Rice Science

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1. 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

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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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2. 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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3. Response of Rice Growth and Nutrient Absorption in a Saline- Alkali Paddy to Different Nitrogen Fertilizer Applications

Wang Xinyi, Zhu Hui, Yan Baixing, Brian Shutes, Zeng Yuan

Rice Science 2024, 31 (3): 245-250. DOI: 10.1016/j.rsci.2024.03.001

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4. 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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5. 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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6. 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

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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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7. 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

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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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8. 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

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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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9. Putrescine Modulates Cadmium Fixation Ability of Cell Wall to Decrease Cadmium Accumulation in Rice, a Process Might Depend on Nitric Oxide

Wang Haoyu, Li Su, Yang Jibo, Huang Jing, Zhu Xiaofang, Shen Renfang, Zeng Dali

Rice Science 2024, 31 (3): 237-240. DOI: 10.1016/j.rsci.2023.11.009

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10. Does Financial Inclusion Influence Economic Efficiency of Rice Farming? Evidence from Ogun State, Nigeria

Shakirat B. Ibrahim, Raheem O. Aminu, Aisha O. Arowolo, Opeyemi O. Okanlawon, Afeez A. Adegbola

Rice Science 2024, 31 (6): 638-642. DOI: 10.1016/j.rsci.2024.10.001

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11. Interaction Between Ustilaginoidea virens and Rice and Its Sustainable Control

Zhang Fengmin, Cao Zhenzhen, Zheng Xin, He Yuntao, Chen Mingxue, Lin Xiaoyan

Rice Science 2024, 31 (3): 269-284. DOI: 10.1016/j.rsci.2023.11.012

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Ustilaginoidea virens is a common rice pathogen that can easily lead to a decline in rice quality and the production of toxins pose potential risks to human health. In this review, we present a comprehensive literature review of research since the discovery of rice false smut. We provide a comprehensive and, at times, critical overview of the main results and findings from related research, and propose future research directions. Firstly, we delve into the interaction between U. virens and rice, including the regulation of transcription factors, the process of U. virens infecting rice panicles, and the plant immune response caused by rice infection. Following that, we discuss the identification and characterization of mycotoxins produced by the pathogenic fungus, as well as strategies for disease management. We emphasize the importance of comprehensive agricultural prevention and control methods for the sustainable management of U. virens. This knowledge will update our understanding of the interaction between U. virens and rice plants, offering a valuable perspective for those interested in U. virens.

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12. Exploring Nutritional Compositions, Volatile Compounds, Health Benefits, Emerging Processing Technologies, and Potential Food Products of Glutinous Rice: A Review

Maimunah Mohd Ali, Norhashila Hashim

Rice Science 2024, 31 (3): 251-268. DOI: 10.1016/j.rsci.2024.02.002

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Glutinous rice (Oryza sativa var. glutinosa) stands out as one of the most popular rice varieties globally, amidst thousands of rice cultivars. Its increasing popularity is attributed to its rich nutritional compositions and health benefits. This review aims to summarize the nutritional compositions, volatile compounds, and health benefits of glutinous rice. Further, in-depth studies are necessary to explore the utilization of glutinous rice in enhancing processing technologies and developing new food products. Glutinous rice has been shown to possess numerous health benefits, including antioxidant activity, bioactive compounds, anti-cancer properties, anti-inflammatory effects, anti-diabetic potential, and cholesterol-lowering effects. Besides its nutritional compositions, the major volatile compounds identified in glutinous rice could serve as a functional food for human consumption. Emerging processing technologies related to glutinous rice are elaborated to improve the latest developments for incorporating them into various food products.

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13. Gapless Genome Assembly of ZH8015 and Preliminary Multi-Omics Analysis to Investigate ZH8015’s Responses Against Brown Planthopper Infestation

Li Dian, Duan Wenjing, Liu Qun’en, Wu Weixun, Zhan Xiaodeng, Sun Lianping, Zhang Yingxin, Cheng Shihua

Rice Science 2024, 31 (3): 317-327. DOI: 10.1016/j.rsci.2024.02.001

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Accurate genomic information is essential for advancing genetic breeding research in specific rice varieties. This study presented a gapless genome assembly of the indica rice cultivar Zhonghui 8015 (ZH8015) using PacBio HiFi, Hi-C, and ONT (Oxford Nanopore Technologies) ultra-long sequencing technologies, annotating 43 037 gene structures. Subsequently, utilizing this genome along with transcriptomic and metabolomic techniques, we explored ZH8015’s response to brown planthopper (BPH) infestation. Continuous transcriptomic sampling indicated significant changes in gene expression levels around 48 h after BPH feeding. Enrichment analysis revealed particularly significant alterations in genes related to reactive oxygen species scavenging and cell wall formation. Metabolomic results demonstrated marked increases in levels of several monosaccharides, which are components of the cell wall and dramatic changes in flavonoid contents. Omics association analysis identified differentially expressed genes associated with key metabolites, shedding light on ZH8015’s response to BPH infestation. In summary, this study constructed a reliable genome sequence resource for ZH8015, and the preliminary multi-omics results will guide future insect-resistant breeding research.

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14. Molecular Mechanism of Rice Necrotic Lesion for Optimized Yield and Disease Resistance

Hou Xinyue, Wang Yuping, Qian Qian, Ren Deyong

Rice Science 2024, 31 (3): 285-299. DOI: 10.1016/j.rsci.2023.12.003

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How to balance rice resistance and yield is an important issue in rice breeding. Plants with mutated necrotic lesion genes often have persistent broad-spectrum resistance, but this broad-spectrum resistance usually comes at the expense of yield. Currently, many necrotic lesion mutants in rice have been identified, and these genes are involved in disease resistance pathways. This review provides a detailed introduction to the characteristics, classification, and molecular mechanisms of necrotic lesion formation. Additionally, we review the molecular regulatory pathways of genes involved in rice disease resistance. Concurrently, we summarize the relationship between resistance and yield in rice using newly developed gene editing methods. We discuss a rational and precise breeding strategy to better utilize molecular design technology for breeding disease-resistant and high-yield rice varieties.

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15. Cell Wall Fixation, Translocation, and Vacuolar Detoxification of Cadmium Contribute to Differential Grain Cadmium Accumulation in Two Rice Cultivars

Zhu Xiaofang, Zhao Ling, Huang Jing, He Jiatong, Song Jiayin, Teng Ying, Shen Renfang

Rice Science 2024, 31 (3): 241-244. DOI: 10.1016/j.rsci.2023.11.010

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16. 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

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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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17. Biofilmed-PGPR: Next-Generation Bioinoculant for Plant Growth Promotion in Rice under Changing Climate

Jeberlin Prabina Bright, Hemant S. Maheshwari, Sugitha Thangappan, Kahkashan Perveen, Najat A. Bukhari, Debasis Mitra, Riyaz Sayyed, Andrea Mastinu

Rice Science 2025, 32 (1): 94-106. DOI: 10.1016/j.rsci.2024.08.008

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The exopolysaccharide matrix of diazotrophic cyanobacteria was used to integrate phosphorus (P) and potassium (K) solubilizing bacteria, enhancing the survival of plant growth-promoting rhizobacteria, and ultimately the survival of bacteria in the rhizosphere for better plant growth. A new biofilm-based formulation comprising the diazotrophic cyanobacteria Anabaena AMP2, P-solubilizing Bacillus megaterium var. phosphaticum PB1, and K-solubilizing Rhizobium pusense KRBKKM1 was tested for efficacy in rice. The growth medium with half-strength BG-11 medium supplemented with 3% glucose showed best for biofilm formation under in vitro conditions. Analysis of the methanolic extract of the cyanobacterial- bacterial biofilm (CBB) showed the activity of antioxidants, such as 2-methoxy phenol and pentadecane, which are proven to improve plant-microbe interactions and plant growth, respectively. Treatment of rice seeds with CBB extract at 100 mL/kg or 200 mL/kg showed significant enhancement in germination rate and seedling length. Therefore, a pot culture experiment with the CBB formulations was carried out, and different growth and yield parameters were recorded. Principal component analysis showed that plant growth, yield, soil dehydrogenase activity, and soil chlorophyll content were positively correlated with rice plants amended with vermiculite-based CBB at 2 kg/hm²followed 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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18. Rice Cultivation under Film Mulching Can Improve Soil Environment and Be Beneficial for Rice Production in China

Zhang Youliang, Zhu Kaican, Tang Yongqi, Feng Shaoyuan

Rice Science 2024, 31 (5): 545-555. DOI: 10.1016/j.rsci.2024.06.009

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Rice cultivation under film mulching is an integrated management technology that can conserve water, increase soil temperature, improve yield, and enhance water and nitrogen use efficiencies. Despite these advantages, the system does have its drawbacks, such as soil organic matter reduction and microplastic pollution, which impede the widespread adoption of film mulching cultivation in China. Nonetheless, the advent of degradable film, controlled-release fertilizer, organic fertilizer, and film mulching machinery is promoting the development of rice film mulching cultivation. This review outlines the impact of rice cultivation under film mulching on soil moisture, soil temperature, soil fertility, greenhouse gas emissions, weed control, and disease and pest management. It also elucidates the mechanism of changes in rice growth, yield and quality, water use efficiency, and nitrogen use efficiency. This paper incorporates a review of published research articles and discusses some uncertainties and shortcomings associated with rice cultivation under film mulching. Consequently, prospective research directions for the technology of rice film mulching cultivation are outlined, and recommendations for future research into rice cultivation under film mulching are proposed.

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19. Genome-Wide Discovery of Candidate Genes Associated with Cold Tolerance in Rice at Various Growth Stages

Liu Jiajun, Wang Cuili, Sun Mingmao, Ma Xiaoding, Han Bing, Guo Xiaohong, Han Longzhi, Cui Di

Rice Science 2025, 32 (2): 137-142. DOI: 10.1016/j.rsci.2024.12.001

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20. 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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