4). doi: 10.1080/10408398.2018.1431763 [Epub ahead of print]. Fifty housekeeping rice genes list used for strong motif validation. We then went over the full publication of each record and identified the gene symbol and gene model in the reference genome. analyzed the data. It is possible to identify candidate genes associated with rice yield using the model of random walk with restart on a functional similarity network. PPI networks have also been used to provide a simplified yet systematic measure of functional similarities between genes (Chen et al., 2017a, 2018a). Additional file 2: Table S2: List of rice gene families. List of primers used for qRT-PCR analysis. Nucleic Acids Res. Two ATP binding cassette G transporters, rice ATP binding cassette G26 and ATP Binding cassette G15, collaboratively regulate rice male reproduction. However, a global view of the interaction networks for all functionally characterized rice genes remains to be elaborated. Inferring MicroRNA-disease associations by random walk on a heterogeneous network with multiple data sources. RESEARCH ARTICLE Open Access Transcriptomic analyses of rice (Oryza sativa) genes and non-coding RNAs under nitrogen starvation using multiple omics technologies Sang-Yoon Shin1,2, Jin Seo Jeong3,5, Jae Yun Lim1, Taewook Kim1, June Hyun Park1, Ju-Kon Kim3 and Chanseok Shin1,2,4* Abstract Background: Nitrogen (N) is a key macronutrient essential for plant growth, and its … Exogenous melatonin (MT) was found to be an interesting tool for enhancing the resistance of rice to Xanthomonasoryzaepv. Proximal phenotyping and machine learning methods to identify Septoria Tritici blotch disease symptoms in wheat. doi: 10.21775/cimb.027.109, Zhu, L., Su, F., Xu, Y., and Zou, Q. Analysis of the chemical toxicity effects using the enrichment of Gene Ontology terms and KEGG pathways. 68, 248–257. The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. Plant Sci. Genomic positions were determined for more than 98.1% of all functionally characterized rice genes based on the corresponding gene models of the Nipponbare reference genome (Additional file 1: Table S1; Fig. 2002 ). Front. Decoding of every DNA element of the rice genome is essential for genetic improvement to address increasing food demands. Each node represents a functionally characterized rice gene. Rice 11:32. doi: 10.1186/s12284-018-0223-4, You, Z. H., Huang, Z. Pipeline for identification of putative long non-coding RNAs in rice. Gramates LS, Marygold SJ, Santos Gd et al. The abscissa represents the top 500 ranking positions, and the ordinate represents the number of matching seed nodes. We conducted GO analysis to assess the functional enrichment of the top 100 candidate genes (Figure 4). Although they can also be based on gene names, it is noted that only Using the latest release of the GO database (Ashburner et al., 2000; Chen L. et al., 2016; Raza, 2016; The Gene Ontology, 2017), edges were scored for a shared functional significance score of genes in the network that were annotated with GO terms. doi: 10.1093/nar/gkn325, Vlaic, S., Conrad, T., Tokarski-Schnelle, C., Gustafsson, M., Dahmen, U., Guthke, R., et al. The past 15 years have witnessed extraordinary advances in rice functional genomics. 18, 218–226. (2018). Interaction networks comprising 1310 functionally characterized rice genes were constructed, which revealed complex regulation and crosstalk of different biological pathways. We also found that 335 genes were involved in different stress signaling pathways, while 139 genes were related to rice diseases, including blast, bacterial blight, and sheath blight. Another study reported that the PR gene (LOC_ Os12g36840) was suppressed in expression in rice during interactions with the plant-growth promoting bacteria, Herbaspirillum seropedicae [ 8 ]. Biochem. Genomics 14, 143–155. Rep. 8:433. doi: 10.1038/s41598-017-18370-2, Wang, F., Song, B. X., Zhao, X., Miao, Y. T., Li, D. Y., Zhou, N., et al. We manually searched the 100 top candidate genes (Table 1) in PubMed1 for their association with yield. Next, we manually curated the dataset based on the full text of each publication and obtained 1297 functionally characterized rice genes. Illustration of the proposed method. Pipeline for identification of putative long non-coding XZ performed the research. Part I. Numerous rice lipids synthesis related genes and quantitative trait loci (QTLs) are summarized for understanding of the genetic basis and metabolism of lipid biosynthesis in rice grain. funRiceGenes was constructed by integrating data from PubMed, Oryzabase, and China Rice Data Center, and it has been updated every 2 weeks using a Shiny application. Genes and QTLs are recently known for the nutritional quality of rice. doi: 10.2174/1574893611666160125220905, Li, P., Guo, M., Wang, C., Liu, X., and Zou, Q. Only 7 genes—RFT1, Ehd4, Hd6, OsCO3, ROC4, Se14, and OsPIL15—were unique to rice. Display of information in this database as static web pages. © The Author 2017. Proteins with accurate functional annotations are vital to biological research. For any of these genes, all relevant publications and a brief summary are available in this database [59]. doi: 10.1039/c2mb25180a. 1860, 2619–2626. Nat. doi: 10.1093/bioinformatics/btt426, Coneva, V., Simopoulos, C., Casaretto, J. Impact Factor 4.402 | CiteScore 7.8More on impact ›, Machine Learning Techniques on Gene Function Prediction BR: brassinosteroid; CRISPR: Clustered Regularly Interspaced Short Palindromic Repeats; GA: gibberellin; GWAS: genome-wide association study; kb: kilo base; RAP-DB: the Rice Annotation Project Database; TAIR: the Arabidopsis Information Resource. In the context of the functional similarity network, the above validation procedure was equivalent to removing one part of the seed genes to candidate genes and determining whether candidates containing these seeds could receive a high rank. Book chapter Full text access. Finally, the robustness of the parameter r leads to a high level of accuracy in making predictions, and the method that achieving parameter can be adapted to other dataset. wrote the paper. (2018). Mol. Cite Gramene Feedback J. Hum. Additionally, determining which genes in quantitative trait loci regulate grain size and number has not been clarified (Borzee et al., 2018; Li et al., 2018). Rice blast disease is one of the most serious and recurrent problems in rice-growing regions worldwide. By comprehensive … Mineral and vitamin deficiency related problems are common in the majority of the population and more specific to developing countries as their staple food is rice. The candidates ranking at the top of the results list were considered to be the most relevant rice yield-related genes. Xu et al. Biophys. List of amino acid/peptide transporter genes and their expression level in rice. In this study, we constructed a comprehensive, up-to-date database of rice functional genes, which includes ∼2800 cloned rice genes and ∼5000 members of different gene families. The rice genome annotation project maintained by the Michigan State University [23] and the Rice Annotation Project Database (RAP-DB) [24] greatly promoted the progress of rice functional genomics. TABLE 1. We found that a cloned rice gene OsSGL (LOC_Os02g04130, chr02:1799733-1800811), which regulated grain weight in rice, was ∼70 kb away from a GWAS peak (chr02:1871732) in terms of grain weight [50, 51]. We would appreciate your sending us (R. W.) information (and reprints, if possible) on your publications pertaining to this matter. List of genes divided into each group is given in Supplementary Tables S2 and S3 for indica and japonica rice, respectively. If genes share similar set of those terms (annotation profile), they are most likely involved in similar biological mechanisms. et al., 2018). Based on these observations, we propose that rice has three BR receptors and OsBRI1 dominantly functions in almost all organs, but the other two proteins, OsBRL1 and OsBRL3, also function in the roots. The first column represents the chromosomal location of the genes (chromosome number). Nine QTLs for grain size were identified by genome-wide association study in a natural rice population. Chen, X., Yan, C. C., Zhang, X., and You, Z. H. (2017b). Then, we constructed a protein–protein network that scores the edges through functional similarities. This data is in form of a 200 by 3 dataframe with genes/gene ids as rownames. Xa1 confers TAL effector-dependent resistance to Xanthomonas oryzae pathovar oryzae (Xoo) in rice, and resistance is suppressed by interfering TAL effectors (iTALEs). ENDEAVOUR update: a web resource for gene prioritization in multiple species. Bioinform. We demonstrated the high performance of this approach by a five-fold cross-validation experiment, as well as the robustness of the parameter r. We also assessed the strength of associations between known seeds and candidate genes in the light of the results scores. As a result, 637 genes were assigned more than 1 symbol (Additional file 1: Table S1). oryzae (Xoo)-caused bacterial blight (BB). Ieee Acm Trans. The shared functional significance score F(i,j) between gene i and j was measured by the Weighted Shared Functions approach, which considered a gene’s functions as a set of functional categories in GO. Of the 50 microsatellites selected, 19 were polymorphic, and a small set of five primer pairs was sufficient to discriminate among the 37 rice varieties studied. Kawahara Y, de la Bastide M, Hamilton J et al. Each green edge indicates a connection between 2 genes. Pyramiding of two or more effective resistance genes/alleles into elite rice lines enhances the durability and spectrum of resistance. This is equivalent to letting the random walker begin from each of the known disease genes with equal probability. FIGURE 3. Oncotarget 7, 57919–57931. Sci. Genes with different number of orthologs are indicated with different colors and shapes. Genes References Rice ID INSD View Cart To all NBRP Rice resource users Thank you for using NBRP Rice resources. In addition, a user-friendly query interface and tidy data for downloading are provided in the funRiceGenes database. The networks were then exported in a data format suitable for Cytoscape, which was used to visualize the network [66]. Long non-coding RNAs and complex diseases: from experimental results to computational models. All the affiliations are marked on the world map as blue circles based on their longitudes and latitudes. Candidate gene prioritization with endeavour. The matching numbers of the five-part seed genes were applied to assess the effectiveness of RWR. Interaction network of genes regulating flowering in rice and the orthologs of these genes in other plants. doi: 10.1039/c2mb00002d, Chen, X., Liu, M. X., and Yan, G. Y. Abe, K., Oshima, M., Akasaka, M., Konagaya, K. I., Nanasato, Y., Okuzaki, A., et al. The gene interaction network comprising 762 genes. Direct interaction with OsNAC14 recruits factors involved in DNA damage repair and defense response, resulting in an improved tolerance to drought (Shim et al., 2018). IRWRLDA: improved random walk with restart for lncRNA-disease association prediction. To have an updated list of WRKY genes in rice, we used the HMMER program (Sonnhammer et al. We would appreciate your sending us (R. W.) information GO terms in which the top 100 candidate genes are enriched. Several of these PR genes are strongly induced in rice upon inoculation with the pathogen, Magnaporthe oryzae, and are considered to be excellent markers for plant defense reactions . Thus, the gene interaction networks provided in this database could also be taken into account when making breeding designs. Reconstruction, topological and gene ontology enrichment analysis of cancerous gene regulatory network modules. (2000). (2013). Probabilistic functional gene societies. Our work in rice would facilitate functional genomic studies of other crops including wheat, sorghum, and maize. doi: 10.1021/acs.jafc.7b06093, Li, F., Xie, J., Zhu, X., Wang, X., Zhao, Y., Ma, X., et al. Bioinform. For example, Ghd8 was responsible for grain number, plant height, and heading date [37]. Project name: funRiceGenes (funRiceGenes, RRID:SCR_015778), Project home page: http://funricegenes.ncpgr.cn/, GitHub repository: https://github.com/venyao/RICENCODE, Operating system(s): platform independent, Other requirements: tested with R packages shiny (1.0.5), shinythemes (1.1.1), shinyBS (0.61), RCurl (, XML (, stringr (1.2.0), plyr (1.8.4), Any restrictions to use by nonacademics: none, Research resource ID: funRiceGenes, RRID:SCR_015778. (2018) used machine learning and integrated this analysis with data obtained from spectroradiometer, infrared thermometer, and chlorophyll fluorescence measurements to identify the most predictive proxy measurements for studying Septoria tritici blotch disease of wheat. GO annotation is the list of all annotated genes linked to ontological terms describing those genes. (2018). 13:e1005455. Each edge indicates a connection between 2 genes. Decoding the genetic reservoirs of rice is the basis for rice phenotype improvement. P.S. funRiceGenes. RWRMDA: predicting novel human microRNA-disease associations. 11, 4–12. The size of the circle represents the number of publications conducted by each affiliation. Curr. A total of 441 keywords were investigated, which generated 21 872 records for 1952 genes (Additional file 10: Table S6). (2012a). Likewise, another gene OsPPKL3 (LOC_Os12g42310, chr12:26273157-26282197), which regulated grain length, is ∼90 kb away from a GWAS peak (chr12:26182880) associated with grain length [52, 53]. doi: 10.2174/1574893611666151119221435, Zhang, M., Li, J., Chen, F., and Kong, Q. In total, 1841 connections supported by 4046 evidences were detected, which comprised 1310 genes constituting 214 interaction networks (Additional file 11: Table S7). doi: 10.2174/1574893611666151203221255. Biosyst. STRING v10: protein-protein interaction networks, integrated over the tree of life. A sentence in which 2 or more genes were observed was regarded as evidence supporting the connection between these genes. Published by Oxford University Press. All records were grouped by published journal. Issues Mol. Rice is one of the most important stable food as well as a monocotyledonous model organism for the plant research community. GO enrichment analysis is used to interpret high-throughput molecular data. Targeting intra-cellular transport combined with efficient uptake and storage significantly increases grain iron and zinc levels in rice. (2018). We further collected ∼3600 members of various gene families by integrating data from the Rice Genome Annotation Project database [29], the Oryzabase database, and research publications. Comparative analysis with one other chilling tolerant rice and two chilling sensitive rice resulted in identification of 182 genes that were cold induced in all four rice cultivars (CCI genes). This work also established a search tool to query a particular gene, and to provide insights into gene functions and locations. Improvement of yield and resistance to multiple biotic and abiotic stresses of rice are essential strategies to cope with the increasing world population and the diminishing arable land. Front. LRSSLMDA: laplacian regularized sparse subspace learning for MiRNA-disease association prediction. Number of WRKY genes classified into each groups and subgroups in indica and japonica rice is given in Table 2. 9:310. doi: 10.3389/fpls.2018.00310, Szklarczyk, D., Franceschini, A., Wyder, S., Forslund, K., Heller, D., Huerta-Cepas, J., et al. Curr. Nucleic Acids Res. The abscissa shows GO terms, and the ordinate represents the number of GO terms. The y-axis indicates the number of publications using a specific biotechnique. All candidate genes were ranked by RWR to determine the ranking of the test gene. Nine QTLs for grain size were identified by genome-wide association study in a natural rice population. Mol. Nomenclature for cloned plant genes. P.S. The second largest network contained 14 genes involved in glutamine metabolism, including OsAMT1;3, GAD3, and GAT1 [42, 43]. Additional file 3: Figure S1: Number of papers on rice functional genomic studies published in each year. (2017). Nomenclature for cloned plant genes. Moreover, the putative homologs of some rice genes were investigated in other crops such as wheat [14–17], barley [18], and maize [19]. We obtained functional annotation information from the GO Consortium (Ashburner et al., 2000), and downloaded GO annotations of O. sativa from the most recent GO version. JJ wrote the manuscript. We constructed interaction networks of functionally characterized genes based on the concurrence of the symbols of 2 or more genes in the same sentence of an abstract or a title of research publications using in-house R script with manual curation. Hori K, Ogiso-Tanaka E, Matsubara K et al. Fifty housekeeping Arabidopsis genes list used for motif validation. The authors declare that they have no competing interests. miREFRWR: a novel disease-related microRNA-environmental factor interactions prediction method. A., El-Kereamy, A., Guevara, D. R., Cohn, J., et al. The work was supported by the Natural Science Foundation of China (Nos. Based on the orthologous groups among 7 plants provided by the Rice Genome Annotation Project [47], we found that 40 of the 77 genes had orthologous genes in sorghum, maize, Brachypodium, Arabidopsis, poplar, and grapevine, and orthologous genes were also identified for another 20 rice genes in sorghum, maize, and Brachypodium (Fig. For optimal parameters, genes were also ranked according to the calculated p scores with nine different r-values (r = 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, and 0.9). Biol. We demonstrated the high performance of the RWR approach via a five-fold cross-validation experiment and showed the robustness of the parameter r. As an application of the RWR approach, we predicted a landscape of associations between known seeds and candidate genes. C. Price, 1989. 1998) and Hidden Markov Model (HMM) trained with rice WRKY genes (Xie et al. The first release of RicyerDB contained more than 400 manually curated gene information entries which were all associated with rice yield. Future development of our research will include the collection of more rice yield-related genes via online databases and the analysis of literature. Curr. Here, we identified, with a high level of confidence, 208 imprinted gene candidates from rice ( Oryza sativa ). (2015). 169, 2064–2079. 12, 312–319. The GO term having the most candidates annotated to was GO: 0005524 ∼ ATP binding, which is a binding motif within the primary structure of an ATP binding protein. Based on massive expression profiles, RED provides a list of housekeeping and tissue-specific genes and dynamically constructs co-expression networks for gene(s) of interest. Table S 9. Information on each gene, including the GenBank accession number and the corresponding gene model in the Nipponbare genome, was extracted. Metabolic and co-expression network-based analyses associated with nitrate response in rice. Hundreds of imprinted genes have been identified from several plant species. Genes controlling important agronomic traits, including grain yield [3, 4], blast [5] and blight [6, 7] disease resistance, insect resistance [8], and abiotic stress resistance [9, 10], were functionally characterized. List of genes divided into each group is given in Supplementary Tables S2 and S3 for indica and japonica rice, respectively. In accessing pseudomolecule data from the Rice Genome Annotation Project web site, terms used internally by the Rice Genome Annotation Project such as TU and gene model can be found. We further downloaded 29 982 publication records by querying the PubMed database with the keyword rice ((rice[Title] OR rice[Title/Abstract]), data until 13 February 2014). Basis Dis. 14:e1006022. Additional file 4: Table S3: Publications on functionally characterized rice genes. Genes related to signal transduction and transcription category may play an important role in transduction and regulation of upstream signals mediated by Al in rice bean because they represent one of the major categories in both forward libraries. Use of the RWR method in the function similarity network can identify candidate genes associated with known rice yield-related genes, while gene ranking saves experimental time in the exploitation of rice as a major crop. Nipponbare [2]. Novel human lncRNA-disease association inference based on lncRNA expression profiles. 9:3. doi: 10.1038/s41419-017-0003-x, Chen, X., Xie, D., Wang, L., Zhao, Q., You, Z. H., and Liu, H. (2018b). S1). For author affiliations that failed to be geocoded at high resolutions, we further used the Mapeasy website [62] to find the accurate latitudes and longitudes. Applications of random walk model on biological networks. Plant Sci., 20 November 2018 doi: 10.2174/1574893611666161008195145, Li, M., Zheng, R. Q., Li, Q., Wang, J. X., Wu, F. X., and Zhang, Z. H. (2016). This procedure applied a RWR algorithm to the network to calculate a score for each candidate gene, and then ranked the candidates to obtain a ranking list as the output (Chen et al., 2012a,b; Chen, 2016; Chen X. et al., 2016; Li et al., 2016; Peng et al., 2016; Zhu et al., 2018). Expression of the key genes involved in ABA biosynthesis in rice implanted by ion beam. Overexpression of OsNAC14 improves drought tolerance in rice. *” in PDF files were inspected utilizing the R tm [64] package. Nucleic Acids Res. 37, D412–D416. Bioinform. Genomic selection of agronomic traits in hybrid rice using an NCII population. (2015). Front. At the beginning, the walker chooses the seeds as the starting point. In this paper, we set default values for parameters r = 0.3 (see Results section for details). All data are deposited in the funRiceGenes database (https://funricegenes.github.io/). In recent years, a protein–protein interaction (PPI) network has been developed to achieve a global inference of entire genes (Liu et al., 2010; Lee, 2011; Rezadoost et al., 2016; Wang et al., 2016; Zeng et al., 2016; Luo and Liu, 2017; Holland and Johnson, 2018; Vlaic et al., 2018). Some of these genes were utilized in rice breeding directly based on marker-assisted strategy and CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) [11–13]. We downloaded O. sativa Japonica protein network data through STRING version 10.5 (Szklarczyk et al., 2015). … J. The RICE2020 project was proposed by rice researchers in 2008 to characterize the functions of all rice genes (~32,000) by the year 2020 (Zhang et al. The largest network was composed of 762 genes including ones associated with flowering, phosphate uptake and homeostasis, iron uptake, stress signaling, blight disease resistance, meiosis, BR (brassinosteroid) and GA (gibberellin) signaling, grain weight, and endosperm development (Fig. The list of reported salinity tolerance related genes in rice based on the literature review, classified into four tissues (including shoot, root, seedling, and leaves) in 4 sheets. Gene 664, 139–151. We adopted a five-fold cross-validation experiment to assess the capability of RWR to identify the left seeds. Usage of various biotechniques in rice functional genomics studies. Reporter 7: 99-103. Curr. doi: 10.1093/nar/gkn760, Jiang, J., Xing, F., Zeng, X. X., and Zou, Q. (2018). doi: 10.1016/j.fcr.2016.09.011, Tranchevent, L. C., Ardeshirdavani, A., ElShal, S., Alcaide, D., Aerts, J., Auboeuf, D., et al. The abstract, the author affiliation, and the full text of each publication were subsequently extracted from the PubMed database. (2011). In our study, 136 known genes were selected as seed genes and other genes as candidate genes. Rice is one of the most important food crops for humans. This procedure was repeated until all seed genes were used up as test genes. Biol. Any rice yield-related gene can therefore be easily queried and the findings downloaded through the webpage, while candidate genes can be screened and prioritized to identify those most likely to be associated with known genes. (2014). (2018) compared six genomic selection methods, such as least absolute shrinkage and selection operation and support vector machine, to evaluate predictabilities for different methods, and demonstrated their implementation to predict the hybrid performance of rice. The GENE menu lists 2900+ From a list comprising 1146 co-expressed genes from Arabidopsis and rice using the ATTED-II database, we identified novel candidates involved in signal transduction, regulation and substrate transport, as well as enzymes directly involved in secondary wall biosynthesis.