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    Biofilmed-PGPR: Next-Generation Bioinoculant for Plant Growth Promotion in Rice under Changing Climate
    Jeberlin Prabina Bright, Hemant S. Maheshwari, Sugitha Thangappan, Kahkashan Perveen, Najat A. Bukhari, Debasis Mitra, Riyaz Sayyed, Andrea Mastinu
    Rice Science    2025, 32 (1): 94-106.   DOI: 10.1016/j.rsci.2024.08.008
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    The exopolysaccharide matrix of diazotrophic cyanobacteria was used to integrate phosphorus (P) and potassium (K) solubilizing bacteria, enhancing the survival of plant growth-promoting rhizobacteria, and ultimately the survival of bacteria in the rhizosphere for better plant growth. A new biofilm-based formulation comprising the diazotrophic cyanobacteria Anabaena AMP2, P-solubilizing Bacillus megaterium var. phosphaticum PB1, and K-solubilizing Rhizobium pusense KRBKKM1 was tested for efficacy in rice. The growth medium with half-strength BG-11 medium supplemented with 3% glucose showed best for biofilm formation under in vitro conditions. Analysis of the methanolic extract of the cyanobacterial- bacterial biofilm (CBB) showed the activity of antioxidants, such as 2-methoxy phenol and pentadecane, which are proven to improve plant-microbe interactions and plant growth, respectively. Treatment of rice seeds with CBB extract at 100 mL/kg or 200 mL/kg showed significant enhancement in germination rate and seedling length. Therefore, a pot culture experiment with the CBB formulations was carried out, and different growth and yield parameters were recorded. Principal component analysis showed that plant growth, yield, soil dehydrogenase activity, and soil chlorophyll content were positively correlated with rice plants amended with vermiculite-based CBB at 2 kg/hm2 followed by a spray with aqueous CBB formulation at 5 mL/L at 15 and 30 d after rice transplanting grown with a 25% reduced level of nitrogen/phosphorus/potassium chemical fertilizers than the recommended dose. Further, Pearson correlation analysis showed that yield was positively correlated with soil dehydrogenase (r = 0.92**) and soil chlorophyll content (r = 0.96**). We concluded that CBB could be used as a novel biofilm-based bio-inoculant to increase rice productivity and crop fitness as a component in integrated nutrient management and sustainable organic farming strategies with reduced chemical fertilizers.

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    Straw Burning Dilemma in Modern Agriculture: A Systematic Review of Driving Factors, Environmental Impacts, and Sustainable Solutions
    Ghada Abd Elsattar Mohammed Oraby, Fadillah Putra, M. Halim Natsir, Dian Siswanto, Meshal M. Abdullah, Ammar Abulibdeh
    Rice Science    2025, 32 (5): 637-648.   DOI: 10.1016/j.rsci.2025.06.007
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    Straw burning has emerged as a persistent and multifaceted challenge within global agricultural systems, particularly across Asia, Africa, and Latin America. This review reframes straw burning not as an isolated behavioral issue, but as the outcome of interlinked structural, technological, and socio-cultural constraints embedded in modern agricultural transitions. Drawing on a synthesis of recent empirical studies, we identify four conceptual turning points that reshape the understanding of straw burning: the structural consequences of mechanization, the trade-offs between high- and low-tech solutions, the cultural legitimacy of burning practices, and the need for systems-based, climate-aligned management paradigms. The analysis reveals that interventions focusing solely on technical innovation often overlook the deeper institutional and cultural factors that sustain burning as a rational choice under constrained conditions. We advocate for hybrid, place-based strategies that combine accessible agronomic practices with long-term investments in infrastructure, policy alignment, and community engagement. Moving beyond fragmented solutions and adopting an integrated systems lens enables this study to contribute a forward-looking framework for sustainable straw management that is environmentally just, socially legitimate, and economically viable.

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    Mixture of Bacillus Amyloliquefaciens and Bacillus Pumilus Modulates Community Structures of Rice Rhizosphere Soil to Suppress Rice Seedling Blight
    Jiang Nan, Qiu Jiehua, Tian Dagang, Shi Huanbin, Liu Zhiquan, Wen Hui, Xie Shuwei, Chen Huizhe, Wu Meng, Kou Yanjun
    Rice Science    2025, 32 (1): 118-130.   DOI: 10.1016/j.rsci.2024.09.001
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    Rice seedling blight, caused by various fungi, including Fusarium oxysporum, poses a severe threat to rice production. As awareness grows regarding the environmental and safety hazards associated with the application of fungicides for managing rice seedling blight, there has been a shift in focus towards biological control agents. In this study, we isolated biocontrol bacteria from paddy fields that significantly inhibited the growth of F. oxysporum in vitro and identified the strains as Bacillus amyloliquefaciens T40 and Bacillus pumilus T208. Additionally, our findings indicated that the combined application of these Bacillus strains in soil was more effective in reducing the incidence of rice seedling blight than their individual use. Analysis of 16S and internal transcribed spacer rRNA gene sequencing data revealed that the mixture of the T40 and T208 strains exhibited the lowest average clustering coefficients, which were negatively correlated with the biomass of F. oxysporum-inoculated rice seedlings. Furthermore, this mixture led to higher stochastic assembly (average |βNTI| < 2) and reduced selection pressures on rice rhizosphere bacteria compared with individual strain applications. The mixture of the T40 and T208 strains also significantly increased the expression of defense-related genes. In conclusion, the mixture of the T40 and T208 strains effectively modulates microbial community structures, enhances microbial network stability, and boosts the resistance against rice seedling blight. Our study supports the development and utilization of biological resources for crop protection.

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    Identification and Characterization of WAKg Genes Involved in Rice Disease Resistance and Yield
    Ayaz Ahmad, Cheng Mingxing, Guo Yu, Luo Xiong, Yang Zihan, Liu Manman, Yuan Huanran, Li Qiancheng, Li Shaoqing, Fan Fengfeng
    Rice Science    2025, 32 (5): 673-684.   DOI: 10.1016/j.rsci.2025.04.011
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    The wall-associated kinases (WAKs) play a crucial role in rice resistance, but their relationship to yield-related traits remains poorly understood. In this study, we analyzed the rice wall-associated kinase galacturonan-binding (WAKg) gene family and evaluated its association with both disease resistance and grain yield. A total of 108 OsWAKg genes were identified in rice. Promoter cis-element analysis revealed that the promoter regions of OsWAKg genes contain abundant resistance- and hormone-related elements. Induced expression analysis of 18 OsWAKg genes highly expressed in both rice leaves and roots showed that 14 genes were pathogen-induced, 9 were induced by development-related hormones, and 8 were responded to both stimuli. Transgenic validation confirmed that OsWAKg16 and OsWAKg52 positively regulate rice disease resistance and yield. Moreover, OsWAKg52 regulates rice disease resistance through multiple pattern-triggered immunity responses. These findings demonstrate that OsWAKgs significantly contribute to the coordinated regulation of disease resistance and grain yield, providing new insights into rice WAKg gene family and potential genetic resources for synergistic crop improvement.

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    Breeding for Heat Tolerant Aromatic Rice Varieties and Identification of Novel QTL Regions Associated with Heat Tolerance During Reproductive Phase by QTL-Seq
    Surangkana Chimthai, Sulaiman Cheabu, Wanchana Aesomnuk, Siriphat Ruengphayak, Siwaret Arikit, Apichart Vanavichit, Chanate Malumpong
    Rice Science    2025, 32 (1): 67-80.   DOI: 10.1016/j.rsci.2024.12.002
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    Extremely high temperatures resulting from climate change have become a major challenge for increasing rice production. Therefore, our objective was to develop heat-tolerant aromatic rice varieties using the pedigree method, focusing on selecting for seed-setting ability under extremely high temperatures along with the use of single nucleotide polymorphism/insertion and deletion (SNP/InDel) markers to improve aromatic properties and grain quality. Furthermore, the QTL-seq approach was utilized to identify QTLs for seed-setting rate in an F2 population subjected to heat stress. The candidate QTL regions were then aligned to confirm SNPs/InDels in synonymous F7 candidate heat-tolerant lines. The results revealed that four promising lines, namely 84-7-1-9, 84-7-1-10, 159-3-3-1, and 159-3-3-10, were classified as heat-tolerant with low amylose content. In addition, lines 84-7-1-9 and 84-7-1-10 were identified as aromatic rice encompassing the aroma gene (badh2). Regarding the QTL-seq results, the qSF2.1 region ranged from 311 051 to 3 929 422 bp on chromosome 2, was identified based on the highest contrasting SNP index between the heat-susceptible and tolerant bulks. The candidate genes within this region include two genes related to heat shock proteins, three genes associated with pollen fertility, and four genes involved in heat stress and other abiotic stress responses. These genes are proposed as potential candidates for heat tolerance and could serve as targets in rice breeding programs aimed at enhancing heat tolerance.

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    Disruption of Energy Metabolism and Reactive Oxygen Species Homeostasis in Honglian Type-Cytoplasmic Male Sterility (HL-CMS) Rice Pollen
    Wang Mingyue, Zhao Weibo, Feng Xiaoya, Chen Yi, Li Junhao, Fu Jinmei, Yan Yingchun, Chu Zhaohui, Huang Wenchao
    Rice Science    2025, 32 (1): 81-93.   DOI: 10.1016/j.rsci.2024.10.003
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    Honglian type-cytoplasmic male sterility (HL-CMS) is caused by the inter-communication between the nucleus and mitochondria. However, the mechanisms by which sterility genes regulate metabolic alterations and changes in mitochondrial morphology in the pollen of HL-CMS remain unclear. In this study, we compared the morphological differences between the pollen of the male sterile line YA and the near-isogenic line NIL-Rf6 using hematoxylin-eosin staining and 4ʹ,6-diamidino-2-phenylindole (DAPI) staining. HL-CMS is characterized by gametophytic sterility, where the aborted pollen grains are empty, and the tapetal layer remains intact. Transmission electron microscopy was employed to observe mitochondrial morphological changes at the microspore stage, revealing significant mitochondrial alterations, characterized by the formation of 'large spherical mitochondria', occurred at the binucleate stage in the YA line. Additionally, metabolomics analysis revealed decreased levels of metabolites associated with the carbohydrate and flavonoid pathways. Notably, the decrease in flavonoids was found to contribute to an elevation in reactive oxygen species (ROS) levels. Therefore, we propose a model in which rice fertility is modulated by the levels of pollen carbohydrates and flavonoid metabolites, with impaired mitochondrial energy production and reduced flavonoid biosynthesis as the main causes of ROS accumulation and pollen abortion in rice.

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    Leucine-Rich Repeat Protein Family Regulates Stress Tolerance and Development in Plants
    Hao Zhiqi, Wang Tingyi, Chen Dongdong, Shen Lan, Zhang Guangheng, Qian Qian, Zhu Li
    Rice Science    2025, 32 (1): 32-43.   DOI: 10.1016/j.rsci.2024.12.003
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    The leucine-rich repeat (LRR) protein family is involved in a variety of fundamental metabolic and signaling processes in plants, including growth and defense responses. LRR proteins can be divided into two categories: those containing LRR domains along with other structural elements, which are further subdivided into five groups, LRR receptor-like kinases, LRR receptor-like proteins, nucleotide-binding site LRR proteins, LRR-extensin proteins, and polygalacturonase-inhibiting proteins, and those containing only LRR domains. Functionally, various LRR proteins are primarily involved in plant development and responses to environmental stress. Notably, the LRR protein family plays a central role in signal transduction pathways related to stress adaptation. In this review, we classify and analyze the functions of LRR proteins in plants. While extensive research has been conducted on the roles of LRR proteins in disease resistance signaling, these proteins also play important roles in abiotic stress responses. This review highlights recent advances in understanding how LRR proteins mediate responses to biotic and abiotic stresses. Building upon these insights, further exploration of the roles of LRR proteins in abiotic stress resistance may aid efforts to develop rice varieties with enhanced stress and disease tolerance.

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    OsACL-A2 Regulates Positive Iron Uptake and Blast Resistance in Rice
    Duan Wenjing, Aaron Chan, Xu Peng, Zhang Yingxin, Sun Lianping, Wang Beifang, Cao Yongrun, Zhang Yue, Li Dian, Chen Daibo, Hong Yongbo, Zhan Xiaodeng, Wu Weixun, Cheng Shihua, Liu Qun’en, Cao Liyong
    Rice Science    2025, 32 (5): 589-593.   DOI: 10.1016/j.rsci.2025.03.007
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    OsPR10b Positively Regulates Blast and Bacterial Blight Resistance in Rice
    He Niqing, Lin Shaojun, Cheng Zhaoping, Huang Fenghuang, Jin Yidan, Wang Wenxiao, Yang Dewei
    Rice Science    2025, 32 (5): 585-588.   DOI: 10.1016/j.rsci.2025.04.014
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    Fluorescence Detection of Bacterial Pathogens in Rice by Recombinant Polymerase Amplification Based on Self-Heating Paper Chip
    Yang Ning, Fu Jiuju, Wang Aiying, Liu Shuhua, Chang Kangpeng, Song Wei, Tao Shoulong, Mao Hanping, Zhang Xiaodong, Xu Lijia
    Rice Science    2025, 32 (2): 131-136.   DOI: 10.1016/j.rsci.2025.01.001
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    Genome-Wide Identification of Dopamine β-Monooxygenase N-Terminal Gene Family in Rice and Its Role in Response to Blast Disease and Abiotic Stress
    Mareyam Mukhtar, Amresh Kumar, Ashfak S. Mujawar, Bhuvnesh Sareen, Suhas G. Karkute, Rohini Sreevathsa, Amitha Mithra Sevanthi, Amolkumar U. Solanke
    Rice Science    2025, 32 (5): 685-703.   DOI: 10.1016/j.rsci.2025.05.004
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    Dopamine β-monooxygenase N-terminal (DOMON) domain-containing genes are present across all taxa and are critical in cell signaling and redox transport. Despite their significance, these genes remain understudied in plant species. In this study, we identified 15 DOMON genes in rice and analyzed their phylogenetic relationships, conserved motifs, and cis-regulatory elements. Phylogenetic analysis revealed distinct clustering of OsDOMON genes in rice and other monocots, compared with Arabidopsis thaliana. Promoter analysis showed a higher abundance of stress-related regulatory elements in Tetep, a well-known blast and abiotic stress-tolerant cultivar, compared with Nipponbare and HP2216. OsDOMON genes displayed differential expression under biotic stress (Magnaporthe oryzae infection) and abiotic stresses (drought, heat, and salinity) in contrasting cultivars. Tetep exhibited significantly higher expression levels of specific OsDOMON genes during early blast infection stages, particularly OsDOMON6.1 and OsDOMON9.2, suggesting their roles in cell wall fortification and reactive oxygen species signaling. Under abiotic stress, genes like OsDOMON3.3, OsDOMON8.1, and OsDOMON9.2 showed higher expression in Tetep, indicating their involvement in stress tolerance mechanisms. This study provides a foundation for future functional studies of OsDOMON genes, paving the way for developing rice cultivars resistant to biotic and abiotic stresses.

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    Accelerating Wild Rice Disease-Resistant Germplasm Exploration: Artificial Intelligence (AI)-Powered Wild Rice Blast Disease Level Evaluation and Disease-Resistance Identification
    Pan Pan, Guo Wenlong, Li Hengbo, Shao Yifan, Guo Zhihao, Jin Ye, Cheng Yanrong, Yu Guoping, Fu Zhenshi, Hu Lin, Zheng Xiaoming, Zhou Guomin, Zhang Jianhua
    Rice Science    2025, 32 (5): 727-746.   DOI: 10.1016/j.rsci.2025.05.005
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    Accurate evaluation of disease levels in wild rice germplasm and identification of disease resistance are critical for developing rice varieties resistant to blast disease. However, existing evaluation methods face limitations that hinder progress in breeding. To address these challenges, we proposed an AI-powered method for evaluating blast disease levels and identifying resistance in wild rice. A lightweight segmentation model for diseased leaves and lesions was developed, incorporating an improved federated learning approach to enhance robustness and adaptability. Based on the segmentation results and resistance identification technical specifications, wild rice materials were evaluated into 10 disease levels (L0 to L9), further enabling disease-resistance identification through multiple replicates of the same materials. The method was successfully implemented on augmented reality glasses for real-time, first-person evaluation. Additionally, high-speed scanners and edge computing devices were integrated to enable continuous, precise, and dynamic evaluation. Experimental results demonstrate the outstanding performance of the proposed method, achieving effective segmentation of diseased leaves and lesions with only 0.22 M parameters and 5.3 G floating-point operations per second (FLOPs), with a mean average precision (mAP@0.5) of 96.3%. The accuracy of disease level evaluation and disease-resistance identification reached 99.7%, with a practical test accuracy of 99.0%, successfully identifying three highly resistant wild rice materials. This method provides strong technical support for efficiently identifying wild rice materials resistant to blast disease and advancing resistance breeding efforts.

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    Understanding Investigational Perspective of Antioxidant and Antibacterial Properties of Rice
    Intan Farahanah, Shariza Sahudin, Hannis Fadzillah Mohsin, Siti Alwani Ariffin, Liyana Dhamirah Aminuddin
    Rice Science    2025, 32 (1): 15-31.   DOI: 10.1016/j.rsci.2024.10.004
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    Whole-grain rice has gained significant attention for its potential health benefits, particularly because of its antioxidant and antibacterial properties. Despite this growing interest, there remains a pressing need for a comprehensive evaluation of the methods used to analyze these bioactive compounds, considering the diversity of rice types and the influence of environmental factors. This review aims to provide an in-depth overview of recent analytical methods, particularly those employed over the last five years, to assess the antioxidant and antibacterial properties of rice. It focuses on commonly used antioxidant assays, such as the 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity assay, which encompasses both single electron transfer and hydrogen atom transfer mechanisms. Other antioxidant assays are also discussed, alongside methods used to evaluate antibacterial properties, including disc diffusion, well diffusion, broth or agar dilution, and advanced techniques such as flow cytofluorometric and bioluminescent assays. The review further explores the bacterial strains most frequently studied, including Bacillus cereus, Listeria monocytogenes, Escherichia coli, and Salmonella species. It highlights the key techniques and parameters employed to ascertain and quantify the antioxidant and antibacterial potential of rice, while critically analysing the strengths and limitations of these approaches. By synthesizing current methods and offering insights into their application, this review can be served as a guide for future research aimed at standardizing and improving the assessment of rice’s bioactive properties, paving the way for broader scientific and practical applications.

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    Regulation of Yield and Eating and Cooking Quality in Rice Through Seed Albumin OsRAL5
    Zhao Chunfang, He Lei, Guan Ju, Luo Lei, Zhao Ling, Zhou Lihui, Yao Shu, Chen Tao, Zhu Zhen, Zhao Qingyong, Wang Cailin, Zhang Yadong
    Rice Science    2025, 32 (1): 6-10.   DOI: 10.1016/j.rsci.2024.08.005
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    Genome-Wide Discovery of Candidate Genes Associated with Cold Tolerance in Rice at Various Growth Stages
    Liu Jiajun, Wang Cuili, Sun Mingmao, Ma Xiaoding, Han Bing, Guo Xiaohong, Han Longzhi, Cui Di
    Rice Science    2025, 32 (2): 137-142.   DOI: 10.1016/j.rsci.2024.12.001
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    NARROW AND ROLLED LEAF 9, a Novel Gene Encoding 20S Proteasome β1 Subunit that Regulates Leaf Morphology and Grain Size in Rice
    Kang Fengyu, Zhou Liang, Chen Wenqiang, Huang Pingliang, Amos Musyoki Mawia, Luo Ju, Hu Peisong
    Rice Science    2025, 32 (2): 143-146.   DOI: 10.1016/j.rsci.2024.12.008
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    Spireoside Controls Blast Disease by Disrupting Membrane Integrity of Magnaporthe oryzae
    Xu Liting, He Kaiwei, Guo Chunyu, Quan Cantao, Ma Yahuan, Zhang Wei, Ren Lifen, Wang Long, Song Li, Ouyang Qing, Yin Junjie, Zhu Xiaobo, Tang Yongyan, He Min, Chen Xuewei, Li Weitao
    Rice Science    2025, 32 (1): 107-117.   DOI: 10.1016/j.rsci.2024.10.005
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    The application of fungicides is an effective strategy for controlling plant diseases. Among these agents, plant-derived antifungal metabolites are particularly promising due to their eco-friendly and sustainable nature. Plant secondary metabolites typically exhibit broad-spectrum antifungal activity without selective toxicity against pathogens. However, only a small fraction of antifungal metabolites have been identified from the tens of thousands of known plant secondary metabolites. In this study, we conducted a metabolomic analysis on both blast-resistant (Digu) and -susceptible (Lijiangxintuanheigu) rice varieties to uncover novel metabolites that enhance blast resistance. We found that 24 and 48 h post-inoculation with Magnaporthe oryzae were critical time points for metabolomic profiling, based on the infected status of M. oryzae in rice and the observed differences in shikimate accumulation between the two varieties. Following metabolomic analysis, we identified nine flavonoids that were differentially accumulated and are considered potential candidates for disease control. Among these, apigenin-7-glucoside, rhamnetin, and spireoside were found to be effective in controlling blast disease, with spireoside demonstrating the most pronounced efficacy. We discovered that spireoside controlled blast disease by inhibiting both spore germination and appressorium formation in M. oryzae, primarily through disrupting cell membrane integrity. However, spireoside did not induce rice immunity. Furthermore, spireoside was also effective in controlling sheath blight disease. Thus, spireoside shows considerable promise as a candidate for the development of a fungicide for controlling plant diseases.

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    Expanding Viral Diversity in Rice Fields by Next-Generation Sequencing
    Wang Haoran, Chen Guoqing, Feng Guozhong
    Rice Science    2025, 32 (1): 44-51.   DOI: 10.1016/j.rsci.2024.12.004
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    In rice fields, rice plants usually grow alongside wild weeds and are attacked by various invertebrate species. Viruses are abundant in plants and invertebrates, playing crucial ecological roles in controlling microbial abundance and maintaining community structures. To date, only 16 rice viruses have been documented in rice-growing regions. These viruses pose serious threats to rice production and have traditionally been identified only from rice plants and insect vectors by isolation techniques. Advances in next-generation sequencing (NGS) have made it feasible to discover viruses on a global scale. Recently, numerous viruses have been identified in plants and invertebrates using NGS technologies. In this review, we discuss viral studies in rice plants, invertebrate species, and weeds in rice fields. Many novel viruses have been discovered in rice ecosystems through NGS technologies, with some also detected using metatranscriptomic and small RNA sequencing. These analyses greatly expand our understanding of viruses in rice fields and provide valuable insights for developing efficient strategies to manage insect pests and virus-mediated rice diseases.

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    Transcriptomic Regulation Analysis Reveals Salt-Induced Response at Early Seedling Stages among Three Rice Genotypes
    Sirinthorn Kongpraphrut, Lü Yang, Wang Yueying, Mohamed Hazman, Tong Hanhua, Qian Qian, Guo Longbiao
    Rice Science    2025, 32 (5): 607-611.   DOI: 10.1016/j.rsci.2025.04.013
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    Effect of Germinated Brown Rice Supplementation on Prediabetes Markers: A 120-Day Dietary Intervention Study in Selected Female Groups
    Hemalatha Ganapathyswamy, Thirukkumar Subramani, Kanmani Kalaivanan, Adiyaman Pannerselvam, Amutha Sundararajan
    Rice Science    2025, 32 (1): 11-14.   DOI: 10.1016/j.rsci.2024.08.006
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