Rice最新文献

{"title":"Genome-Wide Identification of the RhoGAP Gene Family and Main Function of OsRhoGAP2 in Seed Germination of Rice by Transcriptome Analysis.","authors":"Chaowei Fang, Yuanqing Nie, Yifan Bi, Wenjing An, Dongdong Jia, Weihong Liang","doi":"10.1186/s12284-025-00843-y","DOIUrl":"10.1186/s12284-025-00843-y","url":null,"abstract":"<p><p>Rho GTPase-activating proteins (RhoGAPs) play crucial roles in regulating various biological processes. However, the functions of RhoGAP family genes in rice (Oryza sativa) remain largely unexplored. Here, we identified 19 RhoGAP genes in rice, and preliminarily analyzed the genes information, expression patterns, and evolutionary relationship with AtRhoGAPs in Arabidopsis. Using CRISPR/Cas9-mediated gene editing, we generated loss-of-function mutants of OsRhoGAP2 (rhogap2) and found that seed germination was significantly delayed compared to the wild type (WT). Further analysis revealed that α-amylase activity was reduced in rhogap2 germinating seeds. RNA-seq profiling identified 291 upregulated and 130 downregulated genes in the mutant, with differentially expressed genes (DEGs) primarily enriched in phenylpropanoid biosynthesis and other metabolic pathways. Notably, most phenylpropanoid biosynthesis-related genes exhibited increased expression in rhogap2 germinating seeds. These findings establish a foundational framework for future functional studies of RhoGAP genes in rice and provide novel insights into the molecular mechanisms by which RhoGAPs regulate seed germination in plants.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"83"},"PeriodicalIF":5.0,"publicationDate":"2025-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12380660/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144966989","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":"Identification of Leaf Rust-Related Gene Signature in Wheat (Triticum Aestivum L.) Using High-Throughput Sequencing, Network Analysis, and Machine Learning Algorithms.","authors":"Muhammad Farhan, Muhammad Ikram, Jing-E Sun, San-Wei Yang, Yong Wang","doi":"10.1186/s12284-025-00839-8","DOIUrl":"10.1186/s12284-025-00839-8","url":null,"abstract":"","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"82"},"PeriodicalIF":5.0,"publicationDate":"2025-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12374937/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144967100","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":"Alternative polyadenylation and metabolic profiling in young panicle development of hybrid rice and its parents.","authors":"Guangliang Wu, Shangwei Yu, Junru Fu, Linjuan Ouyang, Lifang Hu, Jianmin Bian, Xiaorong Chen, Jie Xu, Dahu Zhou, Haohua He, Haihui Fu","doi":"10.1186/s12284-025-00834-z","DOIUrl":"10.1186/s12284-025-00834-z","url":null,"abstract":"<p><p>Alternative polyadenylation (APA) is a widespread post-transcriptional regulatory mechanism in eukaryotes that modulates gene expression by generating transcript variants. The development of young panicles in rice is a critical stage that determines grain number and weight. However, the regulatory mechanisms and inheritance patterns of APA during this process remain poorly understood. In this study, full-length isoform sequencing (Iso-seq) and metabolome were employed to investigate APA dynamics in the young panicle of hybrid rice variety Wufengyou T025 and in parent lines, Wufeng B and Changhui T025. This analysis revealed that approximately 80% of genes possessed two or more polyadenylation (pA) sites. These APA genes were predominantly enriched in the pathways associated with rice spikelet development, including response to external photoperiod changes, energy production and transportation, protein signal exchange, and amino acid metabolism. Notably, transcripts with a shortened 3'-untranslated region (3'UTR) exhibited elevated expression levels of their corresponding genes, suggesting that APA plays an important role in modulating gene expression. Furthermore, the variable 3'UTR of the 25% differentially expressed APA genes contained numerous miRNA binding sites, including osa-miR1848 and osa-miR5075, which are known to influence spikelet development. In the offspring, the expression levels of core APA factors during young panicle development were generally downregulated compared to the parental lines. Additionally, metabolomic analysis identified 209 and 164 differentially abundant metabolites in the offspring relative to Wufeng B and Changhui T025, respectively. Intriguingly, some of the enriched metabolic pathways overlapped with those of differentially expressed APA genes, implying that APA may influence small-molecule metabolites in pathways related to spike development. Collectively, these findings are valuable for understanding the regulation of APA and its genetic basis in young panicle development, offering new insights into the molecular mechanisms underlying this critical development stage.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"80"},"PeriodicalIF":5.0,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12370618/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144967001","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":"Identification and Candidate Gene Analysis of qCTS11-TK9, a Novel Major Quantitative Trait Locus Associated with Chilling Tolerance in Rice Seedlings.","authors":"Sheng-Shan Wang, Yu-Ting Liu, Pei-Hua Tsai, Shu-Fang Cheng, Kai-Yi Chen, Rong-Kuen Chen","doi":"10.1186/s12284-025-00838-9","DOIUrl":"10.1186/s12284-025-00838-9","url":null,"abstract":"<p><p>Chilling stress can severely damage rice and lead to yield losses. The genetic mechanisms underlying responses of rice to chilling stress are complex and can vary depending on the genetic background, developmental stage, and experimental conditions. In this study, we used the chilling stress-tolerant japonica variety Taiken 9 (TK9) and the chilling stress-sensitive indica variety Taichung Sen 17 (TCS17) to investigate the genetic basis of chilling tolerance in rice seedlings. A BC₃-derived backcross inbred line, NSY1051070, which inherited high chilling tolerance from TK9 within the genetic background of TCS17, was developed through recurrent backcross breeding. A major quantitative trait locus (QTL), qCTS11-TK9, was identified in the distal region of the long arm of chromosome 11 by using F₂ and F₃ populations derived from the cross between TCS17 and NSY1051070. High-resolution linkage analysis delimited qCTS11-TK9 to a 191-kb genomic region containing 16 annotated putative genes in the rice reference genome. Expression and sequence analyses revealed three candidate genes responsible for chilling tolerance in NSY1051070: LOC_Os11g42790, LOC_Os11g42800, and LOC_Os11g42850. Our findings unveiled a novel major QTL associated with chilling tolerance in rice seedlings. The discovery of qCTS11-TK9 highlights a new source of seedling-stage chilling tolerance, and the markers developed in this study may aid future breeding programs.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"81"},"PeriodicalIF":5.0,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12370572/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144967060","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":"Effects of variety degeneration on yield formation, quality traits and 2-acetyl-1-pyrroline biosynthesis in high-quality Japonica rice.","authors":"Qiang Shi, Zexu Zhou, Wenjie Lu, Jinlong Hu, Nianbin Zhou, Qiangqiang Xiong, Hongcheng Zhang, Jinyan Zhu","doi":"10.1186/s12284-025-00837-w","DOIUrl":"10.1186/s12284-025-00837-w","url":null,"abstract":"<p><p>The main purpose of the present study was to study the degeneration of the high-quality japonica rice varieties during long-term cultivation, with a focus on changes in yield, rice quality and indices related to 2-acetyl-1-pyrroline (2-AP) biosynthesis, to provide a scientific basis for the comprehensive purification and improvement of high-quality rice varieties. By selecting the lines from the populations of Nanjing 9108 and Nanjing 46 at Liyang, it was found that the mutant lines showed significant differences in the yield and yield components, processing and appearance quality, cooking and flavor quality, rapid viscosity analyser profile characteristics and 2-AP content. Molecular marker detection can be used as a primary method for seed purity identification. The results revealed that the 2-AP content was positively correlated with proline activity, ProDH activity and δ-OAT activity but negatively correlated with BADH2 activity. Through stepwise discriminant analysis, it was determined that 1000-grain weight and trough viscosity could be used as core indicators for discriminating line variations.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"79"},"PeriodicalIF":5.0,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12364791/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144874934","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":"The endoglucanase gene LOC_Os09g23084 is involved in rice development and susceptibility to sheath rot disease.","authors":"Ping Wan, Chi-Kuan Tu, Kai-Jie Jang, Su-May Yu, Shuen-Fang Lo, Meng-Yi Lin, Zun-Jie Syu, Yu-Hsuan Chiu, Tuan-Hua David Ho, Miin-Huey Lee","doi":"10.1186/s12284-025-00836-x","DOIUrl":"10.1186/s12284-025-00836-x","url":null,"abstract":"<p><p>Sheath rot disease, caused by Sarocladium oryzae, is a severe problem in rice cultivation and can result in significant yield loss worldwide. In this study, we analyzed the function of LOC_Os09G23084, encoding an endoglucanase-1 precursor, through gene overexpression. Two single T-DNA insertion homozygous overexpression lines, 1-16 S and 4-10 S, derived from Oryza sativa cv. TNG67, were used for functional characterization. In field conditions, overexpression of LOC_Os09g23084 resulted in a decrease in rice development and an increase in susceptibility to sheath rot disease at the harvest stage. The overexpression lines showed delayed maturation, reduced internode and panicle neck length, deformed and less protruded vascular bundles, lower lignin content, and decreased yield. To verify the susceptibility of the overexpression lines to sheath rot disease, we set up a leaf-cutting inoculation method on seedlings. Lesion length was used to assess disease severity and was confirmed by fungal colonization using a GFP-tagged S. oryzae transgenic strain. The data confirmed that the overexpression lines were more susceptible to S. oryzae than wild-type lines. The reduced internode length and panicle neck length, less protruded peripheral vascular bundles, and low lignin content might contribute to the susceptibility to sheath rot. In this study, we provide insights into the potential function and mechanism of the endoglucanase gene LOC_Os09g23084 in rice susceptibility to sheath rot disease. Additionally, we demonstrated that LOC_Os09G23084 plays a crucial role in rice growth and development.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"78"},"PeriodicalIF":5.0,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12361039/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144874936","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":"Identification of a Novel Rice Chromosomal Translocation Line that Could Cause the Heterozygote Semi-Sterility and be Overcome by Genomic Duplication.","authors":"Ruilian Deng, Hanli You, Qi Ge, Jinwen Wu, Zhukuan Cheng, Lianjun Zhu, Hang Yu, Lin Chen, Muhammad Qasim Shahid, Zijun Lu, Xiangdong Liu","doi":"10.1186/s12284-025-00835-y","DOIUrl":"10.1186/s12284-025-00835-y","url":null,"abstract":"<p><p>Interspecific and intersubspecific hybrid rice have demonstrated substantial heterosis and increased yield potential, yet they are frequently restricted by complex hybrid sterility (HS). Gene regulation has primarily been used to explain the genetic mechanism of HS; however, it is still unclear how cryptic chromosomal structural hybridity results in heterozygote semi-sterility at the molecular level. This study identified a T-DNA-mediated heterozygous mutant mfss (male and female semi-sterility) in rice, of which the self-pollinated progeny would produce heterozygous semi-sterile mutant plants and homozygous fertile mutant plants, mm, with homozygous in inserted T-DNA. The hybrids derived from mm plants crossing with other rice varieties exhibited conservative semi-sterility. Genomic analyses and fluorescence in situ hybridization (FISH) observation revealed that the end of chromosome 6 (170 genes) translocated with the end of chromosome 2 (566 genes) in mm plants. Among these 736 translocated genes, 102 reproduction-concerned genes, including a new gene, MCM5, were detected, which may result in half of gametes lacking many reproduction-concerned genes to display sterility and caused semi-sterility of mfss-heterozygotes. Hybrids derived from an autotetraploid rice line created from mm plants by genome duplication crossed with a neo-tetraploid rice displayed high fertility, implying that the mfss-heterozygote semi-sterility might be overcome by producing polyploid hybrid rice. These findings elucidate the genetic process of reciprocal translocation causing the heterozygote semi-sterility in rice and offer valuable insights for the production of fertile polyploid hybrid rice.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"77"},"PeriodicalIF":5.0,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12361019/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144874935","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":"OsROXY2 Regulates Stamen Number Through Interaction with OsbZIP47 in Rice.","authors":"Zhongni Wang, Doudou Chen, Xuelei Lin, Jing Wang, Muhammad Arif, Jiali Li, Yanlong Gong, Yue Lei, Xian Wu, Chaoxin Wu, Susong Zhu, Luhua Li","doi":"10.1186/s12284-025-00833-0","DOIUrl":"10.1186/s12284-025-00833-0","url":null,"abstract":"<p><p>Precise regulation of floral primordia initiation is essential for normal flower development. However, the mechanisms regulating floral primordia initiation (PI) are complex and poorly understood. Herein, we identified a natural mutant in rice, stamen less (sl), which develops florets with reduced stamen number and no carpel due to defects in stamen and carpel PI. STAMENLESS (SL) encodes the CC-type glutaredoxin OsROXY2 and is involved in the regulation of stamen PI. OsROXY1, the closest homolog of OsROXY2, showed no function in stamen PI regulation. The osroxy1 single mutant showed normal reproductive development, while the floret phenotypes of osroxy1/2 double mutant were comparable to those of osroxy2 mutant. The TGA transcription factor OsbZIP47 showed a strong interaction with OsROXY2, and the two genes exhibited overlapping subcellular localizations and expression patterns during flower development. The number of stamens in the osbzip47 mutant was increased to seven (around 35%), indicating that OsbZIP47 is a negative regulator of stamen PI, in contrast to OsROXY2. Taken together, our results reveal that OsROXY2 regulates stamen number via interaction with OsbZIP47, indicating GRX-TGA-mediated floral organ number regulation mechanism is conserved in monocots and eudicots.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"76"},"PeriodicalIF":5.0,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12350981/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144837555","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":"Salinity Stress Induces Phase Separation of Plant BARENTSZ to Form Condensates.","authors":"Peigang Li, Lanfeng Wu, Wenchao He, Shanshan Zhang, Chaoying He","doi":"10.1186/s12284-025-00830-3","DOIUrl":"10.1186/s12284-025-00830-3","url":null,"abstract":"<p><p>Phase separation (PS) of BARENTSZ (BTZ), a core member of the exon-junction complex (EJC), is involved in various physiological and developmental processes in animals. However, less is known about plant equivalents. Here, we demonstrated that the loss of function of Oryza sativa BTZ genes (OsBTZs) reduced rice tolerance to salinity stress. Moreover, OsBTZ proteins underwent PS independent of other core members of EJC, forming condensates under salt stress. OsBTZs may recruit proteins that play roles in the salt tolerance response to form cytoplasmic condensates, which act as stress granules. The predicted prion-like domain (PrLD), that originated ancestrally and is functionally conserved, was demonstrated to be key to the PS of OsBTZs upon NaCl treatment. This work revealed a new role for plant BTZs through an evolutionarily conserved mechanism-PS-in the formation of condensates in response to salinity stress, thus providing new insights into the adaptive evolution of plant BTZs under abiotic stress.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"75"},"PeriodicalIF":5.0,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12339837/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144817364","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":"The 14-3-3 Protein OsGF14h Coordinates Brassinosteroid and Gibberellin Signaling to Regulate Plant Growth and Grain Yield in Rice.","authors":"Yonghong Xie, Zhupeng Fan, Kaichong Teng, Zejian Huang, Kaizun Xu, Jianxiong Li","doi":"10.1186/s12284-025-00831-2","DOIUrl":"10.1186/s12284-025-00831-2","url":null,"abstract":"<p><p>Brassinosteroids (BRs) and gibberellins (GAs) are two important phytohormones that regulate plant growth and development. Crosstalk between BR and GA has been unveiled in Arabidopsis but the molecular mechanism by which the concurrence of these two signaling pathways regulates plant growth and development in rice remains elusive. The14-3-3 proteins are a family of conserved molecules that interact with a number of protein clients to regulate fundamental cellular processes including different aspects of plant hormone physiology. Here, we report that the rice 14-3-3 protein OsGF14h (G-box factor 14-3-3 homolog h) negatively modulates BR response and positively regulates GA signaling in rice. Overexpressing OsGF14h in rice increased plant height and grain yield, whereas knocking out OsGF14h increased lamina joint angle and reduced plant height and grain yield. OsGF14h interacted with both OsOFP8, a positive regulator in BR signaling, and SLR1, a negative key regulator in GA signaling. Interaction with OsGF14h led to nuclear export and cytoplasmic retention of OsOFP8, whereas OsGF14h interaction resulted in SLR1 shuttling from the nucleus to the cytoplasm and consequently inducing degradation of SLR1. Our results indicate that OsGF14h functions in both BR and GA signaling pathways and acts as a crosstalk point for BR and GA signaling, which offers new insights into the role of 14-3-3 proteins in regulating plant growth and development by modulating BR and GA signaling crosstalk.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"74"},"PeriodicalIF":5.0,"publicationDate":"2025-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12317962/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144769003","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}