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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

    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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    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/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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    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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    Mixture of Bacillus Amyloliquefaciens and Bacillus Pumilus Modulates Community Structures of Rice Rhizosphere Soil to Suppress Rice Seedling Blight
    Jiang Nan, Qiu Jiehua, Tian Dagang, Shi Huanbin, Liu Zhiquan, Wen Hui, Xie Shuwei, Chen Huizhe, Wu Meng, Kou Yanjun
    Rice Science    2025, 32 (1): 118-130.   DOI: 10.1016/j.rsci.2024.09.001
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    Rice seedling blight, caused by various fungi, including Fusarium oxysporum, poses a severe threat to rice production. As awareness grows regarding the environmental and safety hazards associated with the application of fungicides for managing rice seedling blight, there has been a shift in focus towards biological control agents. In this study, we isolated biocontrol bacteria from paddy fields that significantly inhibited the growth of F. oxysporum in vitro and identified the strains as Bacillus amyloliquefaciens T40 and Bacillus pumilus T208. Additionally, our findings indicated that the combined application of these Bacillus strains in soil was more effective in reducing the incidence of rice seedling blight than their individual use. Analysis of 16S and internal transcribed spacer rRNA gene sequencing data revealed that the mixture of the T40 and T208 strains exhibited the lowest average clustering coefficients, which were negatively correlated with the biomass of F. oxysporum-inoculated rice seedlings. Furthermore, this mixture led to higher stochastic assembly (average |βNTI| < 2) and reduced selection pressures on rice rhizosphere bacteria compared with individual strain applications. The mixture of the T40 and T208 strains also significantly increased the expression of defense-related genes. In conclusion, the mixture of the T40 and T208 strains effectively modulates microbial community structures, enhances microbial network stability, and boosts the resistance against rice seedling blight. Our study supports the development and utilization of biological resources for crop protection.

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    Molecular Evolution of Rice Blast Resistance Gene bsr-d1
    Li Wei, Zhang Mengchen, Yang Yaolong, Weng Lin, Hu Peisong, Wei Xinghua
    Rice Science    2024, 31 (6): 700-711.   DOI: 10.1016/j.rsci.2024.08.004
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    Rice blast, caused by the fungus Magnaporthe oryzae, reduces rice yields by 10% to 35%. Incorporating blast resistance genes into breeding programs is an effective strategy to combat this disease. Understanding the genetic variants that confer resistance is crucial to this strategy. The gene Bsr-d1 encodes a C2H2-like transcription factor, and its recessive allele confers broad-spectrum resistance against infections by various strains of M. oryzae. In this study, we investigated the molecular evolution of the rice blast resistance gene bsr-d1 in a representative population consisting of 827 cultivated and wild rice accessions. Our results revealed that wild rice exhibited significantly higher nucleotide diversity, with polymorphic regions primarily concentrated in the promoter region, in contrast to indica and japonica rice varieties. The Bsr-d1 gene displayed significant differentiation between indica and japonica rice varieties, with the bsr-d1 resistance allele being unique to indica rice. Haplotype network and phylogenetic analyses suggested that the bsr-d1 resistance allele most likely originated from Oryza nivara in the region adjacent to the Indian Peninsula and the Indochina Peninsula. Moreover, we explored the utilization of bsr-d1 resistance alleles in China and designed a pair of DNA primers based on the polymorphic sites for the detection of the bsr-d1 resistance gene. In summary, our study uncovering the origin and evolution of bsr-d1 will enhance our understanding of resistance gene variation and expedite the resistance breeding process.

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    Applying Boron Fertilizer at Different Growth Stages Promotes Boron Uptake and Productivity in Rice
    Sitthikorn Bodeerath, Jeeraporn Veeradittakit, Sansanee Jamjod, Chanakan Prom-U-Thai
    Rice Science    2024, 31 (6): 751-760.   DOI: 10.1016/j.rsci.2024.08.007
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    Boron (B) is an essential micronutrient for plant growth and yield. We investigated the optimal growth stage for B fertilizer application to improve rice production. The study was conducted using a 2 × 4 factorial design in a randomized complete block during the rainy season of 2022. We utilized two premium Thai rice varieties Khao Dawk Mali 105 (KDML105) and Pathum Thani 1 (PTT1), and four soil B fertilizer treatments: a control (no B application), B application at the tillering stage, B application at the flowering stage, and B application at both the tillering and flowering stages. The results showed that the application of B fertilizer at the flowering stage and at both the tillering and flowering stages increased grain yield of KDML105 by 25.0% and 34.0%, respectively. In contrast, the grain yield of PTT1 showed no response to B application. The increased grain yield of KDML105 was attributed to an increased number of panicles per plant and a higher filled grain rate, which was due to the elevated B concentration in all plant parts and the total B uptake, particularly when B was applied at the flowering and tillering stages. Notably, B application increased the fertilized grain rates and reduced the proportion of unfertilized grains, a phenomenon that corresponded with the increased B concentration across all plant parts. The total B uptake ranged from 5.11 to 15.85 mg/m2 in KDML105 and from 8.37 to 24.26 mg/m2 in PTT1, with the highest total B uptake observed when B was applied at both the tillering and flowering stages for both rice varieties.

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    Breeding for Heat Tolerant Aromatic Rice Varieties and Identification of Novel QTL Regions Associated with Heat Tolerance During Reproductive Phase by QTL-Seq
    Surangkana Chimthai, Sulaiman Cheabu, Wanchana Aesomnuk, Siriphat Ruengphayak, Siwaret Arikit, Apichart Vanavichit, Chanate Malumpong
    Rice Science    2025, 32 (1): 67-80.   DOI: 10.1016/j.rsci.2024.12.002
    Abstract151)   HTML7)    PDF (5232KB)(320)       Save

    Extremely high temperatures resulting from climate change have become a major challenge for increasing rice production. Therefore, our objective was to develop heat-tolerant aromatic rice varieties using the pedigree method, focusing on selecting for seed-setting ability under extremely high temperatures along with the use of single nucleotide polymorphism/insertion and deletion (SNP/InDel) markers to improve aromatic properties and grain quality. Furthermore, the QTL-seq approach was utilized to identify QTLs for seed-setting rate in an F2 population subjected to heat stress. The candidate QTL regions were then aligned to confirm SNPs/InDels in synonymous F7 candidate heat-tolerant lines. The results revealed that four promising lines, namely 84-7-1-9, 84-7-1-10, 159-3-3-1, and 159-3-3-10, were classified as heat-tolerant with low amylose content. In addition, lines 84-7-1-9 and 84-7-1-10 were identified as aromatic rice encompassing the aroma gene (badh2). Regarding the QTL-seq results, the qSF2.1 region ranged from 311 051 to 3 929 422 bp on chromosome 2, was identified based on the highest contrasting SNP index between the heat-susceptible and tolerant bulks. The candidate genes within this region include two genes related to heat shock proteins, three genes associated with pollen fertility, and four genes involved in heat stress and other abiotic stress responses. These genes are proposed as potential candidates for heat tolerance and could serve as targets in rice breeding programs aimed at enhancing heat tolerance.

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    Breeding Resilience: Exploring Lodging Resistance Mechanisms in Rice
    Durga Prasad Mullangie, Kalaimagal Thiyagarajan, Manonmani Swaminathan, Jagadeesan Ramalingam, Sritharan Natarajan, Senthilkumar Govindan
    Rice Science    2024, 31 (6): 659-672.   DOI: 10.1016/j.rsci.2024.08.002
    Abstract138)   HTML4)    PDF (6882KB)(214)       Save

    Lodging is more than just plants falling over; it incurs significant economic losses for farmers leading to a decrease in both yield and quality of the final produce. Human management practices, such as dense sowing, excessive nitrogen fertilizer applications, inappropriate sowing dates, and upland rice cultivation, exacerbate the risk of lodging in rice. While breeders have developed high-yielding rice varieties utilizing the sd1 gene, relying solely on this gene is insufficient to enhance lodging resistance. Identifying the traits that contribute to lodging resistance is crucial. Key factors include biochemical, anatomical, and morphological traits, such as the levels of lignin, cellulose, hemicellulose, silicon, and potassium, along with the number and area of vascular bundles and the thickness, diameter, and length of the culm. Moreover, markers associated with lodging-related genes, like SCM2, SCM3, SCM4, and prl4, can be utilized effectively in marker-assisted backcrossing to develop rice varieties with desirable culm traits. This literature review aims to aid rice breeders in addressing the issue of lodging by examining traits that influence lodging resistance, developing phenotyping strategies for these traits, identifying suitable instrumentation, exploring methods for screening lodging-resistant plants, understanding the mathematical relationships involved, and considering molecular breeding aspects for pyramiding genes related to lodging.

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    Fluorescence Detection of Bacterial Pathogens in Rice by Recombinant Polymerase Amplification Based on Self-Heating Paper Chip
    Yang Ning, Fu Jiuju, Wang Aiying, Liu Shuhua, Chang Kangpeng, Song Wei, Tao Shoulong, Mao Hanping, Zhang Xiaodong, Xu Lijia
    Rice Science    2025, 32 (2): 131-136.   DOI: 10.1016/j.rsci.2025.01.001
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    Immune Sensor Xa21 Regulates Bacterial Leaf Blight Infection in Seven Rice Cultivars from Myanmar
    Nay Chi Aye, Rizwana Begum Syed Nabi, Muhammad Shahid, Nkulu Kabange Rolly, Rupesh Tayade, Lee-Bong Choon, Adil Hussain, Byung-Wook Yun
    Rice Science    2024, 31 (6): 634-637.   DOI: 10.1016/j.rsci.2024.06.008
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    Regulation of Yield and Eating and Cooking Quality in Rice Through Seed Albumin OsRAL5
    Zhao Chunfang, He Lei, Guan Ju, Luo Lei, Zhao Ling, Zhou Lihui, Yao Shu, Chen Tao, Zhu Zhen, Zhao Qingyong, Wang Cailin, Zhang Yadong
    Rice Science    2025, 32 (1): 6-10.   DOI: 10.1016/j.rsci.2024.08.005
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    Histone Acetyltransferase GCN5 Regulates Rice Growth and Development and Enhances Salt Tolerance
    Xue Chao, Zhao Xinru, Chen Xu, Cai Xingjing, Hu Yingying, Li Xiya, Zhou Yong, Gong Zhiyun
    Rice Science    2024, 31 (6): 688-699.   DOI: 10.1016/j.rsci.2024.06.002
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    Histone acetylation is indispensable in the process of crops resisting abiotic stress, which is jointly catalyzed by histone acetyltransferases and deacetylases. However, the mechanism of regulating salt tolerance through histone acetyltransferase GCN5 is still unclear. We revealed that GCN5 can catalyze the acetylation of canonical H3 and H4 lysine residues both in vivo and in vitro in rice. The knockout mutants and RNA interference lines of OsGCN5 exhibited severe growth inhibition and defects in salt tolerance, while the over-expression of OsGCN5 enhanced the salt tolerance of rice seedlings, indicating that OsGCN5 positively regulated the response of rice to salt stress. RNA-seq analysis suggested OsGCN5 may positively regulate the salt tolerance of rice by inhibiting the expression of OsHKT2;1 or other salt-responsive genes. Taken together, our study indicated that GCN5 plays a key role in enhancing salt tolerance in rice.

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    Disruption of Energy Metabolism and Reactive Oxygen Species Homeostasis in Honglian Type-Cytoplasmic Male Sterility (HL-CMS) Rice Pollen
    Wang Mingyue, Zhao Weibo, Feng Xiaoya, Chen Yi, Li Junhao, Fu Jinmei, Yan Yingchun, Chu Zhaohui, Huang Wenchao
    Rice Science    2025, 32 (1): 81-93.   DOI: 10.1016/j.rsci.2024.10.003
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    Honglian type-cytoplasmic male sterility (HL-CMS) is caused by the inter-communication between the nucleus and mitochondria. However, the mechanisms by which sterility genes regulate metabolic alterations and changes in mitochondrial morphology in the pollen of HL-CMS remain unclear. In this study, we compared the morphological differences between the pollen of the male sterile line YA and the near-isogenic line NIL-Rf6 using hematoxylin-eosin staining and 4ʹ,6-diamidino-2-phenylindole (DAPI) staining. HL-CMS is characterized by gametophytic sterility, where the aborted pollen grains are empty, and the tapetal layer remains intact. Transmission electron microscopy was employed to observe mitochondrial morphological changes at the microspore stage, revealing significant mitochondrial alterations, characterized by the formation of 'large spherical mitochondria', occurred at the binucleate stage in the YA line. Additionally, metabolomics analysis revealed decreased levels of metabolites associated with the carbohydrate and flavonoid pathways. Notably, the decrease in flavonoids was found to contribute to an elevation in reactive oxygen species (ROS) levels. Therefore, we propose a model in which rice fertility is modulated by the levels of pollen carbohydrates and flavonoid metabolites, with impaired mitochondrial energy production and reduced flavonoid biosynthesis as the main causes of ROS accumulation and pollen abortion in rice.

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    Expanding Viral Diversity in Rice Fields by Next-Generation Sequencing
    Wang Haoran, Chen Guoqing, Feng Guozhong
    Rice Science    2025, 32 (1): 44-51.   DOI: 10.1016/j.rsci.2024.12.004
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    In rice fields, rice plants usually grow alongside wild weeds and are attacked by various invertebrate species. Viruses are abundant in plants and invertebrates, playing crucial ecological roles in controlling microbial abundance and maintaining community structures. To date, only 16 rice viruses have been documented in rice-growing regions. These viruses pose serious threats to rice production and have traditionally been identified only from rice plants and insect vectors by isolation techniques. Advances in next-generation sequencing (NGS) have made it feasible to discover viruses on a global scale. Recently, numerous viruses have been identified in plants and invertebrates using NGS technologies. In this review, we discuss viral studies in rice plants, invertebrate species, and weeds in rice fields. Many novel viruses have been discovered in rice ecosystems through NGS technologies, with some also detected using metatranscriptomic and small RNA sequencing. These analyses greatly expand our understanding of viruses in rice fields and provide valuable insights for developing efficient strategies to manage insect pests and virus-mediated rice diseases.

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    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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    Synergy in Rice Immunity: Exploring Strategies of Coordinated Disease Defense Through Receptor-Like Kinases and Receptor- Like Cytoplasmic Kinases
    Pei Mengtian, Cao Yingying, Xie Xuze, Cao Ying, Chen Jia, Zhang Xi, Wang Zonghua, Lu Guodong, Zhang Shenghang
    Rice Science    2024, 31 (6): 643-658.   DOI: 10.1016/j.rsci.2024.07.002
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    Receptor-like kinases (RLKs) and receptor-like cytoplasmic kinases (RLCKs) play an indispensable role in the perception and transmission of extracellular signals in plants. In rice, these kinases actively participate in immune responses against a variety of pathogens, including fungi, bacteria, and viruses. However, research on the specific response mechanisms and the spectrum of different kinase activities against various pathogens remains insufficient. This review provides an in-depth and comprehensive overview of the types and functions of RLKs and RLCKs involved in disease resistance, emphasizing the central role of certain RLKs and RLCKs in the plant immune system. These kinases can recognize specific molecular patterns of pathogens and rapidly initiate an immune response in rice. Furthermore, the activity and functional regulation of these key kinases are tightly controlled by various post-translational modifications, such as phosphorylation and ubiquitination. This meticulous regulation ensures that the rice immune system’s response is both precise and timely, effectively balancing the intensity of the immune response and preventing potential issues caused by either hyperactivity or insufficiency. By synthesizing current research findings, this review not only broadens our understanding of the role of RLKs and RLCKs in plant immunity but also provides new perspectives and strategies for future research on disease resistance breeding in rice. Future studies are expected to delve deeper into the signaling networks and regulatory mechanisms of these kinases, exploring their potential in agricultural production to develop rice varieties with enhanced disease resistance.

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    Mixed-Oligosaccharides Promote Seedling Growth of Direct-Seeded Rice under Salt and Alkaline Stress
    Yang Yigang, Xu Ya’nan, Bai Yeran, Zhang Yuanpei, Han Wei, Makoto Saito, Lü Guohua, Song Jiqing, Bai Wenbo
    Rice Science    2024, 31 (6): 712-724.   DOI: 10.1016/j.rsci.2024.08.001
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    Rice direct seeding technology is an appealing alternative to traditional transplanting because it conserves labor and irrigation resources. Nevertheless, there are two main issues, salt stress and alkaline stress, which contribute to poor emergence and seedling growth, thereby preventing the widespread adoption and application of this technique in the Ningxia Region of China. Therefore, to determine whether germination can be promoted by mixed-oligosaccharide (KP) priming (in which seeds are soaked in a KP solution before sowing) under salt and alkaline stress, a proteomics study was performed. KP-priming significantly mitigated abiotic stress, such as salt and alkaline stress, by inhibiting root elongation, ultimately improving seedling establishment. By comparing the proteomics analyses, we found that energy metabolic pathway was a vital factor in KP-priming, which explains the alleviation of salt and alkaline stress. Key proteins involved in starch mobilization, pyruvate mobilization, and ATP synthesis, were up-regulated by KP-priming, significantly blocking salt and alkaline-triggered starch accumulation while enhancing pyruvate metabolism. KP-priming also up-regulated ATP synthase to improve energy efficiency, thereby improving ATP production. In addition, it enhanced antioxidant enzymatic activities and reduced the accumulation of reactive oxygen species. All of these factors contributed to a better understanding of the energy regulatory pathway enhanced by KP-priming, which mediated the promotion of growth under salt and alkaline conditions. Thus, this study demonstrated that KP-priming can improve rice seed germination under salt and alkaline stress by altering energy metabolism.

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    NARROW AND ROLLED LEAF 9, a Novel Gene Encoding 20S Proteasome β1 Subunit that Regulates Leaf Morphology and Grain Size in Rice
    Kang Fengyu, Zhou Liang, Chen Wenqiang, Huang Pingliang, Amos Musyoki Mawia, Luo Ju, Hu Peisong
    Rice Science    2025, 32 (2): 143-146.   DOI: 10.1016/j.rsci.2024.12.008
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    Leucine-Rich Repeat Protein Family Regulates Stress Tolerance and Development in Plants
    Hao Zhiqi, Wang Tingyi, Chen Dongdong, Shen Lan, Zhang Guangheng, Qian Qian, Zhu Li
    Rice Science    2025, 32 (1): 32-43.   DOI: 10.1016/j.rsci.2024.12.003
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    The leucine-rich repeat (LRR) protein family is involved in a variety of fundamental metabolic and signaling processes in plants, including growth and defense responses. LRR proteins can be divided into two categories: those containing LRR domains along with other structural elements, which are further subdivided into five groups, LRR receptor-like kinases, LRR receptor-like proteins, nucleotide-binding site LRR proteins, LRR-extensin proteins, and polygalacturonase-inhibiting proteins, and those containing only LRR domains. Functionally, various LRR proteins are primarily involved in plant development and responses to environmental stress. Notably, the LRR protein family plays a central role in signal transduction pathways related to stress adaptation. In this review, we classify and analyze the functions of LRR proteins in plants. While extensive research has been conducted on the roles of LRR proteins in disease resistance signaling, these proteins also play important roles in abiotic stress responses. This review highlights recent advances in understanding how LRR proteins mediate responses to biotic and abiotic stresses. Building upon these insights, further exploration of the roles of LRR proteins in abiotic stress resistance may aid efforts to develop rice varieties with enhanced stress and disease tolerance.

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