Rice最新文献

{"title":"A Cyclin Gene OsCYCB1;5 Regulates Seed Callus Induction in Rice Revealed by Genome Wide Association Study.","authors":"Wenjing Song, Jian Zhang, Wenyu Lu, Siyi Liang, Hairong Cai, Yuanyuan Guo, Shiyi Chen, Jiafeng Wang, Tao Guo, Hong Liu, Dehua Rao","doi":"10.1186/s12284-024-00742-8","DOIUrl":"https://doi.org/10.1186/s12284-024-00742-8","url":null,"abstract":"<p><p>Plant tissue culture is extensively employed in plant functional genomics research and crop genetic improvement breeding. The callus induction ability is critical for utilizing Agrobacterium-mediated genetic transformation. In this study, we conducted a genome-wide association study (GWAS) utilizing 368 rice accessions to identify traits associated with callus induction rate (CIR), resulting in the identification of a total of 104 significant SNP loci. Integrated with gene function annotation and transcriptome analysis, 13 high-confidence candidate genes involved in auxin-related, CYC cyclins, and histone H3K9-specific methyltransferase were identified in significant loci. Furthermore, we also verified a candidate gene, Os05g0493500 (OsCycB1;5), and employed the CRISPR/Cas9 system to generate OsCycB1;5 knockout mutants in rice (Oryza sativa L.). The OscycB1;5 mutant displays significantly reduced callus induction and proliferation capacity, this result indicating OsCycB1;5 is required for the callus formation in rice. Overall, this study provides several reliable loci and high-confidence candidate genes that may significantly affect callus formation in rice. This information will offer valuable insights into the mechanisms underlying callus formation not only in rice but also in other plants.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"17 1","pages":"64"},"PeriodicalIF":4.8,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11473481/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142473685","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":"Involvement of the Metallothionein gene OsMT2b in Drought and Cadmium Ions Stress in Rice","authors":"Yanxin Chen, Ying He, Yibin Pan, Yunyi Wen, Lili Zhu, Jieer Gao, Weiting Chen, Dagang Jiang","doi":"10.1186/s12284-024-00740-w","DOIUrl":"https://doi.org/10.1186/s12284-024-00740-w","url":null,"abstract":"<p>Abiotic stress is one of the major factors restricting the production of rice (<i>Oryza sativa</i> L.). Developing rice varieties with dual abiotic stress tolerance is essential to ensure sustained rice production, which is necessary to illustrate the regulation mechanisms underlying dual stress tolerance. At present, only a few genes that regulate dual abiotic stress tolerance have been reported. In this study, we determined that the expression of <i>OsMT2b</i> was induced by both drought and Cd²⁺ stress. After stress treatment, <i>OsMT2b</i>-overexpression lines exhibited enhanced drought tolerance and better physiological performance in terms of relative water content and electrolyte leakage compared with wild-type (WT). Further analysis indicated that ROS levels were lower in <i>OsMT2b</i>-overexpression lines than in WT following stress treatment, suggesting that <i>OsMT2b</i>-overexpression lines had a stronger ability to scavenge ROS under stress. Reverse transcription-quantitative PCR (RT-qPCR) results demonstrated that under drought stress, <i>OsMT2b</i> influenced the expression of genes involved in ROS scavenging to enhance drought tolerance in rice. In addition, <i>OsMT2b</i>-overexpression plants displayed increased tolerance to Cd²⁺ stress, and physiological assessment results were consistent with the observed phenotypic improvements. Thus, enhancing ROS scavenging ability through <i>OsMT2b</i> overexpression is a novel strategy to boost rice tolerance to both drought and Cd²⁺ stress, offering a promising approach for developing rice germplasm with enhanced resistance to the abiotic stressors.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"4 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142250084","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 Ratio of A400/A1800 Mapping Identifies Chromosomal Regions Containing Known Photoprotection Recovery-Related Genes in Rice","authors":"Shoumik Saha, Nilanjan Sinha Mahapatra, Kriti Bhattacharya, Rimpa Kundu, K. Nimitha, Shamba Ganguly, Sebantee Ganguly, Tirthankar Biswas, Prabir K Bhattacharyya, Somnath Bhattacharyya","doi":"10.1186/s12284-024-00739-3","DOIUrl":"https://doi.org/10.1186/s12284-024-00739-3","url":null,"abstract":"<p>The rice, like other plants, undergoes photoprotection mode by increasing nonphotochemical quenching (NPQ) in high light intensity (&gt; 1200 µmol m^− 2s^− 1 PPFD), which attenuates photosystem II yield (φPSII) drastically. The plant remains in photoprotection mode even after light intensity becomes not stressful for an extended period. While there are significant differences in the time it takes for photoprotection to recover among different genotypes, its use is limited in plant breeding because measuring the chlorophyll fluorescence parameters in progressive actinic light after dark adaptation takes more than forty-five minutes per genotype. The study finds that instantly measured A₄₀₀/A₁₈₀₀ ratio by five minutes in flag leaves of 25 diverse genotypes strongly associated with the φPSII₄₀₀ differences between theoretical and actual, qPd₄₀₀ and NPQ₄₀₀ with R² values 0.74, 0.65 and 0.60, respectively. In two consecutive years, GWAS of A₄₀₀/A₁₈₀₀ ratio identified the regions with genes reported earlier for plant photoprotection recovery. Additionally, QTL analysis in a RIL population also identified the regions carrying known genes related to photoprotection. Thus, the A₄₀₀/A₁₈₀₀ ratio can quickly phenotype many plants for easier introgression of the traits in popular cultivars. The identified genotypes, genes, and QTLs can be used to improve yield potential and allele mining.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"15 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142250080","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":"OsWRKY70 Plays Opposite Roles in Blast Resistance and Cold Stress Tolerance in Rice","authors":"Jiangdi Li, Yating Chen, Rui Zhang, Rujie Wang, Bin Wu, Haiwen Zhang, Guiqing Xiao","doi":"10.1186/s12284-024-00741-9","DOIUrl":"https://doi.org/10.1186/s12284-024-00741-9","url":null,"abstract":"<p>The transcription factor WRKYs play pivotal roles in the adapting to adverse environments in plants. Prior research has demonstrated the involvement of <i>OsWRKY70</i> in resistance against herbivores and its response to abiotic stress. Here, we reported the functional analysis of <i>OsWRKY70</i> in immunity against fungal diseases and cold tolerance. The results revealed that <i>OsWRKY70</i> was induced by various <i>Magnaporthe oryzae</i> strains. Knock out mutants of <i>OsWRKY70</i>, which were generated by the CRISPR/Cas9 system, exhibited enhanced resistance to <i>M. oryzae</i>. This was consistent with fortifying the reactive oxygen species (ROS) burst after inoculation in the mutants, elevated transcript levels of defense-responsive genes (<i>OsPR1b</i>, <i>OsPBZ1</i>, <i>OsPOX8.1</i> and <i>OsPOX22.3</i>) and the observation of the sluggish growth of invasive hyphae under fluorescence microscope. RNA sequencing (RNA-seq) and quantitative real-time PCR (qRT-PCR) validations demonstrated that differentially expressed genes were related to plant-pathogen interactions, hormone transduction and MAPK cascades. Notably, <i>OsbHLH6</i>, a key component of the JA signaling pathway, was down-regulated in the mutants compared to wild type plants. Further investigation confirmed that OsWRKY70 bound to the promoter of <i>OsbHLH6</i> by semi-in vivo chromatin immunoprecipitation (ChIP). Additionally, the loss-function of <i>OsWRKY70</i> impaired cold tolerance in rice. The enhanced susceptibility in the mutants characterized by excessive ROS production, elevated ion leakage rate and increased malondialdehyde content, as well as decreased activity of catalase (CAT) and peroxidase (POD) under low temperature stress was, which might be attributed to down-regulation of cold-responsive genes (<i>OsLti6b</i> and <i>OsICE1</i>). In conclusion, our findings indicate that OsWRKY70 negatively contributes to blast resistance but positively regulates cold tolerance in rice, providing a strategy for crop breeding with tolerance to stress.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"16 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142249758","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":"Physiological Basis of Plant Growth Promotion in Rice by Rhizosphere and Endosphere Associated Streptomyces Isolates from India","authors":"Dhivya P. Thenappan, Rakesh Pandey, Alkesh Hada, Dinesh Kumar Jaiswal, Viswanathan Chinnusamy, Ramcharan Bhattacharya, Kannepalli Annapurna","doi":"10.1186/s12284-024-00732-w","DOIUrl":"https://doi.org/10.1186/s12284-024-00732-w","url":null,"abstract":"<p>This study demonstrated the plant growth-promoting capabilities of native actinobacterial strains obtained from different regions of the rice plant, including the rhizosphere (FT1, FTSA2, FB2, and FH7) and endosphere (EB6). We delved into the molecular mechanisms underlying the beneficial effects of these plant-microbe interactions by conducting a transcriptional analysis of a select group of key genes involved in phytohormone pathways. Through in vitro screening for various plant growth-promoting (PGP) traits, all tested isolates exhibited positive traits for indole-3-acetic acid synthesis and siderophore production, with FT1 being the sole producer of hydrogen cyanide (HCN). All isolates were identified as members of the <i>Streptomyces</i> genus through 16S rRNA amplification. In pot culture experiments, rice seeds inoculated with strains FB2 and FTSA2 exhibited significant increases in shoot dry mass by 7% and 34%, respectively, and total biomass by 8% and 30%, respectively. All strains led to increased leaf nitrogen levels, with FTSA2 demonstrating the highest increase (4.3%). On the contrary, strains FB2 and FT1 increased root length, root weight ratio, root volume, and root surface area, leading to higher root nitrogen content. All isolates, except for FB2, enhanced total chlorophyll and carotenoid levels. Additionally, qRT-PCR analysis supported these findings, revealing differential gene expression in auxin (<i>OsAUX1</i>,<i> OsIAA1</i>,<i> OsYUCCA1</i>,<i> OsYUCCA3</i>), gibberellin (<i>OsGID1</i>,<i> OsGA20ox-1</i>), and cytokinin (<i>OsIPT3</i>,<i> OsIPT5</i>) pathways in response to specific actinobacterial treatments. These actinobacterial strains, which enhance both aboveground and belowground crop characteristics, warrant further evaluation in field trials, either as individual strains or in consortia. This could lead to the development of commercial bioinoculants for use in integrated nutrient management practices.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"58 1","pages":"60"},"PeriodicalIF":5.5,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142184747","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":"Gγ-protein GS3 Function in Tight Genetic Relation with OsmiR396/GS2 to Regulate Grain Size in Rice.","authors":"Lin Zhu, Yanjie Shen, Zhengyan Dai, Xuexia Miao, Zhenying Shi","doi":"10.1186/s12284-024-00736-6","DOIUrl":"10.1186/s12284-024-00736-6","url":null,"abstract":"<p><p>Manipulating grain size demonstrates great potential for yield promotion in cereals since it is tightly associated with grain weight. Several pathways modulating grain size have been elaborated in rice, but possible crosstalk between the ingredients is rarely studied. OsmiR396 negatively regulates grain size through targeting OsGRF4 (GS2) and OsGRF8, and proves to be multi-functioning. Here we showed that expression of GS3 gene, a Gγ-protein encoding gene, that negatively regulates grain size, was greatly down-regulated in the young embryos of MIM396, GRF8OE and GS2OE plants, indicating possible regulation of GS3 gene by OsmiR396/GRF module. Meanwhile, multiple biochemical assays proved possible transcriptional regulation of OsGRF4 and OsGRF8 proteins on GS3 gene. Further genetic relation analysis revealed tight genetic association between not only OsmiR396 and GS3 gene, but also GS2 and GS3 gene. Moreover, we revealed possible regulation of GS2 on four other grain size-regulating G protein encoding genes. Thus, the OsmiR396 pathway and the G protein pathway cross talks to regulate grain size. Therefore, we established a bridge linking the miRNA-transcription factors pathway and the G-protein signaling pathway that regulates grain size in rice.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"17 1","pages":"59"},"PeriodicalIF":4.8,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11384671/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142154951","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: HD-ZIP IV Gene ROC1 Regulates Leaf Rolling and Drought Response Through Formation of Heterodimers with ROC5 and ROC8 in Rice.","authors":"Zhihuan Tao, Xuexia Miao, Zhenying Shi","doi":"10.1186/s12284-024-00738-4","DOIUrl":"10.1186/s12284-024-00738-4","url":null,"abstract":"","PeriodicalId":21408,"journal":{"name":"Rice","volume":"17 1","pages":"58"},"PeriodicalIF":4.8,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11383883/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142154950","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":"OsRopGEF10 Attenuates Cytokinin Signaling to Regulate Panicle Development and Grain Yield in Rice.","authors":"Ming Li, Lianjie Feng, Huanxia Ye, Meiyu Li, Jing Jin, Li-Zhen Tao, Huili Liu","doi":"10.1186/s12284-024-00737-5","DOIUrl":"10.1186/s12284-024-00737-5","url":null,"abstract":"<p><p>Cytokinins, which play crucial roles in shoot development, substantially affect grain yield. In rice, the OsRopGEF10-OsRAC3 module is associated with cytokinin signaling and crown root development. However, the effects of RopGEF-mediated cytokinin signaling on rice shoot development and grain yield remain unclear. In this study, we investigated the role of OsRopGEF10 in SAM development and the underlying mechanism. We showed that overexpression of OsRopGEF10 inhibited SAM and panicle development, leading to decreased grain yield. Intriguingly, the overexpression of a specific amino acid mutant of OsRopGEF10, designated gef10-W260S, was found to promote panicle development and grain yield. Further analysis using the BiFC assay revealed that the gef10-W260S mutation disrupted the recruitment of rice histidine phosphotransfer proteins (OsAHP1/2) to the plasma membrane (PM), thereby promoting cytokinin signaling. This effect was corroborated by a dark-induced leaf senescence assay, which revealed an increased cytokinin response in the gef10-W260S ectopic expression lines, whereas the overexpression lines presented a suppressed cytokinin response. Moreover, we revealed that the enhanced panicle development in the gef10-W260S lines was attributable to the upregulated expression of several type-B response regulators (RRs) that are crucial for panicle development. Collectively, these findings revealed the negative regulatory function of OsRopGEF10 in the development of the shoot apical meristem (SAM) via interference with cytokinin signaling. Our study highlights the promising role of OsRopGEF10 as a potential target for regulating SAM and panicle development in rice, revealing a valuable breeding strategy for increasing crop yield.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"17 1","pages":"57"},"PeriodicalIF":4.8,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11369127/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142120542","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":"OsRAV1 Regulates Seed Vigor and Salt Tolerance During Germination in Rice.","authors":"Yingbo Gao, Xinyi Zhao, Xin Liu, Chang Liu, Kunming Zhang, Xiaoxiang Zhang, Juan Zhou, Guichun Dong, Youping Wang, Jianye Huang, Zefeng Yang, Yong Zhou, Youli Yao","doi":"10.1186/s12284-024-00734-8","DOIUrl":"10.1186/s12284-024-00734-8","url":null,"abstract":"<p><p>Seed vigor is a complex trait encompassing seed germination, seedling emergence, growth, seed longevity, and stress tolerance, all are crucial for direct seeding in rice. Here, we report that the AP2/ERF transcription factor OsRAV1 (RELATED TO ABI3 AND VP1) positively regulates seed germination, vigor, and salt tolerance. Additionally, OsRAV1 was differently expressed in embryo and endosperm, with the OsRAV1 localized in the nucleus. Transcriptomic analysis revealed that OsRAV1 modulates seed vigor through plant hormone signal transduction and phenylpropanoid biosynthesis during germination. Haplotype analysis showed that rice varieties carrying Hap3 displayed enhanced salt tolerance during seed germination. These findings suggest that OsRAV1 is a potential target in breeding rice varieties with high seed vigor suitable for direct seeding cultivation.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"17 1","pages":"56"},"PeriodicalIF":4.8,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11366736/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142111520","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":"Rice Promoter Editing: An Efficient Genetic Improvement Strategy.","authors":"Bowen Wu, Hangfei Luo, Zhongbo Chen, Bakht Amin, Manyu Yang, Zhenghan Li, Shuai Wu, Saleh H Salmen, Sulaiman Ali Alharbi, Zhongming Fang","doi":"10.1186/s12284-024-00735-7","DOIUrl":"https://doi.org/10.1186/s12284-024-00735-7","url":null,"abstract":"<p><p>Gene expression levels in rice (Oryza sativa L.) and other plant species are determined by the promoters, which directly control phenotypic characteristics. As essential components of genes, promoters regulate the intensity, location, and timing of gene expression. They contain numerous regulatory elements and serve as binding sites for proteins that modulate transcription, including transcription factors and RNA polymerases. Genome editing can alter promoter sequences, thereby precisely modifying the expression patterns of specific genes, and ultimately affecting the morphology, quality, and resistance of rice. This paper summarizes research on rice promoter editing conducted in recent years, focusing on improvements in yield, heading date, quality, and disease resistance. It is expected to inform the application of promoter editing and encourage further research and development in crop genetic improvement with promote.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"17 1","pages":"55"},"PeriodicalIF":4.8,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11364747/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142111522","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}