Rice最新文献

{"title":"Trihelix Transcription Factor OsTGS1 Regulates Grain Size and Weight in Rice.","authors":"Qingsong Gao, Jiayi Ding, Shiqing Dong, Kezhi Zheng, Xi Liu, Caiyong Yuan","doi":"10.1186/s12284-025-00792-6","DOIUrl":"https://doi.org/10.1186/s12284-025-00792-6","url":null,"abstract":"<p><p>Grain size is one of the major factors determining rice grain yield. Nevertheless, our knowledge of the molecular mechanisms underlying the control rice grain size remains limited. Trihelix proteins are plant-specific transcription factors that regulate plant growth and development. However, their roles in modulating grain size in cereal crops are largely unknown. Here, we report the rice trihelix family gene Oryza sativa trihelix transcription factor related to grain size 1 (OsTGS1) as a novel regulator of grain size and weight. Mutation of OsTGS1 leads to large and heavy grains, whereas overexpression of OsTGS1 results in small and light grains. OsTGS1 regulates grain size by influencing cell division and cell expansion in spikelet hulls. OsTGS1 is expressed in various tissues, and its expression level increases during panicle development. The OsTGS1 protein is localized to the nucleus and exhibits transcriptional repressor activity. The screening of interacting proteins via a yeast two-hybrid assay revealed that OsTGS1 interacted with GSK3/SHAGGY-LIKE KINASE2 (GSK2), an important regulator of various agronomic traits, including grain size, in rice. Moreover, ostgs1 mutants are hypersensitive to exogenous brassinosteroid treatment, indicating that OsTGS1 may be involved in brassinosteroid signaling. Our study reveals the role of OsTGS1 in controlling grain size and provides a new gene resource for improving grain weight in rice.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"31"},"PeriodicalIF":4.8,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12040797/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144021940","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":"MORE FLORET1 Interacts with C-type Replication Protein A Complex and Regulates Male Meiosis in Rice.","authors":"Lianjun Zhu, Rou Chen, Yu Huang, Guobin Liang, Jinwen Wu, Haibin Guo, Xiangdong Liu, Zijun Lu","doi":"10.1186/s12284-025-00791-7","DOIUrl":"https://doi.org/10.1186/s12284-025-00791-7","url":null,"abstract":"<p><p>Meiosis plays a pivotal role in plant reproduction, which is also crucial for enhancing genetic diversity. Although the impact of MOF1 on floral organ development and its negative regulation of the key tapetal gene PKS2 have been established, the specific function of MOF1 in male meiotic process remains elusive. In this study, we identified two mutant lines of MOF1 in Nipponbare background. Compared to the wild-type controls, MOF1 mutations resulted in significant reductions in seed setting rate and pollen fertility, partially attributed to its defects in the formation of male meiotic bivalents. RNA-seq analyses and RT-qPCR assays revealed that loss-of-function mutation of MOF1 didn't alter expression levels of 60 known meiotic-regulated genes, suggesting that MOF1 may not function as a transcriptional factor in its meiotic regulation. Yeast two-hybrid and bimolecular fluorescence complementation assays demonstrated the protein-protein interactions among MOF1, RPA2c, RPA1c, as well as FAR1, among which RPA1c and RPA2c involved in meiotic bivalent formation. Furthermore, gene expression pattern analyses and subcellular localization studies indicated the co-expression among above interacted proteins in nucleus during anther development. Our findings provide a mechanistic insight into how MOF1 modulate male meiosis possibly through interactions with key meiotic proteins, facilitating a better understanding of male reproductive regulation.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"30"},"PeriodicalIF":4.8,"publicationDate":"2025-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12033130/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144036822","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":"OsERF2 Acts as a Direct Downstream Target of OsEIL1 to Negatively Regulate Salt Tolerance in Rice.","authors":"Jiahao Zhou, Shengliang Fang, Xinjie Liu, Lei Luo, Yuhua Liu, Haiwen Zhang","doi":"10.1186/s12284-025-00787-3","DOIUrl":"https://doi.org/10.1186/s12284-025-00787-3","url":null,"abstract":"<p><p>Salinity is a significant limiting factor that adversely affects plant growth, distribution and crop yield. Ethylene responsive factors play crucial roles in plant responses to and tolerance of various abiotic stresses. Recently, we revealed that OsERF2 is involved in root growth by transcriptionally regulating hormone and sugar signaling in rice. Here, we report that OsERF2 is a direct target gene of OsEIL1 and negatively regulates salt tolerance in rice. Compared to the wild type, the gain-of-function mutant of OsERF2 (nsf2857) and the knockdown of OsERF2 via an artificial microRNA (Ami-ERF2) exhibited decreased and increased salt tolerance, respectively. The enhanced salt tolerance observed in Ami-OsERF2 lines was associated with lower accumulations of malondialdehyde and reactive oxygen species (ROS) under salt stress, while the opposite was true for nsf2857 plants, which exhibited decreased salt tolerance. At the transcriptional level, several stress-related genes encoding ROS and NAD(P)H-related oxidoreductases were downregulated in nsf2857 plants but upregulated in Ami-ERF2 plants. Furthermore, yeast one-hybrid and ChIP assays revealed that OsEIL1 can bind to the of EBS cis element present in the promoter of OsERF2 (-bp), suggesting that OsEIL1 may directly regulate the expression of OsERF2. Collectively, our findings indicate that OsERF2 is a direct downstream factor involved in the regulation of salt tolerance in rice, highlighting its potential application in the genetic improvement of tolerance to abiotic stresses in this crop.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"29"},"PeriodicalIF":4.8,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12021750/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144029252","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 Dual-localized Fructose Bisphosphate Aldolase is Essential for Chloroplast Development and Carbon Metabolism in Rice.","authors":"Xin Liu, Yingbo Gao, Siyuan Tang, Linli Ben, Xiaoxiang Zhang, Guichun Dong, Juan Zhou, Lingshang Lin, Zefeng Yang, Yong Zhou, Jianye Huang, Youli Yao","doi":"10.1186/s12284-025-00779-3","DOIUrl":"https://doi.org/10.1186/s12284-025-00779-3","url":null,"abstract":"<p><p>Fructose-1,6-bisphosphate aldolase (FBA) stands as a pivotal enzyme involved within the Calvin cycle and glycolytic pathways in bacteria and higher plants, but the specific function of OsFBA in rice is still unclear. Here, we identified a chloroplast and mitochondria dual-localized FBA protein, OsFBA1, in rice. Experimental evidence showed that the functionally deficient osfba1 mutants featured a notable decline in chlorophyll content, photosynthetic rate, and severe growth impediment by the three-leaf stage, leading to eventual plant demise. Up-regulation of photosynthetic-pathway genes in the osfba1 mutants indicated the essential role of OsFBA1 in chloroplast development and suggested a compensatory mechanism of other genes in the process. Furthermore, the absence of OsFBA1 impaired the carbon assimilation in young rice seedlings, and supplying exogenous glucose could partially sustain the survival of osfba1 mutant for a few more days. Pathway-specific metabolomics analysis revealed a systemic change of metabolites in the glycolytic pathway, and consequential carbohydrates accumulation due to OsFBA1 disruption. Transcriptomics profiling corroborated the expression changes of photosynthesis, and carbon metabolism pathway genes. We further demonstrated that OsFBA1 serves as the primary FBA enzyme governing energy generation, photosynthesis and carbon metabolism. These results prove that OsFBA1 is an essential core gene in supporting the life cycle of rice, its expression has to be tightly regulated.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"28"},"PeriodicalIF":4.8,"publicationDate":"2025-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12003240/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144006018","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":"Modelling and Using Spatial Effects in Nationwide Historical Data Improve Genomic Prediction of Rice Heading Date in Japan.","authors":"Shoji Taniguchi, Takeshi Hayashi, Hiroshi Nakagawa, Kei Matsushita, Hiromi Kajiya-Kanegae, Jun-Ichi Yonemaru, Akitoshi Goto","doi":"10.1186/s12284-025-00778-4","DOIUrl":"https://doi.org/10.1186/s12284-025-00778-4","url":null,"abstract":"<p><p>Genomic prediction is a promising strategy for enhancing crop breeding efficiency. Historical data of breeding and cultivation tests from geographically wide regions presumably contain rich information for training genomic prediction models. Therefore, it is essential to explore methodologies to effectively handle such data. To improve the prediction accuracy of models using historical data, we incorporated a spatial model to account for spatial structures among field stations, in addition to conventional genomic prediction models. Targeting the rice heading date from historical data across Japan, we first constructed conventional genomic prediction models using genomic and/or meteorological elements as predictors. Next, we obtain the residual terms. Assuming that the residual terms were partly explained by the spatial effects assigned to each field station, a spatial model was applied to the residual terms and the spatial effects were calculated. Our genomic prediction models performed best when the genome, meteorological elements, and genome-meteorology interactions were included (model 3), and they performed second best when the genome and meteorological elements were included (model 2). For these genomic prediction models, residual terms were spatially biased and corrected for spatial effects. For the best model (model 3), the root mean squared errors (RMSE) of genomic prediction combined with spatial effects were approximately 3.6 days under tenfold cross-validation and approximately 5.1 days under leave-one-line-out cross-validation. The inclusion of the spatial effects improved the RMSEs by approximately 15% and 9% for the former and latter, respectively. Lines with highly improved predictions of the spatial effects were developed, mainly in the northern Tohoku region. The spatial effects were heterogeneous and regional patterns were detected. These findings imply that spatial effects are important not only for improving prediction performance but also for dissecting the model itself to identify the factors contributing to model improvement.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"27"},"PeriodicalIF":4.8,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11992326/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144045619","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":"Correction: E3 Ubiquitin Ligase OsRFI2 Regulates Salinity Tolerance by Targeting Ascorbate Peroxidase OsAPX8 for its Degradation in Rice.","authors":"Wenjing Zhao, Junli Wen, Juan Zhao, Linlin Liu, Mei Wang, Menghan Huang, Chaowei Fang, Qingpo Liu","doi":"10.1186/s12284-025-00780-w","DOIUrl":"https://doi.org/10.1186/s12284-025-00780-w","url":null,"abstract":"","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"26"},"PeriodicalIF":4.8,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11985708/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143992531","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":"Microrchidia OsMORC6 Positively Regulates Cadmium Tolerance and Uptake by Mediating DNA Methylation in Rice.","authors":"Jingai Tan, Muhammad Fahad, Lantian Zhang, Liang Wu, Xia Wu","doi":"10.1186/s12284-025-00785-5","DOIUrl":"10.1186/s12284-025-00785-5","url":null,"abstract":"<p><p>Rice (Oryza sativa) is an extremely important global food crop. However, cadmium (Cd) contamination in paddy fields poses a serious threat to human health worldwide. To generate low-Cd or Cd-free rice germplasms, it is essential to understand the molecular mechanisms involved in Cd tolerance, uptake, and translocation from soil to plant. In this study, we identify three Microrchidia proteins, OsMORC6a, OsMORC6b, and OsMORC6c, that regulate Cd tolerance and accumulation, although they do not alter the translocation of Cd from roots to shoots. Knockout of all three genes results in reducing Cd accumulation and increasing sensitivity to Cd stress. Furthermore, transcriptome analysis reveals 1,127 differentially expressed genes (DEGs) in the morc6abc mutants, which are significantly enriched in 'plant-type cell wall' and 'oxidoreductase activity' pathways. Through an integrating DNA methylome and transcriptome data, we identify 247 hyper-DMR-associated DEGs and 325 hypo-DMR-associated DEGs in morc6abc mutants. Gene Ontology (Go) enrichment analysis reveals that OsMORC6 proteins positively regulate Cd tolerance and uptake by mediating DNA methylation, which regulates the proper expression of genes related to plant cell wall and oxidative stress under Cd stress. Taken together, our findings reveal novel genes that mediate Cd tolerance and accumulation by affecting DNA methylation, offering valuable resource for breeding low-Cd or Cd-free rice germplasms.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"25"},"PeriodicalIF":4.8,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11981988/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143812230","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":"Genomic Regions and Molecular Markers Associated with Deeper Rooting to Improve Grain Yield in Aerobic Rice (Oryza sativa L.) Production Systems.","authors":"Wenliu Gong, Ricky Vinarao, Christopher Proud, Shona Wood, Peter Snell, Shu Fukai, Jaquie Mitchell","doi":"10.1186/s12284-025-00784-6","DOIUrl":"10.1186/s12284-025-00784-6","url":null,"abstract":"<p><p>A greater proportion of deep roots could ensure water uptake at depth and is considered a key trait for aerobic adaptation. However, the study of genomic regions and molecular markers related to deep rooting is limited especially for aerobic rice production. This study utilised 705 genotypes composed of recombinant inbred lines and predominantly diverse japonica sets to identify and validate genomic regions associated with the proportion of deep roots below 20 cm (DR20). Six quantitative trait loci (QTL) for DR20 were identified under well-watered aerobic conditions, explaining 5.3-23.7% of the phenotypic variance and introgression of the favourable alleles resulted in 10-21.6% deeper roots. Simultaneous development of high throughput molecular markers and QTL validation demonstrated the effect of four (qADR1, qADR9, qADR10, and qADR11) out of six QTL increasing DR20 up to 29.4% across genetic backgrounds. The four QTL also conferred a mean grain yield advantage of 1.46 t/ha. This study reports for the first time validated genomic regions and high throughput molecular markers associated with deeper rooting and improved grain yield in rice under aerobic conditions. These tools may accelerate the development of rice adapted to aerobic production systems and ultimately enhance sustainable rice production in areas with limited water availability.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"24"},"PeriodicalIF":4.8,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11977055/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143803969","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":"Comprehensive GWAS and Transcriptome Analysis Discovered Candidate Gene Associated with Starch Pasting Properties of Temperate japonica rice (Oryza sativa L.).","authors":"Yoon Kyung Lee, Su Jang, Jihwan Im, Hee-Jong Koh","doi":"10.1186/s12284-025-00782-8","DOIUrl":"10.1186/s12284-025-00782-8","url":null,"abstract":"<p><p>The growing market demand for high eating quality (EQ) rice, driven by improved living standards, highlights the need to better understand its complex genetic architecture. Starch pasting properties are critical determinants of rice EQ, yet their genetic basis remains incompletely understood. This study aimed to unravel the genetic factors underlying starch pasting properties in temperate japonica rice panel of 284 accessions comprising landraces and improved varieties. Genome-wide association studies conducted for two years identified 59 significant lead SNPs. Among them, consistent lead SNPs on chromosomes 2 and 8, in addition to the well-characterized Wx gene on chromosome 6 were detected from multiple traits and years. LD block analysis and transcriptome analysis of accessions with extreme phenotypes identified OsGLUTN (Os02g0224300/LOC_Os02g13130), a gene encoding a high molecular weight glutenin subunit-like protein, as a strong candidate. Clustering patterns of differential gene expressions showed higher expression of OsGLUTN in low-viscosity cultivars and lower expression in high-viscosity cultivars. Haplotype analysis revealed significant variations in viscosity traits associated to OsGLUTN alleles, and functional validation using enhancer active tagging line showed significantly reduced starch viscosity, confirming its role in EQ regulation. While the Wx accounted for most viscosity traits, the identification of novel loci on chromosomes 2 and 8 highlights additional genetic factors to EQ variation. These findings deepen our understanding of how storage protein metabolism impacts rice grain quality. The identification of OsGLUTN provides a foundation for breeding programs focused on developing rice varieties with improved cooking and eating qualities, addressing growing consumer demand for premium rice.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"23"},"PeriodicalIF":4.8,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11961803/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143764954","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 lncRNA22524 from Dongxiang Wild Rice Reduces Drought and Salt Stress Tolerance in Cultivated Rice.","authors":"Yong Chen, Yingying Mao, Hong Xie, Xinjian Zou, Wanling Yang, Rifang Gao, Jiankun Xie, Fantao Zhang","doi":"10.1186/s12284-025-00777-5","DOIUrl":"10.1186/s12284-025-00777-5","url":null,"abstract":"<p><p>Drought and salt stresses are major challenges to rice production, and a deep understanding of the mechanisms for tolerance could help deal with the challenges. Long non-coding RNAs (lncRNAs) play crucial roles in gene regulation. Previously, lncRNA22524 has been identified as a drought stress-responsive lncRNA from Dongxiang wild rice (DXWR). Nevertheless, its reactions to abiotic stresses in genetics and physiology remained unclear. In this study, we employed a rapid amplification of cDNA ends (RACE) to obtain the full-length cDNA of lncRNA22524 from DXWR, analyzed its cellular localization, built an overexpression vector to generate transgenic lines of cultivated rice and evaluated its impact in genetics and physiology. After treated with drought and salt stress, the overexpressed lines exhibited much more injuries and lower rates of survival, more reactive oxygen species (ROS) and malondialdehyde (MDA), lower antioxidant enzymes and lower proline (Pro) and soluble sugar (SS) than their wild-type (WT). Furthermore, transcriptome analysis of overexpressed lines with weaker tolerance than WT revealed 1,233 differentially expressed genes (DEGs), where most DEGs were involved in phenylpropanoid biosynthesis, photosynthesis and glutathione metabolism. These findings demonstrated that lncRNA22524 negatively regulated rice responses to drought and salt stress, which clear way of working from transcription to metabolic products should be worth of further study.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"22"},"PeriodicalIF":4.8,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11933495/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143701079","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}