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    Seed Storability in Rice: Physiological Foundations, Molecular Mechanisms, and Applications in Breeding
    Zhou Tianshun, Yu Dong, Wu Liubing, Xu Yusheng, Duan Meijuan, Yuan Dingyang
    Rice Science    2024, 31 (4): 401-416.   DOI: 10.1016/j.rsci.2024.02.011
    Abstract216)   HTML6)    PDF (4301KB)(806)       Save

    Long-term storage of crop seeds is critical for the conservation of germplasm resources, ensuring food supply, and supporting sustainable production. Rice, as a major food staple, has a substantial stock for consumption and production worldwide. However, its food value and seed viability tend to decline during storage. Understanding the physiological responses and molecular mechanisms of aging tolerance forms the basis for enhancing seed storability in rice. This review outlines the latest progress in influential factors, evaluation methods, and identification indices of seed storability. It also discusses the physiological consequences, molecular mechanisms, and strategies for breeding aging-tolerant rice in detail. Finally, it highlights challenges in seed storability research that require future attention. This review offers a theoretical foundation and research direction for uncovering the mechanisms behind seed storability and breeding aging-tolerant rice.

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    Improving Semi-Dried Brown Rice Noodle Quality via Mixed Fermentation of Lactobacillus and Yeast
    Luo Lijuan, Cheng Zixuan, Qiao Fan, Xiong Gangping, Liu Jun, Huang Qingming, Li Jiangtao, Lin Qinlu, Liu Chun
    Rice Science    2024, 31 (5): 489-493.   DOI: 10.1016/j.rsci.2024.06.005
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    Direct-Seeded Rice: Genetic Improvement of Game-Changing Traits for Better Adaption
    Priyanka Negi, Jagadish Rane, Rajendra Sadashiv Wagh, Tukaram Jayaram Bhor, Dipti Digambar Godse, Priyanka Jadhav, C. Anilkumar, Dasari Sreekanth, K. Sammi Reddy, Sharad Ramrao Gadakh, K. M. Boraih, C. B. Harisha, P. S. Basavaraj
    Rice Science    2024, 31 (4): 417-433.   DOI: 10.1016/j.rsci.2024.04.006
    Abstract195)   HTML9)    PDF (3780KB)(758)       Save

    The sustainability of rice production continues to be a subject of uncertainty and inquiry attributed to shifts in climatic conditions. In light of the impending climate change crisis and the high labor and water costs accompanying it, direct-seeded rice (DSR) is unquestionably one of the most practical solutions. Despite its resource and climate-friendly advantages, early maturing rice faces weed competitiveness and seedling establishment challenges. Resolving these issues is crucial for promoting its wider adoption among farmers, presenting it as a more effective sustainable rice cultivation method globally. Diverse traditional and contemporary breeding methods are employed to mitigate the limitations of the DSR approach, leveraging advanced techniques such as speed breeding and genome editing. Focusing on key traits like mesocotyl length elongation, early seedling vigor, root system architecture, and weed competitiveness holds promise for transformative improvements in DSR adaptation at a broader scale within farming communities. This review aims to summarize how these features contribute to increased crop production in DSR conditions and explore the research efforts focusing on enhancing DSR adaptation through these traits. Emphasizing the pivotal role of these game-changing traits in DSR adaptation, our analysis sheds light on their potential transformative impact and offers valuable insights for advancing DSR practices.

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    Efficient Breeding of Early-Maturing Rice Cultivar by Editing Hd6 via CRISPR/Cas9
    Chen Zhihui, Tao Yajun, Xu Yang, Wu Jingjing, Wang Fangquan, Li Wenqi, Jiang Yanjie, Fan Fangjun, Li Xia, Zhu Jianping, Zhu Qian-Hao, Yang Jie
    Rice Science    2024, 31 (6): 629-633.   DOI: 10.1016/j.rsci.2024.06.007
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    Salinity Stress Deteriorates Grain Yield and Increases 2-Acetyl-1-Pyrroline Content in Rice
    Wei Huanhe, Ma Weiyi, Zhang Xiang, Zuo Boyuan, Geng Xiaoyu, Wang Lulu, Zhu Wang, Chen Yinglong, Huo Zhongyang, Xu Ke, Meng Tianyao, Dai Qigen
    Rice Science    2024, 31 (4): 371-374.   DOI: 10.1016/j.rsci.2024.02.010
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    Effects of Biochar Inoculation with Bacillus megaterium on Rice Soil Phosphorus Fraction Transformation and Bacterial Community Dynamics
    Yu Keru, Xue Zhaokun, Fang Xianzhi, Ma Jiawei, Wang Yongjun, Liu Dan, Ye Zhengqian
    Rice Science    2024, 31 (4): 361-365.   DOI: 10.1016/j.rsci.2024.04.003
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    Rice Heat Tolerance Breeding: A Comprehensive Review and Forward Gaze
    Ravindran Lalithambika Visakh, Sreekumar Anand, Sukumaran Nair Arya, Behera Sasmita, Uday Chand Jha, Rameswar Prasad Sah, Radha Beena
    Rice Science    2024, 31 (4): 375-400.   DOI: 10.1016/j.rsci.2024.02.004
    Abstract169)   HTML11)    PDF (4019KB)(641)       Save

    The yield potential of rice is seriously affected by heat stress due to climate change. Since rice is a staple food globally, it is imperative to develop heat-resistant rice varieties. Thus, a thorough understanding of the complex molecular mechanisms underlying heat tolerance and the impact of high temperatures on various critical stages of the crop is needed. Adoption of both conventional and innovative breeding strategies offers a long-term advantage over other methods, such as agronomic practices, to counter heat stress. In this review, we summarize the effects of heat stress, regulatory pathways for heat tolerance, phenotyping strategies, and various breeding methods available for developing heat-tolerant rice. We offer perspectives and knowledge to guide future research endeavors aimed at enhancing the ability of rice to withstand heat stress and ultimately benefit humanity.

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    Host-Induced Gene Silencing of Effector AGLIP1 Enhanced Resistance of Rice to Rhizoctonia solani AG1-IA
    Zhao Mei, Liu Xiaoxue, Wan Jun, Zhou Erxun, Shu Canwei
    Rice Science    2024, 31 (4): 463-474.   DOI: 10.1016/j.rsci.2024.04.005
    Abstract164)   HTML7)    PDF (4370KB)(611)       Save

    Rice sheath blight, caused by Rhizoctonia solani AG1-IA, is a major disease in rice-growing areas worldwide. Effectors of phytopathogenic fungi play important roles during the infection process of fungal pathogens onto their host plants. However, the molecular mechanisms by which R. solani effectors regulate rice immunity are not well understood. Through prediction, 78 candidate effector molecules were identified. Using the tobacco rattle virus-host induced gene silencing (TRV-HIGS) system, 45 RNAi constructs of effector genes were infiltrated into Nicotiana benthamiana leaves. The results revealed that eight of these constructs resulted in a significant reduction in necrosis caused by infection with the AG1-IA strain GD-118. Additionally, stable rice transformants carrying the double-stranded RNA construct for one of the effector genes, AGLIP1, were generated to further verify the function of this gene. The suppression of the AGLIP1 gene increased the resistance of both N. benthamiana and rice against GD-118, and also affected the growth rate of GD-118, indicating that AGLIP1 is a key pathogenic factor. Small RNA sequencing showed that the HIGS vectors were processed into siRNAs within the plants and then translocated to the fungi, leading to the silencing of the target genes. As a result, AGLIP1 might be an excellent candidate for HIGS, thereby enhancing crop resistance against the pathogen and contributing to the control of R. solani infection.

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    In vivo Haploid Induction via Parthenogenesis Gene ToPAR in Rice
    XIONG Jie, JI Yajie, YANG Shenlin, QIU Xianjin, QIAN Qian, WANG Kejian
    Rice Science   
    Accepted: 11 December 2024

    Estimating Key Phenological Dates of Multiple Rice Accessions Using Unmanned Aerial Vehicle-Based Plant Height Dynamics for Breeding
    Hong Weiyuan, Li Ziqiu, Feng Xiangqian, Qin Jinhua, Wang Aidong, Jin Shichao, Wang Danying, Chen Song
    Rice Science    2024, 31 (5): 617-628.   DOI: 10.1016/j.rsci.2024.04.007
    Abstract151)   HTML11)    PDF (6167KB)(282)       Save

    Efficient and high-quality estimation of key phenological dates in rice is of great significance in breeding work. Plant height (PH) dynamics are valuable for estimating phenological dates. However, research on estimating the key phenological dates of multiple rice accessions based on PH dynamics has been limited. In 2022, field traits were collected using unmanned aerial vehicle (UAV)-based images across 435 plots, including 364 rice varieties. PH, dates of initial heading (IH) and full heading (FH), and panicle initiation (PI), and growth period after transplanting (GPAT) were collected during the rice growth stage. PHs were extracted using a digital surface model (DSM) and fitted using Fourier and logistic models. Machine learning algorithms, including multiple linear regression, random forest (RF), support vector regression, least absolute shrinkage and selection operator, and elastic net regression, were employed to estimate phenological dates. Results indicated that the optimal percentile of the DSM for extracting rice PH was the 95th (R2 = 0.934, RMSE = 0.056 m). The Fourier model provided a better fit for PH dynamics compared with the logistic models. Additionally, curve features (CF) and GPAT were significantly associated with PI, IH, and FH. The combination of CF and GPAT outperformed the use of CF alone, with RF demonstrating the best performance among the algorithms. Specifically, the combination of CF extracted from the logistic models, GPAT, and RF yielded the best performance for estimating PI (R2 = 0.834, RMSE = 4.344 d), IH (R2 = 0.877, RMSE = 2.721 d), and FH (R2 = 0.883, RMSE = 2.694 d). Overall, UAV-based rice PH dynamics combined with machine learning effectively estimated the key phenological dates of multiple rice accessions, providing a novel approach for investigating key phenological dates in breeding work.

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    Bulked Segregant RNA-Seq Analysis of Pollinated Pistils Reveals Genes Influencing Spikelet Fertility in Rice
    Kanokwan Kaewmungkun, Keasinee Tongmark, Sriprapai Chakhonkaen, Numphet Sangarwut, Theerachai Thanananta, Amorntip Muangprom
    Rice Science    2024, 31 (5): 556-571.   DOI: 10.1016/j.rsci.2024.06.001
    Abstract150)   HTML11)    PDF (5103KB)(292)       Save

    Prezygotic isolation is important for successful fertilization in rice, significantly affecting yield. This study focused on F5:6 generation plants derived from inter-subspecific crosses (Nipponbare × KDML105) with low (LS) and high seed-setting rates (HS), in which normal pollen fertility was observed. However, LS plants showed a reduced number of pollen grains adhering to the stigma and fewer pollen tubes reaching the ovules at 4‒5 h post-pollination, compared with HS plants. Bulked segregant RNA-Seq analysis of pollinated pistils from the HS and LS groups revealed 249 and 473 differentially expressed genes (DEGs), respectively. Kyoto Encyclopedia of Genes and Genomes analysis of the HS and LS- specific DEGs indicated enrichment in metabolic pathways, pentose and glucuronate interconversions, and flavonoid biosynthesis. Several of these DEGs exhibited co-expression with pollen development genes and formed extensive clusters of co-expression networks. Compared with LS pistils, enzyme genes controlling pectin degradation, such as OsPME35 and OsPLL9, showed similar expression patterns, with higher levels in HS pistils pre-pollination. Os02g0467600, similar to cinnamate 4-hydroxylase gene (CYP73), involved in flavonoid biosynthesis, displayed higher expression in HS pistils post-pollination. Our findings suggest that OsPME35, OsPLL9, and Os02g0467600 contribute to prezygotic isolation by potentially modifying the stigma cell wall (OsPME35 and OsPLL9) and controlling later processes such as pollen-stigma adhesion (Os02g0467600) genes. Furthermore, several DEGs specific to HS and LS were co-localized with QTLs and functional genes associated with spikelet fertility. These findings provide valuable insights for further research on rice spikelet fertility, ultimately contributing to the development of high-yielding rice varieties.

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    Anticancer Activity of Rice Callus Suspension Cultures from Aromatic Varieties and Metabolites Regulated in Treated Cancer Cell Lines
    Anuradha Kumari, Wusirika Ramakrishna
    Rice Science    2024, 31 (4): 449-462.   DOI: 10.1016/j.rsci.2024.04.002
    Abstract144)   HTML5)    PDF (5768KB)(572)       Save

    Tissue culture techniques were used to produce large amounts of bioactive compounds with medicinal potential, overcoming space and time constraints for cancer prevention. Rice callus suspension cultures (RCSC) and seed extracts prepared from aromatic rice varieties were used to evaluate the cytotoxic impact on human colon and lung cancer cell lines, as well as a normal control cell line, using Taxol as a positive control. RCSC and seed extracts from two Indian aromatic rice varieties were applied at different concentrations to treat the cancer cell lines and normal lung fibroblasts over varying time intervals. Apoptosis was assessed in 1:5 dilutions of the A549 and HT-29 cell lines treated with RCSC for 72 h, using propidium iodide staining and flow cytometry. RCSC showed a more potent cytotoxic effect than seed extracts with minimal effect on the normal cell line, in contrast to Taxol. Confocal microscopy and flow cytometry further confirmed the apoptotic effect of RCSC. Gas chromatography-mass spectrometry-based metabolic profiling identified metabolites involved in cytotoxicity and highlighted altered pathways. RCSC is proposed as an alternative source for the development of novel anticancer drugs with reduced side effects.

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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
    Abstract141)   HTML5)    PDF (1708KB)(418)       Save

    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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    Changes in Metabolites and Allelopathic Effects of Non-Pigmented and Black-Pigmented Lowland Indica Rice Varieties in Phosphorus Deficiency
    Liyana Sara, Sompop Saeheng, Panupong Puttarak, Lompong Klinnawee
    Rice Science    2024, 31 (4): 434-448.   DOI: 10.1016/j.rsci.2024.02.009
    Abstract140)   HTML6)    PDF (6978KB)(524)       Save

    Phosphorus (P) levels alter the allelopathic activity of rice seedlings against lettuce seeds. In this study, we investigated the effect of P deficiency on the allelopathic potential of non-pigmented and pigmented rice varieties. Rice seedlings of the white variety Khao Dawk Mali (KDML105, non-pigmented) and the black varieties Jao Hom Nin (JHN, pigmented) and Riceberry (RB, pigmented) were cultivated under high P (HP) and low P (LP) conditions. Morphological and metabolic responses to P deficiency were investigated. P deficiency inhibited shoot growth but promoted root growth of rice seedlings in all three varieties. Moreover, P deficiency led to decreased cytosolic phosphate (Pi) and total P concentrations in both shoot and root tissues. The subsequent reduction in internal P concentration enhanced the accumulation of phenolic compounds in both shoot and root tissues of the seedlings. Subsequently, allelopathy-based inter- and intra-specific interactions were assessed using water extracts from seedlings of the three varieties grown under HP and LP conditions. These extracts were tested on seeds of lettuce, the weed Dactyloctenium aegyptium, and the same rice variety. The shoot and root extracts from P-deficient seedlings reduced the germination of all recipient plants. Specifically, the shoot extract from P-deficient KDML105 seedlings reduced the germination index (GI) of lettuce seeds to 1%, while those from P-deficient RB and JHN seedlings produced GIs of 32% and 42%, respectively. However, when rice seeds were exposed to their own LP shoot and root extracts, their GIs increased up to 4-fold, compared with the HP extracts. Additionally, the shoot extracts from P-deficient plants also stimulated the germination of D. aegyptium by about 2-3-fold, whereas the root extracts did not have this effect. Therefore, P starvation led to the accumulation and exudation of phenolics in the shoots and roots of rice seedlings, altering their allelopathic activities. To adapt to P deficiency, rice seedlings potentially release signaling chemicals to suppress nearby competing species while simultaneously promoting their own germination and growth.

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    Progress on Molecular Mechanism of Heat Tolerance in Rice
    Fu Yiwei, Wu Jiayelu, Wu Mingming, Ye Shenghai, Zhai Rongrong, Ye Jing, Zhu Guofu, Yu Faming, Lu Yanting, Zhang Xiaoming
    Rice Science    2024, 31 (6): 673-687.   DOI: 10.1016/j.rsci.2024.07.001
    Abstract139)   HTML8)    PDF (2368KB)(242)       Save

    Rice (Oryza sativa L.) is a major food crop in China, and its high and stable yield is crucial for ensuring food security in the country. However, over the past few years, extreme weather events induced by global climate change have impacted rice growth. For example, the effects of heat stress on rice quality and yield have been significant. Therefore, it is fundamental to conduct in-depth research on the heat-tolerance mechanisms of rice and to cultivate superior new thermotolerant rice varieties. This review summarizes the adverse effects of high temperatures on rice growth at various stages, the heat-tolerance mechanisms in rice, and the heat-tolerance genes and QTLs that have been identified in recent years. We also discuss strategies to enhance the heat tolerance of rice, offering new insights for rice breeding research.

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    Random Amplification Polymorphic DNA and Agro-Morphological Traits-Based Fingerprinting for Detection of Genetic Divergence in Indian Black Rice
    Manisha Sharma, Dhananjay Raturi, Vijay Rani Rajpal, Manju Chaudhary, Soom Nath Raina, Apekshita Singh
    Rice Science    2024, 31 (4): 366-370.   DOI: 10.1016/j.rsci.2024.03.002
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    Next Generation Nutrition: Genomic and Molecular Breeding Innovations for Iron and Zinc Biofortification in Rice
    Kunhikrishnan Hemalatha Dhanyalakshmi, Reshma Mohan, Sasmita Behera, Uday Chand Jha, Debashis Moharana, Ahalya Behera, Sini Thomas, Preman Rejitha Soumya, Rameswar Prasad Sah, Radha Beena
    Rice Science    2024, 31 (5): 526-544.   DOI: 10.1016/j.rsci.2024.04.008
    Abstract134)   HTML4)    PDF (3211KB)(262)       Save

    Global efforts to address malnutrition and hidden hunger, particularly prevalent in low- and middle-income countries, have intensified, with a focus on enhancing the nutritional content of staple crops like rice. Despite serving as a staple for over half of the world’s population, rice falls short in meeting daily nutritional requirements, especially for iron (Fe) and zinc (Zn). Genetic resources, such as wild rice species and specific rice varieties, offer promising avenues for enhancing Fe and Zn content. Additionally, molecular breeding approaches have identified key genes and loci associated with Fe and Zn accumulation in rice grains. This review explores the genetic resources and molecular mechanisms underlying Fe and Zn accumulation in rice grains. The functional genomics involved in Fe uptake, transport, and distribution in rice plants have revealed key genes such as OsFRO1, OsIRT1, and OsNAS3. Similarly, genes associated with Zn uptake and translocation, including OsZIP11 and OsNRAMP1, have been identified. Transgenic approaches, leveraging transporter gene families and genome editing technologies, offer promising avenues for enhancing Fe and Zn content in rice grains. Moreover, strategies for reducing phytic acid (PA) content, a known inhibitor of mineral bioavailability, have been explored, including the identification of low-PA mutants and natural variants. The integration of genomic information, including whole-genome resequencing and pan-genome analyses, provides valuable insights into the genetic basis of micronutrient traits and facilitates targeted breeding efforts. Functional genomics studies have elucidated the molecular mechanisms underlying Fe uptake and translocation in rice. Furthermore, transgenic and genome editing techniques have shown promise in enhancing Fe and Zn content in rice grains through the manipulation of key transporter genes. Overall, the integration of multi-omics approaches holds significant promise for addressing global malnutrition and hidden hunger by enhancing the nutritional quality of rice, thereby contributing to improved food and nutritional security worldwide.

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    RISE Method Based on Rare Allele Infusion and Sanger Sequencing Estimation: A Simple, Cheap, and Efficient Method for Detecting Transgene Copy Number in Rice
    Liu Tingchang, Huang Lifang, Liu Peng, Cui Yanchun, Chen Caiyan, Mao Donghai
    Rice Science    2024, 31 (5): 499-502.   DOI: 10.1016/j.rsci.2024.05.001
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    Biochar Decreases Soil Cadmium (Cd) Availability and Regulates Expression Levels of Cd Uptake/Transport-Related Genes to Reduce Cd Translocation in Rice
    Wang Han, Huang Qina, Zhang Yan, Shao Guosheng, Hu Yijun, Xu Youxiang
    Rice Science    2024, 31 (5): 494-498.   DOI: 10.1016/j.rsci.2024.04.004
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    Development of Machine Vision-Based Algorithm for Counting and Discriminating Filled and Unfilled Paddy Rice in Overlapping Mode
    Mahdieh Hoseingholizadeh-Alashti, Davood Kalantari
    Rice Science    2024, 31 (5): 503-506.   DOI: 10.1016/j.rsci.2024.04.001
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