Rice Science

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1. 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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2. 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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3. 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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4. 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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5. 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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6. 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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7. Molecular and Functional Roles of Tapetum Organelles: A Nursing Staff for Pollen Development

Asif Ali, Sumer Zulfiqar, Asad Riaz, Maneesh Lingwan, Sun Lianping, Wu Xianjun

Rice Science 2025, 32 (5): 617-636. DOI: 10.1016/j.rsci.2025.06.003

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Male gametes are produced in the anthers and are essential for fertilization and seed setting. A transverse section of the anther reveals four layers: the epidermis, endothecium, middle layer, and tapetum. The tapetum, being the innermost layer, plays a critical role in supplying nutrients, enzymes, and protection to microspores. Detailed microscopic and ultrastructural analyses have revealed highly active and well-organized structures within the tapetum, referred to as tapetal organelles. Molecular studies have highlighted the significance of tapetal cell death and the nurturing role of the tapetum for microspores. However, the mechanisms by which these processes are mediated by tapetal organelles at the cellular level remain elusive. The discovery of mutants defective in tapetal organelles has enabled further investigations into their structure, morphology, and function. This review discusses the molecular and functional roles of various tapetal organelles, such as plastids (amyloplasts and elaioplasts), mitochondria, tapetosomes, endoplasmic reticulum, and lipid bodies. We provide an overview of their roles, highlight key organelles in the tapetum, and address recent challenges and potential applications of genes regulating tapetal organelles in enhancing crop fertility.

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8. 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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9. 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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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. 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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13. 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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14. 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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15. Amino Acid Transporter OsAAP18 Modulates Nitrogen Allocation to Boost Yield and Grain Quality in Rice

He Chongchong, Yang Xiaochuan, Zhang Jie, Wu Wenhao, Wang Chuanbo, Chen Wenbo, Wu Bowen, Huang Weiting, Fang Zhongming

Rice Science 2026, 33 (2): 151-154. DOI: 10.1016/j.rsci.2026.01.005

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16. Identification and Functional Characterization of TPL/TPR Genes in Rice Disease Resistance

Zhan Chengfang, Lu Xueli, Chen Yingtong, Li Shunyuan, Zhang Xiaoyan, Chen Siqi, Xie Huan, Jin Lei, Ding Lin, Ge Yi, Yang Ting, Dai Liping, Cao Junfeng, Wang Mengcen, Tang Zhengbin, Zeng Dali

Rice Science 2026, 33 (2): 232-244. DOI: 10.1016/j.rsci.2025.12.002

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TOPLESS/TOPLESS-RELATED (TPL/TPR) proteins are transcriptional corepressors that play pivotal roles in plant development, hormone signaling, and stress responses. Although TPL/TPR proteins have been identified in various organisms, their functions in rice disease resistance remain largely unexplored. Here, we conducted a comprehensive analysis of the three rice TPL/TPR proteins, designated OsTPR1, OsTPR2, and OsTPR3, examining their evolutionary relationships, expression patterns, and subcellular localization, and assessing their roles in disease resistance. Phylogenetic analysis revealed that the three OsTPRs belonged to distinct evolutionary clades. Expression analysis demonstrated tissue-specific patterns and responsiveness to jasmonate (JA), with all three genes being induced upon infection with Xanthomonas oryzae pv. oryzae (Xoo). Consistent with their roles as transcriptional corepressors, all three OsTPRs localized to the nucleus. Disease resistance assays showed that, after inoculation with Xoo, lesion lengths on ostpr2 and ostpr3 mutants were significantly shorter than those on wild-type plants. Protein interaction assays demonstrated that OsTPR2 interacted with JA ZIM-domain protein (OsJAZ12), whose expression is also induced by Xoo. Furthermore, haplotype analysis of OsTPRs revealed natural variation, leading to the identification of superior allelic variants that confer improved resistance to bacterial blight without a yield penalty. Collectively, our findings provide a systematic characterization of TPL/TPR proteins in rice, highlight their potential roles in resistance to bacterial leaf blight, and identify valuable allelic resources for molecular breeding aimed at improving both disease resistance and yield.

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17. Role of OsPHB2 in Rice Plant Architecture and Salt Stress Tolerance: Mining High-Yielding Haplotype 2

Wang Zhonghao, Yu Ruoqian, Tian Yahong, Hu Ping, Wang Yueying, Luo Chenxi, Wei Qianya, Song Xinyang, Liu Wenjun, Tang Mengna, Yin Lu, Nong Wen, Lu Caolin, Li Sanfeng, Mao Yijian, Zhang Guangheng, Zhu Xudong, Lou Guangming, Wang Yuexing

Rice Science 2026, 33 (2): 146-150. DOI: 10.1016/j.rsci.2026.01.004

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18. Grain Zinc 7 Contributes to Zinc Deficiency Tolerance and Accumulation in Rice

Tang Jichun, Zhan Junhui, Liu Yuxi, Li Shuangyuyan, Lu Xiang, Meng Lijun, Ye Guoyou

Rice Science 2025, 32 (5): 594-598. DOI: 10.1016/j.rsci.2025.04.007

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19. NRAMPs: Versatile Transporters Involved in Metal Ion Homeostasis and Their Applications in Rice Breeding

Huang Qina, Wu Lijuan, Jiang Hongrui, He Yan, Liu Song, Yang Changdeng, Liang Yan

Rice Science 2026, 33 (1): 39-58. DOI: 10.1016/j.rsci.2025.10.010

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The NRAMP (natural resistance-associated macrophage protein) family plays a pivotal role in metal ion transport, regulating both essential micronutrient uptake and toxic heavy metal accumulation in plants. In rice (Oryza sativa), OsNRAMP transporters critically influence metal homeostasis, stress adaptation, and grain safety. Among them, OsNRAMP5 serves as a major entry point for cadmium (Cd) and manganese (Mn) uptake, making it a prime target for low-Cd rice breeding. However, knockout of OsNRAMP5 leads to severe Mn deficiency, highlighting the need for precise genetic modifications (e.g., OsNRAMP5-Q337K), which reduce Cd accumulation while maintaining Mn nutrition. Additionally, OsNRAMP1 and OsNRAMP2 contribute to Cd translocation and plant immunity, whereas OsNRAMP3/4/6/7 participate in Mn, iron, and zinc distribution and stress responses. This review systematically summarizes the structural, functional, and regulatory mechanisms of OsNRAMPs, emphasizing their roles in metal transport, pathogen resistance, and abiotic stress adaptation. Furthermore, we discuss strategies for developing low-Cd rice varieties, including QTL-based breeding, CRISPR/Cas9-mediated gene editing, and multi-gene stacking approaches. Finally, we outline future research directions, such as structural engineering of metal-binding sites and field validation of engineered rice lines, to ensure sustainable rice production in heavy metal-contaminated soils.

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20. Genetic Investigation Reveals That High Heterozygous Frequency in Selfing Offspring Promotes Multi-Generational Heterosis in Polyploid Rice

Zhu Lianjun, Huang Yu, Yang Jia, Chen Rou, Wu Jinwen, Liu Xiangdong, Lu Zijun

Rice Science 2025, 32 (5): 603-606. DOI: 10.1016/j.rsci.2025.04.010

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