Rice最新文献

{"title":"PRX102 Participates in Root Hairs Tip Growth of Rice.","authors":"Sunok Moon, Behnam Derakhshani, Yun Shil Gho, Eui-Jung Kim, Su Kyoung Lee, Xu Jiang, Choonseok Lee, Ki-Hong Jung","doi":"10.1186/s12284-023-00668-7","DOIUrl":"10.1186/s12284-023-00668-7","url":null,"abstract":"<p><p>Root hairs are extensions of epidermal cells on the root tips that increase the root contract surface area with the soil. For polar tip growth, newly synthesized proteins and other materials must be incorporated into the tips of root hairs. Here, we report the characterization of PRX102, a root hair preferential endoplasmic reticulum peroxidase. During root hair growth, PRX102 has a polar localization pattern within the tip regions of root hairs but it loses this polarity after growth termination. Moreover, PRX102 participates in root hair outgrowth by regulating dense cytoplasmic streaming toward the tip. This role is distinct from those of other peroxidases playing roles in the root hairs and regulating reactive oxygen species homeostasis. RNA-seq analysis using prx102 root hairs revealed that 87 genes including glutathione S-transferase were downregulated. Our results therefore suggest a new function of peroxidase as a player in the delivery of substances to the tips of growing root hairs.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"16 1","pages":"51"},"PeriodicalIF":5.5,"publicationDate":"2023-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10654324/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136398947","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 Thematic Special Issue: Beneficial Plant-Microbe Interactions in Rice.","authors":"Concha Domingo,&nbsp;Blanca San Segundo","doi":"10.1186/s12284-023-00659-8","DOIUrl":"10.1186/s12284-023-00659-8","url":null,"abstract":"","PeriodicalId":21408,"journal":{"name":"Rice","volume":"16 1","pages":"50"},"PeriodicalIF":5.5,"publicationDate":"2023-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10624776/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71434635","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":"GWAS Combined with WGCNA of Transcriptome and Metabolome to Excavate Key Candidate Genes for Rice Anaerobic Germination.","authors":"Dandan Li,&nbsp;Kai Liu,&nbsp;Chuanchao Zhao,&nbsp;Siyi Liang,&nbsp;Jing Yang,&nbsp;Ziai Peng,&nbsp;Aoyun Xia,&nbsp;Meng Yang,&nbsp;Lixin Luo,&nbsp;Cuihong Huang,&nbsp;Jiafeng Wang,&nbsp;Ming Huang,&nbsp;Wuming Xiao,&nbsp;Hui Wang,&nbsp;Ling Su,&nbsp;Tao Guo","doi":"10.1186/s12284-023-00667-8","DOIUrl":"https://doi.org/10.1186/s12284-023-00667-8","url":null,"abstract":"<p><p>Direct seeding of rice is a lightweight and simple cultivation method, which can effectively promote rice production. Anaerobic germination tolerance is one of the main traits of rice adaptability to direct seeding. The mining of related genetic loci, analysis of anaerobic traits and screening of tolerance genes provided valuable genetic resources for improving the anaerobic germination ability of direct seeding rice. This study conducted a dynamic genome-wide association study (GWAS) based on coleoptile-related traits of 591 rice natural populations, and a total of 317 SNP sites were detected. Integrated dynamic widely targeted metabolomics analysis, we found that xanthine, L-alanine and GABA may be key biomarkers that are sensitive and respond strongly to hypoxic stress perception. By WGCNA analysis of targeted metabolomics and transcriptomics, a total of 3 modules were obtained that were significantly correlated with the above three marker metabolites, namely dark green, dark gray and light green modules, respectively, and several key structural genes of OsAlaAT1, OsGAD4, OsAAH and Os09g0424600 that may affect hypoxic germination were screened from the 3 modules. Among them, OsAlaAT1 (Os10g0390500), located in Chr10-12877840, which is within the GWAS location range of CVAN3d, is considered to be a more reliable candidate gene. Overall, in addition to providing new insight into the metabolic regulation of L-alanine, GABA and xanthine during hypoxic germination of rice. This study also provided a reference for the basic theoretical research and breeding application research on the related traits of anaerobic germination in direct-seeding rice.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"16 1","pages":"49"},"PeriodicalIF":5.5,"publicationDate":"2023-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10618154/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71426522","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":"Impact of Seed Origin and Genetic Drift of Improved Rice Variety IR841 in Benin.","authors":"Paulin Sedah, Lambert Gustave Djedatin, Laura Yêyinou Estelle Loko, Eben-Ezer Baba Kayodé Ewedje, Azize Orobiyi, Chalemagne Dossou Seblodo Judes Gbemavo, Joelle Toffa, Cyrille Tchakpa, Philippe Cubry, Francois Sabot","doi":"10.1186/s12284-023-00657-w","DOIUrl":"10.1186/s12284-023-00657-w","url":null,"abstract":"<p><strong>Background: </strong>Rice production is important for food security in Benin, with a national production largely dominated by the cultivation of the aromatic ecotype IR841, by far the most appreciated by Beninese consumers. However, to maintain agronomical qualities of a given cultivar, the origin and quality of seeds are mandatory and at the heart of the maintenance of yield and of market requests. Following this idea, the objective of the current study was thus to investigate the genetic purity of IR841 varieties collected from rice producers across 22 villages in Benin in relation to their agronomical performances.</p><p><strong>Results: </strong>For this, agromorphological evaluation of 72 accessions based on 13 quantitative descriptors followed by genotyping with the Illumina Infinium rice 7 K SNP array of 9 accessions was carried out in the presence of 2 controls. Agromorphologic as well as genetic and phylogenetic analyses revealed two groups, the first one Okouta97, Koum47, Nana30, Man118, Ang1 and control sample IR841-2) was characterized by seed accessions provided by the formal seed system, while the second (Koum53, Tchaka41 and Koud46) comprising seeds from local markets or from previous harvests and showing a depression in agronomic performances.</p><p><strong>Conclusion: </strong>We showed that IR841 seed purity is mandatory for the completion of agronomical performance, and that the farmers' choice of seeds must be guided and informed to ensure sustainability and food security.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"16 1","pages":"48"},"PeriodicalIF":5.5,"publicationDate":"2023-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10600083/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50158682","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":"OsSTS, a Novel Allele of Mitogen-Activated Protein Kinase Kinase 4 (OsMKK4), Controls Grain Size and Salt Tolerance in Rice.","authors":"Jianguo Liu, Lan Shen, Longbiao Guo, Guangheng Zhang, Zhenyu Gao, Li Zhu, Jiang Hu, Guojun Dong, Deyong Ren, Qiang Zhang, Qing Li, Dali Zeng, Changjie Yan, Qian Qian","doi":"10.1186/s12284-023-00663-y","DOIUrl":"10.1186/s12284-023-00663-y","url":null,"abstract":"<p><p>Soil salinization is one of the most common abiotic stresses of rice, which seriously affects the normal growth of rice. Breeding salt-tolerant varieties have become one of the important ways to ensure food security and sustainable agricultural development. However, the mechanisms underlying salt tolerance control still need to be clarified. In this study, we identified a mutant, termed salt-tolerant and small grains(sts), with salt tolerance and small grains. Gene cloning and physiological and biochemical experiments reveal that sts is a novel mutant allele of Mitogen-activated protein Kinase Kinase 4 (OsMKK4), which controls the grain size, and has recently been found to be related to salt tolerance in rice. Functional analysis showed that OsSTS is constitutively expressed throughout the tissue, and its proteins are localized to the nucleus, cell membrane, and cytoplasm. It was found that the loss of OsSTS function enhanced the salt tolerance of rice seedlings, and further studies showed that the loss of OsSTS function increased the ROS clearance rate of rice seedlings, independent of ionic toxicity. In order to explore the salt tolerance mechanism of sts, we found that the salt tolerance of sts is also regulated by ABA through high-throughput mRNA sequencing. Salt and ABA treatment showed that ABA might alleviate the inhibitory effect of salt stress on root length in sts. These results revealed new functions of grain size gene OsMKK4, expanded new research ideas related to salt tolerance mechanism and hormone regulation network, and provided a theoretical basis for salt-tolerant rice breeding.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"16 1","pages":"47"},"PeriodicalIF":5.5,"publicationDate":"2023-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10597928/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49692255","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 Seed Vigor-Related QTL Cluster Associated with Weed Competitive Ability in Direct-Seeded Rice (Oryza Sativa L.).","authors":"Shan Xu, Yuexin Fei, Yue Wang, Wenjia Zhao, Luyan Hou, Yujie Cao, Min Wu, Hongkai Wu","doi":"10.1186/s12284-023-00664-x","DOIUrl":"10.1186/s12284-023-00664-x","url":null,"abstract":"<p><p>Direct seeding of rice (Oryza sativa L.) is a low-labor and sustainable cultivation method that is used worldwide. Seed vigor and early vigor are important traits associated with seedling stand density (SSD) and weed competitive ability (WCA), which are key factors in direct-seeded rice (DSR) cultivation systems. Here, we developed a set of chromosome segment substitution lines with Xiushui134 as receptor parent and Yangdao6 as donor parent and used these lines as a mapping population to identify quantitative trait loci (QTLs) for seed vigor, which we evaluated based on germinability-related indicators (germination percentage (GP), germination energy (GE), and germination index (GI)) and seedling vigor-related indicators (root number (RN), root length (RL), and shoot length (SL) at 14 days after imbibition) under controlled conditions in an incubator. Ten QTLs were detected across four chromosomes, of which a cluster of QTLs (qGP11, qGE11, qGI11, and qRL11) co-localized on Chr. 11 with high LOD values (12.03, 8.13, 7.14, and 8.75, respectively). Fine mapping narrowed down the QTL cluster to a 0.7-Mb interval between RM26797 and RM6680. Further analysis showed that the QTL cluster has a significant effect (p < 0.01) on early vigor under hydroponic culture (root length, total dry weight) and direct seeding conditions (tiller number, aboveground dry weight). Thus, our combined analysis revealed that the QTL cluster influenced both seed vigor and early vigor. Identifying favorable alleles at this QTL cluster could facilitate the improvement of SSD and WCA, thereby addressing both major factors in DSR cultivation systems.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"16 1","pages":"45"},"PeriodicalIF":5.5,"publicationDate":"2023-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10575835/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41211203","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":"Glucan Synthase-like 2 is Required for Seed Initiation and Filling as Well as Pollen Fertility in Rice.","authors":"Ronghua Qiu, Yang Liu, Zhengzheng Cai, Jieqiong Li, Chunyan Wu, Gang Wang, Chenchen Lin, Yulin Peng, Zhanlin Deng, Weiqi Tang, Weiren Wu, Yuanlin Duan","doi":"10.1186/s12284-023-00662-z","DOIUrl":"10.1186/s12284-023-00662-z","url":null,"abstract":"<p><strong>Background: </strong>The Glucan synthase-like (GSL) genes are indispensable for some important highly-specialized developmental and cellular processes involving callose synthesis and deposition in plants. At present, the best-characterized reproductive functions of GSL genes are those for pollen formation and ovary expansion, but their role in seed initiation remains unknown.</p><p><strong>Results: </strong>We identified a rice seed mutant, watery seed 1-1 (ws1-1), which contained a mutation in the OsGSL2 gene. The mutant produced seeds lacking embryo and endosperm but filled with transparent and sucrose-rich liquid. In a ws1-1 spikelet, the ovule development was normal, but the microsporogenesis and male gametophyte development were compromised, resulting in the reduction of fertile pollen. After fertilization, while the seed coat normally developed, the embryo failed to differentiate normally. In addition, the divided endosperm-free nuclei did not migrate to the periphery of the embryo sac but aggregated so that their proliferation and cellularization were arrested. Moreover, the degeneration of nucellus cells was delayed in ws1-1. OsGSL2 is highly expressed in reproductive organs and developing seeds. Disrupting OsGSL2 reduced callose deposition on the outer walls of the microspores and impaired the formation of the annular callose sheath in developing caryopsis, leading to pollen defect and seed abortion.</p><p><strong>Conclusions: </strong>Our findings revealed that OsGSL2 is essential for rice fertility and is required for embryo differentiation and endosperm-free nucleus positioning, indicating a distinct role of OsGSL2, a callose synthase gene, in seed initiation, which provides new insight into the regulation of seed development in cereals.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"16 1","pages":"44"},"PeriodicalIF":5.5,"publicationDate":"2023-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10560172/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41132897","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":"Optimization of Multi-Generation Multi-location Genomic Prediction Models for Recurrent Genomic Selection in an Upland Rice Population.","authors":"Hugues de Verdal, Cédric Baertschi, Julien Frouin, Constanza Quintero, Yolima Ospina, Maria Fernanda Alvarez, Tuong-Vi Cao, Jérôme Bartholomé, Cécile Grenier","doi":"10.1186/s12284-023-00661-0","DOIUrl":"10.1186/s12284-023-00661-0","url":null,"abstract":"<p><p>Genomic selection is a worthy breeding method to improve genetic gain in recurrent selection breeding schemes. The integration of multi-generation and multi-location information could significantly improve genomic prediction models in the context of shuttle breeding. The Cirad-CIAT upland rice breeding program applies recurrent genomic selection and seeks to optimize the scheme to increase genetic gain while reducing phenotyping efforts. We used a synthetic population (PCT27) of which S₀ plants were all genotyped and advanced by selfing and bulk seed harvest to the S_0:2, S_0:3, and S_0:4 generations. The PCT27 was then divided into two sets. The S_0:2 and S_0:3 progenies for PCT27A and the S_0:4 progenies for PCT27B were phenotyped in two locations: Santa Rosa the target selection location, within the upland rice growing area, and Palmira, the surrogate location, far from the upland rice growing area but easier for experimentation. While the calibration used either one of the two sets phenotyped in one or two locations, the validation population was only the PCT27B phenotyped in Santa Rosa. Five scenarios of genomic prediction and 24 models were performed and compared. Training the prediction model with the PCT27B phenotyped in Santa Rosa resulted in predictive abilities ranging from 0.19 for grain zinc concentration to 0.30 for grain yield. Expanding the training set with the inclusion of the PCT27A resulted in greater predictive abilities for all traits but grain yield, with increases from 5% for plant height to 61% for grain zinc concentration. Models with the PCT27B phenotyped in two locations resulted in higher prediction accuracy when the models assumed no genotype-by-environment (G × E) interaction for flowering (0.38) and grain zinc concentration (0.27). For plant height, the model assuming a single G × E variance provided higher accuracy (0.28). The gain in predictive ability for grain yield was the greatest (0.25) when environment-specific variance deviation effect for G × E was considered. While the best scenario was specific to each trait, the results indicated that the gain in predictive ability provided by the multi-location and multi-generation calibration was low. Yet, this approach could lead to increased selection intensity, acceleration of the breeding cycle, and a sizable economic advantage for the program.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"16 1","pages":"43"},"PeriodicalIF":5.5,"publicationDate":"2023-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10533757/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41164892","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":"Disruption of the Novel Small Protein RBR7 Leads to Enhanced Plant Resistance to Blast Disease.","authors":"Hui Shi, Qing Xiong, Zhangjie Zhao, Lian Zhou, Junjie Yin, Xiang Lu, Xuewei Chen, Jing Wang","doi":"10.1186/s12284-023-00660-1","DOIUrl":"10.1186/s12284-023-00660-1","url":null,"abstract":"<p><p>Plant disease is a threat to global food security. Breeding crops carrying broad-spectrum resistance loci is an effective way to control infectious disease. Disease-resistant mutants are valuable resources for deciphering the underlying mechanisms of plant immunity and could provide genetic loci to generate disease-resistant crops. Here, we identified a rice mutant, rbr7 (rice blast resistance 7), that confers resistance against different strains of Magnaporthe oryzae. Disease-mimicking necrotic lesions started to appear on the leaves of rbr7 four weeks after sowing. Histochemical analysis revealed reactive oxygen species accumulation and cell death accompanied by spontaneous lesion formation in rbr7. Map-based cloning and bulk segregation analysis showed a 2855 bp fragment deletion on chromosome 5, leading to the disruption of the LOC_Os05g28480-coding protein. Transgenic rbr7 complementation plants showed compromised resistance to rice blast, indicating that LOC_Os05g28480, or Rbr7, regulates the rice immune response. Rbr7 encodes a small protein of unknown function with 85 amino acids. Transcriptomic analysis revealed that disruption of RBR7 led to the upregulation of genes responding to salicylic acid, systemic acquired resistance and pathogenesis-related genes. Taken together, our findings reveal insights into a novel small protein involved in regulating plant resistance to rice blast and provide a potential target for crop breeding.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"16 1","pages":"42"},"PeriodicalIF":5.5,"publicationDate":"2023-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10513991/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41135038","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":"Explanation Generated for Sequential Recommendation based on Transformer model","authors":"Yuanpeng Qu, H. Nobuhara","doi":"10.1109/SCISISIS55246.2022.10002066","DOIUrl":"https://doi.org/10.1109/SCISISIS55246.2022.10002066","url":null,"abstract":"Generating recommendation reasons for recommended items can play an essential role in personalization such as by summarizing users’ comments on their purchased items. However, existing methods only utilize general recommendations, ignoring the fact that items purchased by users are often related to their purchase history. To address this issue, we propose a multitask model referred to as Explanation Generated for Sequential Recommendation (EG4SRec), which is designed to generate recommendation reasons based on a Transformer model for sequential recommendations. First, we predicted and recommended items based on the time series information from the user’s purchase history. Additionally, we used the proposed method to generate recommendation reasons for a target user based on these features by assigning linguistic meaning to the user’s purchase history and the items they may be interested in buy. Moreover, we applied context prediction to generate features for recommendation reasons. The results of experiments conducted using the constructed review dataset, which includes approximately 1. 29M explanations from the Yelp dataset, show that the proposed approach is reasonably effective for sequential recommendations. The model achieved performance similar to that of an existing SOTA model in terms of the evaluation matrix and performed even better in some other terms.","PeriodicalId":21408,"journal":{"name":"Rice","volume":"12 1","pages":"1-6"},"PeriodicalIF":5.5,"publicationDate":"2022-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77960279","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}