Rice最新文献

{"title":"TaCIPK19-3D Improves Photosynthetic Machinery, Growth, Yield, and Salt Tolerance in Transgenic Rice.","authors":"Muhammad Arif, Dingli Hong, Ruhong Xu, Mo Xian Chen, Hafiz Mamoon Rehman, Zhongni Wang, Luhua Li","doi":"10.1186/s12284-025-00827-y","DOIUrl":"https://doi.org/10.1186/s12284-025-00827-y","url":null,"abstract":"<p><p>Calcineurin B-like interacting protein kinases (CIPKs) are central regulators of plant development and stress adaptation. However, the specific roles of individual CIPK family members remain largely unexplored in major crops like wheat and rice. In this study, we characterized the function of TaCIPK19-3D through overexpression in transgenic rice and CRISPR-Cas9-mediated oscipk19 knockout lines. Expression profiling and subcellular localization analyses revealed that TaCIPK19-3D is associated with chloroplast development and metabolic activity. Overexpression lines exhibited enhanced chloroplast structure, increased chlorophyll biosynthesis, stomatal conductance, net photosynthetic rate, transpiration, and elevated levels of K⁺/Na⁺, Ca²⁺, and Mg²⁺, resulting in improved growth and yield compared to wild-type and mutant lines. Notably, TaCIPK19-3D overexpression conferred increased salt tolerance by upregulating ABA signaling, antioxidant responses, and proline biosynthesis. Key genes involved in chlorophyll synthesis (OsCAO, OsCHLH) and salt stress responses (OsAPX2, OsP5CS, OsABA2) were significantly upregulated in transgenic plants. Protein interaction studies using yeast two-hybrid and bimolecular fluorescence complementation (BiFC) assays demonstrated that TaCIPK19-3D interacts with TaFBA-4D and four CBL proteins (TaCBL1, TaCBL3, TaCBL4, and TaCBL7). Collectively, our findings reveal that TaCIPK19-3D positively regulates photosynthesis, ion homeostasis, and stress-responsive signaling pathways, highlighting its potential for improving crop productivity and stress resilience in wheat and rice.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"67"},"PeriodicalIF":4.8,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144643318","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrated Transcriptomic, Proteomic, and Metabolomic Analyses Reveal Mechanisms Underlying Day-Night Differences in Carbohydrate Metabolism between Diploid and Tetraploid Rice.","authors":"Weilong Meng, Yuchen Liu, Changjiang Zhang, Xiaohong Zhan, Yingkai Wang, Xinfang Yu, Chunying Zhang, Ningning Wang, Jian Ma","doi":"10.1186/s12284-025-00826-z","DOIUrl":"https://doi.org/10.1186/s12284-025-00826-z","url":null,"abstract":"<p><p>Polyploidy plays a crucial role in plant evolution, as polyploid plants possess larger genomes compared to their diploid counterparts. This genomic expansion leads to changes in gene redundancy and interactions, which alter the physiological metabolism of polyploids. Carbohydrate metabolism is a crucial energy metabolism pathway in plants, significantly impacting plant growth and development. In this study, we employed multi-omics analysis to investigate the differences in carbohydrate metabolism between diploid and tetraploid flag leaves during both day and night periods at the grain-filling stage. Our results revealed significant differences in carbohydrate metabolism between diploid (GFD-2X) and autopolyploid (GFD-4X) rice during both day and night periods. Chromosome doubling resulted in GFD-4X exhibiting reduced sucrose catabolism during the daytime, while starch synthesis and catabolism were stronger in GFD-4X compared to GFD-2X during both daytime and nighttime. Additionally, the phosphorylation of monosaccharides was enhanced in GFD-4X, suggesting that changes in chromosome ploidy altered carbohydrate metabolism, thereby benefiting the regulation and redistribution of carbohydrates in tetraploid rice. Furthermore, analysis of respiration-related pathways indicated that tetraploid rice may have more vigorous respiratory activity. Specifically, GFD-4X exhibited enhanced glycolysis and TCA cycle activity at night, resulting in more efficient energy production, which in turn influenced growth and the developmental process. This study examined the regulatory networks of genes, proteins, and metabolites involved in carbohydrate metabolism in diploid and tetraploid rice during both day and night periods. Our findings offer insights into how chromosome ploidy affects carbohydrate metabolism and reveal the distinct growth and developmental mechanisms of tetraploid rice.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"65"},"PeriodicalIF":4.8,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144643317","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Endophytes Enhance Rice Inorganic Nitrogen Use Efficiency and Mitigate Nitrogen Loss Via Dissimilatory Nitrate Reduction To Ammonium in Paddy Soils.","authors":"Mengting Liu, Ting Liu, Zixian Zhang, Jinzhi Yao, Xiao Xiao, Huanhuan An, Pangzhi Wei, Xubiao Luo, Shuping Qin","doi":"10.1186/s12284-025-00814-3","DOIUrl":"https://doi.org/10.1186/s12284-025-00814-3","url":null,"abstract":"<p><p>Rice cultivation involves the large amounts of fertilizers application, but nitrogen (N) use efficiency remains low. Endophytes are considered key microorganisms that regulate nitrogen utilization and gaseous nitrogen loss in rice paddy ecosystems. However, systematic studies on the effectiveness and underlying mechanisms of endophytes in nitrogen utilization by crops within paddy fields are still scarce. This study employed microcosmic experiments to investigate the effects of endophytes on gaseous nitrogen loss from paddy soil and inorganic nitrogen utilization in rice plants. Results demonstrated that colonization of endophytes increased the efficiency of inorganic N use by approximately twofold. The simultaneous addition of rice roots colonized with endophytes to the soil resulted in a significant increase in ammonium (NH₄⁺) concentrations by 121-138% as well. Notably, colonization with endophytes reduced cumulative nitrous oxide (N₂O) emissions by 13-21% compared to the control. Importantly, the endophytes were shown to enhance soil redox capacity by increasing Clostridium abundance and Fe²⁺ concentration, thereby promoting the dissimilatory nitrate reduction to ammonium (DNRA) and mitigating soil N loss. These findings underline the potential of rice endophytes in paddy field management to enhance soil nitrogen retention and reduce nitrogen loss.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"66"},"PeriodicalIF":4.8,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144643316","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Histidine-25-Arginine Mutation in the Rice MACPF Protein OsCAD1 Induces Cell Death and Activates Defense Responses in the Lesion Mimic Mutant spl17.","authors":"Dongsheng Tian, Yanchang Luo, Shuye Jiang, Yuejing Gui, Raji Mohan, Ignatius Ren Kai Phang, In-Cheol Jang, Zhongchao Yin","doi":"10.1186/s12284-025-00823-2","DOIUrl":"https://doi.org/10.1186/s12284-025-00823-2","url":null,"abstract":"<p><p>Plants defend themselves against pathogens through pattern-triggered immunity (PTI) and effector-triggered immunity (ETI), with the latter often inducing a hypersensitive response (HR) characterized by localized programmed cell death (PCD). Lesion mimic mutants (LMMs), which spontaneously form HR-like lesions in the absence of pathogen infection, have served as valuable genetic resources for dissecting the molecular mechanisms underlying cell death and immune signaling in plants. In this study, we characterize the rice lesion mimic mutant spl17, derived from the IR64 cultivar, and identify the mutation responsible for its phenotype. We demonstrate that the spl17 mutation leads to the accumulation of reactive oxygen species (ROS), induces light-dependent cell death and lesion formation, elevates levels of salicylic acid (SA) and jasmonic acid (JA), activates defense-related genes, and confers enhanced resistance to Xanthomonas oryzae pv. oryzae. Using map-based cloning, we identified a single Histidine-25-Arginine substitution (OsCAD1^H25R) in OsCAD1, a gene encoding a membrane attack complex/perforin (MACPF) domain-containing protein in rice, as the causal mutation. CRISPR/Cas9 genome editing revealed that a knockout of OsCAD1 (OsCAD1^KO) results in seedling lethality, whereas a weak allele (OsCAD1^D8) leads to a viable lesion mimic phenotype and enhances resistance to X. oryzae pv. oryzae. Subcellular localization studies demonstrated that eGFP-OsCAD1 is broadly distributed in Nicotiana benthamiana cells. Transcriptome analyses, including RNA-Seq and Gene Set Enrichment Analysis (GSEA), indicate that differentially expressed genes (DEGs) in spl17 are enriched in catalytic activity, metabolic processes, and membrane functions. Together, these results suggest that OsCAD1 is indispensable for rice growth and development, and that its mutation triggers cell death and defense responses.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"68"},"PeriodicalIF":4.8,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144643319","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Omics-Based Characterization of BTB Gene Family in T. aestivum, Reveals the Potential of TaBTB11/56/57/58 in Combined Heat and Drought Stress Regulation.","authors":"Zhiwei Wang, Aimen Shafique, Areej S Jalal, Bofeng Yu, Mingjiu Liu, Kotb A Attia, Sajid Fiaz, Muhammad Salman Mubarik","doi":"10.1186/s12284-025-00808-1","DOIUrl":"10.1186/s12284-025-00808-1","url":null,"abstract":"<p><p>Wheat (Triticum aestivum) is a globally important staple crop that faces increasing challenges from climate change, particularly the combined effects of heat and drought stress. The BTB (Broad Complex, Tramtrack, and Bric-à-Brac) gene family is involved in diverse biological processes, including stress responses, but its characterization in T. aestivum remains limited. This study aimed to comprehensively investigate the BTB gene family in T. aestivum and identify key genes potentially involved in resilience to abiotic stress.In the current study, we identified 62 BTB genes in T. aestivum using BLAST and Hidden Markov Model (HMM) approaches. Phylogenetic analysis classified these genes into nine subgroups based on conserved domain architecture. Gene structure analysis revealed diverse exon-intron organizations, supporting evolutionary divergence among subgroups. Chromosomal mapping demonstrated an uneven distribution of BTB genes across the A, B, and D sub-genomes, with the highest number localized on sub-genome D. Cis-regulatory element analysis highlighted the presence of multiple stress-responsive motifs, particularly those associated with heat and drought responses, i.e., ABRE, G-box, CAAT-box, TATA-box. Expression profiling using transcriptome data from two T. aestivum varieties (Atay 85 and Zubkov) revealed differential regulation of BTB gene family members under drought, heat, and combined stress conditions. Furthermore, qRT-PCR validation showed that TaBTB11, TaBTB56, TaBTB57, and TaBTB58 were consistently regulated across all three stress conditions, highlighting their potential as key targets for stress-resilient T. aestivum breeding. Furthermore, Green fluorescent protein (GFP) localization confirmed that these genes were expressed in the nucleus.This study highlights key genes, i.e., TaBTB11, TaBTB56, TaBTB57, and TaBTB58, as potential targets for marker-assisted selection and genetic improvement of T. aestivum for enhanced resilience to combined heat and drought stress.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"64"},"PeriodicalIF":4.8,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12254111/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144609248","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Multi-omics Approach Reveals the Effects of Bio- and Chemical- Pesticides on Rice Yield and Quality under Disease Stress.","authors":"Chongchong Lu, Yingzhe Yue, Baoyou Liu, Yanke Jiang, Zimeng Li, Muhammad Zunair Latif, Xiaoying Zhang, Dayin Chen, Lili Dai, Lingguang Kong, Qian Du, Ziyi Yin, Yang Li, Hansong Dong, Xinhua Ding","doi":"10.1186/s12284-025-00822-3","DOIUrl":"10.1186/s12284-025-00822-3","url":null,"abstract":"<p><p>Rice production is gravely threatened by bacterial leaf streak (BLS). BLS prevention and control rely heavily on chemical pesticides, which contaminate the environment and endanger human health. Here, we evaluated the effects of inducer of plant resistance ZhiNengCong (ZNC), which is derived from endophytic fungi Paecilomyces variotii, the chemical pesticide dioctyl diethylenetriamine (DDL) and the antibiotic pesticide zhongshengmycin (ZSM) on grain size and quality of diseased- rice (DR). BLS significantly reduced the thousand-grain weight and seed setting rate of rice plants, which could be restored by ZNC rather than DDL or ZSM. Transcriptome and metabolomics profiling showed that ZNC increased the expression levels of resistance-, growth- and sugars, amino acids and lipid metabolism-related genes in DR leaves and restored the levels of carbohydrates, vitamins, nucleotides and amino acids in DR grains, which is better than DDL and ZSM. This study demonstrates that plant immune inducers are more effective than conventional pesticides in restoring DR yield and quality, which provides novel insights into the innovation of green biopesticides in sustainable crop production.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"63"},"PeriodicalIF":4.8,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12234920/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144576175","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Targeting eIF4A with RNA Aptamers Enhances Salt Stress Tolerance in Rice Through Modulation of Translation Initiation.","authors":"Haomin Chen, Zhihao Xie, Mingming Chen, Peiyi Zhu, Daming Chen, Yongxiang Huang, Shuangfeng Dai","doi":"10.1186/s12284-025-00819-y","DOIUrl":"10.1186/s12284-025-00819-y","url":null,"abstract":"<p><p>Salt stress is a major limiting factor for rice productivity worldwide, and improving salt tolerance is crucial for ensuring sustainable agricultural production. In this study, we investigate the use of RNA aptamers to modulate eukaryotic initiation factor 4 A (eIF4A), a key regulator of translation initiation under stress conditions, to enhance salt stress tolerance in rice (Oryza sativa). Using Systematic Evolution of Ligands by EXponential enrichment (SELEX), we isolated high-affinity RNA aptamers that specifically bind to eIF4A. One aptamer, eApt-2, was found to bind eIF4A with high affinity, selectively blocking cap-dependent translation initiation. Radioisotope‑based helicase assays confirmed that eApt‑2 does not impair eIF4A's intrinsic RNA‑unwinding activity. Transfected rice expressing eApt-2 exhibited enhanced salt stress tolerance, with improved growth, biomass accumulation, and photosynthetic activity under saline conditions. Moreover, stable transgenic rice lines expressing eApt‑2 maintained enhanced growth and biomass accumulation under 150 mM NaCl stress, mirroring transient expression results, and transgenic Arabidopsis lines showed similar tolerance. Our results demonstrate the potential of RNA aptamers as a precise, reversible tool for enhancing stress resilience in crops, offering an alternative to conventional genetic modification methods. This study opens new avenues for engineering salt-tolerant rice and highlights the broader applicability of RNA aptamers in improving plant responses to abiotic stresses.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"62"},"PeriodicalIF":4.8,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12234956/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144576186","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Overexpression of the ABA Synthesis Gene OsABA2 Enhances Seed Storability in Rice.","authors":"Yongxiang Liao, Pengfei Jiang, Mingming Zhang, Fangli Jin, Mengyuan Li, Jiazhi Dong, Daiming Guo, Yingxiu Liao, Asif Ali, Saira Saleem, Xiangyang Zhang, Qinggui Jiang, Su Liu, Hongyu Zhang, Xiaoqiong Chen, Kangxi Du, Hao Zhou, Duo Xia, Peizhou Xu, Xianjun Wu","doi":"10.1186/s12284-025-00817-0","DOIUrl":"10.1186/s12284-025-00817-0","url":null,"abstract":"<p><p>Seed storability is critical for seed production and germplasm conservation. Numerous studies have linked seed storability to abscisic acid (ABA) metabolism; however, the use of biotechnological approaches to strategically and rapidly enhance seed storability in rice through manipulation of ABA biosynthesis genes remains unexplored. In the current study, we developed overexpression lines (OE) of OsABA2, which encodes a XANTHOXIN DEHYDROGENASE, a key enzyme in the ABA synthesis pathway. Our experimental results showed that the relative expression of OsABA2 was upregulated in response to artificial aging treatment. The germination rate of OsABA2-OE lines was significantly higher, while the electrical conductivity of the seed leachate was lower compared to the wild type (WT), indicating improved seed vigor. Following artificial aging treatments, OsABA2-OE lines exhibited less pronounced changes in storage substances such as sugars and total starch, relative to WT. Reduced diaminobenzidine (DAB) staining intensity in OsABA2-OE lines suggested lower levels of reactive oxygen species (ROS). Correspondingly, the contents of hydrogen peroxide and malondialdehyde were lower, whereas catalase activity and total antioxidant capacity were higher in OsABA2-OE lines after artificial aging treatments. Comparative transcriptome analysis further revealed that the overexpression of OsABA2 may enhance seed storability by modulating the expression of ROS scavenging genes. For practical application, Gang46B-a hybrid rice parental line with poor storability-significantly improved its post-aging germination rates. These findings demonstrate that the overexpression of OsABA2 enhances seed storability by regulating ABA biosynthesis pathway and associated oxidative response. Thus, OsABA2 represents a promising molecular target for precise improvement of seed storage traits. This approach could be utilized for the improvement of seed storability in rice and other crops, offering valuable implications for the seed industry.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"61"},"PeriodicalIF":4.8,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12227392/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144560952","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"OsDISMO1: A Novel Transporter for Molybdenum Distribution in Rice Shoots.","authors":"Prashant Kandwal, Toru Fujiwara, Takehiro Kamiya","doi":"10.1186/s12284-025-00821-4","DOIUrl":"10.1186/s12284-025-00821-4","url":null,"abstract":"<p><p>Molybdenum (Mo) is an essential micronutrient for plants, forming the Mo cofactor (Moco) necessary for molybdoenzyme activity. While only a single type of molybdate transporter (MOT) has been identified in plants, other Mo transporters remain unknown. In this study, we identified a novel Mo transporter gene, OsDISMO1 (Oryza sativa Distributor of Molybdenum 1), through the characterization of a high Mo grain mutant in rice. Gene mapping of the mutant and the phenotype of knockout mutants demonstrated that OsDISMO1 is responsible for the observed mutant phenotype. Mo concentration analysis in various leaf tissues of three-week-old seedlings revealed higher Mo levels in the young leaves of the mutant compared to the wild type Hitomebore (HB), while the flag leaf of the mutant had lower Mo levels than the HB. OsDISMO1 promoter-GUS analysis indicated expression in the vascular bundles of shoots, particularly in the phloem. Additionally, a GFP-fused OsDISMO1 protein was localised to the endoplasmic reticulum (ER) membrane in rice protoplasts. The ability of OsDISMO1 to transport Mo was confirmed through heterologous expression in Saccharomyces cerevisiae. These findings suggest that OsDISMO1 is a Mo transporter, facilitating the movement of Mo from old to new or source tissues.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"59"},"PeriodicalIF":4.8,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12227400/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144560951","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"RSLpred2: An Integrated Web Server for the Annotation of Rice Proteome Subcellular Localization Using Deep Learning.","authors":"Naveen Duhan, Rakesh Kaundal","doi":"10.1186/s12284-025-00767-7","DOIUrl":"10.1186/s12284-025-00767-7","url":null,"abstract":"<p><p>Rice is one of the most important staple crops, providing food for more than one-half of the world's population worldwide. Identifying the localization of encoded proteins is the key to understanding their functional characteristics and facilitating their purification. The prediction of protein localization experimentally is time-consuming due to the need for meticulous experimentation, validation, and data analysis; computational methods provide a quick and accurate alternative. We propose RSLpred-2.0, an extension of our previously developed and widely used RSLpred-1.0 tool for annotating the rice proteome. RSLpred-2.0 is implemented in four levels to accurately predict protein subcellular localization. The first level differentiates between single and dual localization with accuracy (97.66% in 5-fold training/testing, 98.12% on an independent data) and Matthews correlation coefficient (0.88 training, 0.90 independent). Single localized proteins are classified into ten classes at the second level, with accuracy (98.33% in 5-fold training/testing, 98.46% on an independent data) and Matthews correlation coefficient (0.95 training, 0.95 independent). The third level categorizes dual localized proteins into six classes with accuracy (99.20% in 5-fold training/testing, 96.75% on an independent data) and Matthews correlation coefficient (0.98 training, 0.90 independent). The fourth level classifies membrane proteins predicted in level 1 into single-pass and multi-pass membranes with accuracy (99.83% in 5-fold training/testing, 98.81% on an independent data) and Matthews correlation coefficient (0.99 training, 0.97 independent). The RSLpred2 tool will help the researchers understand many organelle-specific functions, cellular processes, and regulatory mechanisms essential for plant growth, development, and response to environmental stimuli. The web server as well as its standalone version of the software developed from this study is available freely at https://kaabil.net/RSLpred2/ .</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"58"},"PeriodicalIF":4.8,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12227404/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144560953","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}