Rice Grain Research Articles

Machine learning with analysis-of-variance-based method for identifying rice varieties

Rice, which has the highest production and consumption rates worldwide, is one of the main nutrients in our country because it is economical and nutritious. Rice undergoes various stages of production from the field to the dinner tables, with the cleaning phase involving separation of rice from unwanted materials. There are different varieties of rice such as arborio, basmati, aracadaga, ipsala, and jasmine. Therefore, it is necessary to identify rice varieties based on customer demands. Rice variety identification is primarily based on its outer appearance, including color, size, and shape. In this study, 75,000 rice grain images, including 15,000 images for each variety, were considered. Using a combination of 12 morphological features, four shape features, and 90 color features obtained from five different color spaces, 106 features were extracted from the images. An analysis of variance (ANOVA) was employed to select high-rank features, which were then fed to a support vector machine (SVM) for classification. The experimental results demonstrated that the utilization of 40 high-rank features yielded impressive outcomes, with a validation accuracy of 99.89 %, cost value of 16, test accuracy of 99.81 %, and cost value of 28. These high accuracy rates are particularly noteworthy, as they indicate the robustness and reliability of the proposed methodology in distinguishing between different rice varieties with minimal error. This high level of precision is critical for practical applications, such as quality control in rice production, to ensure that customers receive the specific rice variety they demand. Implementing this methodology in real-world scenarios could significantly enhance the efficiency and accuracy of the rice variety identification processes, benefiting both producers and consumers.

Effects of silicate stabilizers on cadmium reduction and the quality of rice grains in acidic paddy soil

Silicate has been proven to be highly-effective at immobilizing soil heavy metals, but the effects of silicate stabilizers on rice grain cadmium (Cd) reduction and rice quality under field conditions are not clear. In this study, a field experiment was conducted over three consecutive years was conducted to examine the Cd reduction in rice grains and to reveal the potential effects of silicate stabilizers on rice grain nutrients, by setting different amounts of bentonite (B), silica‒calcium fertilizer (SC) and zeolite powder (ZP). The results revealed that the application of the B, SC and ZP significantly decreased the soil CaCl2‒Cd concentration (> 39%) and significantly reduced the grain Cd concentration in both early rice (> 70%) and late rice (> 18%) under field conditions; the silicate stabilizers reduced the soil available iron (Fe) but did not limit rice grain Fe nutrition. Additionally, the three silicates promoted rice yield and improved the rice grain Ca and Mg contents; and the application of B increased the amylose concentration of the late rice grains. In conclusion, high amounts of silicate stabilizers did not adversely influence the soil conventional nutrient indices, rice minerals or rice taste, but changes in rice selenium content need attention. Overall, in comparison with lime, silicate stabilizers can improve not only the safety of rice but also the nutritional and taste qualities of rice and are more eco-friendly for long-term use in soil.

Effect of pH on growth and Cd accumulation in different rice varieties under hydroponics

ABSTRACT Currently, applying lime to cadmium (Cd)-contaminated paddy fields to increase pH and reduce Cd availability is an effective method to control excessive Cd levels in rice grain. However, under hydroponic conditions, the impact of increased pH on Cd accumulation in different rice varieties remains unclear. This study employed three rice varieties (Yuzhenxiang, Shaoxiang 100, Xiangwanxian 12) with different Cd accumulation characteristics under different pH and long-term treatment with 1 μM CdCl2, to study the effect of pH on growth and Cd accumulation in different rice varieties. The result showed that as pH shifted from 5 to 8, the SPAD values, shoot dry weight, and plant height of the three rice varieties significantly decreased. The main root length, root volume, and root dry weight of Yuzhenxiang, and Shaoxiang100 significantly decreased. Conversely, the root architecture indicators of Xiangwanxian 12 did not change significantly. As for element accumulation, increasing the pH significantly increased the content of Mn in both the shoots and roots of all three varieties. Yuzhenxiang significantly reduced Cd content in both the shoots and roots of rice, while Shaoxiang100 significantly increased Cd content in both parts. Xiangwanxian 12 showed a significant increase in Cd content in the shoots but a decrease in the roots. In terms of subcellular distribution, Yuzhenxiang significantly reduced Cd concentrations in the cell wall and organelles of root cells, resulting in lower Cd concentrations in the root tissue. Conversely, Shaoxiang100 significantly increased Cd concentrations in the cell wall, organelles, and soluble fractions of root cells, leading to higher Cd concentrations in the root tissue. Xiangwanxian 12 also exhibited a decrease in Cd concentrations in the cell wall, organelles, and soluble fraction of root cells, resulting in lower Cd concentrations in the root tissue. Additionally, the expression of the OsNRAMP5 and OsHMA3 gene was significantly increased in Shaoxiang 100, while no significantly change in Yuzhenxiang and Xiangwanxian 12. These results provide important guidance on the impact of pH on Cd accumulation during the vegetative growth stage of different rice varieties.

OsRopGEF10 Attenuates Cytokinin Signaling to Regulate Panicle Development and Grain Yield in Rice

Cytokinins, which play crucial roles in shoot development, substantially affect grain yield. In rice, the OsRopGEF10-OsRAC3 module is associated with cytokinin signaling and crown root development. However, the effects of RopGEF-mediated cytokinin signaling on rice shoot development and grain yield remain unclear. In this study, we investigated the role of OsRopGEF10 in SAM development and the underlying mechanism. We showed that overexpression of OsRopGEF10 inhibited SAM and panicle development, leading to decreased grain yield. Intriguingly, the overexpression of a specific amino acid mutant of OsRopGEF10, designated gef10-W260S, was found to promote panicle development and grain yield. Further analysis using the BiFC assay revealed that the gef10-W260S mutation disrupted the recruitment of rice histidine phosphotransfer proteins (OsAHP1/2) to the plasma membrane (PM), thereby promoting cytokinin signaling. This effect was corroborated by a dark-induced leaf senescence assay, which revealed an increased cytokinin response in the gef10-W260S ectopic expression lines, whereas the overexpression lines presented a suppressed cytokinin response. Moreover, we revealed that the enhanced panicle development in the gef10-W260S lines was attributable to the upregulated expression of several type-B response regulators (RRs) that are crucial for panicle development. Collectively, these findings revealed the negative regulatory function of OsRopGEF10 in the development of the shoot apical meristem (SAM) via interference with cytokinin signaling. Our study highlights the promising role of OsRopGEF10 as a potential target for regulating SAM and panicle development in rice, revealing a valuable breeding strategy for increasing crop yield.

Effect of Chinese Milk Vetch on Zinc Content and Zinc Absorption of Rice in Purple Tidal Mud Soil

Rice is a staple food crop that feeds billions globally. Addressing Zn deficiency in rice is crucial for improving nutrition and food security. Zn deficiency in rice is a widespread issue, especially in purple tidal mud substrates, which often exhibit low Zn availability. The objective of this two-year pot study was to explore the relationship between Zn content, yield components, and Zn absorption in rice grown in purple tidal mud substrate with varying amounts of Chinese milk vetch (Astragalus sinicus L.) incorporation. The experimental design consisted of seven treatments: an unfertilized control, a Chinese milk vetch control, a chemical fertilizer control, and four treatment variations incorporating Chinese milk vetch alongside chemical fertilizer applications. The results indicated that planting and applying Chinese milk vetch improved the grain yield of rice in purple tidal mud substrate, and the yield increased with higher levels of Chinese milk vetch applied. The increased grain yield resulted in higher Zn absorption in rice grains. The application of Chinese milk vetch, both solely and in combination with chemical fertilizers, had varying effects on zinc uptake and grain zinc formation efficiency in early and late rice, with the control and low-level Chinese milk vetch treatments generally exhibiting the highest performance across the two-year period. By introducing Chinese milkvetch following the use of chemical fertilizers, the Zn content in rice grains increased starting from the second year. The treatment with Chinese milkvetch applied at a rate of 2.25 t/hm2 showed the best results in increasing the Zn content in rice grains. The increase in Zn content and Zn uptake by the rice plants gave rise to a lowering of the DTPA-extractable Zn content in the purple tidal mud substrate. Sole Chinese milk vetch application and using Chinese milk vetch following chemical fertilizer application both increased Zn content extracted by DTPA in purple tidal mud substrate.

Uptake and Accumulation of Cobalt Is Mediated by OsNramp5 in Rice.

Cobalt (Co) contamination in soils potentially affects human health through the food chain. Although rice (Oryza sativa) as a staple food is a major dietary source of human Co intake, it is poorly understood how Co is taken up by the roots and accumulated in rice grain. In this study, we physiologically characterized Co accumulation and identified the transporter for Co2+ uptake in rice. A dose-dependent experiment showed that Co mainly accumulated in rice roots. Further analysis with LA-ICP-MS showed Co deposited in most tissue of the roots, including exodermis, endodermis and stele region. Co accumulation analysis using mutants defective in divalent cation uptake showed that Co2+ uptake in rice is mediated by the Mn2+/Cd2+/Pb2+ transporter OsNramp5, rather than OsIRT1 for Fe2+ and OsZIP9 for Zn2+. Knockout of OsNramp5 enhanced tolerance to Co toxicity. Heterologous expression of OsNramp5 showed transport activity for Co2+ in Saccharomyces cerevisiae. Co2+ uptake was inhibited by either Mn2+ or Cd2+ supply. At the reproductive stage, the Co concentration in the straw and grains of the OsNramp5 knockout lines was decreased by 41%-48% and 28%-36%, respectively, compared with that of the wild-type rice. The expression level of OsNramp5 in the roots was not affected by Co2+. Taken together, our results indicate that OsNramp5 is a major transporter for Co2+ uptake in rice, which ultimately mediates Co accumulation in the grains.

Mutation of KAP, which encodes a keratin-associated protein, affects grain size and yield production in rice.

Grain size and shape are critical agronomic traits that directly impact rice grain yield. Identifying genes that control these traits can provide new strategies for yield improvement. In this study, we characterized a rice mutant, reduced grain length (rgl), which exhibited decreased grain length due to reduced cell proliferation. Map-based cloning identified a base deletion in OsRGL2, a gene encoding a keratin-associated protein (KAP), as the cause of the mutant phenotype. CRISPR-Cas9-generated OsRGL2 knockout mutants also displayed reduced grain length, confirming its role. OsRGL2 transcripts were detected in various tissues, with relative higher gene expression in young panicles, and OsRGL2 was localized to the plasma membrane. Overexpression of OsRGL2 increased grain size by promoting cell proliferation in the spikelet hull and significantly enhanced grain yield per plant. Importantly, OsRGL2 was found to interact with RGB1, indicating that OsRGL2 positively regulates grain size and yield through its interaction with RGB1. Additionally, OsRGL2 regulated the expression of cell cycle-related genes, further elucidating its role in grain development. These findings demonstrate that OsRGL2 is a positive regulator of grain size in rice, and manipulating its expression may offer a novel strategy for enhancing rice grain yield.

Distribution of tetracycline resistance genes within an organic fertilizer-amended soil–rice continuum

The transmission of antibiotic resistance genes (ARGs) to humans through the consumption of plants grown in manure-amended soils is a critical concern. However, the effect of manure application on the profiles of tetracycline resistance genes (TRGs) within the soil–rice continuum remains unclear. In this study, tetracycline (TC) content, bacterial communities, abundance of 8 TRGs, and class 1 integron (intI1) were characterized using high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS), Illumina sequencing, and quantitative PCR (qPCR) in rhizosphere soils, roots, and grains of rice exposed to pig manure (PM), rapeseed cake (RC), and chemical fertilizer (CF), respectively. Our findings indicate that the type of sample was the primary determinant of TRGs abundance variation within the soil-rice continuum, with a consistent decline from rhizosphere soils to roots to grains. Furthermore, fertilization type significantly influenced TRGs abundance, with the highest levels observed in PM treatment. TetZ and tetX were predominant, constituting over 90% of total TRGs abundance across all samples. In addition, the mechanism of TRGs profile formation varies with sample types. Bacterial communities-TC content-intI1 interactions determined the change in TRGs abundance in rhizosphere soils, and bacterial communities constituted the most important factor affecting TRGs abundance within the roots. However, bacterial communities and/or intI1 poorly explained the change in TRGs abundance within the grains. Our study attempts to explore the underlying mechanism for the profiles of TRGs in soil–rice continuums exposed to manure, as well as provides a theoretical basis for controlling the spread of endogenous antibiotic resistance within rice grown in soil receiving pig manure.

Dissecting the molecular basis of the ultra-large grain formation in rice.

The shape of rice grains not only determines the thousand-grain weight but also correlates closely with the grain quality. Here we identified an ultra-large grain accession (ULG) with a thousand-grain weight exceeding 60 g. The integrated analysis of QTL, BSA, de novo genome assembled, transcription sequencing, and gene editing was conducted to dissect the molecular basis of the ULG formation. The ULG pyramided advantageous alleles from at least four known grain-shaping genes, OsLG3, OsMADS1, GS3, GL3.1, and one novel locus, qULG2-b, which encoded a leucine-rich repeat receptor-like kinase. The collective impacts of OsLG3, OsMADS1, GS3, and GL3.1 on grain size were confirmed in transgenic plants and near-isogenic lines. The transcriptome analysis identified 112 genes cooperatively regulated by these four genes that were prominently involved in photosynthesis and carbon metabolism. By leveraging the pleiotropy of these genes, we enhanced the grain yield, appearance, and stress tolerance of rice var. SN265. Beyond showcasing the pyramiding of multiple grain size regulation genes that can produce ULG, our study provides a theoretical framework and valuable genomic resources for improving rice variety by leveraging the pleiotropy of grain size regulated genes.

Predictive modeling of rice milling degree for three typical Chinese rice varieties using interpretative machine learning methods.

Brown rice over-milling causes high economic and nutrient loss. The rice degree of milling (DOM) detection and prediction remain a challenge for moderate processing. In this study, a self-established grain image acquisition platform was built. Degree of bran layer remaining (DOR) datasets is established with image capturing and processing (grain color, texture, and shape features extraction). The mapping relationship between DOR and the DOM is in-depth analyzed. Rice grain DOR typical machine learning and deep learning prediction models are established. The results indicate that the optimized Catboost model can be established with cross-validation and grid search method, with the best accuracy improving from 84.28% to 91.24%, achieving precision 91.31%, recall 90.89%, and F1-score 91.07%. Shapley additive explanations analysis indicates that color, texture, and shape feature affect Catboost prediction accuracy, the feature importance: color>texture>shape. The YCbCr-Cb_ske and GLCM-Contrast features make the most significant contribution to rice milling quality prediction. The feature importance provides theoretical and practical guidancefor grain DOM prediction model. PRACTICAL APPLICATION: Rice milling degree prediction and detection are valuable for rice milling process in practical application. In this paper, image processing and machine learning methods provide an automated, nondestructive, and cost-effective way to predict the quality of rice. The study may serve as a valuable reference for improving rice milling methods, retaining rice nutrition, and reducing broken rice yield.

Predictive modeling of mineral content in rice grains: Insights from support vector and adaboost regression

Predictive modeling of mineral content in rice grains: Insights from support vector and adaboost regression

Crop Residue Biochar Rather Than Manure and Straw Return Provided Short Term Synergism Among Grain Production, Carbon Sequestration, and Greenhouse Gas Emission Reduction in a Paddy Under Rice‐Wheat Rotation

ABSTRACTReturn of crop residues directly as straw, animal manure, or biochar are recommended management options for biowaste recycling and soil organic carbon (SOC) maintenance in agriculture. However, to address the soil health challenges associated with soil degradation and climate change, it is critical to determine if or which of these different forms of crop residues could deliver a synergic improvement in SOC storage, emission reduction, and crop productivity following field application. In this study, maize straw in the form of air‐dried biomass (CS), manure via cattle digestion (CM), and biochar via pyrolysis (CB) was respectively amended once at a dose of 10 t C ha−1, in comparison to no maize straw addition (CK), in a paddy field under rice‐wheat rotation. Changes in soil properties, SOC storage, greenhouse gas (GHG) emissions, and rice/wheat yield were examined over two consecutive rice/wheat rotation cycles following soil amendment. The total rice grain yield considerably increased by 6% under CM and CB, while it reduced by 6% under CS compared to CK. Soil nutrient content persistently increased under CM and CB by 4.2% ~ 17% and 11% ~ 26% for total nitrogen, 26% ~ 61% and 20% ~ 53% for available P, and 2% ~ 82% and 30% ~ 115% for available K, respectively. Topsoil SOC storage increased considerably by 8% under CM and 20% under CB, while remained unchanged under CS, compared to CK. The total methane (CH4) and nitrous oxide (N2O) emissions were considerably increased by 7 folds and 15% under CS and 3.5 folds and 61% under CM, respectively, compared to CK. In contrast, these emissions considerably decreased under CB by 33% for CH4 and 29% for N2O. Consequently, the C emission efficiency considerably reduced under CS and CM but increased under CB over the two rotation cycles monitored. Moreover, the soil quality index (SQI) considerably improved under CM and CB but remained unchanged under CS compared to CK. Among the different forms of straw return, manure, and biochar, straw amendments differed considerably in their effects on C sequestration, GHG emissions, and crop productivity. Only biochar from crop residues synergistically improved these functions in the short‐term following application to paddy soil.

Early Maturing Rice Variety ‘Saeodae1’ with Translucent Rice Grain and Excellent Cultivation Stability

Early Maturing Rice Variety ‘Saeodae1’ with Translucent Rice Grain and Excellent Cultivation Stability

Comprehensive Effect of Zinc Boron with NPK and Salicylic Acid Foliar Application Treatments on Rice Yield and Grain Quality Under Salty Soil Conditions

Comprehensive Effect of Zinc Boron with NPK and Salicylic Acid Foliar Application Treatments on Rice Yield and Grain Quality Under Salty Soil Conditions

Effects of soaking treatment on water distribution of rice grains, starch characteristics and eating quality of wet rice noodles

Herein, rice was subjected to different soaking processes on water distribution of rice grains, starch characteristics, and eating quality of fresh wet rice noodles. Results demonstrated that, when soaked at temperatures between 10 °C and 40 °C for 120 min, rice grains reached saturation in water absorption, and the hardness gradually stabilized. However, the moisture continued to penetrate the interior of rice grains after 120 min, leading to an increase in moisture content, higher water permeability, and enlarged water migration channels. With extended soaking time periods, the content of damaged starch in rice flour considerably decreased. Although the gelatinization temperature of rice starch decreased after soaking, the enthalpy required for gelatinization increased. The relative crystallinity of rice starch demonstrated an increasing trend, followed by a decreasing trend, and reached its highest value of 18.18 % after 60 min of soaking. To summarize, the texture indices of fresh rice noodles demonstrated an increasing trend, although stretching and cooking quality demonstrated a trend of initially increasing and then decreasing with no considerable changes observed between 120 and 240 min of soaking. In summary, moderate soaking treatment can enhance the edible quality of fresh wet rice noodles.

Effects of different fermentation processes on cooking and eating quality of brown rice noodles

While brown rice noodles are nutritionally dense, their subpar cooking and eating attributes render them unpalatable to consumers. Fermentation serves as a viable method to enhance food quality and taste. In our previous study, the quality of brown rice noodles was notably enhanced through solid-state fermentation of rice flour (SFRF) with Limosilactobacillus fermentum. In this study, we investigated the impact of SFRF, solid-state fermentation of rice grains (SFRG), and liquid-state fermentation of rice grains (LFRG) on the cooking attributes, sensory qualities, and processing characteristics of brown rice noodles (BRN). The findings indicated that the quality of brown rice noodles (BRN) could be notably enhanced through the application of these three fermentation techniques. In comparison to the BRN produced via SFRF and LFRG, the rice noodles processed using SFRG exhibited superior visual appeal, reduced cooking losses (4.87%), minimal breakage rates (4.00%), and enhanced taste profile. Following fermentation, the gelatinization temperature (Tp) and peak viscosity of rice flour decreased, with SFRG demonstrating the lowest gelatinization temperature. Pasting and rheological assessments revealed that solid-state fermentation of rice grains led to a reduction in the pasting viscosity of rice flour by hindering starch granule swelling and disintegration. In summary, noodles processed through SFRG exhibited enhanced cooking and sensory characteristics, luminosity (L*), and superior gel structure.

Predicting the risk of arsenic accumulation in soil-rice system in Asian monsoon region

Rice is a staple food for a significant portion of the global population. Arsenic (As) accumulated in rice grains influences rice quality which threatens human health. In this study, we used three machine learning models to predict arsenic accumulation in rice based on over 300 surveys. The prediction results of soil arsenic indicate that high-arsenic soil areas are mainly distributed in South and Southeast Asia such as India, China, and Thailand. In addition, higher bioaccumulation factors (BAF), associated with higher temperature, are predominantly observed in eastern India and southern Myanmar. However, arsenic content in soil is relatively lower in these areas. About 5.5 billion population may be threatened by the consumption of high-arsenic rice. It can be concluded that temperatures may influence the BAF except for soil arsenic, and soil physicochemical properties. Further research on the relationship between climate parameters and BAF should be conducted to address and adapt to future climate change. Additionally, understanding the mechanism of arsenic accumulation under different climatic conditions is crucial for developing agricultural technologies to reduce arsenic accumulation in rice.

SCREENING OF RICE GERMPLASM AGAINST DROUGHT STRESS USING MORPHOLOGICAL PARAMETERS

Oryza sativa L. is a staple diet for billions of people in the world. Different rice varieties' drought stress responses and their effects on both qualitative and quantitative variables. Rice is the second main exportable product of Pakistan and the agriculture sector has shown remarkable growth, with the crop sector posting a growth of 6.58% in Fiscal year 2022. Drought have a bad effect on the vegetative and reproductive stages of crops. Drought stress can reduce crop yield production. The RCBD design, two-way ANOVA factorial analysis, Tukey test, Genetic advance and Heritability were used for this experiment. This study specifically focuses on the response of rice genotypes to drought stress and its effect on morphological parameters such as plant height, panicle length, stem diameter, flag leaf length and width, number of panicles per plant, and 1000-grain weight. Drought tolerance genotypes were screened out and used to the standard Index of IRRI to identify morphological processing in Rice Research Institute Kala Shah Kaku, Pakistan. Total 35 rice genotypes were sown under drought stress with checked variety. Six varieties perform better production under drought stress conditions. These varieties like Pokkoli, Vehari, Nonabokra, Kalomonk, PK10683, and Basmati 375 show better perform under drought stress. The findings of this research can contribute to the development of drought-tolerant rice varieties and enhance food security in drought-prone areas. The importance of qualitative parameters, such as panicle curvature and awning, is also explored, with potential implications for the visual appearance and market preferences of rice grains. Overall, this research provides valuable insights into the genetic basis and potential breeding strategies for improving drought tolerance in rice.

The quantitative trait locus GWY10 controls rice grain width and yield.

The quantitative trait locus GWY10 controls rice grain width and yield.

Effects of Water Clover Density and Submerged NPK Fertilizer on Rice Production

Water clover is an important weed that causes a decrease in rice yields by 15-42%. This study examined the effects of water clover density andNPK fertilizer application on rice yields. This study was arranged in a complete randomized block design with two factors. The first factor was water clover density with three levels, consisting of no water clover, one water clover, and two water clover. The second factor was the application of NPK, which was applied to the surface, submerged in 3, 6, and 9 cm—performed with three replications. Water clover density affected the number of rice panicles, the number of rice grains per panicle, the weight of 100 seeds, rice biomass, and water clover biomass. The application of submerged NPK affected rice biomass. The application of NPK on the surface reduced the highest rice biomass. Two water clovers per rice plant reduced the number of rice panicles by 39% compared to without weeds. Rice biomass decreased by 40% and 50% at weed density of one and two water clover weeds per rice plant, respectively. The higher the density of clover weeds, the higher the decline in harvest yields and the higher the biomass of clover weeds.