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Plant Physiology 140:12-17 (2006) © 2006 American Society of Plant Biologists OPEN ACCESS ARTICLE Oryzabase. An Integrated Biological and Genome Information Database for Rice1,[OA]Genetic Strains Research Center (N.K.) and Center for Genetic Resource Information (Y.Y.), National Institute of Genetics, Mishima, Shizuoka 411–8540, Japan; and Department of Genetics, School of Life Science, Graduate University for Advanced Studies (Sokendai), Mishima, Shizuoka 411–8540, Japan (N.K., Y.Y.)
The aim of Oryzabase is to create a comprehensive view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information (http://www.shigen.nig.ac.jp/rice/oryzabase/top/top.jsp). The database contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. The anatomical description of rice development is unique and is the first known representation for rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. The systematic presentation of a large number of rice mutant and mutant trait genes is indispensable, as is description of research in wild strains, core collections, and their detailed characterization. Several genetic, physical, and expression maps with full genome and cDNA sequences are also combined with biological data in Oryzabase. These datasets, when pooled together, could provide a useful tool for gaining greater knowledge about the life cycle of rice, the relationship between phenotype and gene function, and rice genetic diversity. For exchanging community information, Oryzabase publishes the Rice Genetics Newsletter organized by the Rice Genetics Cooperative and provides a mailing service, rice-e-net/rice-net.
Rice (Oryza sativa) is one of three major dietary staple foods in the world and has a highly syntenic genomic and gene structure with respect to the other two major foods, maize (Zea mays) and wheat (Triticum aestivum). The genome sequence of a japonica variety, Nipponbare, was completed in 2004 and, prior to this, considerable information relating to the genome and gene structures of rice (such as the nuclear, chloroplast and mitchondrion genome, cDNA, expressed sequence tag [EST], and protein sequences) was compiled. In addition, data has been gathered on the functional genomic resources of rice, such as Tos17 and T-DNA-tagged lines, along with their flanking sequences. Several major databases for rice genome research can be accessed through the International Rice Genome Sequencing Project Web site (http://rgp.dna.affrc.go.jp/IRGSP/index.html). A rice expression database called Rice Expression Database (http://red.dna.affrc.go.jp/RED/), a rice full-length cDNA database designated KOME (http://cdna01.dna.affrc.go.jp/cDNA/), a rice Tos17 insertion mutant database (http://tos.nias.affrc.go.jp/  miyao/pub/tos17/), and a rice proteome database and integrated rice genome explorer INE (http://rgp.dna.affrc.go.jp/giot/INE.html) have also been established. The Institute for Genomic Research (http://www.tigr.org/tigr-scripts/tgi/T_index.cgi?species=rice, http://www.tigr.org/tdb/e2k1/osa1/), Cold Spring Harbor Laboratory (http://mccombielab.cshl.edu/external/riceweb/), and other major rice projects and institutions have constructed databases that have assembled and/or processed full genome sequences. A Chinese group has published indica rice sequences (Yu et al., 2005 ) and the Oryza Map Alignment Project (http://www.omap.org/), which is a wild rice (Zizania palustris) bacterial artificial chromosome (BAC) alignment project, is another major activity at Arizona University. Gramene (http://www.gramene.org/) and GrainGenes (http://wheat.pw.usda.gov/GG2/index.shtml) are databases organized for cereal comparative genomics at Cornell University. Recently there has been much effort and progress into biologically characterizing rice in terms of mutants and their genes, phenotypes, developmental features, and other events related to the ontology of rice. To date, biological characteristics for rice phenotypes, traits, habitats, and other growth and developmental information have not been described in rice databases. Therefore, the Oryzabase aims to prepare such basic biological information collected from all developmental stages, mutants, natural variants, and so on. Genomic information and genetic resources are also provided for correlating biological events and/or strains with molecular evidence. Data structures that combine biological features (such as phenotype, development, mutants, and natural variants) with molecular attributes (such as cDNA and genome sequences, gene ontology [GO] terms, and gene expression profile) will help researchers gain a more comprehensive view of rice. The data in Oryzabase are divided into 15 sections: development/anatomy, mutants, trait genes, linkage maps, physical maps, comparative maps, references, basic biological data, DNA sequence, BLAST search, chloroplast and mitochondrion, tools and protocols, strains, stock centers, and wild rice. Design, data collection, and construction of the database are organized by the Rice Genetic Resources Committee along with members of the Rice Gene Nomenclature Committee that belongs to the Rice Genetics Cooperative (RGC). Several experts in a special field are pointed to curate each section of Oryzabase. The Genetic Strains Information Laboratory in the National Institute of Genetics (NIG) in Japan is responsible for building and maintaining the database.
Oryzabase is a unique rice database that shows morphological and gene expression characteristics of this organism at different developmental stages and in various mutants. The biological information in Oryzabase is both unique and basic and is composed of four sections: Development/Anatomy, Trait Genes, Mutants, and Basic Biological Information. Items in each section are not only shown by their own characters but also accompanied with in situ gene expression information, references, and other relevant data. Developmental and anatomical data have been gathered from researchers who are experts in each tissue (Itoh et al., 2005 ) and combined with related expression and mutant data mostly from published information.
This section is the core and most distinctive part of Oryzabase (http://www.shigen.nig.ac.jp/rice/oryzabase/development/organAndStage.jsp). Rice organ development is dissected stage by stage, and the anatomical characteristics of each stage are described. The developmental stages and/or organs shown in Oryzabase, which have recently been finalized by Itoh et al. (2005) Thus, the Development/Anatomy section enables specific rice organ developmental stages to be linked to related biological and molecular events and phenomena. To provide easy access to all organ development, we present as much data as possible in single tables linking individual items to more detailed description sources. From this, users can quickly obtain an entire view of organ development in rice and easily find necessary data about mutants, expression patterns of genes, and references. A search system using keywords is also provided. Gene expression profiles, created by microarray analysis, are the next target for including in the database. Determination of critical developmental stages and precise gene expression profiling in those stages makes it possible to unravel genetic programs in the development and gene expression networks.
Over the past decades, nearly 1,700 rice mutants or natural variants with visible or physiological phenotypes have been revealed. In our recent review we reported many interesting mutants and genes responsible for the phenotypes (Kurata et al., 2005
A large collection of the n-methyl n-nitrosourea (MNU)-induced mutant population is also provided (http://www.shigen.nig.ac.jp/rice/oryzabase/nbrpStrains/kyushuGrc.jsp). Only 12 classes of visible phenotypes, including 49 easily identifiable phenotypes, have been used to classify these mutant lines (Table I). Phenotypic classification of the MNU-induced mutants is identical to that used for Tos17-induced mutant lines. It is presumed that the Tos17 mutagenesis cannot be performed to saturation because of several types of preferential insertion sites of Tos17 (Miyao et al., 2003 ). Consequently, mutation-enriched, chemically induced mutants are the next promising resource for characterizing mutant genes using reverse genetic tools such as TILLING (Till et al., 2003).
Basic Biological Data and References Access to several other biological datasets is available in the section called Basic Biological Data at http://www.shigen.nig.ac.jp/rice/oryzabase/basic/basicBiologicalData.jsp. This is composed of six subsections and describes basic information for wild rice, mutants, genetic maps, chromosomes and cultivation, crossing, and harvesting of rice for beginners in rice research. The content of the six subsections are as follows: (1) species and their geographical distribution of wild and cultivated strains of rice in the world; (2) organs of rice, their morphology, and names; (3) mutants of rice (collection of selected mutant phenotypes identified and characterized); (4) genetic maps of rice (RFLP and visible marker maps); (5) chromosomes of rice; and (6) cultivation of rice (cultivation manual for rice genetic experiments).
Oryzabase has gathered information on nearly 20,000 useful strains. Wild rice accessions, cultivars, mutant lines, chromosome substitution lines, recombinant inbred lines (RILs), marker gene lines, and other lines useful for rice research are incorporated and distributed in Oryzabase. These unique resources have been collected, generated, and maintained for several decades through many researchers in several key laboratories.
Once the genome sequencing of the cultivated rice O. sativa (AA genome) is complete, information of the wild rice genomes of AA, BB, CC, BBCC, CCDD, EE, FF, GG, and HHJJ (comprising 23 species, including two cultivated species of O. sativa and Oryza glaberrima), gathered in the Oryzabase, should become one of the most valuable genetic resources in the post sequencing era (http://www.shigen.nig.ac.jp/rice/oryzabase/wild/coreCollection.jsp). Short descriptions about biological and molecular characteristics, habitats, and the world distribution of these Oryza species appear in the Basic Biological Data section. For more than 40 years, nearly 1,700 wild rice accessions from all over the world have been collected in the NIG. The International Rice Research Institute (IRRI) in the Philippines also has about 1,900 wild rice accessions (Vaughan, 1994 For convenience in accessing, we chose a core collection of 289 accessions from wild species, which were grouped into ranks 1, 2, and 3. Rank 1 contains highly desirable accessions, with two or three accessions from 18 wild species (19, if Oryza nivara is counted as a separate species). Rank 2 is the next recommended collection with 64 accessions taken from all species. Rank 3 is a supplementary collection that includes 171 accessions. These accessions are spread worldwide and cover as much genetic variation as possible. The phenotype and detailed characterization of the core collection have been recorded. Genomic DNA of the core collection accessions is available upon request. The wild rice species and accessions characterized so far can provide valuable sources for analyzing speciation and cultivation processes, where ancestor genes could have been selectively maintained, varied, or lost.
RILs of four japonica x indica crosses have been generated, and their information will be incorporated in the near future. Also, chromosome substitution lines with japonica backgrounds crossed with other AA genome species (indica of O. sativa, O. glaberrima, Oryza glumaepatula, Oryza meridionalis, Oryza rufipogon, Oryza barthii, and O. nivara) are now partially available and the remainder will be available in the near future in the section of NBRP stains. Each wild strain-crossed AA species substitution population is composed of about 40 to 80 lines that cover entire genome segments. A schematic description of the population is shown in Figure 2 . Information regarding another 11,724 strains includes several special mutants and useful parent lines for crossing. This information can be easily accessed and distributed between institutions and researchers for research purposes and is available in the sections called Strains (http://www.shigen.nig.ac.jp/rice/oryzabase/strains/summary.jsp) and Stock Center (http://www.shigen.nig.ac.jp/rice/oryzabase/strains/stockCenter.jsp).
Many databases of rice genomic information are available, as mentioned in the introduction. In Oryzabase, we selected and reorganized genomic and genetic information provided in the public sources to show relations among strains, phenotypes, genotypes, gene expression data, and sequences. We incorporated several genetic and physical maps together to the sequenced genome and expressed sequences.
A number of genetic linkage maps have been created for rice (http://www.shigen.nig.ac.jp/rice/oryzabase/maps/map.jsp). In Oryzabase, four basic linkage maps (classical linkage [CL], integrated [IT], recombinant inbred [RI], and Nipponbare-Kasalath) have been combined using common markers.
The CL map has been constructed with 209 phenotypically identified genes reported originally in 1998 in a committee report for the RGC (Nagato and Yoshimura, 1998
The IT map locates 83 RFLP markers and 40 phenotypic marker genes (Yoshimura et al., 1997
The RI map is an RFLP framework map that has been constructed using 375 RFLP markers using RILs of a japonica strain Asominori crossed with an indica strain IR24 (Tsunematsu et al., 1996
The Nipponbare-Kasalath map is the densest molecular genetic map carrying 2,275 DNA markers for rice (Harushima et al., 1998
In the physical map section (http://www.shigen.nig.ac.jp/rice/oryzabase/genome/chromosomeList.jsp), 12 chromosome maps are being constructed by collecting publicly available DNA sequences from DNA Data Bank of Japan/EMBL/GenBank nucleotide sequence databases and their predicted coding sequences as well as full-length cDNA regions from the KOME. The genomic viewer is planned to provide a chromosome view, which displays entire chromosomes in a line, together with other views by a range of 250 K to 1 M and of 10 to 100 K. Complete maps will be available soon. Rice DNA sequence accessions (over 64,000 entries in National Center for Biotechnology Information-GenBank Release 149.0) extracted from the plant division section of the DNA data bank of Japan/EMBL/GenBank database are also available in a separate section titled DNA sequence (http://www.shigen.nig.ac.jp/rice/oryzabase/dna/sequences.jsp).
The Oryzabase comparative map is a map that has added barley (Hordeum vulgare) and wheat EST clones to the rice EST/cDNA linkage map (http://www.shigen.nig.ac.jp/rice/oryzabase/comparative/comparative.jsp). The EST data used for this map was obtained from a barley database (http://earth.lab.nig.ac.jp/%7Edclust/cgi-bin/barley_pub/) and the KOMUGI (http://shigen.lab.nig.ac.jp/wheat/komugi/t) wheat database. To allow sharing of clones among monocot plant researchers, EST clone names, instead of their contig numbers, are displayed on the comparative maps. An assembly viewer for each contig is currently in preparation.
Enormous progress has been made, over a very short period of time, in the field of biological ontology. Indeed, ontologies are becoming indispensable for effective use of accumulated information. The section titled Development/Anatomy in Oryzabase strongly relates to the Plant Ontology Consortium (http://www.plantontology.org/) project that aims to develop, curate, and share controlled vocabularies describing plant structures and their growth and developmental stages. This will provide a semantic framework for meaningful cross-species queries across databases, despite the fact that these two tasks began independently. Oryzabase is now collaborating with the Plant Ontology Consortium and will contribute to the establishment of Plant Ontology (PO). Meanwhile, in Phenotype and Trait Ontology (PATO), a phenotype or trait is expressed with a combination of attributes and values such that a phenotypic mutant, for example, can be described with a combination of PO and PATO. Zebrafish Information Network (http://zfin.org/cgi-bin/webdriver?MIval=aa-ZDB_home.apg) leads the PATO ontology project and has established the ontologies required for describing mutant phenotype information. An integrated viewer, O3, is being developed in Oryzabase to show both the concept of ontology and the associated data. The O3 viewer was named after three-dimensional ontologies: time, space, and features, which correspond to PO developmental stage, PO plant structure, and PATO, respectively.
All trait genes in Oryzabase are manually annotated by researchers and some are associated with GO-IDs. Oryzabase GO is soon to be submitted to the central GO database through the Gramene database. GOALL (Yamazaki and Jaiswal, 2005
Rice Genetics Newsletter
The RGC began in 1984 and instigated the International Rice Genetics Symposium and the publishing of the Rice Genetics Newsletter (RGN; http://www.shigen.nig.ac.jp/rice/oryzabase/rgn/newsletter.jsp; Oka and Khush, 1984
The Oryzabase started to support the Rice Net interactive Web site service for Japanese rice researchers in 2001. Recently this network service has expanded to worldwide rice researchers as a Rice-E-Net (http://chanko.lab.nig.ac.jp/list-touroku/rice-e-net-touroku.html). Participation of more rice and other cereal researchers in the Oryzabase Rice-E-Net will culminate in greater interactive sharing of rice information. Thus, Oryzabase covers and compiles information from the rapidly progressing fields of biology such as genetics, physiology, and molecular biology for rice. In particular, detailed biological information from developmentally and anatomically analyzed data presents an indispensable resource for further ontology studies and functional genomics. The main objective of the database is to present ways of correlating biological information with molecular events for understanding the complex genome of rice. Oryzabase continues to collect and relate new information for improving our understanding of the genus Oryza and its effective use as an important staple food.
We wish to thank Drs. H. Morishima and S. Iyama and Ms. T. Miyabayashi for their helpful suggestions and assistance with this work. We are grateful to many colleagues, especially to Drs. A. Yoshimura and Y. Nagato, for offering plenty of invaluable data and for supporting Oryzabase construction. Received March 17, 2005; returned for revision November 2, 2005; accepted November 2, 2005.
1 This work was supported by the National Bioresource Project organized by the Ministry of Education, Culture, Sports, Science and Technology (Japan) and the Rice Genome Simulator Project (no. GS2107) organized by the Ministry of Agriculture, Forestry and Fisheries (Japan).  The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Nori Kurata (nkurata{at}lab.nig.ac.jp).
[OA] Open Access articles can be viewed online without a subscription. www.plantphysiol.org/cgi/doi/10.1104/pp.105.063008. * Corresponding author; e-mail nkurata{at}lab.nig.ac.jp; fax 81–55–981–6879.
Ammiraju JSS, Luo M, Goicoechea JL, Wang W, Kudrna D, Muller C, Talag J, Kim H, Sisneros NB, Blackmon B, et al (2006) The Oryza bacterial artificial chromosome library resource: construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genomes types of the genus Oryza. Genome Res (in press) Harushima Y, Yano M, Shomura A, Sato M, Shimano T, Kuboki Y, Yamamoto T, Lin SY, Antonio BA, Parco A, et al (1998) A high density rice genetic linkage map with 2275 markers using a single F2 population. Genetics 148: 479–494 Ito Y, Eiguchi M, Kurata N (2004) Establishment of an enhancer trap system with Ds and GUS for functional genomics in rice. Mol Genet Genomics 271: 639–650[Web of Science][Medline] Itoh JI, Nonomura KI, Ikeda K, Yamaki S, Inukai Y, Yamagishi H, Kitano H, Nagato Y (2005) Rice plant development: from zygote to spikelet. Plant Cell Physiol 46: 23–47 Kurata N, Miyoshi K, Nonomura K, Yamazaki Y, Ito Y (2005) Rice mutants and genes related to organ development, morphogenesis and physiological traits. Plant Cell Physiol 46: 48–62 Miyao A, Tanaka K, Murata K, Sawaki H, Takeda S, Abe K, Shinozuka Y, Onosato K, Hirochika H (2003) Target site specificity of the Tos17 retrotransposon shows a preference for insertion within genes and against insertion in retrotransposon-rich regions of the genome. Plant Cell 15: 1771–1780 Nagato Y, Yoshimura A (1998) Report of the committee on gene symbolization, nomenclature and linkagemap. Rice Genet Newsl 15: 13–74 Oka HI, Khush GS, editors (1984) Rice Genetics Newsletter 1. Rice Genetics Cooperative, Mishima, Japan, pp 1–91 Till BJ, Reynolds SH, Greene A, Codomo CA, Enns LC, Johnson JE, Burtner C, Odden AR, Young K, Taylor NE, et al (2003) Large-scale discovery of induced point mutations with high-throughput TILLING. Genome Res 13: 524–530 Tsunematsu H, Yoshimura A, Harushima Y, Nagamura Y, Kurata N, Yano M, Sasaki T, Iwata N (1996) RFLP framework map using recombinant inbred lines in rice. Breed Sci 46: 279–284 Vaughan DA, editor (1994) The Wild Relatives of Rice: A Genetic Resources Handbook. International Rice Research Institute, Los Baños, Philippines, pp 85–87 Yamazaki Y, Jaiswal P (2005) Biological ontologies in rice databases: an introduction to the activities in Gramene and Oryzabase. Plant Cell Physiol 46: 63–68 Yoshimura A, Ideta O, Iwata N (1997) Linkage map of phenotype and RFLP markers in rice. Plant Mol Biol 35: 49–60[CrossRef][Web of Science][Medline] Yu J, Wang J, Lin W, Li S, Li H, Zhou J, Ni P, Dong W, Hu S, Zeng C, et al (2005) The genomes of Oryza sativa: a history of duplication. PLoS Biol 3: 1–16[CrossRef][Medline] This article has been cited by other articles:
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ABSTRACT
BIOLOGICAL DATA
-glucuronidase-staining patterns of enhancer trap lines (Itoh et al., 2004
