the fixation index (Fst) and nucleotide diversity (Pi) ratios, three prominent selective sweep regions (qSS1, qSS10, and qSS12) driving subspecific differentiation were captured on chromosomes 1, 10, and 12. Notably, the qSS12 locus harbors the sucrose transporter gene OsSUT2, indicating that carbohydrate transport and energy metabolism served as core genomic targets driving the indica–japonica divergence. Furthermore, genome-wide association studies (GWAS) successfully mapped 9 significant loci modulating heading date, effective tiller number, and grain size. Subsequent gene-based haplotype analyses within these target intervals pinpointed elite allelic variations in core candidate genes, including OsSPX1 (phosphate homeostasis, 1000-grain weight), Chl9 (chlorophyll synthesis, grain width), and OsCER1 (wax biosynthesis, panicle length). Collectively, this study deciphers the genomic landscape and subspecies differentiation patterns of Zhejiang rice germplasm, providing pivotal molecular targets and invaluable genomic resources for germplasm conservation and precision molecular breeding. Full article

Anther length is a crucial agronomic trait that directly correlates with pollen number and pollination efficiency, thereby affecting rice grain yield and hybrid seed production. However, the specific molecular mechanisms regulating rice anther length remain largely unclear. In this study, we identified a short anther (san) mutant generated by CRISPR/Cas9, which exhibited significantly shortened anthers and reduced pollen number, without affecting other agronomic traits or pollen viability. Cytological observations revealed that the shortened anther phenotype in san mutants was caused by reduced epidermal cell number, rather than altered cell size. SAN was highly expressed in spikelets and developing anthers and encodes a nucleus-localized C1-1iG subclass C₂H₂ zinc finger protein with a conserved QALGGH motif and a C-terminal EAR motif. Further assays demonstrated that SAN functions as a transcriptional repressor, and could interact with the corepressor TPR2 in the nucleus. RNA-seq analysis indicated that SAN influences expression of genes associated with cell cycle and cytokinin, which are critical for epidermal cell division during anther development. Phylogenetic analysis showed that SAN was evolutionarily conserved in plants and was closely related to Arabidopsis SUP/ZFP11 and rice SRO. Collectively, our findings revealed that SAN specifically modulated rice anther length by promoting epidermal cell division and providing new insights into the molecular mechanism of anther size regulation. Full article

Selenium nanoparticles (Se NPs) have shown potential for regulating cadmium (Cd) accumulation in rice; however, their particle-size-dependent effects in the paddy soil–rice system remain unclear. In this study, a whole-growth-period pot experiment was conducted to investigate the mechanisms of Se NPs with different particle sizes (50, 100, and 200 nm) applied at different rates (20 and 50 mg/kg) in regulating Cd accumulation in rice grown in Cd-contaminated paddy soil. Se NP application significantly altered rhizosphere pH and redox potential, decreased Cd concentrations in soil solution and DTPA-extractable Cd, and increased soil solution Se and KH₂PO₄-extractable Se. In the 20 mg/kg treatment, Se NPs promoted the transformation of Cd from exchangeable fractions to Fe–Mn oxide-bound fractions, indicating reduced Cd mobility. Se NPs also enhanced root iron plaque formation and increased the retention of Fe, Cd, and Se on the root surface. XPS analysis showed that 50 and 100 nm Se NPs increased the proportion of Fe(III) in root iron plaque, thereby strengthening Cd adsorption and immobilization at the root–soil interface. In addition, Se NP treatments reshaped rhizosphere microbial communities. The 50 nm treatment showed stronger effects on fungal taxa related to organic matter decomposition and Se activation, whereas the 100 nm treatment more effectively enriched bacterial groups associated with Fe and S cycling, including Thermodesulfobacteriota and Sideroxydans. Among all treatments, 100 nm Se NPs at 20 mg/kg reduced grain Cd from 0.466 to 0.050 mg/kg, representing an 89.27% reduction, while maintaining grain Se at 0.384 mg/kg, which is within the acceptable range for selenium-enriched rice. Overall, 100 nm Se NPs showed the best balance among Cd mitigation, Se biofortification, and ecological safety, suggesting their potential for application in safe rice production in Cd-contaminated paddy soils. Full article

A polysaccharide with water solubility named RRBP was extracted from red rice bran (Oryza sativa L.), and its structural characterization was analyzed. The polysaccharide exhibited a monodisperse molecular weight distribution with an average of 51.4 kDa, and also comprised glucose (98.1%, w/w) and small amounts of arabinose, galactose, xylose, and mannose. Structural investigations using methylation analysis combined with UV and FT-IR spectroscopy demonstrated that RRBP is a structurally complex hyperbranched glucan characterized by an extensive branch with “→4)-α-d-Glcp-(1“→linkages constituting 30.6% of the backbone. RRBP demonstrated concentration-dependent stimulation of nitric oxide (NO) generation along with elevated secretion levels of IL-6 and TNF-α but showed minimal effect on IL-12 production in assays with RAW264.7 macrophage cells. Gene expression profiling verified the enhanced transcription of genes encoding iNOS and pro-inflammatory cytokines including IL-6, TNF-α, and IL-12 following RRBP treatment. Moreover, it is important to note that RRBP was able to promote M1 macrophage activation and exhibited no cytotoxicity, and this implied that RRBP could serve as a biocompatible pro-inflammatory immunostimulant. In summary, these findings suggested that RRBP is a distinctive glucan that possesses selective immunomodulatory properties and could be applied in the development of functional food products designed for targeted immune system modulation. Full article

Rice yield is a complex polygenic trait influenced by intricate interactions among component characters. In this study, integrative quantitative genetics and multivariate models were used to dissect yield architecture and trait networks, and identify the promising genotypes among 21 rice genotypes that were tested in a randomized block design with three replicates. Analysis of variance revealed highly significant genotypic differences (p < 0.001) for most agronomic, yield, and grain-quality traits. Genetic variability analysis revealed high genotypic and phenotypic coefficients of variation, together with high heritability and genetic advance, for grain density per panicle, number of grains per panicle, biomass, flag leaf area, tillering ability, harvest index, and grain yield, indicating considerable genetic potential for genetic improvement. Pearson’s correlation and path coefficient analyses revealed that biomass and number of grains per panicle were the major determinants of grain yield per hill, with biomass exhibiting the strongest positive association (r = 0.678) and the largest direct effect. Principal component analysis indicated that the first two principal components explained 51.4% of the total phenotypic variation, with yield components, biomass, tillering traits, and grain-quality attributes contributing most strongly to genotype differentiation. Hierarchical cluster analysis grouped the genotypes into four distinct clusters, revealing substantial phenotypic divergence and valuable parental combinations for hybridization. The multi-trait selection index identified VAR16 as the most promising genotype, followed by VAR1, VAR17, VAR18, and VAR12, owing to their desirable combination of high grain yield and superior grain quality. Overall, this study offers a robust foundation for ideotype breeding and parental selection to enhance rice productivity and grain quality under subtropical conditions. Full article

The brown planthopper (BPH, Nilaparvata lugens) is a major insect pest of rice (Oryza sativa L.) causing severe yield losses across Asia. Although the resistance gene OsBph32 from the cultivar Ptb33 enhances BPH resistance, its molecular and physiological mechanisms remain unclear. Here, we investigated its function using OsBph32-overexpressing lines combined with physiological, transcriptomic, and metabolomic analyses. Overexpression of OsBph32 in the susceptible cultivar 9311 significantly increased resistance to BPH, as indicated by reduced plant damage and suppressed insect growth. This was associated with increased reactive oxygen species accumulation and callose deposition, suggesting activation of early defense responses. Multi-omics analyses revealed that OsBph32 is associated with transcriptional changes in genes involved in cell wall biosynthesis, phenylpropanoid metabolism, and carbon metabolism. Metabolomic profiling further showed increased accumulation of flavonoids, phenolamides, and lignin-related metabolites under BPH infestation, together with changes in carbon metabolism and starch accumulation. Collectively, these results suggest that OsBph32 is associated with coordinated changes in structural reinforcement, secondary metabolism, and carbon metabolism during insect attack, which may contribute to enhanced rice resistance and provide new insights into non-NLR-mediated insect defense mechanisms in plants. Full article