Oryza Sativa Research Articles

Impact of Zinc Solubilizing Bacteria and Microbial Consortia on Growth and Yield of Rice (Oryza sativa L.)

Rice (Oryza sativa L.) is a staple food for over half the world's population, particularly in Asia. This study explores the potential of Zn-solubilizing microbes to enhance micronutrient content in rice, aiming to address these deficiencies sustainably. Beneficial free-living soil bacteria, specifically plant growth-promoting rhizobacteria (PGPR), were investigated for their role in improving plant health and yield. Twenty-two bacterial isolates were screened for Zn solubilization, with Enterobacter hormaechei identified as the most promising. Field experiments with rice varieties PD 26 and NDR 359 involved treatmentssuch asT1 (Control), T2 (ZnSB1: Enterobacter hormaechei MT507226.1), T3 (Consortium1: Pantoearodasii MZ397586 + Seratiamarcesecens MW843567), and T4 (Consortium2: Enterobacter hormaechei MT507226.1 + Pantoearodasii MZ397586 + Seratiamarcesecens MW843567). with individual and consortia of Zn-solubilizing bacteria. Significant improvements were shown in plant height, leaf area index (LAI), total chlorophyll, total dry matter (TDM), and grain yield. Results showed that Consortium1 (T3) significantly increased plant height by 7.94% for PD26 and 10.16% for NDR 359. Leaf Area Index (LAI) also improved notably under Consortium1, with increases of 15.56% for PD26 and 24.39% for NDR 359. Total chlorophyll content was highest under Consortium1 for PD26 (36.63% increase) and under Consortium2 for NDR 359 (31.41% increase). Total dry matter (TDM) showed substantial gains, especially in NDR 359 with Consortium2 treatment, achieving a 36.51% increase. Grain yield increased significantly across all treatments, with Consortium1 showing the highest yields: 12.26% for PD26 and 23.01% for NDR 359.Correlation analysis indicated strong positive relationships between plant height, TDM, and grain yield, underscoring the importance of these parameters in determining crop productivity. The findings suggest that microbial consortia, particularly Consortium1, can effectively replace traditional zinc fertilizers, enhancing sustainable agriculture by promoting plant growth and yield. These results are consistent with recent studies on the role of plant growth-promoting rhizobacteria (PGPR) in improving nutrient uptake and crop performance.

Tillage practices on soil penetration resistance, soil infiltration, percolation and yield of rice (Oryza sativa) in rice-based cropping system

The experiment was conducted during 2019–23 at Tamil Nadu Rice Research Institute (Tamil Nadu Agricultural University, Coimbatore), Aduthurai, Tamil Nadu to analyse the effect of conservation tillage methods on bulk density, soil penetration resistance and soil infiltration rate of clay soil and rice yield in rice-based cropping system. Experiment consisted of three tillage practices, viz. conventional tillage/puddling (CT); zero tillage (ZT); and minimal tillage/dry ploughing (MT) and two rice (Oryza sativa L.) cultivars (ADT 43 and CORH 3), replicated four times. The result of the study revealed that the bulk density was significantly lower with zero tillage due to presence of crop residues and addition of organic matter. The mean infiltration rate under zero tillage was 0.16 cm/h as compared to puddling (0.14 cm/h) and dry ploughing (0.20 cm/h). The study further showed that the mean soil percolation rate was significantly altered by the tillage methods and soil percolation rate was 0.12 cm/h in zero tillage as compared to puddling (0.10 cm/h) and dry ploughing (0.16 cm/h). In contrary to the other physical properties, the soil penetration resistance was in the order of dry ploughing>zero tillage>puddling. The mean soil penetration resistance under zero tillage was reduced from 690–500 Kpa, 740–600 Kpa and 760–620 Kpa respectively at 0–5, 5–10 and 10–15 cm depth as compared to puddling. The results further indicated that the yield parameters and rice did not differ among the different tillage practices.

Protective Effects of an Octapeptide Identified from Riceberry™ (Oryza sativa) Protein Hydrolysate on Oxidative and Endoplasmic Reticulum (ER) Stress in L929 Cells

Reactive oxygen species (ROS) play a critical role in oxidative stress and cellular damage, underscoring the importance of identifying potent antioxidants. This research focuses on the antioxidant capabilities of Riceberry™-derived peptides and their protective effects against oxidative and endoplasmic reticulum (ER) stress in L929 cells. By simulating human digestion, Riceberry™ protein hydrolysate was generated, from which antioxidant peptides were isolated using OFFGEL electrophoresis and LC-MS/MS. Notably, an octapeptide (VPAGVAHW) from the hydrolysate demonstrated significant antioxidant activity, particularly against oxidative stress induced by iodoacetic acid (IAA) or hydrogen peroxide (H2O2) and ER stress caused by tunicamycin (TM) in L929 cells. This peptide’s effectiveness was evident in its dose-dependent ability to enhance cell viability and mitigate stress effects, although its efficiency varied with the stress inducer. Our study suggests that Riceberry™-derived peptides could serve as a promising natural antioxidant with potential benefits for health promotion and applications in the food industry, offering an environmentally friendly alternative to synthetic antioxidants.

The characteristic analysis of TaTDF1 reveals its function related to male sterility in wheat (Triticum aestivum L.)

BackgroundThe male sterile lines are an important foundation for heterosis utilization in wheat (Triticum aestivum L.). Thereinto, pollen development is one of the indispensable processes of wheat reproductive development, and its fertility plays an important role in wheat heterosis utilization, and are usually influencing by genes. However, these key genes and their regulatory networks during pollen abortion are poorly understood in wheat.ResultsDEFECTIVE IN TAPETAL DEVELOPMENT AND FUNCTION 1 (TDF1) is a member of the R2R3-MYB family and has been shown to be essential for early tapetal layer development and pollen grain fertility in rice (Oryza sativa L.) and Arabidopsis thaliana. In order to clarify the function of TDF1 in wheat anthers development, we used OsTDF1 gene as a reference sequence and homologous cloned wheat TaTDF1 gene. TaTDF1 is localized in the nucleus. The average bolting time of Arabidopsis thaliana overexpressed strain (TaTDF1-OE) was 33 d, and its anther could be colored normally by Alexander staining solution, showing red. The dominant Mosaic suppression silence-line (TaTDF1-EAR) was blue-green in color, and the anthers were shrimpy and thin. The TaTDF1 interacting protein (TaMAP65) was confirmed using Yeast Two-Hybrid Assay (Y2H) and Bimolecular-Fluorescence Complementation (BiFC) experiments. The results showed that downregulated expression of TaTDF1 and TaMAP65 could cause anthers to be smaller and shrunken, leading to pollen abortion in TaTDF1 wheat plants induced by virus-induced gene-silencing technology. The expression pattern of TaTDF1 was influenced by TaMAP65.ConclusionsThus, systematically revealing the regulatory mechanism of wheat TaTDF1 during anther and pollen grain development may provide new information on the molecular mechanism of pollen abortion in wheat.

Microbial degradation of paddy (Oryza sativa) straw by submerged state fermentation

This study elucidates the effective lignocellulose degrading potential of microbial consortium by using paddy straw as the sole source under submerged fermentation conditions. Straw degradation was enhanced by bioaugmentation procedures where consortia of isolated and standard cultures resulted in maximum enzyme activities of endoglucanase (1 U/ml), exoglucanase (1.31 U/ml), β-glucosidase (2.42 U/ml), xylanase (12.63 U/ml) and manganese peroxidase (5.43 U/ml) after 28 days of incubation along with laccase (4.36 U/ml) and lignin peroxidase (6.71 U/ml) after 21 days of incubation. By the action of consortium, maximum reduction of cellulose, hemicellulose and lignin was found to be 35.31, 22.50 and 44.72%, respectively after 28 days of incubation. A significant increase in percentage loss in dry matter of paddy straw was observed till 4 weeks of fermentation. Field emission scanning electron microscope (FE-SEM) micrographs revealed sufficient loosening of cellulose and hemicellulose showing successful degradation of straw tissue. Overall, the above stated findings emphasize on potential of lignocellulosic microorganisms to be used as an alternative to traditional stubble burning practice. Although, these extracellular enzymes are well equipped in breaking down lignocelluloses to their monomeric or oligomeric subunits, but they may not be exploited at commercial level due to very slow rate of reaction. The efficacy of these cultures for straw degradation in field condition further needs elaborative experimental trials as environmental parameters are quite variable in the field.

Yield Trait Association Studies through Principal Component Analysis in Bi-Parental Population Derived from indica/tropical japonica Inter Sub-Specific Cross in Rice (Oryza sativa L.)

In the present investigation, a mapping population consisting of 189 lines derived from an inter sub-specific cross between an indica cultivar, ‘Samba Mahsuri’ and a tropical japonica accession, ‘Cuba 65’ was investigated to assess the trait contribution to variability employing principal component analysis (PCA). The study aimed at determination of inter-relationships among various yield attributing traits vis-à-vis individuals of the mapping population. Out of eleven principal components (PC), first four PCs exhibited Eigen value more than one accounting to a total of 68.73% cumulative variance among the characters. The first PC accounted for the highest variability (PC1 31.6%) to the total variability, followed by 14.51% (PC2), 12.69% (PC3) and 9.91% (PC4). The highest positive Eigen value observed for the tiller number (0.33) and panicle number (0.32) in PC1 indicated their pronounced effect in the overall variation in the population. The analysis revealed the traits that contribute maximum for the variation. PCA also revealed negligible effect of days to fifty percent flowering, grain size and spikelet fertility to the variability in the mapping population. Although all the studied traits except grain size showed significant positive association with grain yield; negative correlation was observed between some of the component traits. Panicle weight, thousand grain weight and grain number showed negative association with tiller number and panicle number. The latter two traits contributed to the maximum variability in the population. The trait associations identified in the present investigation will help in determining the selection criteria to be adopted in the development of high yielding cultivars involving indica/tropical japonica populations.

Deciphering the genetic basis of agronomic, yield, and nutritional traits in rice (Oryza sativa L.) using a saturated GBS-based SNP linkage map

Developing high-yielding rice varieties that possess favorable agronomic characteristics and enhanced grain Zn content is crucial in ensuring food security and addressing nutritional needs. This research employed ICIM, IM, and multi-parent population QTL mapping methods to identify important genetic regions associated with traits such as DF, PH, NT, NP, PL, YLD, TGW, GL, GW, Zn, and Fe. Two populations of recombinant inbred lines consisting of 373 lines were phenotyped for agronomic, yield and grain micronutrient traits for three seasons at IRRI, and genotyped by sequencing. Most of the traits demonstrated moderate to high broad-sense heritability. There was a positive relationship between Zn and Fe contents. The principal components and correlation results revealed a significant negative association between YLD and Zn/Fe. ICIM identified 81 QTLs, while IM detected 36 QTLs across populations. The multi-parent population analysis detected 27 QTLs with six of them consistently detected across seasons. We shortlisted eight candidate genes associated with yield QTLs, 19 genes with QTLs for agronomic traits, and 26 genes with Zn and Fe QTLs. Notable candidate genes included CL4 and d35 for YLD, dh1 for DF, OsIRX10, HDT702, sd1 for PH, OsD27 for NP, whereas WFP and OsIPI1 were associated with PL, OsRSR1 and OsMTP1 were associated to TGW. The OsNAS1, OsRZFP34, OsHMP5, OsMTP7, OsC3H33, and OsHMA1 were associated with Fe and Zn QTLs. We identified promising RILs with acceptable yield potential and high grain Zn content from each population. The major effect QTLs, genes and high Zn RILs identified in our study are useful for efficient Zn biofortification of rice.

Comprehensive mapping and modelling of the rice regulome landscape unveils the regulatory architecture underlying complex traits

Unraveling the regulatory mechanisms that govern complex traits is pivotal for advancing crop improvement. Here we present a comprehensive regulome atlas for rice (Oryza sativa), charting the chromatin accessibility across 23 distinct tissues from three representative varieties. Our study uncovers 117,176 unique open chromatin regions (OCRs), accounting for ~15% of the rice genome, a notably higher proportion compared to previous reports in plants. Integrating RNA-seq data from matched tissues, we confidently predict 59,075 OCR-to-gene links, with enhancers constituting 69.54% of these associations, including many known enhancer-to-gene links. Leveraging this resource, we re-evaluate genome-wide association study results and discover a previously unknown function of OsbZIP06 in seed germination, which we subsequently confirm through experimental validation. We optimize deep learning models to decode regulatory grammar, achieving robust modeling of tissue-specific chromatin accessibility. This approach allows to predict cross-variety regulatory dynamics from genomic sequences, shedding light on the genetic underpinnings of cis-regulatory divergence and morphological disparities between varieties. Overall, our study establishes a foundational resource for rice functional genomics and precision molecular breeding, providing valuable insights into regulatory mechanisms governing complex traits.

Seed priming and subsequent inoculation of drought-tolerant plant growth-promoting rhizobacteria Bacillus tropicus KH90 improves rice (Oryza sativa L.) plant health under drought and non-drought conditions

Seed priming and subsequent inoculation of drought-tolerant plant growth-promoting rhizobacteria Bacillus tropicus KH90 improves rice (Oryza sativa L.) plant health under drought and non-drought conditions

Dynamics of Fe, Mn, and potentially harmful elements under reducing conditions in iron ore tailings after dam collapse in the Doce River basin-Brazil: flooded and non-flooded rice cultivations.

Potentially harmful element (PHE) bioavailability is important to environmental contamination and must be checked under several soil conditions. This study aimed to assess Fe, Mn, and PHE uptake by rice (Oryza sativa) grown on flooded and non-flooded Fe tailings collected from the Doce River basin after its collapse in Brazil. After 65days of sowing, shoots and roots were harvested to determine PHE concentrations. The mean concentrations of Mn in shoots and Fe in the roots of rice grown on the flooded tailings were 2140mgkg-1 and 15,219mgkg-1, respectively. Mn was extensively translocated from roots to shoots (translocation factor (TF) = 2). Conversely, Fe accumulated in roots (TF = 0.015) and caused morphological damage to this rice organ. The application of macro and micronutrients lessened Fe toxicity in the roots of rice cultivated on the flooded tailings. The flooding of tailings influenced more Fe accumulation than Mn accumulation by rice plants. The PHE Ag, As, Cd, Ni, Hg, Pb, and Sb exhibited low total concentrations (maximum of 9mgkg-1 for Ni and a minimum of 0.2mgkg-1 for Cd, Hg, and Sb), and it was not observed an increase in their availability under tailings flooding conditions.

Cytokinin oxidase2-deficient mutants improve panicle and grain architecture through cytokinin accumulation and enhance drought tolerance in indica rice.

The Osckx2 mutant accumulates cytokinin thereby enhancing panicle branching, grain yield, and drought tolerance, marked by improved survival rate, membrane integrity, and photosynthetic function. Cytokinins (CKs) are multifaceted hormones that regulate growth, development, and stress responses in plants. Cytokinins have been implicated in improved panicle architecture and grain yield; however, they are inactivated by the enzyme cytokinin oxidase (CKX). In this study, we developed a cytokinin oxidase 2 (Osckx2)-deficient mutant using CRISPR/Cas9 gene editing in indica rice and assessed its function under water-deficit and salinity conditions. Loss of OsCKX2 function increased grain number, secondary panicle branching, and overall grain yield through improved cytokinin content in the panicle tissue. Under drought conditions, the Osckx2 mutant conserved more water and demonstrated improved water-saving traits. Through reduced transpiration, Osckx2 mutants showed an improved survival response than the wild type to unset dehydration stress. Further, Osckx2 maintained chloroplast and membrane integrity and showed significantly improved photosynthetic function under drought conditions through enhanced antioxidant protection systems. The OsCKX2 function negatively affects panicle grain number and drought tolerance, with no discernible impact in response to salinity. The finding suggests the utility of the beneficial Osckx2 allele in breeding to develop climate-resilient, high-yielding cultivars for future food security.

Integrated transcriptome and metabolome analysis of salinity tolerance in response to foliar application of choline chloride in rice (Oryza sativa L.)

Integrated transcriptome and metabolome analysis of salinity tolerance in response to foliar application of choline chloride in rice (Oryza sativa L.)

Specialized Metabolites From the Husks of Rice Oryza sativa L. and Their Biological Activities.

Rice (Oryza sativa L.) husk harbors a substantial proportion of biological metabolites, as one of the most plentiful agriculture by-products in rice milling process, rice husk remains poorly utilized. As a continuing search for potential bioactive molecules from the husk of rice, a totally of twelve conponents (1-12), including six sterol ferulates (1-6), one flavonoid (7), one dipeptide (8), and four phenylpropanoid derivatives (9-12) were obtained. All the chemical structures were elucidated based on comprehensive spectroscopic data. Wherein, compounds 1 and 2 were yield as previous undescribed metabolites, and the comprehensive NMR data for compounds 3 and 4 were first presented in its entirety. Motivated by the similarity of the structural motifs of components 1-6 to that of reported sterol ferulates, the antioxidant and anti-inflammatory effects for compounds 1-6 were evaluated in vitro. Among them, compounds 5/6 had a significant antioxidant activity compare to that of vitamin E in both DPPH and reducing power assay up to the concentration 40 μg/ml; while compounds 1 and 2 exhibited weak suppressive effect on the production of nitric oxide, with the IC50 values of 53.27 ± 1.37 μM.

The structural and digestive properties of indica rice starch-fatty acid complexes

The structural and digestive properties of indica rice starch-fatty acid complexes and the effects of lipoxygenase on the structural and digestive properties of the complexes were examined in this study. The complexes were characterized by scanning electron microscopy, X-ray diffraction, Fourier transform-infrared spectroscopy and Raman spectroscopy. The results showed that indica rice starch had the highest molecular chain order and the highest crystallinity, and the crystallization disappeared after gelatinization, and the formation of indica rice starch-fatty acid complexes promoted the transformation of starch crystal structure from A-type to V-type. Lipoxygenase reduced the regularity of starch molecular crystal structure in the complexes, while enzyme protein improved the order of starch molecular structure in the complexes. The regularity of starch crystal structure in the complexes could improve with the increase of composite temperature and the increase of fatty acid unsaturation. In vitro digestibility and in vitro digestion kinetics showed that the formation of indica rice starch-fatty acid complexes reduced the digestibility of indica rice starch to a certain extent. The RDS content of indica rice starch was 66.42 ± 0.39 %, and lipoxygenase reduced the reduction of rapidly digested starch content during complexes digestion, while enzyme protein increased the content of resistant starch.

Detection and Evaluation of Blast Resistance Genes in Backbone Indica Rice Varieties from South China

Detection and Evaluation of Blast Resistance Genes in Backbone Indica Rice Varieties from South China

A maize semi-dwarf mutant reveals a GRAS transcription factor involved in brassinosteroid signaling.

Brassinosteroids (BR) and gibberellins (GA) regulate plant height and leaf angle in maize (Zea mays). Mutants with defects in BR or GA biosynthesis or signaling identify components of these pathways and enhance our knowledge about plant growth and development. In this study, we characterized three recessive mutant alleles of GRAS transcription factor 42 (gras42) in maize, a GRAS transcription factor gene orthologous to the DWARF AND LOW TILLERING (DLT) gene of rice (Oryza sativa). These maize mutants exhibited semi-dwarf stature, shorter and wider leaves, and more upright leaf angle. Transcriptome analysis revealed a role for GRAS42 as a determinant of BR signaling. Analysis of the expression consequences from loss of GRAS42 in the gras42-mu1021149 mutant indicated a weak loss of BR signaling in the mutant, consistent with its previously demonstrated role in BR signaling in rice. Loss of BR signaling was also evident by the enhancement of weak BR biosynthetic mutant alleles in double mutants of nana plant1-1 and gras42-mu1021149. The gras42-mu1021149 mutant had little effect on GA-regulated gene expression, suggesting that GRAS42 is not a regulator of core GA signaling genes in maize. Single-cell expression data identified gras42 expressed among cells in the G2/M phase of the cell cycle consistent with its previously demonstrated role in cell cycle gene expression in Arabidopsis (Arabidopsis thaliana). Cis-acting natural variation controlling GRAS42 transcript accumulation was identified by expression genome-wide association study (eGWAS) in maize. Our results demonstrate a conserved role for GRAS42/SCARECROW-LIKE 28 (SCL28)/DLT in BR signaling, clarify the role of this gene in GA signaling, and suggest mechanisms of tillering and leaf angle control by BR.

Starch Characteristics and Amylopectin Unit and Internal Chain Profiles of Indonesian Rice (Oryza sativa)

Indonesia is arguably a major player in worldwide rice production. Though white rice is the most predominantly cultivated, red, brown, and red rice are also very common. These types of rice are known to have different cooking properties that may be related to differences in their starch properties. Investigating the starch properties, especially the fine structure of their amylopectin, can help understand these differences. This study aims to investigate the starch characteristics of some Indonesian rice varieties by evaluating the starch granule morphology and size, molecular characteristics, amylopectin unit and internal chain profiles, and thermal properties. Starches were extracted from white rice (long grain (IR-64) and short grain (IR-42)), brown rice, red rice, and black rice cultivated in Java Island, Indonesia. IR-42 had the highest amylose content of 39.34% whilst the black rice had the least of 1.73%. The enthalpy of gelatinization and onset temperature of the gelatinization of starch granules were between 3.2 and 16.2 J/g and 60.1 to 73.8 °C, respectively. There were significant differences between the relative molar amounts of the internal chains of the samples. The two white rice and black rice had a significantly higher amount of A-chains, but a lower amount of B-chains and fingerprint B-chains (Bfp) than the brown and red rice. The average chain length (CL), short chain length (SCL), and external chain length (ECL) were significantly longer for the red rice and the black rice in comparison to both the white rice amylopectins. The long chain length (LCL) and internal chain length (ICL) of the sample amylopectins were similar. Rice starches were significantly different in the internal structure but not as much in their amylopectin unit chain profile. These results suggest the differences in their amylopectin clusters and building blocks.

Effect of Arbuscular Mycorrhizal Fungi on the growth and Yield of Rice (Oryza sativa L.) in Bauchi, Nigeria

Effect of Arbuscular Mycorrhizal Fungi on the growth and Yield of Rice (Oryza sativa L.) in Bauchi, Nigeria

Prediction of protein content in paddy rice (Oryza sativa L.) combining near-infrared spectroscopy and deep-learning algorithm

Rice is a staple crop in Asia, with more than 400 million tons consumed annually worldwide. The protein content of rice is a major determinant of its unique structural, physical, and nutritional properties. Chemical analysis, a traditional method for measuring rice’s protein content, demands considerable manpower, time, and costs, including preprocessing such as removing the rice husk. Therefore, of the technology is needed to rapidly and nondestructively measure the protein content of paddy rice during harvest and storage stages. In this study, the nondestructive technique for predicting the protein content of rice with husks (paddy rice) was developed using near-infrared spectroscopy and deep learning techniques. The protein content prediction model based on partial least square regression, support vector regression, and deep neural network (DNN) were developed using the near-infrared spectrum in the range of 950 to 2200 nm. 1800 spectra of the paddy rice and 1200 spectra from the brown rice were obtained, and these were used for model development and performance evaluation of the developed model. Various spectral preprocessing techniques was applied. The DNN model showed the best results among three types of rice protein content prediction models. The optimal DNN model for paddy rice was the model with first-order derivative preprocessing and the accuracy was a coefficient of determination for prediction, Rp2 = 0.972 and root mean squared error for prediction, RMSEP = 0.048%. The optimal DNN model for brown rice was the model applied first-order derivative preprocessing with Rp2 = 0.987 and RMSEP = 0.033%. These results demonstrate the commercial feasibility of using near-infrared spectroscopy for the non-destructive prediction of protein content in both husked rice seeds and paddy rice.

Transcription factor NAC78 cooperates with NAC78 INTERACTING PROTEIN6 to confer drought tolerance in rice.

NAC (NAM, ATAF1/2, and CUC2) family transcription factors are involved in several cellular processes, including responses to drought, salinity, cold, and submergence. However, whether or how certain NAC proteins regulate drought tolerance in rice (Oryza sativa) remain unclear. In this study, we show that over-expression of OsNAC78 enhanced rice resistance to drought treatment, whereas Osnac78 mutant plants were susceptible to drought stress. We further characterized the OsNAC78 interacting protein, named NAC78 interacting protein6 (OsNACIP6), and found that it conferred rice drought tolerance. Our results demonstrate that OsNACIP6 enhanced transcription of OsNAC78 and promoted the expression of its downstream target OsGSTU37, encoding a glutathione reductase. The ABRE4 cis-element in the promoter region of OsNACIP675-1-127 conferred significant up-regulation of OsNACIP6 expression and initiated the OsNACIP6/OsNAC78-OsGSTU37 module that facilitates rice growth under drought conditions. Together, our results uncover a transcriptional module composed of OsNACIP6, OsNAC78, and OsGSTU37 and provide insights into the molecular mechanisms underlying the drought stress response in rice.