oryza

Summary

Summary: A genus of grass family (Poaceae) that include several rice species.

Top Publications

  1. . The map-based sequence of the rice genome. Nature. 2005;436:793-800 pubmed
    ..The additional single-nucleotide polymorphisms and simple sequence repeats identified in our study should accelerate improvements in rice production. ..
  2. Yuan C, Liu L, Qi X, Fu Y, Ye J. Assessing the impacts of the changes in farming systems on food security and environmental sustainability of a Chinese rural region under different policy scenarios: an agent-based model. Environ Monit Assess. 2017;189:322 pubmed publisher
    ..Despite its limitations, ABM could be considered a useful tool in analyzing, exploring, and discussing the comprehensive effects of the changes in farming system on food security and environmental sustainability. ..
  3. Shibuya M, Sasaki K, Tanaka Y, Yasukawa M, Takahashi T, Kondo A, et al. Development of combined nanofiltration and forward osmosis process for production of ethanol from pretreated rice straw. Bioresour Technol. 2017;235:405-410 pubmed publisher
    ..5-fold and then concentrated by the NF(+H2O)-FO hybrid process. The NF(+H2O)-FO hybrid process has the potential for optimized ethanol production from pretreated lignocellulosic biomass. ..
  4. Wei Y, Li H, Zhang J, Xiong J, Yi X, You J. Legacy and Current-Use Insecticides in Agricultural Sediments from South China: Impact of Application Pattern on Occurrence and Risk. J Agric Food Chem. 2017;65:4247-4254 pubmed publisher
    ..Pyrethroids and fipronil were restricted to use in paddy fields, but their occurrence and risk in agricultural waterways were high, calling for better measures to regulate the illegal use of insecticides. ..
  5. Chung I, Kim J, Lee K, Park S, Lee J, Son N, et al. Geographic authentication of Asian rice (Oryza sativa L.) using multi-elemental and stable isotopic data combined with multivariate analysis. Food Chem. 2018;240:840-849 pubmed publisher
    Rice (Oryza sativa L.) is the world's third largest food crop after wheat and corn. Geographic authentication of rice has recently emerged asan important issue for enhancing human health via food safety and quality assurance...
  6. Choudhary G, Ranjitkumar N, Surapaneni M, Deborah D, Vipparla A, Anuradha G, et al. Molecular Genetic Diversity of Major Indian Rice Cultivars over Decadal Periods. PLoS ONE. 2013;8:e66197 pubmed publisher
    ..It was obvious from the present findings, that genetic diversity was progressively on the rise in the varieties released during the decadal periods, between 1970s and 2000s. ..
  7. Kaur A, Pati P, Pati A, Nagpal A. In-silico analysis of cis-acting regulatory elements of pathogenesis-related proteins of Arabidopsis thaliana and Oryza sativa. PLoS ONE. 2017;12:e0184523 pubmed publisher
    ..attempt has been made to analyze promoter regions of PR1, PR2, PR5, PR9, PR10 and PR12 of Arabidopsis thaliana and Oryza sativa...
  8. Kouzai Y, Mochizuki S, Nakajima K, Desaki Y, Hayafune M, Miyazaki H, et al. Targeted gene disruption of OsCERK1 reveals its indispensable role in chitin perception and involvement in the peptidoglycan response and immunity in rice. Mol Plant Microbe Interact. 2014;27:975-82 pubmed publisher
    ..It is also suggested that OsCERK1 mediates the signaling pathways of both fungal and bacterial molecular patterns by interacting with different LysM-containing receptor-like proteins. ..
  9. Campbell M, Bandillo N, Al Shiblawi F, Sharma S, Liu K, Du Q, et al. Allelic variants of OsHKT1;1 underlie the divergence between indica and japonica subspecies of rice (Oryza sativa) for root sodium content. PLoS Genet. 2017;13:e1006823 pubmed publisher
    Salinity is a major factor limiting crop productivity. Rice (Oryza sativa), a staple crop for the majority of the world, is highly sensitive to salinity stress...

More Information

Publications62

  1. Newbigging A, Paliwoda R, Le X. Rice: Reducing arsenic content by controlling water irrigation. J Environ Sci (China). 2015;30:129-31 pubmed publisher
  2. Liu J, Ma Z, Zhu H, Caiyin Q, Liang D, Wu H, et al. Improving xylose utilization of defatted rice bran for nisin production by overexpression of a xylose transcriptional regulator in Lactococcus lactis. Bioresour Technol. 2017;238:690-697 pubmed publisher
    ..In HD medium, the highest nisin titer of the engineered strain FEXR was 3824.53IU/mL, which was 1.37 times of that in sucrose medium by the original strain F44. ..
  3. Kobayashi M, Ohyanagi H, Takanashi H, Asano S, Kudo T, Kajiya Kanegae H, et al. Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput sequencing data. DNA Res. 2017;24:397-405 pubmed publisher
    ..Code and documentation of Heap are freely available from https://github.com/meiji-bioinf/heap (29 March 2017, date last accessed) and our web site (http://bioinf.mind.meiji.ac.jp/lab/en/tools.html (29 March 2017, date last accessed)). ..
  4. Chen L, Xiong G, Cui X, Yan M, Xu T, Qian Q, et al. OsGRAS19 may be a novel component involved in the brassinosteroid signaling pathway in rice. Mol Plant. 2013;6:988-91 pubmed publisher
  5. Narayanan J, Sanjeevi V, Rohini U, Trueman P, Viswanathan V. Postprandial glycaemic response of foxtail millet dosa in comparison to a rice dosa in patients with type 2 diabetes. Indian J Med Res. 2016;144:712-717 pubmed publisher
    ..Thus, millets may have a protective role in the management of hyperglycaemia. Further studies need to be done in a systematic manner to confirm these findings. ..
  6. Rubinelli P, Kim S, Park S, Roto S, Nealon N, Ryan E, et al. Differential effects of rice bran cultivars to limit Salmonella Typhimurium in chicken cecal in vitro incubations and impact on the cecal microbiome and metabolome. PLoS ONE. 2017;12:e0185002 pubmed publisher
    ..In addition, Calrose rice bran inclusion leads to changes in cecal microbiological composition and metabolite profile...
  7. Tian G, Gao L, Kong Y, Hu X, Xie K, Zhang R, et al. Improving rice population productivity by reducing nitrogen rate and increasing plant density. PLoS ONE. 2017;12:e0182310 pubmed publisher
  8. Xu E, Wu Z, Jiao A, Jin Z. Effect of exogenous metal ions and mechanical stress on rice processed in thermal-solid enzymatic reaction system related to further alcoholic fermentation efficiency. Food Chem. 2018;240:965-973 pubmed publisher
  9. Alagappan L, Shanmugasundaram P, Ramachandra B, Gumpu M, Nesakumar N, Jayanth Babu K, et al. Fabrication of electrochemical biosensor with vanadium pentoxide nano-interface for the detection of methylglyoxal in rice. Anal Biochem. 2017;528:19-25 pubmed publisher
    ..99, sensitivity of 1130.86 ?A cm-2 ?M-1, limit of detection of 2 nM and response time of less than 18 s. The developed bioelectrode was used for the detection of MG in raw and par-boiled rice samples. ..
  10. Wang J, Yu H, Xiong G, Lu Z, Jiao Y, Meng X, et al. Tissue-Specific Ubiquitination by IPA1 INTERACTING PROTEIN1 Modulates IPA1 Protein Levels to Regulate Plant Architecture in Rice. Plant Cell. 2017;29:697-707 pubmed publisher
    ..encodes a key transcription factor with pleiotropic effects on regulating plant architecture in rice (Oryza sativa), and IPA1 expression is controlled at the posttranscriptional level by microRNA156 and ..
  11. Holtcamp W. Suspect sweetener: arsenic detected in organic brown rice syrup. Environ Health Perspect. 2012;120:A204 pubmed publisher
  12. Sun Y, Ning T, Liu Z, Pang J, Jiang D, Guo Z, et al. The OsSec18 complex interacts with P0(P1-P2)2 to regulate vacuolar morphology in rice endosperm cell. BMC Plant Biol. 2015;15:55 pubmed publisher
    ..Our results revealed that the OsSec18 regulates vacuolar morphology in both yeast and rice endosperm cell and the OsSec18 interacts with P0(P1-P2)2 complex in rice endosperm cell. ..
  13. Xu G, Yuan M, Ai C, Liu L, Zhuang E, Karapetyan S, et al. uORF-mediated translation allows engineered plant disease resistance without fitness costs. Nature. 2017;545:491-494 pubmed publisher
    ..This broadly applicable strategy may lead to decreased pesticide use and reduce the selective pressure for resistant pathogens. ..
  14. Yokotani N, Tsuchida Mayama T, Ichikawa H, Mitsuda N, Ohme Takagi M, Kaku H, et al. OsNAC111, a blast disease-responsive transcription factor in rice, positively regulates the expression of defense-related genes. Mol Plant Microbe Interact. 2014;27:1027-34 pubmed publisher
    ..These results indicate that OsNAC111 positively regulates the expression of a specific set of PR genes in the disease response and contributes to disease resistance. ..
  15. Xiao L, Guan D, Peart M, Chen Y, Li Q, Dai J. The influence of bioavailable heavy metals and microbial parameters of soil on the metal accumulation in rice grain. Chemosphere. 2017;185:868-878 pubmed publisher
    ..The results suggested that Pb accumulation in rice grain was mainly influenced by the multi-metal interactive effects, and less affected by soil bioavailable Pb. ..
  16. Truong H, Luu P, Imamura K, Matsubara T, Takahashi H, Takenaka N, et al. Binary Solvent Extraction of Tocols, ?-Oryzanol, and Ferulic Acid from Rice Bran Using Alkaline Treatment Combined with Ultrasonication. J Agric Food Chem. 2017;65:4897-4904 pubmed publisher
    ..These results are in good agreement with those reported for rice bran samples from Thailand. ..
  17. Zhang Y, Li Y, Zhu X, Li M, Chen H, Lv X, et al. Development and validation of a solid-phase extraction method coupled with HPLC-UV detection for the determination of biogenic amines in Chinese rice wine. Food Addit Contam Part A Chem Anal Control Expo Risk Assess. 2017;34:1172-1183 pubmed publisher
    ..Thus, the proposed method was demonstrated as being suitable for simultaneous detection, with accurate and precise quantification, of BAs in Chinese rice wine. ..
  18. Zhou J, Yang J, Yu Q, Yong X, Xie X, Zhang L, et al. Different organic loading rates on the biogas production during the anaerobic digestion of rice straw: A pilot study. Bioresour Technol. 2017;244:865-871 pubmed publisher
    ..This study provides new information regarding the OLR and the differences in the spatial distribution of specific microbiota in a rice straw biogas plant. ..
  19. Cao A, Jin J, Li S, Wang J. Integrated analysis of mRNA and miRNA expression profiling in rice backcrossed progenies (BC2F12) with different plant height. PLoS ONE. 2017;12:e0184106 pubmed publisher
    ..Taken together, these results provided valuable information on the molecular mechanisms of hybrid backcrossing and plant height variations based on the gene and miRNA expression levels in the three progeny lines. ..
  20. Bui T, Hoa N, Yen J, Schafleitner R. PCR-based assays for validation of single nucleotide polymorphism markers in rice and mungbean. Hereditas. 2017;154:3 pubmed publisher
    ..CEL-I genotyping performed better in terms of genotyping accuracy and costs than tetra markers. The method is highly useful for validating SNPs in small to medium size germplasm panels. ..
  21. Wei X, Handoko D, Pather L, Methven L, Elmore J. Evaluation of 2-acetyl-1-pyrroline in foods, with an emphasis on rice flavour. Food Chem. 2017;232:531-544 pubmed publisher
    ..The analysis of 2-AP by instrumental techniques, particularly gas chromatography-mass spectrometry and gas chromatography-olfactometry, alongside the use of sensory studies, is also discussed. ..
  22. Acevedo F, Stanley B, Stanley A, Peiffer M, Luthe D, Felton G. Quantitative proteomic analysis of the fall armyworm saliva. Insect Biochem Mol Biol. 2017;86:81-92 pubmed publisher
    ..Based on these results, we conclude that the FAW saliva contains a complex mixture of proteins involved in different functions that are specific for each strain and its composition can change plastically in response to diet type. ..
  23. Mao Y, Zhang H, Xu N, Zhang B, Gou F, Zhu J. Application of the CRISPR-Cas system for efficient genome engineering in plants. Mol Plant. 2013;6:2008-11 pubmed publisher
  24. Guo J, Chen C. Sludge conditioning using the composite of a bioflocculant and PAC for enhancement in dewaterability. Chemosphere. 2017;185:277-283 pubmed publisher
    ..5 g kg-1, PAC of 19.4 g kg-1, and pH of 8.1. Under this optimal condition, DS and SRF of the sludge appeared as 24.1% and 3.0 × 1012 m kg-1, respectively. ..
  25. Hirota T, Tsuboi H, Takahashi H, Asashima H, Ohta M, Wakasa Y, et al. Suppression of GPI-induced arthritis by oral administration of transgenic rice seeds expressing altered peptide ligands. Nihon Rinsho Meneki Gakkai Kaishi. 2017;40:28-34 pubmed publisher
    ..APL12-TG improved the severity of GIA through a decrease in production of IL-17 and anti-GPI antibodies via upregulation of Foxp3 and GITR expression on regulatory T cells in spleen. ..
  26. Sawicki A, Zhou S, Kwiatkowski K, Luo M, Willows R. 1-N-histidine phosphorylation of ChlD by the AAA+ ChlI2 stimulates magnesium chelatase activity in chlorophyll synthesis. Biochem J. 2017;474:2095-2105 pubmed publisher
    ..Formation of the ChlI/ChlD complex in both Chlamydomonas reinhardtii and Oryza sativa is accompanied by phosphorylation of ChlD by ChlI, but the orthologous protein complex from ..
  27. Shi Z, Riley M, Taylor A, Noakes M. Meal-specific food patterns and the incidence of hyperglycemia in a Chinese adult population. Br J Nutr. 2017;118:53-59 pubmed publisher
    ..A traditional wheat-based breakfast is associated with a decreased risk of hyperglycaemia. A rice-based traditional lunch and dinner is associated with an increased risk of hyperglycaemia in Chinese adults. ..
  28. Zhan Y, Sun X, Rong G, Hou C, Huang Y, Jiang D, et al. Identification of two transcription factors activating the expression of OsXIP in rice defence response. BMC Biotechnol. 2017;17:26 pubmed publisher
    ..These results reveal a coordinated regulatory mechanism of OsXIP, which may probably be involved in defence responses via a JA-mediated signaling pathway. ..
  29. Zia Z, Bakhat H, Saqib Z, Shah G, Fahad S, Ashraf M, et al. Effect of water management and silicon on germination, growth, phosphorus and arsenic uptake in rice. Ecotoxicol Environ Saf. 2017;144:11-18 pubmed publisher
    ..The experiments were conducted during September-December 2014, and 2016 to optimize Si concentration for rice (Oryza sativa L.) exposed to As stress...
  30. Yang Y, Wang M, Chen W, Li Y, Peng C. Cadmium Accumulation Risk in Vegetables and Rice in Southern China: Insights from Solid-Solution Partitioning and Plant Uptake Factor. J Agric Food Chem. 2017;65:5463-5469 pubmed publisher
    ..0 and 345 mg kg-1, respectively. Our work illustrates that re-establishing a balance in trace elements in soils' labile pool provides an effective risk-based approach for safer crop practices. ..
  31. He J, Shao G, Wei X, Huang F, Sheng Z, Tang S, et al. Fine mapping and candidate gene analysis of qTAC8, a major quantitative trait locus controlling tiller angle in rice (Oryza sativa L.). PLoS ONE. 2017;12:e0178177 pubmed publisher
    ..Our results provide a foundation for the cloning of qTAC8 and genetic improvement of the rice plant architecture. ..
  32. Cai Y, Hua B, Gao L, Hu Y, Yuan X, Cui Z, et al. Effects of adding trace elements on rice straw anaerobic mono-digestion: Focus on changes in microbial communities using high-throughput sequencing. Bioresour Technol. 2017;239:454-463 pubmed publisher
    ..Methane yield was positively correlated with bacterial diversity and negatively correlated with archaeal diversity for most treatments. ..
  33. Chung E, Yoon H, Kim K, Jeon C, Chung Y. Roseomonas oryzicola sp. nov., isolated from the rhizosphere of rice (Oryza sativa L.). Int J Syst Evol Microbiol. 2015;65:4839-44 pubmed
    ..nov. is proposed. The type strain is YC6724T (=KCTC 22478T=NBRC 109439T). ..
  34. Sun S, Qi G, Gao Q, Wang H, Yao F, Hussain J, et al. Protein kinase OsSAPK8 functions as an essential activator of S-type anion channel OsSLAC1, which is nitrate-selective in rice. Planta. 2016;243:489-500 pubmed
    ..Together, this research suggests that OsSAPK8 is a counterpart of AtOST1 for the activation of OsSLAC1, which is a nitrate-selective anion channel. ..
  35. Liu Z, Wang Z, Lv X, Zhu X, Chen L, Ni L. Comparison study of the volatile profiles and microbial communities of Wuyi Qu and Gutian Qu, two major types of traditional fermentation starters of Hong Qu glutinous rice wine. Food Microbiol. 2018;69:105-115 pubmed publisher
    ..Ultimately, this study provides detailed insight into the volatile profiles and microbial communities presented in Hong Qu. ..
  36. Järvi A, Karlström B, Granfeldt Y, Björck I, Vessby B, Asp N. The influence of food structure on postprandial metabolism in patients with non-insulin-dependent diabetes mellitus. Am J Clin Nutr. 1995;61:837-42 pubmed
    ..001; PI: -39%, P < 0.01), respectively, compared with the corresponding high-GI meals. The results shows the importance of preserved structure in common foods and support the applicability of the GI concept to mixed meals. ..
  37. Shen G, Xing Y. Two novel QTLs for heading date are identified using a set of chromosome segment substitution lines in rice (Oryza sativa L.). J Genet Genomics. 2014;41:659-62 pubmed publisher
  38. Hirano K, Ordonio R, Matsuoka M. Engineering the lodging resistance mechanism of post-Green Revolution rice to meet future demands. Proc Jpn Acad Ser B Phys Biol Sci. 2017;93:220-233 pubmed publisher
  39. Xiao P, Liu F, Liu Y, Yao S, Zhu G. Effects of Pesticide Mixtures on Zooplankton Assemblages in Aquatic Microcosms Simulating Rice Paddy Fields. Bull Environ Contam Toxicol. 2017;99:27-32 pubmed publisher
    ..There was no synergy effect on the microcosm from combinations of pesticides on the assemblages. The zooplankton assemblages affected by chlorpyrifos did not recover at the termination of the experiment, i.e., after 56 days. ..
  40. Lv X, Jiang Y, Liu J, Guo W, Liu Z, Zhang W, et al. Evaluation of different PCR primers for denaturing gradient gel electrophoresis (DGGE) analysis of fungal community structure in traditional fermentation starters used for Hong Qu glutinous rice wine. Int J Food Microbiol. 2017;255:58-65 pubmed publisher
  41. Li X, Wang X, Peng Y, Wei H, Zhu X, Chang S, et al. Quantitative descriptions of rice plant architecture and their application. PLoS ONE. 2017;12:e0177669 pubmed publisher
    ..Furthermore, the combination of vertical and compact architecture indices is the indicator for evaluating the effects of plant architecture on biomass accumulation...
  42. Huang K, Xu Y, Zhang J, Chen C, Gao F, Zhao F. Arsenicibacter rosenii gen. nov., sp. nov., an efficient arsenic methylating and volatilizing bacterium isolated from an arsenic-contaminated paddy soil. Int J Syst Evol Microbiol. 2017;67:3186-3191 pubmed publisher
    ..nov., sp. nov. is proposed. The type strain of Arsenicibacter rosenii is SM-1T (=CCTCC AB 2017086T=KCTC 52624T). ..
  43. Chuah C, Tan E, Sermswan R, Ziegler A. Hydrological connectivity and Burkholderia pseudomallei prevalence in wetland environments: investigating rice-farming community's risk of exposure to melioidosis in North-East Thailand. Environ Monit Assess. 2017;189:287 pubmed publisher
    ..Further, it may be important to investigate melioidosis through transdisciplinary approaches that consider the complex social and ecological contexts in which the disease occurs. ..
  44. Yang D, Cha S, Choi J, Seo T. Hydrogenophaga soli sp. nov., isolated from rice field soil. Int J Syst Evol Microbiol. 2017;67:4200-4204 pubmed publisher
    ..nov. is proposed. ..
  45. Yu L, Ma T, Zhang Y, Hu Y, Yu K, Chen Y, et al. Identification and analysis of the stigma and embryo sac-preferential/specific genes in rice pistils. BMC Plant Biol. 2017;17:60 pubmed publisher
    ..In addition, these novel genes are valuable for the supplementation and perfection of the existing transcriptome in rice, which provides an effective method of detecting novel rice genes. ..
  46. Lee G, Bang D, Lim J, Yoon S, Yea M, Chi Y. Simultaneous determination of ethyl carbamate and urea in Korean rice wine by ultra-performance liquid chromatography coupled with mass spectrometric detection. J Chromatogr B Analyt Technol Biomed Life Sci. 2017;1065-1066:44-49 pubmed publisher
    ..0-7.7?g/L. The method developed in this study, which has the advantages of simplified sample preparation, low detection limits, and good selectivity, was successfully applied for the rapid analysis of EC and urea. ..
  47. Sandhi A, Greger M, Landberg T, Jacks G, Bhattacharya P. Arsenic concentrations in local aromatic and high-yielding hybrid rice cultivars and the potential health risk: a study in an arsenic hotspot. Environ Monit Assess. 2017;189:184 pubmed publisher
    ..Furthermore, due to the low AF, growing LAR instead of HYVs in soils with slightly elevated As levels could help improve the food safety level in the food chain. ..
  48. Sun W, Wang A, Xu D, Wang W, Meng J, Dai J, et al. New Ustilaginoidins from Rice False Smut Balls Caused by Villosiclava virens and Their Phytotoxic and Cytotoxic Activities. J Agric Food Chem. 2017;65:5151-5160 pubmed publisher
    ..Ustilaginoidins R (2), S (3), V (7), W (8), B (17), C (18), and H-J (23-25) were cytotoxic to the tested human cancer cell lines (HCT116, NCI-H1650, BGC823, Daoy, and HepG2), with IC50 values in the range of 4.06-44.1 ?M. ..
  49. Wu H, Dai X, Zhou S, Gan Y, Xiong Z, Qin Y, et al. Ultrasound-assisted alkaline pretreatment for enhancing the enzymatic hydrolysis of rice straw by using the heat energy dissipated from ultrasonication. Bioresour Technol. 2017;241:70-74 pubmed publisher
    ..91vs. 2.73gL-1). The ultrasound-assisted alkaline pretreatment by using the heat energy dissipated from ultrasonication was proved to be a reliable and effective method for rice straw pretreatment. ..
  50. Li Y, Zhang X, Hu S, Liu H, Xu J. PKA activity is essential for relieving the suppression of hyphal growth and appressorium formation by MoSfl1 in Magnaporthe oryzae. PLoS Genet. 2017;13:e1006954 pubmed publisher
    ..oryzae, and phosphorylation of MoSfl1 by PKA relieves its interaction with the Cyc8-Tup1 co-repressor and suppression of genes important for hyphal growth. ..
  51. Li T, Chang Q, Yuan X, Li J, Ayoko G, Frost R, et al. Cadmium transfer from contaminated soils to the human body through rice consumption in southern Jiangsu Province, China. Environ Sci Process Impacts. 2017;19:843-850 pubmed publisher
    ..The chain model approach proposed in this study can be used for the fast and accurate evaluation of human Cd exposure through rice consumption based on the soil conditions in contaminated regions. ..
  52. Zhu Q, Yu S, Chen G, Ke L, Pan D. Analysis of the differential gene and protein expression profile of the rolled leaf mutant of transgenic rice (Oryza sativa L.). PLoS ONE. 2017;12:e0181378 pubmed publisher
    The importance of leaf rolling in rice (Oryza sativa L.) has been widely recognized...
  53. Ji C, Li H, Chen L, Xie M, Wang F, Chen Y, et al. A novel rice bHLH transcription factor, DTD, acts coordinately with TDR in controlling tapetum function and pollen development. Mol Plant. 2013;6:1715-8 pubmed publisher