Rice Science

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1. Three-Line Hybrid Rice in China: Fifty Years of Sustained Improvement in Yield, Quality, and Stress Resistance

Gong Junyi, Zhang Xiaobo, Zhang Jianfu, Zeng Bo, Zhang Xiaoqing, Xu Xia, Cheng Benyi, Hou Yuxuan, Xia Junhui, Wu Jianli, Yang Shihua, Cheng Shihua, Han Bin, Xie Huaan

Rice Science 2026, 33 (4): 499-513. DOI: 10.1016/j.rsci.2026.04.004

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China pioneered the global commercial application of hybrid rice (Oryza sativa L.). Chinese scientists not only proved that heterosis can be realized in self-pollinating crops, a groundbreaking theoretical advance, but also developed commercial hybrid rice breeding into one of China’s most sophisticated agricultural technology models, making outstanding contributions to national food security. This study systematically reviews the 50-year developmental trajectory of officially approved three-line hybrid rice varieties at national and provincial levels in China, through analyzing the approval statistics of individual restorer lines and male sterile lines, the dynamic changes in the popularized planting area of major varieties, and the phenotypic variation in core agronomic traits including grain yield, grain quality, and disease/pest resistance. The paper comprehensively summarizes the remarkable progress, major achievements and practical experience accumulated over half a century of three-line hybrid rice breeding in China, and prospects future research directions for this system.

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2. OsELF3.1-OsCATA-Ghd7 Pathway Regulates Rice Heading

Wu Zhaozhong, Zhong Zhengzheng, Xu Peng, Liu Ling, Wang Beifang, Yang Qinqin, Wen Xiaoxia, Ma Guifang, Luo Mili, Zhang Yingxin, Liu Qun’en, Peng Zequn, Zhan Xiaodeng, Cao Liyong, Cheng Shihua, Wu Weixun

Rice Science 2025, 32 (5): 658-672. DOI: 10.1016/j.rsci.2025.06.001

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Rice, a critical global staple crop, relies heavily on heading date, a key agronomic trait marking the transition from vegetative to reproductive growth. Understanding the genetic regulation of heading date is vital for enhancing the adaptability of high-quality rice varieties across diverse geographical regions and for bolstering local food security. In this study, we uncovered a novel role for OsCATA, a catalase gene, in the regulation of photoperiodic flowering in rice. We identified a novel allele of OsELF3.1, whose mutation resulted in delayed heading. Further analyses revealed that OsELF3.1 physically interacted with OsCATA. Notably, OsCATA exhibited rhythmic expression patterns similar to OsELF3.1 and, when mutated, also delayed flowering. Expression analyses showed that the delayed heading phenotype could be attributed to elevated Ghd7 expression under both long-day and short-day conditions, with OsCATA expression positively regulated by OsELF3.1. Double mutants of OsELF3.1 and OsCATA displayed a heading delay similar to that of oself3.1 single mutants. Additionally, OsELF3.1 could interact with Ghd7 in vivo, alleviating its suppression of Ehd1. Luciferase assays confirmed that Ghd7 repressed Ehd1 expression, while OsELF3.1 mitigated this repression. Collectively, our findings reveal that OsCATA is critical in suppressing Ghd7 expression through the OsELF3.1-OsCATA-Ghd7 transcriptional pathway, thereby regulating rice heading.

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3. Functions of Rice E3 Ubiquitin Ligases in Response to Environmental Stress and in Regulating Grain Size

Li Haifeng, Fan Jiayi

Rice Science 2025, 32 (5): 649-657. DOI: 10.1016/j.rsci.2025.06.005

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The ubiquitin-proteasome system involves three types of enzymes (E1, E2, and E3) that promote protein ubiquitination and degradation. Among these, the E3 ubiquitin ligase mediates substrate specificity. In rice, over 1 500 E3 enzymes have been identified, playing diverse roles in growth, developmental processes, and responses to biotic and abiotic stresses. In recent years, significant progress has been made, with some breakthroughs in regulating disease resistance. Here, we summarize the roles of rice E3 ubiquitin ligases in responding to biotic and abiotic stresses, as well as their functions in regulating key agronomic traits such as seed size. Additionally, future research directions are discussed. This review aims to facilitate further studies on E3 ubiquitin ligases in rice.

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4. 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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5. 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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6. Regulatory Strategies for Alleviating Anaerobic and Submergence Stress in Rice

Zhang Xiaoli, Tao Wei, Tang Maoyan, Gao Guoqing, Chen Lei, Zhong Xiaoyuan, Lü Ronghua, Qin Dongming, Liang Tianfeng, Guo Hui

Rice Science 2026, 33 (2): 186-202. DOI: 10.1016/j.rsci.2026.01.001

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Rice production is increasingly challenged by flooding stress because of global warming and rising sea levels. As the world’s most important staple crop, rice is highly vulnerable to anaerobic and submergence conditions that occur during flooding, particularly at the germination and vegetative stages. Anaerobic environments hinder seedling establishment during germination, while prolonged submergence during the vegetative stage impairs growth, ultimately reducing yield and grain quality. These stresses, driven by extended inundation, trigger a cascade of detrimental physiological responses and represent a major barrier to stable rice production and global food security. In this review, we examine the effects of flooding on rice growth at both the germination and vegetative stages. We further summarize recent advances in the identification of flooding-tolerant germplasm, QTL mapping, genome-wide association study, transcriptomic and proteomic analyses, and other molecular studies. Subsequently, we highlight potential cultivation and regulatory strategies, including genetic, morphological, physiological, and endogenous hormone-related approaches, aimed at enhancing tolerance to anaerobic and submergence stress. Together, these approaches underscore the promise of integrating molecular insights with agronomic practices to mitigate flooding damage and support sustainable rice production.

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7. 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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8. 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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9. Cross-Species Induction of Plant Immunity by Oryza-Specific Small Secreted Peptide, OsRALF26

Oh-Kyu Kwon, A-Ram Jeong, Hyeran Moon, Ryoung Shin, Chang-Jin Park

Rice Science 2025, 32 (6): 747-750. DOI: 10.1016/j.rsci.2025.04.016

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10. Towards Climate-Smart Rice Cultivation: Addressing Methane Emission Mechanisms and Mitigation Strategies for a Sustainable Future

Saleem Asif, Sajjad Asaf, Rahmat Ullah Jan, Du Xiaoxuan, Jae-Ryoung Park, Kyung-Min Kim

Rice Science 2026, 33 (2): 203-220. DOI: 10.1016/j.rsci.2025.11.002

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Rice fields are one of the largest sources of methane (CH₄), a potent greenhouse gas contributing significantly to global warming. Elucidating the underlying mechanisms and mitigating CH₄ emissions from paddy fields is crucial for combating climate change while ensuring sustainable food production. This review investigates the biological processes governing CH₄ generation in rice fields, focusing on how soil microorganisms generate CH₄ under waterlogged, anaerobic conditions. It also explores the mechanisms by which CH₄ escapes into the atmosphere through plant-mediated transport, diffusion, and ebullition. Several factors influencing CH₄ emissions are discussed, including soil composition, water management, exogenous organic matter application, rice variety selection, and local climate conditions. Strategies that can be implemented to reduce CH₄ emissions are assessed, such as alternate wetting and drying, urea deep placement, biochar application, optimized fertilizer application, and breeding of rice varieties with low CH₄ emissions. Novel solutions, such as the enhancement of methane-consuming bacteria in soils using microbial-based approaches, are also explored. The importance of integrating innovative technologies, improved farming practices, and interdisciplinary research is emphasized to develop practical and scalable strategies for reducing CH₄ emissions. By addressing these challenges, we can advance towards the attainment of sustainable agriculture and global climate goals. This review aims to serve as a comprehensive resource for researchers, policymakers, and practitioners seeking to understand and mitigate CH₄ emissions from rice cultivation.

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11. Production of Authentic Hybrid Seedlings by Conferring Parents with Resistance to Different Herbicides

Wu Jingjing, Xia Shijian, Cai Yue, Zhang Qijun, Zong Shouyu, Zhu Qianhao, Yang Jie

Rice Science 2025, 32 (5): 612-616. DOI: 10.1016/j.rsci.2025.05.001

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12. 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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13. QTL-Seq Identifies Genomic Regions Associated with Resistance to Bipolaris oryzae and Their Association with Defense Related Enzyme Activity in Rice

Jagjeet Singh Lore, Sanjay Kumar, Dharminder Bhatia, Mandeep Singh Hunjan, Rishabh Maheshwari, Dayananda Veeriah Patil, Jyoti Jain

Rice Science 2026, 33 (1): 15-20. DOI: 10.1016/j.rsci.2025.08.012

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14. 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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15. Long-Range Admixture Linkage Disequilibrium and Allelic Responses of Sub1 and TPP7 under Consecutive Stress in Rice Validated Through Mendelian Randomization

Sabarinathan Selvaraj, Parameswaran Chidambaranathan, Goutam Kumar Dash, Priyadarsini Sanghamitra, Kishor Pundlik Jeughale, Cayalvizhi Balasubramaniasai, Devraj Lenka, Basavantraya Navadagi Devanna, Seenichamy Rathinam Prabhukarthikeyan, Sanghamitra Samantaray, Amaresh Kumar Nayak

Rice Science 2025, 32 (5): 704-716. DOI: 10.1016/j.rsci.2025.06.009

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Consecutive stresses, such as initial submergence during germination followed by water deficit during the seedling stage, pose significant challenges to direct-seeded rice cultivation. By Linkage disequilibrium analysis, Sub1 and Dro1 (Δbp: 10 Mb), as well as Sub1 and TPP7 (Δbp: 6 Mb) were identified to exhibit long-range linkage disequilibrium (LRLD). Meta-QTL analysis further revealed that Sub1 and TPP7 co-segregated for tolerance to submergence at the germination and seedling stages. Based on this, we hypothesized that LRLD might influence plant responses to consecutive stresses. To test this hypothesis, we developed a structured recombinant inbred line population from a cross between Bhalum 2 and Nagina 22, with alleles (Sub1 and TPP7) in linkage equilibrium. Mendelian randomization analysis validated that the parental alleles, rather than the recombinant alleles of Sub1 and TPP7, significantly influenced 13 out of 41 traits under consecutive stress conditions. Additionally, 16 minor additive effect QTLs were detected between the genomic regions, spanning Sub1 and TPP7 for various traits. A single allele difference between these genomic regions enhanced crown root number, root dry weight, and specific root area by 11.45%, 15.69%, and 33.15%, respectively, under flooded germination conditions. Candidate gene analysis identified WAK79 and MRLK59 as regulators of stress responses during flooded germination, recovery, and subsequent water deficit conditions. These findings highlight the critical role of parental allele combinations and genomic regions between Sub1 and TPP7 in regulating the stress responses under consecutive stresses. Favourable haplotypes derived from these alleles can be utilized to improve stress resilience in direct-seeded rice.

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16. 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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17. An Endosperm-Specific Early Nodulin-Like Gene Regulates Amylose Content in Rice

Zhao Dongsheng, Wu Dengfei, Chen Siyu, Fan Xiaolei, Li Qianfeng, Zhang Changquan, Liu Qiaoquan

Rice Science 2026, 33 (2): 155-158. DOI: 10.1016/j.rsci.2025.12.001

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18. Evaluating Efficacy of ZnO and MgO Nanoparticles on Post-Harvested Rice to Enhance Food Security Against Agroterrorism

Daisy Wilson, Valeria Gonzalez, Hamidreza Sharifan

Rice Science 2025, 32 (5): 717-726. DOI: 10.1016/j.rsci.2025.04.012

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Assessing the resilience of rice varieties against bioterrorism agents is critical to safeguarding food security. This study evaluated Food and Drug Administration-approved and recognized as safe metallic oxide nanoparticles (NPs) of zinc oxide (ZnO) and magnesium oxide (MgO) as protective strategies to reduce susceptibility in imported rice varieties to a biothreat model, Escherichia coli. Two types of rice (brown and white) from four countries (USA, Mexico, India, and Thailand) were treated with 60 mg/L NPs or their ionic forms and sterilized before inoculation. The treatments were analyzed for nutritional profiles, heavy metal content, and pathogen susceptibility. Rice organic compositions were characterized by Fourier transform infrared spectroscopy, and metal were contents quantified using inductively coupled plasma optical emission spectroscopy. Pathogenic response was monitored using ultraviolet mass spectrophotometry. The findings revealed that nutrient-rich varieties like brown rice from Mexico displayed reduced susceptibility to E. coli compared with white rice from India, which showed the highest susceptibility. NP fortification demonstrated significant antimicrobial efficacy, particularly with ZnO and MgO NPs, which were more effective than their ionic counterparts in inhibiting bacterial growth. Results showed that ZnO and MgO NP treatments reduced E. coli growth by 72% and 68%, respectively, compared with untreated controls. Brown rice from Mexican treated with MgO NPs exhibited the lowest optical density at 600 nm (OD₆₀₀ 0.01), indicating significantly enhanced resistance to bacterial proliferation. This research underscores the potential of nano-fortification not only to improve pathogen resilience in rice but also to maintain its nutritional integrity. This study provides a foundational framework for enhancing food safety against bioterrorism agents and supports the development of resilient agricultural practices.

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19. Genetic Regulation of Phytic Acid Biosynthesis in Rice: Pathways and Breeding Approaches for Low-Phytate Varieties

Lishali Desingu, R. L. Visakh, R. P. Sah, Uday Chand Jha, R. V. Manju, Swapna Alex, Radha Beena

Rice Science 2025, 32 (6): 797-812. DOI: 10.1016/j.rsci.2025.10.003

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Phytic acid (PA), or myo-inositol 1,2,3,4,5,6-hexakisphosphate, is the main storage form of phosphorus (P) in seeds, accounting for 65% to 85% of their total P content. The negative charge of PA attracts metal cations, forming insoluble salts called phytates. These phytates, contain six negatively charged ions, can bind divalent cations such as Fe²⁺, Zn²⁺, Mg²⁺, and Ca²⁺, preventing their absorption in monogastric animals. To overcome P deficiency in non-ruminants, phytase is usually given as a supplement, which then results in excess P excretion, leading to environmental problems such as eutrophication. Improved fertilizer management, food processing techniques, and the development of low-PA crops through plant breeding are envisioned as effective ways to improve P-utilization and lessen the environmental impact while minimizing the effect of PA. A better understanding of the molecular and physiological basis of PA biosynthesis, grain PA distribution, the effects of genetic and environmental factors on PA accumulation, and methods to increase micronutrient bioavailability by lowering the effects of PA is essential for developing low-PA crops.

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20. Optimized Leaf Morphology and Delayed Senescence Boost Rice Yield via Enhanced Leaf and Canopy Photosynthesis

Ye Miao, Mao Yuxin, Yuan Rong, Zhang Dehai, Zhang Zujian

Rice Science 2026, 33 (2): 245-259. DOI: 10.1016/j.rsci.2025.12.005

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Four modern hybrid and four japonica rice varieties differing in biomass, yield, and daily biomass production rate during the grain-filling period (DBP_GF), were used to reveal the eco-physiological photosynthetic characteristics of high-yield and high-efficiency rice. Varietal differences were analyzed in leaf and canopy photosynthetic parameters, associated leaf morphological and anatomical traits (e.g., stomatal density, vein density, mesophyll cell arrangement), as well as differences in canopy light interception and leaf area index, and their effects on yield and biomass accumulation. Hybrid rice with yield higher than 11.0 t/hm² and DBP_GF higher than 200 kg/(hm²·d), and japonica rice with yield higher than 9.0 t/hm² and DBP_GF higher than 200 kg/(hm²·d), were classified as high-yield and high-efficiency varieties; other varieties were considered general types. Based on this criterion, two hybrid (Yongyou 2640 and Shanyou 63) and two japonica varieties (Huaidao 5 and Nangeng 5718) were categorized as high-yield and high-efficiency types, while the remaining two hybrid (Liangyoupeijiu and C Liangyou 513) and two japonica varieties (Suxiu 867 and Yangnongdao 1) were classified as general types. Results indicated that high-yield and high-efficiency varieties generally have higher leaf and canopy photosynthesis, superior leaf stomatal, vascular, and mesophyll structures that facilitate CO₂ diffusion and hydraulic transport, higher canopy light transmittance, and slower leaf area attenuation. Rice yield and biomass were positively correlated with photosynthetic parameters and closely linked to associated photosynthetic traits. Efficient rice production was attributed to coordinated improvements in leaf structure, canopy architecture, and delayed leaf area attenuation. This study provides important theoretical guidance for breeding high-efficiency rice varieties.

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