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Plant Physiol. Jan 2006; 140(1): 12–17.
PMCID: PMC1326027

Oryzabase. An Integrated Biological and Genome Information Database for Rice1,[OA]

Abstract

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.

BIOLOGICAL DATA

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.

Development/Anatomy

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), are embryo/endosperm, leaf, root, panicle, spikelet, stamen, ovule, reproductive organ, and juvenile-adult transitional stages. Most organs are divided into five to 10 developmental stages that are characterized by several items such as stage names, tissue sizes, stage-specific events, in situ gene expression information, related mutants, and β-glucuronidase-staining patterns of enhancer trap lines (Itoh et al., 2004, 2005; Kurata et al., 2005). Besides morphological descriptions, many photographic figures of distinctive stages have been incorporated. Furthermore, mutants that have been analyzed morphologically and their abnormalities assigned to specific stages or organs are also arranged in the developmental stage tables.

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.

Trait Genes and Mutants

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). Mutant or natural variant genes are classified into seven organs or characters: vegetative organ, reproductive organ, heterochrony, coloration, seed, tolerance and resistance, and quantitative trait loci. These classes are further categorized into 38 subclasses according to their characteristic features. For instance, reproductive organ is classified into four subclasses: heading date, influorescence, spikelet, and pollination/fertilization/fertility. Information regarding 1,698 mutant genes and 136 unclassified genes is accessible in the Oryzabase section called Trait Genes at http://www.shigen.nig.ac.jp/rice/oryzabase/genes/geneClasses.jsp. A trait gene is a gene that has been identified from a mutant or natural variant and is defined by a name that describes its phenotype. Each entry is shown with a gene symbol, gene name, chromosome (location if identified), mutant class name, GO, and/or trait ontology number. From the gene symbol, users can access a short explanation for each mutant phenotype, original and related publications, and, in some cases, mutant photographs (Fig. 1). Correlation between mutant phenotypes and developmental stages is important for analyzing gene function. Therefore, we also arranged as many mutants as possible to relevant stages or organs showing their defects in the section called Development/Anatomy.

Figure 1.
An example of the shootless 1 mutant as described in the sections Trait Genes and Mutants. For this mutant the gene symbol is shown along with a short description of the mutant phenotype, photographs comparing the mutant with a wild-type plant, and references ...

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).

Table I.
Classification of mutants induced by MNU

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).

GENETIC RESOURCES

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.

Wild Rice Strains

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), including a few hundred derived from those of the NIG. To avoid user confusion, information regarding original and derivative accessions is included in both the Oryzabase (NIG) and the IRRI database. Construction of a large-scale BAC library and a BAC end-sequencing project for wild rice species carried out at the University of Arizona (Ammiraju et al., 2006; http://www.genome.arizona.edu/BAC_special_projects/#Rice) used a total of 13 accessions for 12 species from IRRI, with half of the accessions originally collected in the NIG.

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.

Crossed Lines and Other Strains

RILs of four japonica × 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).

Figure 2.
Indica IR24 genome (red block) substitution lines with a japonica Asominori (white block) background. Eighty-seven lines almost cover all the regions of the indica genome. The purple blocks indicate regions needed for discriminating between homozygosity ...

GENOME MAPS AND SEQUENCES

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.

Linkage Maps

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 chromosomal locations of additional 362 phenotypic genes have also been assigned to 12 chromosomes.

The IT map locates 83 RFLP markers and 40 phenotypic marker genes (Yoshimura et al., 1997). Common phenotypic and RFLP markers in CL, IT, and RI maps are used for positional references. Lines carrying marker genes are available in the section called Strains.

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). Genotype segregation data and descendant seed sets of these RILs (beyond F7) are available in project 4 of the National Bioresource Project.

The Nipponbare-Kasalath map is the densest molecular genetic map carrying 2,275 DNA markers for rice (Harushima et al., 1998).

Physical Maps

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).

Comparative Maps

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.

FUTURE DESIGN FOR PLANT, TRAIT, AND GO

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) is a GO database equipped with an original viewer and is accessible through Oryzabase (http://shigen.lab.nig.ac.jp/ontology/top.jsp). The unique feature of the GOALL viewer is that it can provide a bird's-eye view of all GO terms. In this viewer each dot represents a term, and information relating to the term can be associated with a dot object. This makes it possible to display entire terms associated only with a gene query from certain species. The viewer also allows comparative studies between two different species. Biological ontology should perform best when it is applied to databases with comprehensive viewers. Oryzabase serves as a central resource for monocot plant research, and provides up-to-date knowledge of rice science to researchers.

ACTIVITIES IN RICE RESEARCH COMMUNITY

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 aim and scope of the newsletter is to promote cooperation and exchange of information and material among rice geneticists. For 20 years the RGC organized gene symbolization and nomenclature, establishment of a genetic linkage group, and a chromosome numbering system. These were published in the RGN and have been used as a base for establishing rice genetic and physical maps. All contents of the RGN from volumes 1 to 20 are available in the Oryzabase. From 2005, RGN will be published as an online journal that is uploaded twice a year.

Rice-E-Net/Rice-Net

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.

Acknowledgments

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.

Notes

1This 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 (pj.ca.gin.bal@atarukn).

[OA]Open Access articles can be viewed online without a subscription.

www.plantphysiol.org/cgi/doi/10.1104/pp.105.063008.

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