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28 March 2025, Volume 32 Issue 2 Previous Issue   
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Letters

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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 2025, 32(2): 131-136.  DOI: 10.1016/j.rsci.2025.01.001 Abstract ( )   HTML ( )   PDF (7276KB) ( )

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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 2025, 32(2): 137-142.  DOI: 10.1016/j.rsci.2024.12.001 Abstract ( )   HTML ( )   PDF (6402KB) ( )

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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 2025, 32(2): 143-146.  DOI: 10.1016/j.rsci.2024.12.008 Abstract ( )   HTML ( )   PDF (7089KB) ( )

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Mapping of Red Hull Gene OsRH3 and Its Great Value in Mechanized Hybrid Rice Seed Production Fang Pengpeng, Sun Pingyong, Zhang Li, Wang Pengfei, Zeng Jia, He Qiang, Shu Fu, Xing Yongzhong, Deng Huafeng, Zhang Wuhan 2025, 32(2): 147-151.  DOI: 10.1016/j.rsci.2024.12.005 Abstract ( )   HTML ( )   PDF (8016KB) ( )

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Submergence-Tolerant Rice Cultivar FR13A Harbors Floating Genes SNORKELs but Lacks Floating Ability Daisuke Sasayama, Natsuki Hayashi, Shunsuke Oe, Hiroshi Fukayama, Tomoko Hatanaka, Tetsushi Azuma 2025, 32(2): 152-155.  DOI: 10.1016/j.rsci.2024.12.013 Abstract ( )   HTML ( )   PDF (5146KB) ( )

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Efficient Production of Pyrrolnitrin by Optimizing Culture Medium and Blocking Competitive Secondary Metabolic Pathways in Pseudomonas protegens JP2-4390 Shen Jiamin, Zhang Xinxin, Wang Yucong, Chen Guoqing, Feng Guozhong 2025, 32(2): 156-159.  DOI: 10.1016/j.rsci.2024.12.007 Abstract ( )   HTML ( )   PDF (6441KB) ( )

Reviews

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Discerning Genes to Deliver Varieties: Enhancing Vegetative- and Reproductive-Stage Flooding Tolerance in Rice Sanchika Snehi, Ravi Kiran Kt, Sanket Rathi, Sameer Upadhyay, Suneetha Kota, Satish Kumar Sanwal, Lokeshkumar Bm, Arun Balasubramaniam, Nitish Ranjan Prakash, Pawan Kumar Singh 2025, 32(2): 160-176.  DOI: 10.1016/j.rsci.2025.01.002 Abstract ( )   HTML ( )   PDF (52819KB) ( )   Flooding in rice fields, especially in coastal regions and low-lying river basins, causes significant devastation to crops. Rice is highly susceptible to prolonged flooding, with a drastic decline in yields if inundation persists for more than 7 d, especially during the reproductive stage. Although the SUB1 QTL, which confers tolerance to complete submergence during the vegetative stage, has been incorporated into breeding programs, the development of alternative sources is crucial. These alternatives would broaden the genetic base, mitigate the influence of the genomic background, and extend the efficacy of SUB1 QTL to withstand longer submergence periods (up to approximately 21 d). Contemporary breeding strategies predominantly target submergence stress at the vegetative stage. However, stagnant flooding (partial submergence of vegetative parts) during the reproductive phase inflicts severe damage on the rice crop, leading to reduced yields, heightened susceptibility to pests and diseases, lodging, and inferior grain quality. The ability to tolerate stagnant flooding can be ascribed to several adaptive traits: accelerated aerenchyma formation, efficient underwater photosynthesis, reduced radial oxygen loss in submerged tissues, reinforced culms, enhanced reactive oxygen species scavenging within cells, dehydration tolerance post-flooding, and resistance to pests and diseases. A thorough investigation of the genetics underlying these traits, coupled with the integration of key alleles into elite genetic backgrounds, can significantly enhance food and income security in flood-prone rice-growing regions, particularly in coastal high-rainfall areas and low-lying river basins. This review aims to delineate an innovative breeding strategy that employs genomic, phenomic, and traditional breeding methodologies to develop rice varieties resilient to various dimensions of flooding stress at both the vegetative and reproductive stages.

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Regulation of Regeneration Rate to Enhance Ratoon Rice Production Nie Lixiao, Guo Xiayu, Wang Weiqin, Qi Yucheng, Ai Zhiyong, He Aibin 2025, 32(2): 177-192.  DOI: 10.1016/j.rsci.2024.11.001 Abstract ( )   HTML ( )   PDF (7181KB) ( )   Ratoon rice (Oryza sativa L.) is a sustainable planting model, and its planting area has been increasing year by year. However, there is a lack of literature reviewing the measures and mechanisms to regulate the regeneration rate, as well as the challenges in the production of ratoon rice. This study explores the effects of different varieties, climatic conditions (light and temperature), and cultivation measures (fertilizer management, cropping system, harvest method, water management, and plant growth regulators) on the regeneration rate and grain yield of the ratoon season. It summarizes and analyzes the possible mechanisms that affect the germination of regenerated buds from the perspectives of material accumulation and transportation, hormone metabolism, and molecular mechanisms, and identifies main factors currently limiting the development of ratoon rice. A significant positive correlation between the regeneration rate and grain yield of the ratoon season was found, regulated by varieties, temperatures, light resources, and cultivation measures. Improving the regeneration rate can effectively increase the production of ratoon rice. Notably, rice varieties with high regeneration ability exhibit characteristics such as a suitable growth period, a developed root system, high single-stem weight, a relatively small ratio of grain number to green leaf area, and strong lodging resistance in the main season. Additionally, the germination of regenerated buds is regulated by the accumulation and transport of endogenous hormones (indole-3-acetic acid, gibberellins, and cytokinins), photoassimilates (non-structural carbohydrates), and reactive oxygen metabolism. To further demonstrate the grain yield potential of the ratoon season, improvements are needed in three key areas: the cultivation system of low-stubble ratoon rice, the development of specialized harvesters, and the breeding of rice varieties with high-temperature tolerance during the main crop and low-temperature tolerance during the ratoon crop.

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Progress on Physiological Mechanisms of Rice Spikelet Degeneration at Different Panicle Positions Caused by Abiotic Stress Wang Jingqing, Wang Yaliang, Chen Yulin, Chen Huizhe, Xiang Jing, Zhang Yikai, Wang Zhigang, Zhang Yuping 2025, 32(2): 193-202.  DOI: 10.1016/j.rsci.2024.09.002 Abstract ( )   HTML ( )   PDF (6489KB) ( )   Rice yield is heavily reliant on the number of spikelets per panicle, a factor determined by the processes of spikelet differentiation and degeneration. In rice cultivars with large panicles, spikelet degeneration negates the advantages of large panicle and constrains yield potential. Environmental stress-induced metabolic disorders in plants aggravate spikelet degeneration, with the sensitive period for this process commencing approximately 15‒20 d before panicle heading. Notable positional variations occur within the panicle, with significantly higher spikelet degeneration rates at the basal than at the upper positions. An imbalance of carbon and nitrogen metabolism represents the primary physiological basis for aggravated spikelet degeneration under abiotic stress. Impaired carbon and nitrogen metabolism leads to disordered energy metabolism and disrupted respiratory electron transport, which accelerates the apoptosis of young spikelets through excessive reactive oxygen species accumulation. Sucrose serves as the main carbohydrate source for spikelet development, demonstrating an apical dominance pattern that favors spikelet formation. However, under abiotic stress, the inhibition of sucrose decomposition, rather than sucrose transport impairment, predominantly contributes to aggravated spikelet degeneration at the basal panicle positions. Brassinolide and auxin have a significant relationship with spikelet formation, potentially mediating apical dominance. Specifically, brassinolide enhances sucrose accumulation and utilization, thereby alleviating spikelet degeneration. At present, the mechanisms underlying rice spikelet degeneration have not been fully revealed, and the joint effects of hormones, carbohydrates, and carbon and nitrogen metabolism on this process require further investigation. To reduce the spikelet degeneration, the strategic application of water and fertilizer to establish a stable rice population can enhance the rice plants’ resilience to abiotic stress. An effective approach to reducing spikelet degeneration is to increase the dry matter occupancy of each spikelet during the panicle initiation period.

Research Papers

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OsCERK1 Interacts with OsHPP08 to Regulate Copper Uptake and Blast Resistance in Rice Chen Ya, Liu Zhiquan, Yang Linyin, Wu Fujie, Cao Zijian, Shi Huanbin, Qiu Jiehua, Kou Yanjun 2025, 32(2): 203-216.  DOI: 10.1016/j.rsci.2025.02.001 Abstract ( )   HTML ( )   PDF (110231KB) ( )   The cell surface receptor chitin elicitor receptor kinase 1 (CERK1) is a well-known component of plant immunity. OsCERK1 is involved in regulating copper (Cu) uptake in rice, though the underlying mechanisms remain elusive. In this study, we identified proteins interacting with OsCERK1 and uncovered a novel heavy metal-associated domain-containing protein, OsHPP08. Our findings demonstrate that OsCERK1 phosphorylated and stabilized OsHPP08. Through structural analysis using AlphaFold, a yeast sensitivity assay of the Cu uptake-deficient yeast mutant, and Cu level measurements in oshpp08 mutants and overexpression plants (OsHPP08OE), we revealed that OsHPP08 facilitated Cu uptake. Additionally, rice seedling infection assays demonstrated that OsHPP08 positively contributed to blast resistance, with both OsCERK1 and OsHPP08 being essential for Cu-modulated blast resistance. Further analyses suggested that OsCERK1 and OsHPP08 likely enhanced blast resistance by regulating the antioxidant system and increasing H2O2 accumulation. In conclusion, OsCERK1 promoted Cu uptake by stabilizing OsHPP08, and together they contributed to Cu-modulated blast resistance, likely through the modulation of reactive oxygen species accumulation. These findings deepen our understanding of the intricate interplay between biotic and abiotic signals in rice.

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Establishing Programmable CRISPR/Cas13b-Mediated Knockdown System in Rice Wang Shuman, Zhang Linqi, Gao Ruiren, Wei Guangbo, Dong Weiguo, Xu Jiming, Wang Zhiye 2025, 32(2): 217-227.  DOI: 10.1016/j.rsci.2024.12.012 Abstract ( )   HTML ( )   PDF (103263KB) ( )   CRISPR-Cas endonucleases mediate prokaryotic adaptive immunity by targeting foreign nucleic acids. CRISPR/Cas13b is a class 2 type VI-B ribonuclease that targets and cleaves single-stranded RNA. It exhibits higher RNA interference activity than Cas13a and Cas13c and causes fewer collateral effects than RxCas13d in mammalian cells. However, a programmable CRISPR/Cas13b-mediated RNA interference system for endogenous transcripts in rice has not yet been established. Here, we developed a CRISPR/Cas13b-mediated system to target endogenous transcripts in rice. Our CRISPR/Cas13b system could inhibit multiple endogenous mRNAs simultaneously. In addition, this system efficiently repressed endogenous long noncoding RNAs with more than 50% inhibition in stable transgenic plants. Furthermore, we found only weak collateral effects of the CRISPR/Cas13b-mediated system at the transcriptome-wide level, and no difference in the agronomic traits of stable transgenic rice in the field. We present a programmable CRISPR/Cas13b-mediated knockdown system for rice, offering a potential biotechnological tool for functional genomics and crop improvement.

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A Novel Approach for Screening Salinity-Tolerant Rice Germplasm by Exploring Redox-Regulated Cytological Fingerprint Uthpal Krishna Roy, Babita Pal, Soumen Bhattacharjee 2025, 32(2): 228-242.  DOI: 10.1016/j.rsci.2025.03.006 Abstract ( )   HTML ( )   PDF (38162KB) ( )   Although metabolic homeostasis disruption, cellular damage, and premature senescence caused by salinity stress are well-documented in the literature, there are few studies investigating cytological changes induced by salinity stress within the altered metabolic landscape of rice, and this study aims to fill that gap. The cytological characterization of root tips (in terms of mitotic index and chromosomal abnormalities such as stickiness, laggards, fragments, bridges, micronuclei, ring chromosomes, and total mitotic abnormalities) was conducted on 10 experimental rice landraces from coastal Bangladesh, grown under post-imbibitional salinity stress (PISS), while correlating these changes with their metabolic status. The results revealed a strong correlation between salinity-induced cytological changes in root cells (mitotic index and chromosomal abnormalities) and the redox interactome status of all experimental rice landraces. The landraces Kutepatnai, Talmugur, Nonakochi, and Benapol, which exhibited a higher ability to mitigate PISS-induced chromosomal abnormalities and improve mitotic index, also showed lower accumulation of oxidative stress markers (protein carbonylation, lipid peroxidation, prooxidant accumulation, oxidative stress index, reactive oxygen species (ROS)-antioxidative stress index, and efficiency of ROS processing via the Halliwell-Asada pathway) compared with more susceptible landraces (Charobalam, Jotaibalam, Kachra, and Lalmota). These findings underscore the role of redox biology in preventing chromotoxic effects under salinity stress. Hierarchical cluster analysis and principal component analysis, used to determine variations and similarities among the experimental rice landraces based on cytological attributes, redox interactome, and physiological phenotypes, classified the landraces according to their salinity tolerance and sensitivity. This study proposes a novel approach for exploring redox-regulated cytological fingerprints as a tool for identifying salinity-tolerant rice landraces.

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Molecular and Biological Characterization of Novel Mitovirus Infecting Phytopathogenic Fungus Ustilaginoidea virens He Zhenrui, Zhao Wenhua, Cheng Baoping, Yang Mei, Yang Yingqing, Zhu Yiming, Zhou Erxun 2025, 32(2): 243-258.  DOI: 10.1016/j.rsci.2024.11.002 Abstract ( )   HTML ( )   PDF (102932KB) ( )   Rice false smut (RFS), caused by the ascomycete fungus Ustilaginoidea virens (Cooke) Takahashi, is a notable panicle disease of rice. Mycoviruses represent a category of viruses capable of infecting various fungal groups, garnering interest for their potential application in the biological control of plant fungal diseases. We identified a novel positive-sense single-stranded RNA virus, named Ustilaginoidea virens mitovirus 1 (UvMV1), from an abnormal U. virens strain Uv488. The complete genome sequence of UvMV1 is 2 474 nt in length and contains a large open reading frame encoding RNA-dependent RNA polymerase. UvMV1 is classified as a new member of the genus Unuamitovirus in the family Mitoviridae based on phylogenetic analysis. It is effectively transmitted vertically through conidia of strain Uv488 and horizontally through hyphal fusion between vegetatively compatible individuals with an 80% transmission efficiency. We further demonstrated that UvMV1 significantly influenced conidiation, colony morphology, growth rate, secondary metabolite production, and the response to environmental stress in U. virens. Furthermore, qRT-PCR results aimed at detecting the expression levels of autophagy-related genes suggested that UvMV1 infection had the potential to induce autophagy in U. virens. Activation or inhibition of autophagy through chemical experiments demonstrated that UvMV1 enhances viral titers by inducing autophagy in U. virens, while inhibition of autophagy results in decreased UvMV1 titers. Transcriptome analyses consistently demonstrated that UvMV1 regulated the expression of genes associated with secondary metabolism, mycelial growth, virulence, and the mitogen-activated protein kinase signaling pathway, thereby influencing both the antiviral response and the virulence of U. virens. The data presented collectively identified a novel mycovirus responsible for inducing growth abnormalities in U. virens, and elucidated the regulatory mechanisms during mycovirus-host fungus interactions, particularly the autophagy pathway. These findings offer new perspectives and potential control strategies for managing RFS in agricultural settings.

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A Meta-Analysis of 30 Years in China and Micro-District Experiments Shows Organic Fertilizer Quantification Combined with Chemical Fertilizer Reduction Enhances Rice Yield on Saline-Alkali Land He Chen, Ruan Yunze, Jia Zhongjun 2025, 32(2): 259-272.  DOI: 10.1016/j.rsci.2025.01.004 Abstract ( )   HTML ( )   PDF (11086KB) ( )   To improve the yield and quality of rice grown on saline-alkali soil, a meta-analysis combined with micro-district experimental studies was conducted in China to examine the impact of humic acid- based organic fertilizer and chemical fertilizer on rice yield and quality. This study employed a two-factor fully randomized experimental design, incorporating four levels of humic acid (F0, 0.0 g/pot; F1, 4.8 g/pot; F2, 12.0 g/pot; and F3, 19.2 g/pot) and three levels of chemical fertilizer (A1, full conventional dosage; A2, 85% of conventional dosage; and A3, 70% of conventional dosage). The meta-analysis revealed that the application of organic fertilizer (at a rate of 1500‒3000 kg/hm2) combined with chemical fertilizer had a significantly positive effect on the theoretical yield, tiller number, partial factor productivity, and SPAD value of rice. Temperature, organic fertilizer application, and chemical fertilizer levels were identified as critical factors affecting rice yield. The micro-experiments demonstrated that the application of humic acid organic fertilizer with treatment F3 significantly elevated the SPAD value at the full heading and grain filling stages. Increased panicle number and seed-setting rate were the main contributors to the rise in yield, with the F3 treatment yielding the highest overall. The effective leaf area, high-efficiency leaf area, and dry matter accumulation in rice treated with F3 were all higher compared with the F0 treatment. Our findings indicated that the addition of humic acid organic fertilizer can markedly improve the partial factor productivity and agronomic efficiency of rice. In conclusion, the application of F3 organic fertilizer combined with A3 chemical fertilizer (F3A3) significantly increased the yield of saline-alkali rice, which was 6.62% higher than that of the F0A1 treatment, thereby validating the meta-analysis outcomes. We propose that the combined use of humic acid organic fertilizer and chemical fertilizer can promote the growth of rice in saline-alkali soils. Consequently, these management practices provide a means to foster the green and healthy development of rice in saline-alkali regions across China.