Search Results (1,394)

Rice (Oryza sativa L.) production is severely threatened by rice blast disease caused by the hemibiotrophic fungus Magnaporthe oryzae. Chemical fungicides, although effective, cause environmental pollution, disrupt soil microbiomes, and select for resistant pathogen populations, creating an urgent need for sustainable alternatives. In this study, we isolated Kitasatospora hibisci strain 21007 from mangrove soil and evaluated its biocontrol potential through integrated phenotypic and transcriptomic analyses. The cell-free culture filtrate (CFCF) extract showed potent antifungal activity, inhibiting M. oryzae mycelial growth and suppressing conidial germination as well as appressorium formation in a concentration-dependent manner via antibiosis. Fermentation optimization identified Gauze’s Synthetic Medium No. 1 as optimal for metabolite production. Both inoculation of M. oryzae spores with 21007 CFCF extract and pre-treatment of rice seedlings with 21007 CFCF significantly reduced disease severity under greenhouse conditions. Transcriptomic analysis revealed extensive reprogramming of gene expression in leaves of rice seedlings cultured with 21007 CFCF extract. KEGG pathway enrichment analysis indicated activation of the plant–pathogen interaction and MAPK signaling pathways in rice seedlings cultured with 5% and 10% CFCF extract, suggesting that 21007 CFCF induces host defense signaling. These results support the potential of K. hibisci 21007 as a candidate for sustainable biocontrol of rice blast disease and establish a foundation for future metabolomic and genomic investigations. Full article

Rice (Oryza sativa L.) is a staple food crop, feeding more than 3.5 billion people. With the increasing demand for food in the 21st century, weed infestation poses the most significant biotic threat to global food security, and herbicides remain the most effective and economic way to manage it in field. However, weeds can rapidly adapt under herbicide selection pressure due to their high competitiveness, rapid growth, and reproductive capacity. Hence, we collected Echinochloa crus-galli populations from Heilongjiang and Hebei provinces in China and investigated their resistance mechanisms to pyrazosulfuron-ethyl (PSE), a sulfonylurea herbicide that inhibits acetolactate synthase (ALS). Dose–response experiments confirm that the resistant (R) population exhibits 52.9-fold resistance to PSE compared with the susceptible (S) population. Inhibitor bioassays with malathion and NBD-Cl, together with ALS activity assays, ALS gene sequencing, and molecular docking, collectively suggest that resistance is strongly associated with the ALS Trp-574-Leu target-site substitution, with a possible additional contribution from enhanced herbicide metabolism. However, because the S and R populations originate from geographically distinct locations, some of the observed physiological and molecular differences may also reflect inherent population variation. Specifically, the ALS W574L substitution is predicted to reduce key interactions between ALS and PSE. This study provides valuable evidence for the risk of PSE resistance evolution in E. crus-galli and elucidates the molecular mechanism conferring resistance to ALS inhibitors. Full article

Rice (Oryza sativa L.) straw-return can improve soil carbon (C) sequestration, but its adoption in intensive rice systems is limited by short fallow periods (<30 days), which likely lead to incomplete straw decomposition and increase methane emissions under continuous flooding (CF). Brittle rice straw, characterized by lower recalcitrant fiber content and rapid decomposition, may overcome this constraint; however, its environmental performance under alternate wetting and drying (AWD) remains unclear, such as broader C allocation. This 150-day microcosm study evaluated the interaction of straw type (brittle vs. non-brittle) and water management (CF vs. AWD) on greenhouse gas (GHG) emissions, dissolved C production, soil C storage, and aggregate formation in two contrasting paddy soils (sandy loam vs. silty clay loam). Compared with non-brittle straw, brittle straw returns reduced net GHG emissions by approximately 28.4% under CF and 39.6% under AWD. The combination of brittle straw with AWD produced the lowest net GHG emissions (0.61 kg CO₂-eq m⁻²), indicating that intermittent oxygen input effectively mitigated the early decomposition-related emission risk. Brittle straw also increased the concentrations of dissolved inorganic C by 14.2% and nitrate by 64.3% under AWD, suggesting enhanced mineralization and potential inorganic C stabilization. Regardless of straw type, straw return improved soil C stocks by 27.3% in sandy loam and 29.6% in silty clay loam, while also promoting macroaggregate formation. Overall, this study demonstrated that coupling brittle rice straw with AWD can reduce GHG emissions while maintaining soil C benefits, offering a promising residue management strategy for intensive rice cultivation. Full article

Cotton is recognized as the primary source of essential natural fibers for the global textile industry, supporting its sustainability and development. However, adverse environmental conditions such as drought severely constrain cotton production; thus, developing stress-tolerant cultivars via molecular breeding is essential for maintaining yield stability. Here, a comprehensive functional dissection was conducted on GhGA2ox15, a gibberellin 2-oxidase gene derived from Gossypium hirsutum L. This gene encodes a key catabolic enzyme implicated in the deactivation of endogenous bioactive GAs and the modulation of stress adaptation. We characterized GhGA2ox15, a GA2ox gene from upland cotton that modulates endogenous bioactive GA levels and abiotic stress tolerance. Bioinformatics and sequence analyses confirmed that GhGA2ox15 is a canonical C₂₀-GA2ox subfamily member, with conserved DIOX_N and 2OG-FeII_Oxy domains and marked similarity to orthologs in Arabidopsis and rice. Tobacco subcellular localization assays indicated that GhGA2ox15 resides in both the nucleus and the cytoplasm. In transgenic Arabidopsis and Oryza sativa lines, GhGA2ox15 overexpression was shown to increase drought tolerance, while virus-induced gene silencing (VIGS) of GhGA2ox15 yielded significantly compromised drought resistance. Physiological assays linked GhGA2ox15 silencing to impaired reactive oxygen species (ROS) detoxification. The suppressed lines displayed markedly lower antioxidant enzyme activities, concomitant ROS accumulation in leaves, and attenuated transcription of drought-responsive marker genes. Our findings delineate the mechanistic role of GhGA2ox15 in drought adaptation and highlight its potential utility in breeding drought-tolerant cotton. Full article

Rice depends on its root system to perceive drought, a major environmental constraint that leads to severe yield losses worldwide. To dissect the underlying molecular basis, we conducted a comparative analysis of drought-sensitive (WAB) and drought-tolerant (IR65) rice genotypes that exhibited divergent drought tolerance at the seedling stage. After exposure to 15% PEG6000 (−0.4 MPa) for two days, the shoot and root architectural traits of IR65 were better than those of WAB seedlings. Measurements of physio-biochemical parameters (SOD, CAT, POD, APX, H₂O₂, and proline) suggest that IR65 seedling roots exhibit greater ROS scavenging and osmotic adjustment capacity than WAB, aligning with tolerance to PEG-induced water deficiency. Transcriptomic assessments of roots identified 802 commonly differentially expressed genes (DEGs) during the drought time course (12, 24, and 48 h) in WAB and IR65. They were clustered into eight groups based on their expression profiles and mainly enriched in phytohormone signaling, protein phosphorylation, and transcription factors. Using weighted gene co-expression network analysis (WGCNA), nine significant modules were identified based on n = 382 of the DEGs. A total of 12 DEGs up-regulated in IR65 were distributed in five modules, and five of them were selected for rapid functional validation through in vivo yeast expression. The results showed that transgenic yeasts were tolerant to simulated drought conditions (135 mM PEG3350), indicating that these genes would be potential targets for rice improvement in drought tolerance in the future. Full article

Accurate in-season rice (Oryza sativa L.) yield prediction is crucial for improved nitrogen management and climate-smart decision making, yet rigorous comparative benchmarking of machine learning (ML) models using multi-temporal UAV spectral data with independent temporal validation remains limited. This study systematically evaluated four ML algorithms (Random Forest, XGBoost, Neural Network, and Linear Regression) and two Bayesian model averaging ensembles for rice yield prediction using UAV multispectral imagery. Field experiments spanning three growing seasons (2023–2025) at Louisiana State University comprised 9–10 varieties and six nitrogen rates (0–235 kg N ha⁻¹; 576 plots). Vegetation indices and spectral bands from three growth stages were extracted as predictors. Models were compared using 300 random train–test iterations with systematic hyperparameter optimization, followed by independent validation on 2025 data. Among the individual models, XGBoost achieved the highest internal accuracy (R² = 0.87, RMSE = 0.85 t ha⁻¹), substantially outperforming Linear Regression (R² = 0.66, RMSE = 1.32 t ha⁻¹), while reduced BMA reached R² = 0.89. XGBoost demonstrated robust temporal generalization (R² = 0.62, NRMSE = 8.47%) despite environmental variation. The Enhanced Vegetation Index and Normalized Difference Red Edge at 90 days after planting (reproductive stage) were the most stable predictors across 300 iterations. Tree-based ML models substantially outperform traditional linear approaches, providing reliable pre-harvest yield forecasting for operational precision rice production. Full article

Maize (Zea mays L.), a typical thermophilic crop originating from tropical regions, exhibits an inherent sensitivity to low-temperature stress. Cold stress severely restricts maize seed germination, seedling growth, the physiological metabolism, and the final grain yield, which greatly limits its geographical cultivation range and sustainable industrial development. Elucidating the molecular regulatory mechanisms underlying maize cold tolerance and excavating cold-resistant functional genes are essential for the molecular breeding of cold-tolerant maize varieties and expanding maize planting areas in high-latitude and low-temperature-prone regions. In this study, using the strongly cold-tolerant maize inbred line B144 as the experimental material, we cloned the ZmMAPKKKA gene (NCBI accession: LOC103651289) and systematically screened and verified its cold-stress-specific interacting proteins via multiple molecular biological assays. The full-length coding sequence (CDS) of ZmMAPKKKA is 1134 bp, encoding a 377-amino-acid protein with a predicted molecular weight of 40.37 kDa. The quantitative real-time PCR (qRT-PCR) results demonstrated that the ZmMAPKKKA expression was significantly upregulated by 16.56-fold in maize roots after 12 h of low-temperature treatment, indicating a tissue-specific and robust cold response in root tissues. A total of 25 interacting proteins were identified through yeast two-hybrid screening, among which three stress-responsive proteins, including a protein kinase (LOC100286253), a protein phosphatase 2C (PP2C) (LOC542176), and a NAC transcription factor (LOC118474710), were selected for subsequent verification. The Pull-Down, Co-immunoprecipitation (Co-IP), and bimolecular fluorescence complementation (BiFC) assays consistently confirmed that ZmMAPKKKA specifically interacts with these three proteins both in vitro and in vivo under cold stress conditions. This study is the first to construct a ZmMAPKKKA-centered protein interaction module in the maize mitogen-activated protein kinase (MAPK) cascade under cold stress, establishing a novel kinase–phosphatase–transcription factor regulatory cascade that improves the current understanding of cold signal transduction mechanisms in maize. Homologous genes of ZmMAPKKKA in gramineous crops including rice (Oryza sativa) and sorghum (Sorghum bicolor) have been proven to participate in diverse abiotic stress responses, suggesting the conserved functional roles of MAPKKK family genes across gramineous species. Collectively, our findings provide comprehensive insights into the molecular mechanism of the maize MAPK signaling pathway mediating cold stress adaptation and supply valuable functional gene resources for cold-tolerant maize germplasm innovation and molecular breeding. Full article

Alternate wetting and drying (AWD) is a crucial water-saving irrigation strategy in rice production, yet its regulatory mechanisms during drought–rewatering cycles remain unclear, particularly across recovery stages. Using a polyethylene glycol (PEG-6000) hydroponic system, we analyzed physiological, metabolomic, and transcriptomic responses of Oryza sativa L. ssp. japonica under control, continuous drought, and rewatering treatments. The net photosynthetic rate (P_n) recovered within one day after rewatering, and subsequently exceeded control levels, indicating a photosynthetic compensatory effect. In contrast, instantaneous water-use efficiency (WUE) showed only a transient increase before declining thereafter and remaining lower than under continuous drought, revealing an asynchronous recovery in which carbon assimilation precedes the recovery of transpiration. Metabolomic analysis indicated a shift from drought-induced accumulation to recovery-driven metabolic reprogramming, with coordinated up-regulation of central carbon metabolism and chlorophyll biosynthesis. Decreases in citrate, malate, and glutamate suggested their sustained utilization to support nitrogen assimilation and chlorophyll synthesis. Transcriptomic data further revealed large-scale reprogramming during late recovery, including up-regulation of nitrogen assimilation genes (e.g., NIA, NiR), linking carbon–nitrogen coordination with photosynthetic compensation. Overall, these results demonstrate that stage-specific integration of physiological recovery, metabolic restructuring, and transcriptional regulation underlies AWD-induced efficiency and identify early rewatering as a critical window for optimizing WUE. Full article

Rice cultivation faces major environmental challenges due to climate change, particularly soil salinity, which limits plant growth and productivity. Salt tolerance in rice is typically evaluated using physiological and biochemical traits, whereas leaf anatomical traits combined with advanced statistical analyses remain underexplored. This study investigated leaf anatomical characteristics of the rice cultivar Tubtim Chumphae at the seedling stage under different salinity levels (0, 25, 50, 75, and 100 mM NaCl). Seedlings were cultivated in a soil-based pot system for 42 days prior to treatment, and salinity stress was applied for 4 weeks. Data were analyzed using the Kruskal–Wallis test and multivariate approaches, including Discriminant Analysis of Principal Components (DAPC) and Partial Least Squares Discriminant Analysis (PLS-DA). The results revealed that several anatomical traits significantly varied with salinity, including vertical epidermal cell size of long cells (Epi-VL-LC), major vascular bundle size in the lamina (MVB-la-HL), major vascular bundle size in the midrib (MVB-mid-HL and MVB-mid-VL), as well as stomatal size (St-HL and St-VL) and stomatal density (StD) (p < 0.01). DAPC effectively distinguished salinity levels based on leaf anatomical traits, and the PLS-DA results further supported the robustness of the classification. Epidermal cell size, cell wall and cuticle thickness, stomatal traits, and vascular bundle dimensions were identified as key candidate anatomical biomarkers of salt tolerance. S75 (75 mM NaCl treatment) was suitable as a screening level and S100 (100 mM NaCl treatment) as a confirmation level. The findings provide a useful reference for evaluating salt tolerance in this rice cultivar and may be integrated with morphological, physiological, and biochemical traits to support future rice breeding programs. These findings provide a reference for evaluating salt tolerance in this cultivar and may complement morphological, physiological, and biochemical traits in future rice breeding programs. Full article

Hydrogen sulfide (H₂S) functions as a pivotal gaseous signaling molecule in plants, yet its role in promoting crop yield remains elusive. Here, we demonstrate that sodium hydrosulfide (NaHS) application, a donor of hydrogen sulfide (H₂S), significantly accelerates growth, promotes flowering, and enhances grain yield in rice (Oryza sativa L.). Optimal NaHS treatment increased plant height, root length, and biomass accumulation, concomitant with elevated sucrose, starch, chlorophyll contents, and nitrate reductase activity. Integrated transcriptomic and proteomic analyses revealed that NaHS reprograms key biological pathways, including photosynthesis, carbon metabolism, lipid metabolism, the hormone signal transduction pathway, and reactive oxygen species (ROS) homeostasis. NaHS also remodels fatty acid metabolism, significantly increasing unsaturated fatty acids, linoleic acid (C18:2n6c), and α-linolenic acid (C18:3n3)—the latter serving as the direct precursor for JA biosynthesis—thereby fueling jasmonic acid (JA) biosynthesis. NaHS treatment also induced ROS accumulation while simultaneously activating antioxidant enzymes, maintaining redox homeostasis, and promoting cell proliferation in root meristems. Transmission electron microscopy revealed that NaHS enlarges peroxisomes and increases chloroplast oil body number, linking organellar dynamics to enhanced JA synthesis and ROS signaling. Collectively, our findings establish NaHS as a novel chemical regulator that coordinates JA and ROS signaling to boost rice growth, flowering, and grain yield, offering a promising strategy to improve crop productivity. Full article

Cadmium (Cd) contamination in rice paddies poses serious threats to food safety. This study investigated the effects of bamboo biochar, a microbial agent, and their combination on Cd accumulation, soil properties, and rhizosphere microbial communities in the rice cultivar ‘Ning 47’ (Oryza sativa L.) under Cd stress (20 mg·kg⁻¹). Cd stress significantly reduced plant height, root length, and yield. However, combined treatment with biochar and microbial agent (CdMB) effectively mitigated these effects, reducing Cd content in grains, stems, and roots by 85.98%, 88.66%, and 73.89%, respectively, compared to Cd treatment alone. The CdMB treatment also significantly increased soil organic matter and total nitrogen content while decreasing soil Cd levels by 88.38%. Network analysis identified Flavisolibacter as a keystone taxon under CdMB treatment, indicating enhanced microbial network stability. This also provides a theoretical reference for the management of heavy metal contamination in agricultural soils. By reducing grain Cd contamination and enhancing soil health, this integrated approach addresses key targets of the United Nations Sustainable Development Goals, including SDG 2 (Zero Hunger), SDG 3 (Good Health and Well-being), and SDG 15 (Life on Land). Full article

Trichomes are specialized epidermal structures that play pivotal roles in plant defense against biotic and abiotic stresses. Inositol polyphosphate kinase 2 (IPK2) is a key enzyme in inositol phosphate metabolism with diverse functions in eukaryotic cellular processes. However, its involvement in trichome development remains uncharacterized. Here, we systematically analyzed the function of a rice inositol polyphosphate kinase gene (OsIPK2) in trichome development using transgenic rice lines and heterologously expressing Arabidopsis lines. Scanning electron microscopy (SEM) analysis revealed that OsIPK2 acts as an organ-specific modulator of trichome development in rice. Its overexpression repressed macrohair initiation and microhair elongation in leaves, while promoting trichome development on the glumes. Metabolomic profiling revealed that OsIPK2 overexpression reprogrammed cuticular wax metabolism in transgenic rice leaves, shifting fatty acid flux toward long-chain wax precursors and increasing soluble carbohydrate levels. Transcriptomic and qPCR analysis confirmed that OsIPK2 modulated the expression of genes involved in cuticular wax biosynthesis, auxin homeostasis, and the core trichome regulatory cascade in rice. Conversely, heterologous overexpression of OsIPK2 in Arabidopsis strongly suppressed trichome initiation and branching, resulting in drastically reduced trichome density and fewer trichome branches. These phenotypes were associated with the downregulation of the MYB-bHLH-WD40 (MBW) transcriptional complex and its downstream target genes. Collectively, our findings suggest that OsIPK2 modulated trichome development through organ- and species-specific mechanisms. In rice, it coordinated wax metabolism and the OsSPL10-OsSCR1/2-OsWOX3B-OsHL6 cascade to affect organ-specific trichome formation. In Arabidopsis, it inhibited trichome development by repressing the MBW complex. These results uncover a novel role of OsIPK2 in plant epidermal cell fate specification and advance our understanding of the molecular mechanisms underlying organ- and species-specific regulation of trichome development. Full article

Salinity stress is one of the major obstacles to glycophytic crop production worldwide, including rice. It alters cellular metabolism, causing significant crop destruction that results in substantial reductions in yield. The overexpression of C₄ enzymes, such as phosphoenolpyruvate carboxykinase (PEPCK), at high levels in C₃ transgenic plants through genetic engineering can decrease oxidative stress while increasing photosynthetic capabilities. In this research, we evaluate the efficiency of transgenic rice plants (Oryza sativa L. cv. IR64) overexpressing PEPCK genes in mitigating salinity stress and increasing photosynthetic efficiency. The T1 transgenics showed increased levels of several biochemical factors, including ascorbate peroxidase (APX), catalase (CAT), proline, glutathione reductase (GR), and guaiacol peroxidase (GPX) activities. This was accompanied by reduced levels of malondialdehyde (MDA), hydrogen peroxide (H₂O₂), and electrolytic leakage, suggesting an effective antioxidant defense mechanism against the oxidative damage driven by salt stress. Photosynthetic parameters—such as chlorophyll content, net photosynthetic rate, intercellular CO₂ content, and stomatal conductance—were elevated in transgenic plants compared to control plants. The transgenics also exhibited superior agronomic characteristics. Our findings provide conclusive evidence of the PEPCK gene’s potential role in regulating salt stress response and tolerance in rice plants. Full article

Immature rice is a distinctive cereal product widely consumed in Asian countries due to its natural green color, soft texture, unique flavor, and high nutritional value. However, its fragile structure and pigment sensitivity create significant processing challenges. This study investigates the effects of infrared (IR) roasting temperature (550–650 °C) and time (20–40 min) on the physicochemical, nutritional, and cooked-rice qualities of immature rice (Oryza sativa L., cv. RD6). A two-factor study with three level of factorials was designed and response surface methodology (RSM) was used to evaluate roasting variables and to identify optimal processing conditions (p ≤ 0.05). Increasing roasting severity decreased rice yield, moisture content, water activity, and chlorophyll content, while promoting grain darkening, increasing phenolic content, and enhancing cooked-rice expansion and hardness. Several responses exhibited significant linear and quadratic relationships with roasting conditions, with model coefficients of determination (R²) ranging from 0.676 to 0.829. Multi-response optimization using desirability analysis identified the optimal roasting condition as 650 °C for 20 min, which produced predicted values that closely matched experimental validation (p > 0.05). These results demonstrate that IR roasting provides an effective green-energy processing approach for producing value-added immature rice while maintaining desirable color, nutritional properties, and cooked-rice texture. Full article

Nitrogen (N) is a key nutrient for upland rice (Oryza sativa L.), and plant growth-promoting rhizobacteria (PGPR) have been investigated as a sustainable strategy to improve plant nutrition and crop performance. This study evaluated the effects of N topdressing and PGPR inoculation on leaf chlorophyll index (LCI), leaf nutrient concentrations, and yield components in upland rice. A field experiment was conducted in a randomized block design (4 × 6 factorial) with four N rates (0, 40, 80, and 120 kg ha⁻¹) and five PGPR strains (Azospirillum brasilense, Nitrospirillum amazonense, Bacillus subtilis, Priestia aryabhattai, and Methylobacterium symbioticum), plus a non-inoculated control. No significant interaction between N rates and PGPR inoculation was observed. Nitrogen increased leaf phosphorus (P), potassium (K), and magnesium (Mg) concentrations and panicle number; however, it also increased unfilled grains, reduced grain weight, and did not affect grain yield. Azospirillum brasilense increased LCI by 25.7%. Bacillus subtilis and A. brasilense increased leaf N, K, Mg, copper (Cu) and manganese (Mn) concentrations. Azospirillum brasilense, B. subtilis, N. amazonense, and P. aryabhattai reduced unfilled grains, increased grain weight and grain yield by up to 10.7%, whereas M. symbioticum did not differ from the control in grain yield. Under the conditions of this study, nitrogen was not limiting for grain yield, and all strains, except M. symbioticum, were associated with increases in grain yield and changes in plant nutritional status. Full article