Search Results (1,733)

Improving rice grain quality while reducing nitrogen (N) fertilizer input is a key challenge for sustainable rice production. Although biochar can enhance soil fertility and N use efficiency, its effects on grain quality and starch functionality under reduced N input remain unclear. Two-year pot experiments involving japonica rice cultivars were conducted with different N rates (0.7N–1.1N) under no-biochar (NB) and biochar (BI) conditions. Under non-biochar conditions, grain yield increased with N input, with no significant difference between 1.0N and 1.1N. Biochar application increased grain yield by 4.0–13.3% compared with the corresponding no-biochar treatments, and the yield of BI-0.9N was comparable to that of NB-1.0N. Nitrogen reduction decreased grain chalkiness and improved eating quality, whereas excessive N reduction lowered head rice rate. Biochar improved milling quality and eating quality, while its effects on appearance quality were relatively limited. Compared with 1.0N, 1.1N increased protein content but reduced amylose content and starch viscosity parameters, whereas 0.9N showed the opposite trend. Biochar further increased starch viscosity parameters, with peak and final viscosities increasing by 4.4–30.2% and 2.9–38.9%, respectively, under reduced N conditions, and altered starch thermal properties. Correlation analysis indicated that milling quality correlated with protein content and starch solubility, while eating quality correlated with peak viscosity and breakdown value. In this study, biochar combined with 10% N reduction (BI-0.9N) maintained grain yield while improving grain quality and starch functional properties compared with conventional N management (NB-1.0N), indicating its potential as a nitrogen-saving management option for japonica rice production. Full article

Salinity limits early rice establishment by imposing osmotic stress, ionic imbalance, and poor early seedling growth. Magnetic-field seed treatment has been explored mainly using static magnetic fields (SMFs), whereas low-intensity pulsed electromagnetic fields (PEMFs) remain less defined as physical seed-treatment inputs under salinity. Here, we directly compared SMF and 10 Hz PEMF under matched low-intensity conditions to determine whether PEMF can function as an effective physical seed treatment in rice. Seeds of Oryza sativa L. cv. Phitsanulok 2 were exposed to SMF (2.0 mT) or PEMF (10 Hz, approximately 2.0 mT peak) using three protocols—1 h before sowing, 10 min daily after sowing, or a combined schedule—followed by germination under 150 mM NaCl. Magnetic exposure had limited effect on final germination percentage, but a single 1 h pre-sowing treatment with either SMF or PEMF significantly increased the germination rate index under salinity. This protocol also improved root length, seedling dry weight, and seedling vigour, whereas repeated daily exposure produced less consistent benefits. Redox analysis showed that PEMF increased H₂O₂ at 48 h but reduced H₂O₂ at 96 and 120 h compared with the untreated saline control at the corresponding sampling time. PEMF also produced the clearest increase in extractable DPPH radical-scavenging activity at 120 h. Ion analysis showed that the 1 h pre-sowing treatment improved tissue ion balance, as reflected by lower Na⁺ accumulation, improved K⁺ status, and a reduced Na⁺/K⁺ concentration ratio, particularly in roots. Overall, this study identifies a timing-specific low-intensity magnetic-treatment window for improving early rice establishment under salinity and positions 10 Hz PEMF as a testable non-chemical physical treatment associated with redox remodeling and improved ion homeostasis. Full article

N⁶-methyladenosine (m⁶A) is a vital epitranscriptomic modification that regulates plant development and stress responses. In rice (Oryza sativa L.), the identity of the catalytic subunit (MTA) of the core m⁶A writer complex has remained controversial because of inconsistent annotations based primarily on sequence homology. Here, phylogenetic analysis identified LOC_Os02g45110 as the putative catalytic subunit OsMTA, whereas LOC_Os01g16180 and LOC_Os03g05420 were classified as the structural subunits OsMTB1 and OsMTB2, respectively. All three proteins showed nuclear enrichment. Yeast two-hybrid, luciferase complementation imaging, and bimolecular fluorescence complementation assays demonstrated that OsMTA interacts independently with OsMTB1 and OsMTB2. Moreover, transient co-expression of OsMTA with either OsMTB1 or OsMTB2 increased global m⁶A levels in a heterologous system. No homozygous plants carrying frameshift mutations in OsMTA were obtained, suggesting that complete loss of OsMTA function is lethal. Knockdown of OsMTA or CRISPR/Cas9-mediated knockout of OsMTB1 and OsMTB2 significantly delayed heading date and reduced 1000-grain weight. Conversely, overexpressing OsMTA accelerated heading, whereas overexpressing OsMTB1 or OsMTB2 generally accelerated heading but significantly reduced 1000-grain weight. Together, these findings define the core composition of the rice m⁶A writer complex and reveal its effects on heading date and grain weight. Full article

Single-nucleotide polymorphism (SNP) arrays provide reproducible, accurate, and scalable genotyping for rice research and cultivar development. This review critically evaluates the design and development of major rice SNP platforms and defines their value within a rapidly changing genotyping landscape. In contrast to earlier platform-centered summaries, this review connects array selection with the complete breeding pathway from germplasm assessment and locus discovery to functional validation, marker-assisted transfer, genomic selection, varietal authentication, and pre-breeding. SNP arrays are compared with genotyping-by-sequencing, double-digest restriction site-associated DNA sequencing, low-pass sequencing, whole-genome resequencing, targeted sequencing, and long-read sequencing in terms of cost, throughput, data completeness, computational demand, marker discovery, and population transferability. Candidate-locus validation through gene-expression analysis, haplotype analysis, near-isogenic lines, RNA interference, transgenic complementation, clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas) editing, and field evaluation is also examined. Pangenome resources and the contributions of structural variants, presence/absence variations, and copy number variations to probe design and trait analysis receive particular attention. The review further assesses ascertainment bias, weak detection of rare alleles, genotype-cluster errors, limited portability across distant germplasm, and reduced genomic prediction across populations or environments. Future priorities include multi-omics integration, climate-resilient rice improvement, modular panels, imputation anchor loci, and economical deployment through low-density assays, shared facilities, and kompetitive allele-specific polymerase chain reaction conversion. The value of SNP arrays is greatest when stable genotype calls, large sample numbers, and repeated use across breeding cycles are required. Their practical contribution should be judged by prediction accuracy, selection cost, cycle duration, donor-segment control, realized genetic gain, and cultivar deployment. Full article

Background: Domain of Unknown Function 1645 (DUF1645) is a conserved but poorly characterized plant gene family whose evolutionary history and roles in stress adaptation remain unclear. We performed an integrated genomic, evolutionary, transcriptomic, and Quantitative Trait Locus (QTL) characterization of the DUF1645 family in rice (Oryza sativa). Methods and Results: We identified 14 intronless, non-redundant OsDUF1645 genes distributed across eight chromosomes. Phylogenetic and collinearity analyses suggested that family expansion within Poaceae involved ancestral segmental and localized tandem duplication events. Promoter analysis identified stress- and phytohormone-responsive cis-acting elements, including ABRE, MBS, and MeJA-associated motifs. Public transcriptome datasets revealed diverse OsDUF1645 expression patterns under abiotic and hormonal treatments. Integration with the Quantitative Trait Loci Annotation Rice Online (Q-TARO) QTLome identified physical co-localization of multiple OsDUF1645 loci with stress- and agronomic-trait QTLs, including salinity-, drought-, root architecture-, and water-deficit-associated regions. On Chromosome 1, OsDUF1645.1, OsDUF1645.2, OsDUF1645.3, and OsDUF1645.4 overlapped QTL intervals associated with salinity-related physiological traits, including Na⁺ uptake and Na⁺ balance, and drought-related root traits. On Chromosome 5, the tandemly arranged OsDUF1645.8, OsDUF1645.9, and OsDUF1645.10 co-localized with QTLs related to root architecture and water-deficit responses. qRT-PCR validation under salinity, osmotic stress, and cadmium exposure confirmed distinct stress-responsive expression profiles; OsDUF1645.6 exhibited broad multi-stress responsiveness, whereas OsDUF1645.3 was downregulated under several conditions. Conclusions: The OsDUF1645 family exhibits substantial functional diversification, supported by distinct regulatory architectures, expression profiles, and QTL associations. These findings provide a framework for prioritizing OsDUF1645 candidates for functional validation and their potential application in molecular breeding and development of climate-resilient rice cultivars. Full article

Background/Objectives: Phytocystatins are plant-specific inhibitors of papain-like cysteine proteinases that participate in plant development and responses to biotic and abiotic stresses. The roles of rice (Oryza sativa L.) phytocystatins under cold stress remain poorly understood. Xiaomagu (XMG), a cold-tolerant japonica rice landrace, provides valuable material for exploring phytocystatin transcript responses to low-temperature stress. This study characterizes 12 rice phytocystatin genes isolated from XMG and investigates their transcript profiles under cold and abscisic acid (ABA) treatments. Methods: Twelve phytocystatin genes were isolated from the cold-tolerant japonica rice landrace Xiaomagu. Sequence characterization and conserved domain analysis were performed for these phytocystatin family members. Real-time quantitative PCR was performed to examine transcript abundance of phytocystatin genes: low-temperature stress was applied to leaf and root tissues, while ABA treatment was carried out for leaf tissues only. Results: Conserved domain analysis revealed structural differences among the identified phytocystatin members. Real-time quantitative PCR detected distinct transcriptional responses to cold stress among these phytocystatin genes. In leaves, OsCST1, OsCST8, and OsCST12 were up-regulated, whereas OsCST11 was down-regulated. In roots, OsCST2, OsCST3, OsCST6, and OsCST12 showed increased transcript levels, while OsCST1 and OsCST11 were down-regulated. OsCST2, OsCST6, and OsCST11 exhibited significantly altered transcript abundance under ABA treatment. Conclusions: This study characterizes transcript-level responses of 12 phytocystatin genes from the cold-tolerant rice landrace Xiaomagu (XMG) under cold and ABA treatments. The detected expression changes reflect stress-responsive transcriptional regulation of rice phytocystatin family genes. Further in planta functional assays and comparisons with cold-sensitive genotypes are needed to elucidate their precise roles in rice cold adaptation. Full article

Organic amendments (biochar, manure, and straw) are widely used as soil-applied functional materials in polluted soils; however, integrated comparative assessments within crop rotation systems remain limited. We established a rice (Oryza sativa L.: Hanyou 3015 and Yangtaiyou 128)–celery (Apium graveolens L.: Queen Celery) rotation system on farmland contaminated with heavy metals (HMs). Biochar (B), manure (M), and straw (S) were applied to assess HM dynamics, greenhouse gas emissions (CO₂, CH₄ and N₂O), and overall system responses. B showed limited but generally stabilizing effects on crop performance and greenhouse gas emissions in the rice–celery rotation system; however, it significantly reduced Cd, Pb, and Zn uptake in celery during the later stages of the rotation. Although M enhanced soil N transformation and microbial biomass C, increased yield by 50%, and improved total system carbon sequestration, the associated risk of heavy metal accumulation during the initial rice phase should be considered in agricultural management. S increased rice and celery yields, reduced Pb and Zn accumulation in edible parts, and enhanced carbon sequestration in both crops and soil during the celery phase. These results highlight amendment-specific functions and associated trade-offs in the management of contaminated soils. Full article

Cadmium (Cd) contamination in paddy soils represents a major risk to global food security and human health because Cd can readily enter the food chain through rice consumption. Therefore, clarification of the key processes and mechanisms by which agronomic practices regulate Cd accumulation in rice is essential. Based on integrated two-year pot and field experiments, we showed that different nitrogen fertilizer formulations, including nitrate-N (N), ammonium-N (A), and urea (U), had distinct effects on Cd accumulation and grain yield in rice. The N treatment reduced Cd concentrations in brown rice by 25.29% to 70% in the pot experiment and by 4.25% to 89.97% in the field experiment but decreased grain yield by 5% to 25%. By contrast, the A treatment increased Cd concentrations in brown rice by 17.86% to 58.62%, while maintaining or slightly increasing grain yield (−3% to +5%), and the U treatment showed intermediate responses. These responses were mainly associated with nitrogen-induced shifts in rhizosphere chemistry, especially changes in soil Cd availability linked to pH and exchangeable H⁺, although unmeasured redox-related processes may have also contributed under flooded conditions. Further analyses of internal Cd distribution and translocation, together with exploratory random forest modeling, suggested that Cd transport efficiency at key stem internodes and Cd redistribution from the panicle to the grain were important regulatory nodes associated with Cd concentrations in brown rice. These regulatory nodes were markedly affected by fertilizer formulation. Overall, our results describe a continuous pathway from rhizosphere Cd availability to internal transport and partitioning, through which nitrogen fertilizer formulations regulate Cd accumulation in rice. This study aimed to clarify how different nitrogen fertilizer formulations regulate the trade-off between grain yield and Cd accumulation in rice, based on the hypothesis that these formulations differentially modify rhizosphere chemistry and Cd bioavailability, that specific stem nodes contribute to control of grain Cd accumulation, and that the main regulatory processes differ between pot and field systems. This study provides s a scientific basis for developing practical nitrogen-management strategies to support safe rice production in Cd-contaminated paddy fields. Full article

Cold stress (CS) severely limits the growth and productivity of rice (Oryza sativa L.), particularly in temperate regions where abrupt temperature declines frequently occur during early developmental stages. In recent years, nanoparticle (NP) application has emerged as a promising approach for alleviating CS; however, systematic comparisons of different NPs across multiple growth stages remain unclear. This study evaluated the effectiveness and physiological mechanisms of four NPs (Fe₂O₃, ZnO, TiO₂, and CeO₂) in enhancing CS tolerance of rice seedlings using four cultivars with contrasting cold tolerance: two conventional cultivars (ZJZ-17, cold-sensitive; XZX-6, cold-tolerant) and two hybrid cultivars (LLY-7108, cold-tolerant; LLY-32, cold-sensitive). Seedlings were subjected to CS (14 °C day/10 °C night) for 5 days at three developmental stages (14, 21, and 28 days after emergence), followed by a 7-day recovery period under optimal conditions. CS markedly reduced plant height (34.8%), fresh weight (57.2%), dry weight (50.0%), and chlorophyll a and b contents (48%) following recovery. Foliar application of NPs significantly mitigated the adverse effects of CS, with Fe₂O₃ and ZnO showing the highest effectiveness. Fe₂O₃ treatment increased plant height, fresh weight, and dry weight by 25.6%, 43.5%, and 40.6%, respectively, relative to cold-stressed plants, while chlorophyll a and b contents increased by 41.6% and 42.2%. NPs application alleviated oxidative damage by reducing reactive oxygen species (up to 67.4%), malondialdehyde (up to 51.2%), and proline accumulation (up to 60.4%). Enhanced antioxidant defense was evidenced by increased activities of superoxide dismutase (66.6%), peroxidase (59.6%), and catalase (34.3%) under Fe₂O₃ treatment. Yield-related traits also showed significant recovery, with Fe₂O₃ increasing tiller number, spikelets per panicle, and grain yield per plant. The hybrid cultivar LLY-7108 consistently exhibited greater CS tolerance than conventional cultivars, while the cold-sensitive cultivar ZJZ-17 showed the greatest susceptibility. CS imposed at later growth stages (28-day-old seedlings) caused less damage and allowed greater recovery than early-stage stress (14-day-old seedlings). Overall, NP-mediated enhancement of photosynthesis and antioxidant capacity significantly improves CS tolerance and yield performance in rice, with Fe₂O₃ NPs emerging as a promising strategy for mitigating CS. These findings provide practical insights for rice cultivation in regions prone to chilling events and contribute to the development of nanoparticle-based approaches for rice production under climate stress. Full article

Rice (Oryza sativa L.) is a staple food crop worldwide, and improving disease resistance is a core target in rice breeding. In this study, we employed CRISPR/Cas9 genome editing to modify the coding sequence (CDS) of two susceptibility genes, Bsr-d1 and Pi21, in the elite maintainer line Gengxiang B to enhance its blast resistance. We generated Bsr-d1/Pi21 double homozygous mutants via Agrobacterium-mediated genetic transformation. Quantitative RT-PCR revealed significantly suppressed transcript accumulation of both target genes in the edited lines compared with the wild type Gengxiang B. Upon inoculation with Magnaporthe oryzae, multiple defense-related marker genes were markedly upregulated in the double mutants. Phenotypic assays demonstrated significantly reduced disease severity for both leaf and panicle blast in the edited lines compared with the wild type. Importantly, no statistically detectable differences were found between the double mutants and wild-type plants for key agronomic or grain quality traits. Collectively, these results demonstrate that CRISPR/Cas9-mediated editing of susceptibility loci generates genetically stable blast-resistant rice germplasm without compromising agronomic traits or grain quality, providing valuable genetic resources for future rice varietal improvement. Full article

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

This study evaluated the effect of chickpea and rice incorporation to replace corn in extruded snacks on protein digestibility, mineral bioaccessibility, and estimated glycemic index (eGI) using a standardized in vitro digestion model (INFOGEST 2.0). Four formulations were analyzed: a control (100% corn, CF) and chickpea-enriched snacks (F30, F60, and the commercial flavored F60 formulation, CCP). Chickpea replacement increased protein, dietary fiber, and mineral contents while reducing total starch. Protein digestibility remained high across all samples (89.5–96.6%), although slightly lower in chickpea/rice-enriched formulations. However, these formulations provided a higher amount of digestible protein because of their increased protein content. Mineral bioaccessibility varied depending on the element, but chickpea and rice incorporation generally enhanced mineral concentrations in the fraction potentially available for absorption despite the presence of phytic acid and insoluble dietary fiber. Starch hydrolysis was rapid during the early stages of digestion, leading to high estimated glycemic index (eGI) values in all samples. Nevertheless, chickpea/rice-enriched formulations exhibited lower eGI values compared to the corn control, likely due to reduced starch content and matrix effects. Overall, chickpea and rice replacement improved the nutritional profile of extruded snacks by enhancing protein quality and mineral availability, despite its impact on glycemic response being limited, highlighting opportunities for further product optimization. Full article