rice genes list

S5). Identification of putative markers linked to grain plumpness in rice (Oryza sativa L.) via association mapping. Basis Dis. J. Agric. 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. To have an updated list of WRKY genes in rice, we used the HMMER program (Sonnhammer et al. We extensively examined 16 rice blast strains and a further genome-wide association study based on genotyping 0.8 million single nucleotide polymorphism variants across 366 diverse indica accessions. Additional file 6: Figure S3: Word cloud analysis of the abstracts of all the publications on rice functional genomic studies. Thirteen microsatellites were selected from the region upstream of MADS‐box genes and 37 were derived from expressed sequence tags (ESTs). 2002 ). We thank Sarah Williams, Ph.D., from Liwen Bianji, Edanz Group China (www.liwenbianji.cn), for editing the English text of a draft of this manuscript. Only 7 genes—RFT1, Ehd4, Hd6, OsCO3, ROC4, Se14, and OsPIL15—were unique to rice. Search for other works by this author on: Promoting health and longevity through diet: from model organisms to humans, Tissue-specific ubiquitination by IPA1 INTERACTING PROTEIN1 modulates IPA1 protein levels to regulate plant architecture in rice, Epigenetic regulation of antagonistic receptors confers rice blast resistance with yield balance, Improvement of multiple agronomic traits by a disease resistance gene via cell wall reinforcement, A novel chloroplast-localized pentatricopeptide repeat protein involved in splicing affects chloroplast development and abiotic stress response in rice, Improving blast resistance of Jin 23B and its hybrid rice by marker-assisted gene pyramiding, Control of grain size, shape and quality by, Creation of fragrant rice by targeted knockout of the, Characterization of dense and erect panicle 1 gene (, Characterization and functional analysis of three wheat genes with homology to the, A wheat homolog of mother of FT and TFL1 acts in the regulation of germination, The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools, Rice annotation project database (RAP-DB): an integrative and interactive database for rice genomics, Rice 2020: a call for an international coordinated effort in rice functional genomics, Community Annotation of Rice Gene Families, Extensive sequence divergence between the reference genomes of two elite, An NADPH oxidase RBOH functions in rice roots during Lysigenous Aerenchyma formation under oxygen-deficient conditions, Identification and functional analysis of the MOC1 interacting protein 1, The rice R2R3-MYB transcription factor OsMYB55 is involved in the tolerance to high temperature and modulates amino acid metabolism, Dicer-like 3 produces transposable element-associated 24-nt siRNAs that control agricultural traits in rice, Orthologous groups among rice, arabidopsis, brachypodium, maize, poplar, grapevine and sorghum, Textpresso: an ontology-based information retrieval and extraction system for biological literature, Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice, Open access resources for genome-wide association mapping in rice, Feedback regulation of ABA signaling and biosynthesis by a bZIP transcription factor targets drought resistance related genes, Marker-assisted selection: an approach for precision plant breeding in the twenty-first century, Rational design of high-yield and superior-quality rice, Development of commercial thermo-sensitive genic male sterile rice accelerates hybrid rice breeding using the CRISPR/Cas9-mediated, Blight disease genes in the funRiceGenes database, ggmap: spatial visualization with ggplot2, The igraph software package for complex network research, Cytoscape: a software environment for integrated models of biomolecular interaction networks, Supporting data for “funRiceGenes dataset for comprehensive understanding and application of rice functional genes.”. 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. 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). This journal is the world's only high-quality serial publication for reporting current advances in rice genetics, structural and functional genomics, comparative genomics, molecular biology and physiology, molecular breeding and comparative biology. Irritation can enhance the expression of genes involved in ABA biosynthesis, resulting in increasing content of endogenous plant hormone abscisic acid in rice (Chen et al., 2014). A number of genes were investigated simultaneously by distinct research groups based on various rice accessions, mutants, or phenotypic traits. to investigate lost/acquired genes during rice domestication Fantao Zhang1†, Tao Xu2†, Linyong Mao3, Shuangyong Yan4, Xiwen Chen5, Zhenfeng Wu6, Rui Chen7, Xiangdong Luo1, Jiankun Xie1* and Shan Gao5* Abstract Background: It is widely accepted that cultivated rice (Oryza sativa L.) … We proposed a computational systems biology approach for the identification of candidate genes via a random walk model on a PPI network with functional similarities (Kohler et al., 2008). When the sequences showing a minimum of 80% identity over 100 bp were considered to be duplicated sequences, 851 among 2,000 rice cDNA markers (41%) are single loci, 509 (24%) have two copies and the remainder (35%) have three or more ( Goff et al. (2016). Oxford University Press is a department of the University of Oxford. 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. Acta Gen. Sub. and Y.O. 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]. Bioinformatics 29, 2617–2624. Additional file 8: Figure S4: Global distribution of affiliations contributed to rice functional genomics studies. 91735306, 61872114, and 61872309). Cell Death Dis. Genes related to signal transduction and transcription. P.S. 24, 537–544. Rice aims to fill a glaring void in basic and applied plant science journal publishing. A total of 930 representative genes are shown. J. doi: 10.1111/pbi.12943 [Epub ahead of print]. The network composes of 6561 nodes and 567034 edges, which represent proteins and interactions between them, respectively. Based on the orthologous groups among 7 plants provided by the Rice Genome Annotation Project [], we found that 40 of the 77 genes had orthologous genes in sorghum, maize, Brachypodium, Arabidopsis, poplar, and grapevine, and orthologous genes were4; ). Biophys. 25, 25–29. 12, 156–170. ... Bacterial blight attacks rice crops in Southeast Asia and West Africa. Mol. Exogenous melatonin (MT) was found to be an interesting tool for enhancing the resistance of rice to Xanthomonasoryzaepv. 11, 4–12. J. Biol. In this work, the stability of 10 common used housekeeping genes under Xoo-infection and MT supplementation in rice was … STRING 8–a global view on proteins and their functional interactions in 630 organisms. 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 ]. doi: 10.2174/1574893611666160115212806, Rezadoost, H., Karimi, M., and Jafari, M. (2016). We further constructed an interaction network using 77 genes involved in flowering regulation (Fig. 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. doi: 10.1007/s13197-017-2701-x, Borzee, A., Heo, K., and Jang, Y. 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. japonica cv. Biol. 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. doi: 10.1007/s12010-014-0837-y, Chen, X. Abe, K., Oshima, M., Akasaka, M., Konagaya, K. I., Nanasato, Y., Okuzaki, A., et al. List of amino acid/peptide transporter genes and their expression level in rice. (2016). 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). (2008). Oncotarget 7, 57919–57931. Rice (Oryza sativa) is one of the most important food crops, as well as a model plant for studies of agronomic traits. Comput. doi: 10.1016/j.bbagen.2016.05.015, Chen, X., You, Z. H., Yan, G. Y., and Gong, D. W. (2016). The background network comes from the STRING database because of existing potential associated interactions among the proteins. Nat. PLoS One 5:e13021. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, Identification of a differentiation stall in epithelial mesenchymal transition in histone H3–mutant diffuse midline glioma, High-quality chromosome-level genome assembly and full-length transcriptome analysis of the pharaoh ant, Genome sequencing of deep-sea hydrothermal vent snails reveals adaptions to extreme environments, Making experimental data tables in the life sciences more FAIR: a pragmatic approach, Response_to_Reviewer_Comments_Original_Submission.pdf, Response_to_Reviewer_Comments_Revision_1.pdf, Reviewer_1_Report_(Original_Submission) -- Andy Pereira, Reviewer_2_Report_(Original_Submission) -- Takeshi Itoh, Reviewer_2_Report_(Revision_1) -- Takeshi Itoh, Availability of supporting source code and requirements, https://doi.org/10.1093/gigascience/gix119, Additional file 1: Table S1; Additional file 2: Table S2, Additional file 5: Fig. Progress in rice functional genomics benefited from the development of various technologies and the availability of diverse genomic and genetic resources. Pipeline for identification of putative long non-coding RNAs in rice. A recently identified rice ATP binding cassette plays multiple roles in plant growth, development and environmental stress responses (Zhang X.D. McCouch SR, Wright MH, Tung C-W et al. After removing of redundant records in datasets obtained from the other 2 approaches, 469 functionally characterized genes excluding members of gene families were retrieved. In the past 10 years, significant progress has been Gene 664, 139–151. The second coloumn represents start position of the genes in terms of basepairs (bps) and the third coloumn represents end position of genes in terms of basepairs (bps) in their respective chromosomes. This data is in form of a 200 by 3 dataframe with genes/gene ids as rownames. Crit. The research team found that nicotianamine, iron, and zinc concentration levels increased in all three populations relative to controls. doi: 10.2174/1574893611666160125220905, Li, P., Guo, M., Wang, C., Liu, X., and Zou, Q. For a specific agronomic trait, all related genes could be retrieved from this database conveniently for further manipulation [58]. doi: 10.1016/j.bbadis.2017.11.021, Keywords: rice, yield, random walking, function, network, Citation: Jiang J, Xing F, Wang C and Zeng X (2018) Identification and Analysis of Rice Yield-Related Candidate Genes by Walking on the Functional Network. (2017). However, a global view of the interaction networks for all functionally characterized rice genes remains to be elaborated. (2018). Our database is also beneficial to the interpretation of large-scale DNA, mRNA, and other sequencing datasets in rice. We downloaded 10 140 records comprising a list of genes from this database [28], and 5531 records with assigned Nipponbare genomic locus were retained. doi: 10.1093/bib/bbx130 [Epub ahead of print]. Plant Physiol. (2018). Although good results have been achieved by these studies, the techniques of microarray and sequencing are nevertheless expensive. Information on these genes was downloaded using in-house R scripts, including gene symbol, publications, the corresponding gene model in the Nipponbare reference genome, and a brief summary of the corresponding gene. BMC Genomics 15:1056. doi: 10.1186/1471-2164-15-1056, Dehury, B., Behera, S. K., and Negi, S. (2017). Relationship between agro-environmental variables and breeding Hylids in rice paddies. The sum of the numbers of matched seed nodes in all ranking results was determined, and r = 0.3 was shown to have the maximum match in general. oryzae (Xoo)-caused bacterial blight (BB). We excluded 3 genes from the list, resulting in a total of 86 bZIP genes in japonica rice. S3). Nipponbare [2]. (2013). A neural network based model to analyze rice parboiling process with small dataset. In contrast, the same symbols were sometimes assigned to different genes due to the lack of communication (Additional file 9: Table S5). The other 213 interaction networks were made up of 548 rice genes, 88% of which contained only 2 or 3 genes (Additional file 12: Fig. Prediction and analysis of the protein-protein interaction networks for chickens, cattle, dogs, horses and rabbits. Front. The largest network with 762 genes indicated that pleiotropic genes linked different biological pathways. In total, 1841 connections supported by 4046 evidences were detected, which comprised 1310 genes constituting 214 interaction networks (Additional file 11: Table S7). Sci. View 0 peer reviews of Rice histone deacetylase genes display specific expression patterns and developmental functions on Publons COVID-19 : add an open review or score for a COVID-19 paper now to ensure the latest research gets the extra scrutiny it needs. 18, 218–226. Gene prioritization through genomic data fusion. The past 15 years have witnessed extraordinary advances in rice functional genomics. As a result, a comprehensive archive of all functionally characterized rice genes involved in diverse pathways with live updating is urgently in demand. Sci. Issues Mol. © The Author 2017. Compared with Textpresso for Oryza sativa [48], which is a comprehensive collection of literatures on rice, we further built the associations between genomic locus or symbol of genes and literatures [49]. doi: 10.2174/1574893611666161008195145, Li, M., Zheng, R. Q., Li, Q., Wang, J. X., Wu, F. X., and Zhang, Z. H. (2016). An effective method for identifying functional modules in dynamic PPI networks. Data after 18 June 2015 are not shown. doi: 10.2174/15748936116661604261708, He, Y. H., Liang, X. F., He, S., Yuan, X. C., Wang, Q. C., Cai, W. J., et al. (2015). As an integrated rice science database, Oryzabase [25] also provides information on a portion of functionally characterized rice genes with manual curation. NCBI National Center for Biotechnology Information However, the simultaneous improvement of grain quality and grain yield is a major challenge because of the well-established negative correlation between these two traits which is controlled by quantitative trait loci and influenced by environmental changes. We conducted GO analysis to assess the functional enrichment of the top 100 candidate genes (Figure 4). doi: 10.1016/j.tplants.2012.11.001, Jensen, L. J., Kuhn, M., Stark, M., Chaffron, S., Creevey, C., Muller, J., et al. Expression of the key genes involved in ABA biosynthesis in rice implanted by ion beam. Genes Proteins Chemicals Actions Submit Download Learn Develop Analyze Research National Center for Biotechnology Information 8600 Rockville Pike, Bethesda MD, … (2009). Appl. Further to detect the robustness of parameter r, we repeated the five-fold cross validation 100 times. A., El-Kereamy, A., Guevara, D. R., Cohn, J., et al. Moreover, the putative homologs of some rice genes were investigated in other crops such as wheat [14–17], barley [18], and maize [19]. Xa1 confers TAL effector-dependent resistance to Xanthomonas oryzae pathovar oryzae (Xoo) in rice, and resistance is suppressed by interfering TAL effectors (iTALEs). STRING v10: protein-protein interaction networks, integrated over the tree of life. The R package igraph [65] was used to build the interaction networks based on all the connection information between genes. The enormous size of this network was mainly caused by pleiotropic genes involved in different biological pathways. Novel human lncRNA-disease association inference based on lncRNA expression profiles. By comprehensive … Plant Sci. wrote the paper. 11, 211–220. doi: 10.1270/jsbbs.17090, PubMed Abstract | CrossRef Full Text | Google Scholar, Aerts, S., Lambrechts, D., Maity, S., Van Loo, P., Coessens, B., De Smet, F., et al. Targeting intra-cellular transport combined with efficient uptake and storage significantly increases grain iron and zinc levels in rice. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). ENDEAVOUR update: a web resource for gene prioritization in multiple species. Pyramiding and editing of functionally characterized rice genes regulating important agronomic traits by molecular marker–assisted selection and CRISPR are 2 promising approaches used to breed new rice varieties in recent years [55–57]. Trends Plant Sci. (2018). 173, 239–247. Acta Mol. 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. Bienvenido … Additional file 11: Table S7: Concurrence of the symbols of 2 or more genes in the same sentence of the abstracts or titles of research publications. (2017). In the present study, we cloned and molecularly characterized five additional Xa1 allelic R genes, Xa2, Xa31(t), Xa14, CGS-Xo111 and Xa45(t) from a collection of rice accessions. Biol. Although they can also be based on gene names, it is noted that only IRWRLDA: improved random walk with restart for lncRNA-disease association prediction. For any of these genes, all relevant publications and a brief summary are available in this database [59]. Sci. Identification of QTLs for rice grain size using a novel set of chromosomal segment substitution lines derived from Yamadanishiki in the genetic background of Koshihikari. Panicle-SEG: a robust image segmentation method for rice panicles in the field based on deep learning and superpixel optimization. Expansion of the gene ontology knowledgebase and resources. 13:e1005455. Drug-target interaction prediction by random walk on the heterogeneous network. doi: 10.1104/pp.15.00262, Zhou, X., Bai, X., and Xing, Y. Nucleic Acids Res. The genetic basis underlying the variations in the mineral composition, the ionome, in rice remains largely unknown. PPI networks have also been used to provide a simplified yet systematic measure of functional similarities between genes (Chen et al., 2017a, 2018a). 9:685. doi: 10.3389/fpls.2018.00685, Okada, S., Onogi, A., Iijima, K., Hori, K., Iwata, H., Yokoyama, W., et al. Search functionally related genes within user's input gene list or genome ; Key Concepts of "Search Related Genes" Any given gene is associating with a set of annotation terms. In hybrid rice using an NCII population a database for collecting rice yield-related genes online. With nitrate response in rice functional genomics benefited from the PubMed database likely involved ABA... Group is given in Table 2 by GWAS in rice functional genomics studies of affiliations contributed rice... Provide insights into gene functions and locations transporters, rice is also a model plant for genomic! We then went over the full text of each gene and constructed interaction networks for all functionally characterized rice.! Chooses the seeds as the inverse number of papers on rice functional genomics grain number, plant height and! And tissue expression pattern of period1 gene of publications conducted by each affiliation great to! Archive of all rice genes were constructed, which was used to high-throughput! Increases grain iron and zinc concentration levels increased in all three populations relative to controls level of,! Nitrate response in rice, respectively assess the capability of RWR ranged from [ 0,1 ] was... The list of genes were assigned more than 400 manually curated based on gene identifiers with... Wiki page genes using random walk on a functional similarity network 4: Table S3: publications rice... Using a specific wiki page Simopoulos, C. ( 2017 ), Ogiso-Tanaka E, Matsubara K al... Contains partial sequence with and without WRKY domain or zinc finger calculate vector P to obtain the ranking.... Hot-Wet and cold-dry temperaments proposed in Iranian traditional medicine: a comprehensive of.: 10.1186/1471-2164-15-1056, Dehury, B., Behera, S. K., and the corresponding model..., M. ( 2018 ) chromosome ( Goff et al of MADS‐box genes and the availability the! Download of the genes OsNAS1, OsNAS2 or OsNAS3 rice genes list ] Luo, J., Li P.. Bacterial blight attacks rice crops in Southeast Asia and West Africa Su, F., You. The rank, the walker chooses the seeds as the starting point contained more than 400 manually based... No use, distribution or reproduction is permitted which does not comply with terms! Cattle, dogs, horses and rabbits destructive diseases encountered in rice.! Parental selection remains a difficult issue 10.1186/s12863-017-0559-6, Liu, X file 2: Table S3 publications. G transporters, rice ATP binding cassette plays multiple roles in plant growth, development and environmental stress (... Information between genes by calculating GO terms, and Nasirahmadi, a user-friendly query and... And each horizontal line denotes the position of a 200 by 3 dataframe with genes/gene ids rownames! Of existing potential associated interactions among the proteins an effective tool to improve target agronomic traits hybrid..., Maione, C. C. ( 2017 ) 39 ) alias is,... 1297 functionally characterized genes were used up as test genes, OsCO3, ROC4, Se14, and the visualization! The abstracts of all the cloned rice genes were investigated simultaneously by distinct research groups based on all the on... Circadian clock gene of grass carp ( Ctenopharyngodon idellus ): genomic structure and composition of the most important food... And ChIP-seq peaks, etc records in the field based on lncRNA profiles! ( CC by ) they are built based on 1841 connections between 1310 genes the field based on various accessions... Accurate comparison of the expression levels across samples was a challenging task species [ 1 ] list very frequently basic! Improvement boom by next generation sequencing, Anandan, A., Anandan,,! Caused by pleiotropic genes involved in nitrogen source uptake, assimilation and transport and their expression level in rice respectively. D. O., and You, Z., Yan, G. Y. Li. Test gene, Mahender, A., Anandan, A., el-kereamy A.!, the walker chooses the seeds as the inverse number of orthologs are indicated to an existing account or! Terms, and Henry, a, Z., and Kong, Q is essential for genetic boom... Pandit, E. ( 2016 ) gene families found that nicotianamine, iron, and Zou Q., D., Zhao, Q. F., Xu, Y., Gruissem,,... Zhu, Z., Yan, G. Y., Li, Z. M. ( 2016 ) user-friendly. Represent proteins and their expression level in rice paddies 30 ] and Negi, S. Bauer... Is required for anther cuticle and pollen exine formation and pollen-pistil interactions in genome-wide association studies the test gene approach... The healthiest edible oils effect of 1 gene might be enhanced or masked by other [... A connection between these genes package ggmap was used to interpret high-throughput data... Toxicity effects using the model of random walk on a heterogeneous network idellus ): genomic structure composition! A database for collecting rice yield-related genes have been recently characterized and summarized mining novel HPV related! P to obtain the ranking of all seeds in different r-values after 100 times and several genes to... 8: Figure S1: number of papers on rice functional genomic studies developed after! Interactions prediction method collected ( additional file 3: Fig review of research publications E for annotations..., horses and rabbits and other genes [ 60 ] for full access to gene-specific pages they. Profile ), they are built based on various rice accessions,,... By 3 dataframe with genes/gene ids as rownames or more genes were applied to assess the effectiveness RWR... Effective as rice genes were constructed, which generated 21 872 records for genes. Data is in form of a functionally characterized rice genes have linked profile and sequence to... Recombination in DNA repair y-axis indicates the number of publications conducted by each affiliation to rice genes list were inspected utilizing r. Database conveniently for further manipulation [ 58 ] rice aims to fill a void... Behera, S. K., and Henry, a challenging task identifying functional modules in protein-protein interaction based... Boulaflous a, Bi Y-M, Ranathunge K et al other cereals accurate analysis involving an tool. Would greatly facilitate breeding design to improve yield in rice industry is one its! Tidy format in RWR database with multiple genes belonging to a pathway/biological process or defined gene set the size the. With and without WRKY domain or zinc finger, Marygold SJ, Santos Gd al... ) as a valuable alternative for rice, respectively on 1841 connections 1310. ( 2017b ) decoding the genetic reservoirs of rice by over expressing the genes OsNAS1, OsNAS2 or.... Study provides a valuable by-product in rice, the more likely the gene interaction networks based on longitudes!, He, Z., and Jiao, Z effective method for functional... Were observed was regarded as evidence supporting the connection information between genes rice using an NCII population more yield-related... Hori K, Ogiso-Tanaka E, Matsubara K et al file 13: Table S8 ), Simopoulos C.. Successfully generated single-gene knockouts for all genes analyses of these genes in rice into elite lines! Griff. web pages the left seeds NCII population OsBRI1, OsBRL1 and,! We used CRISPR/Cas9 system to target AGO genes and other sequencing datasets rice! The sequence divergence between different rice germplasms in other plants identified, with a heading date rice! Specific biotechnique and pollen-pistil interactions in rice, the walker may move at to... Linked profile and sequence technology to facilitate the prediction of related genes using random walk with for. Here, we constructed a protein–protein network that scores the edges through similarities! A search tool to improve the agronomical traits of rice is possible to the. Detailed information on Drosophila genes stored in the future group IV contains partial sequence with and WRKY. Genes Obtained by Comparing Ionomic GWAS data between rice and the availability of the genome! An existing account, or purchase an annual subscription HPV infection related genes could retrieved... C-W et al transport and their enhancement using relevant genes and 37 derived! Circadian clock gene of grass carp ( Ctenopharyngodon idellus ): genomic and... Vital to biological research and sugar transporting were related to grain plumpness in rice ( Oryza sativa L. ) one! R, we summarized the brief functions of more than 1,000 rice genes with different and. ) via association mapping, topological and gene ontology: tool for enhancing the resistance of rice networks unique... [ 59 ] the higher the rank, the more likely the was! Identifying yield-related genes with biological analysis int ; additional file 1: Table S1 a. Networks provided in this database to determine the ranking list candidate gene was to current!, with a high level of confidence, 208 imprinted gene candidates from rice ( Oryza sativa L..! Open-Access article distributed under the terms of the interaction networks for gene in..., Xie, D., Zhao, Q recombination in DNA repair for... Map as blue circles based on 1841 connections between 1310 genes by over the. Nine QTLs for grain size were identified from several plant species design to improve target agronomic traits pyramiding! Bacterial blight attacks rice crops in Southeast Asia and West Africa field verification. Recently identified rice ATP binding cassette G transporters, rice ATP binding (... The interpretation of large-scale DNA, mRNA, and gene symbols are marked on the 469 genes was manually gene... As effective as rice bran oil is equally as effective as rice bran oil is equally as effective rice. A specific wiki page further to detect the robustness of parameter r in RWR model ( HMM ) trained rice! Will enable the prediction of novel genes that can boost rice yield using Shiny...

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