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Useful Resources
Complete Rice (Oryza sp.) Sequences
Cereal Genome Sequencing Efforts
Rice
- International Rice Genome Sequencing Project (IRGSP) - The International Rice Genome Sequencing Project (IRGSP), a consortium of publicly funded laboratories, was established in 1997 to obtain a high quality, map-based sequence of the rice genome using the cultivar Nipponbare of Oryza sativa ssp. japonica. It is currently comprised of ten members: Japan, the United States of America, China, Taiwan, Korea, India, Thailand, France, Brazil, and the United Kingdom. The IRGSP adopts the clone-by-clone shotgun sequencing strategy so that each sequenced clone can be associated with a specific position on the genetic map and adheres to the policy of immediate release of the sequence data to the public domain. In December 2004, the IRGSP completed the sequencing of the rice genome. The high-quality and map-based sequence of the entire genome is now available in public databases.
IRGSP Members:
- Rice Genome Program (RGP), Japan RGP is a joint project of the National Institute of Agrobiological Sciences (NIAS) and the Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries (STAFF) and a part of the Japanese Ministry of Agriculture, Forestry and Fisheries (MAFF) Genome Research Program.
- US Rice Genome Sequencing Project -In 1999 CSREES, as the lead U.S. agency in partnership with the National Science Foundation (NSF) and Department of Energy (DOE), competitively funded two U.S. projects to participate in the IRGSP, which includes investigators from Arizona, South Carolina, Missouri, New York, Wisconsin, and Maryland.
- ACWW Rice Genome Sequencing Project: Chromosome 3 & 10. In the fall of 1999, the ACWW (Arizona Genomics Institute (AGI), Rice Genome Analysis, Genome Sequencing Center, & Wisconsin Rice Genome Project) consortium was awarded a grant from the USDA -CSREES/NSF/DOE rice genome initiative to sequence and annotate the short arms of chromosomes 3 and 10, working with TIGR and PGIR.
- TIGR Rice Genome Project The Institute for Genomic Research (TIGR) is a not-for-profit center dedicated to deciphering and analyzing genomes - the complex molecular chains that constitute each organism's unique genetic heritage.
- Plant Genome Initiative at Rutgers (PGIR) Historically, PGIR was established as a high-throughput sequencing facility of medium capacity to participate in an international effort to sequence the rice genome. PGIR had been assigned the middle portion of chromosome 10 from 29.8 to 41.8 cM. During the course of sequencing clones from chromosomes 10 and 11, we also sequenced one clone from chromosome 12 and two smaller clones from the indica variety Teqing that have also been deposited to GenBank.
- National Center for Gene Research (NCGR) was established jointly by the Ministry of Science and Technology, the Chinese Academy of Sciences (CAS), and the Shanghai local government to provide a major focus in China for mapping and sequencing the rice genome, and genomes of other organisms.Since 1998 NCGR has been a member of the International Rice Genome Sequencing Project (IRGSP) to completely sequence the entire rice japonica genome. NCGR has been fully working on the chromosome 4 sequencing in close collaboration with the IRGSP members, the Chinese National Human Genome Center at Shanghai , and Institute of Genetics and Developmental Biology of CAS.
- Genoscope, France
- Rice Genome Project in Republic of China, Taiwan
- John Innes Centre
- Indian Initiative for Rice Genome Sequencing
- Korea Rice Genome Research Program
- National Center for Genetic Engineering and Biotechnology, Thailand
- Brazilian Rice Genome Initiative
- Clemson University Genomics Institute (CUGI)
- National Center for Gene Research Chinese Academy of Sciences, China
- Monsanto Rice Genome Project
Maize- Maize Genome Sequencing Project (mgsp)
- MaizeSequence.org
TOP Cereal Genomic Databases
- Gramene - A comparative resource for cereal genomics. With a focus on rice, Gramene has marker, maps, gene, proteins, QTL, literature, diversity, pathway and ontology information on rice, maize, wheat, sorghum, barley, millet,rye, oats and wild rice.
- Oryzabase, JapanThe Oryzabase consists of five parts, (1) genetic resource stock information, (2) gene dictionary, (3) chromosome maps, (4) mutant images, and (5) fundamental knowledge of rice science.
- International Rice Information System (IRIS) is the rice implementation of the International Crop Information System (ICIS) which is a database system that provides integrated management of global information on genetic resources and crop cultivars. This includes germplasm pedigrees, field evaluations, structural and functional genomic data (including links to external plant databases) and environmental (GIS) data.
- community Rice Genome annotation, Rice oliognucleotide Array Project, Rice Repeat Database - a part of the TIGR Plant Repeat Databases, wheat genome database, Comprehensive Phytopathogen Genomics Resource, Maize database, the Arabidopsis thaliana project and others.
- Rice Expression Database (RED) - RED holds raw and normalized data from expression profiles obtained by the Rice Microarray Project and other research groups.
- RIS - Rice Information System (BGI-RIS) is targeted to be the most up-to-date integrated information resource for rice genomes as well as a workbench for comparative genomic analysis among cereal crops.
- Sundaresan Lab for Functional Genomics of Model Plants, including Rice Sequence Indexed Transposon Insertion Library
- PLEXdb (Plant Expression Database) is a unified public resource for gene expression for plants and plant pathogens. PLEXdb serves as a bridge to integrate new and rapidly expanding gene expression profile data sets with traditional structural genomics and phenotypic data. The integrated tools of PLEXdb allow investigators to use commonalities in plant biology for a comparative approach to functional genomics through use of large-scale expression profiling data sets.
- Pedigrees of Oat Lines (POOL) A Curated Internet Database of Oat Pedigrees, from Eastern Cereal and Oilseed Research Centre
- UK Crop Plant Bioinformatics Network As well as the six UK CropNet databases, they also mirror many other plant-related databases
- Plant Genome Research - Project to develop plant species-specific EST and GSS databases, to provide web-accessible tools and inter-species query capabilities, and to provide genome browsing and annotation capabilities.
- Oryza Sativa Plant Genome DB (OsGDB)
- Arabidopsis (AtGDB)
- ZmGDB
- SRGDB(Splicing Related Genes DB)
- Alternative Splicing in Plants (ASIP)
- Maize GDB the community database for biological information about the crop plant Zea mays ssp. mays. Genetic, genomic, sequence, gene product, functional characterization, literature reference, and person/organization contact information are among the datatypes accessible through this site.
- Panzea Molecular and Functional Diversity of the Maize Genome
- MaizeSequence.org provides sequence and annotation of the Zea mays ssp. mays genome resulting from the Maize Genome Sequencing Project.
- GrainGenes, a database for Triticeae and Avena
- Rice Diversity Project - This project makes use of the wealth of sequence information available for rice to bridge the study of molecular genetic variation with that of whole plant phenotypic variation. The plan is to develop an association mapping platform that will provide new insights into the relationship between molecular and phenotypic diversity, leading to a more efficient utilization of natural variation in crop improvement.
- Phytozome is a joint project of the Department of Energy's Joint Genome Institute and the Center for Integrative Genomics to facilitate comparative genomic studies amongst land plants. Clusters of orthologous and paralogous genes that represent the modern descendents of ancestral gene sets are constructed at key phylogenetic nodes. These clusters allow easy access to clade specific orthology/paralogy relationships as well as clade specific genes and gene expansions. As of version 2.0, Phytozome provides access to five sequenced and annotated land plant genomes, clustered at six evolutionarily significant nodes. Where possible, each gene has been annotated with PFAM, KOG, KEGG, and PANTHER assignments, and publicly available annotations from RefSeq, UniProt, TAIR, JGI are hyper-linked and searchable, including Sorghum bicolor and Oryza sativa.
- Rice TOS17 insertion mutant database, Japan
- RGP High-Density Rice Genetic Map
- The Comparative Saccharinae Genomics Resource (CSGR), from the University of Georgia, formerly known as the Comparative Grass Genomics Center.
- Wheat Genetic and Genomic Resources Center The WGGRC has established a national and international network to conduct and coordinate genetic studies in wheat. The WGGRC maintains a gene bank, along with evaluation and passport data, on 2,500 wheat species accessions. In addition, the WGGRC houses 2,200 cytogenetic stocks, the genetic treasures produced by a lifetime of work by wheat scientists.
- GenomesOnline.org
- Brachypodium.org serves as a simple information repository, but in the future it will serve as the major genome sequence database and tool resource for Brachypodium distachyon
TOP Genome Research and Education
- Department of Energy Joint Genome Institute - JGI brings the expertise of five national laboratories, Lawrence Berkeley, Lawrence Livermore, Los Alamos, Oak Ridge, and Pacific Northwest, and the Stanford Human Genome Center to bear on the frontiers of genome sequencing and related biology. Our sequencing targets encompass a rapidly expanding range of microbes, animals, and plants. The Community Sequencing Program (CSP) aims to broaden the range still further. JGI is operated by the University of California for the U.S. Department of Energy.
- National Plant Genome Initiative 2003-2008 The National Science and Technology Council (NSTC) believes it is critical to continue and even accelerate research efforts in plant genomics in order to take advantage of exciting scientific opportunities that will lead to improved agriculture, energy and health, thus ensuring a high quality of life for future generations. The scientific community has established extensive interdisciplinary and international collaborations to achieve the goals of the NPGI.
- Genetics Review
- Introduction to Molecular Biology Information Resources (a 3-day course)
- International Rice Research Institute (IRRI) - The International Rice Research Institute (IRRI) is an autonomous, nonprofit agricultural research and training organization with offices in more than ten nations. The Institute's main goal is to find sustainable ways to improve the well-being of pr esent and future generations of poor rice farmers and consumers while at the same time protecting the environment. Most of IRRI's research is done in cooperation with natio nal agricultural research and development institutions, farming communities, and other organizations of the world's rice- producing nations.
- Cornell's New Life Sciences Initiative (NLSI)
- Rice genomics at Purdue
- IRD Rice Genetics Group, France
- National Research Centre for Plant Biotechnology - India. Research and Education.
- LSU publications on rice research
- The Rice Technical Working Group (RTWG) - Research and Extension
- RiceCap The overall objective of the outreach component of the RiceCAP project is "to effectively communicate the science and potential of rice plant genomics, including progress and description of the RiceCAP to the U.S. rice industry". An outreach team, consisting of cooperating scie ntists and extension specialists from several of the institutions participating in the project has been assembled.
- Dale Bumpers National Rice Research Center
- UC Cooperative Extension Rice Project.
- CCRRF, California Cooperative Rice Research Foundation
- US Barley Genome Project (formerly North American Barley Genome Project
- Computational Biology at Cornell
- Genetics and Genomics Links compiled at UC Irvine
- African Crop Improvement Website and their resources on rice , sorghum, millet, and maize improvement
- Cold Spring Harbor Laboratory Cold Spring Harbor Laboratory is a private, non-profit basic research and educational institution. Under the leadership of Dr. Bruce Stillman, a member of the National Academy of Sciences and a Fellow of the Royal Society (London), some 330 scientists conduct groundbreaking research in cancer, neurobiology, plant genetics and bioinformatics. Cold Spring Harbor Laboratory is one of eight National Cancer Institute-designated basic research centers in the U.S. and the only such center in the tri-state area.
TOP Functional Genomics
- A shift of emphasis is now occurring from genome mapping and sequencing to determination of genome function. This is the area known as functional genomics
- European Science Foundation Programme on Integrated Approaches for Functional Genomics.
- International Rice Functional Genomics Consortium (IRFGC)
- The Rice Functional Genomics Program (RIFGP), China
- Rice Microarray Opening Site, Japan - Microarray is the powerful tool for understanding comprehensive gene expression at genome-wide level.
- Functional Genomics
- Mu Transposon Information Resource
TOP Tools for Nucleotide and Protein Sequence Analyses
- EMBnet EMBnet is a science-based group of collaborating nodes throughout Europe and a number of nodes outside Europe. The combined expertise of the nodes allows EMBnet to provide services to the European molecular biology community which encompasses more than can be provided by a single node. This site gives an overview of the organization and of it's members. It provides the visitors with news of the EMBnet community and new links related to bioinformatics. It also combines the services available on the nodes and publishes EMBnet.news, the letter devoted to provide information about what is happening at the national and special nodes.
- EBI to search and retrieve the sequences, structures, references, etc, including:
- EMBL Nucleotide Database, Europe's primary collection of nucleotide sequences is maintained in collaboration with Genbank (USA) and DDBJ (Japan),
- Interpro- a Database of protein domains and functional sites
- UniProt Knowledgebase - a complete annotated protein sequence database
- ArrayExpress- for gene expression data
- Ensembl Provides up to date completed metazoic genomes and the best possible automatic annotation
- IntAct Provides a freely available, open source database system and analysis tools for protein interaction data.
- ClustalW for multiple sequence alignment
- ExPASy (Expert Protein Analysis System) Proteomics Server of the Swiss Institute of Bioinformatics (SIB) is dedicated to the analysis of protein sequences and structures s well as 2-D PAGE. Proteomic tools Databases include:
- SWISS-PROT and TrEMBL to search and retrieve protein sequences
- Prosite a Database of protein families and domains
- PDB Databank - a repository of protein 3D structures
- NCBI National Center for Biotechnology Information , hosts:
- NCBI-ENTREZ to search and retrieve the sequences, structures, references, etc.
- BLAST Basic Local Alignment Search Tool, finds regions of local similarity between sequences
- PubMed - a service of the National Library of Medicine, includes over 15 million citations from MEDLINE and additional life science journals for biomedical articles back to the 1950's. PubMed includes links to full text articles and other related resources.
- VAST NCBI's structure-structure similarity search service
- Stanford Genomic Resources offers various resources for genomics and database repositories
- Quick Links (for searches in various databases )
- Bio-Tool Kit an annotated directory of over 900 links to online molecular biology and neuroinformatics resources, includes basic research tools as well as advanced tools enabling integrated, multi-level analysis of the genome, transcriptome, and proteome.
- Predict Protein offers sequence analysis, and structure prediction.
- PEDANT - Protein Extraction, Description and ANalysis Tool provides exhaustive automatic analysis of genomic sequences by a large variety of bioinformatics tools. automatic and exhaustive analysis of protein sequence sets
- GeneDoc - A Full Featured Multiple Sequence Alignment Editor, Analyzer and Shading Utility for Windows
- Resources for Genomics, Molecular Biology and Evolutionary Research
TOP Tools for Plant Genome Analysis
- MAPMAKER/QTL A linkage analysis package designed to help construct primary linkage maps of markers segregating in experimental crosses
- QTL Cartographer A suite of programs for mapping quantitative trait loci (QTLs) onto a genetic linkage map
- SRS - A tool for biosequences.
- QGene A Macintosh software application written for the visualization and rapid statistical analysis of molecular-marker and phenotypic trait data
- MapDisto A program for mapping genetic markers in experimental segregating populations like backcross, doubled haploids, single-seed descent
- Maize Genetics from Buckler Lab genetic and evolution software
- GDPC Provides access to genomic diversity data such as SNPs, SSRs, sequences, etc. and phenotypic data that may be collected in field, genetic, or physiological experiments
- TASSEL Trait Analysis by aSSociation, Evolution and Linkage. This application evaluates linkage disequilibrium, nucleotide diversity, and trait associations
- Genomic Diversity and Phenotype Data Model (GDPDM) captures both Molecular and Phenotypic Diversity data
- Phylogeographer
- MaizeMeister
- Biolign
- STRUCTURE is a free software package for using multi-locus genotype data to investigate population structure
- DISTRUCT is a program that can be used to graphically display results produced by the genetic clustering program STRUCTURE
- POWERMARKER is a comprehensive set of statistical methods for genetic marker data analysis, designed especially for SSR/SNP data analysis.
- BRENDA - The Comprehensive Enzyme Information System
TOP Bioinformatics
- Plant Biology Databases: A Needs Assessment - a white paper
- Plant Genome Research "Outreach" activities, programs and resources.
- Ensembl
- Generic Model Organism Project (GMOD)
- Rice Bioinformatics:- IRRI-hosted Rice Bioinformatics information site set up in response to the Bioinformatics Workshop at the 4th Rice Genetics Symposium held in October 2000.
- Transgenic Crops - a site providing information and links to resources on the technology and issues surrounding transgenic crops (also known as genetically modified or GM crops)
- Plant Ontology - aims to develop, curate and share controlled vocabularies (ontologies) that describe plant structures and growth/developmental stages providing a semantic framework for meaningful cross-species queries across databases.
- A tutorial on Plant Genome Databases.
- Plant Genetics from Oregon State University.
- About genomics
- Biotechnology at Pioneer
- PLAZA- a resource for plant comparative genomics
TOP Plant Breeding
- Global Plant Breeding - website was organized to provide information and support for plant breeders in all parts of the world, working on all crop plants, in public service and private industry
- Department of Plant Breeding and Genetics at Cornell University
- RiceCap The overall objective of the outreach component of the RiceCAP project is "to effectively communicate the science and potential of rice plant genomics, including progress and description of the RiceCAP to the U.S. rice industry". An outreach team, consisting of cooperating scientists and extension specialists from several of the institutions participating in the project has been assembled.
- The Generation Challenge Programme Farmers in the developing world face agricultural challenges far different from their counterparts in industrialized countries, and have different access to resources. This program aims to bridge that gap.
- OSU Barley Breeding Program
TOP Germplasm Resources
- GRIN National Germplasm Resources Information Network)
- ICIS (International Crop Information System on genetic resources, crop improvement, crop management)
- SINGER (Network for Genetic Resources)
- The Chinese Crop Germplasm Information System (CGRIS) is a central repository for all type of plant genetic resources information. It mainly consists of six subsystems: the management system of the National Crop Gene Bank(NCGB), the management system of the long-term storage in Qinghai, the management system of National germplasm Resources Nursery, crop characterization and evaluation database system , the database system for germplasm exchange at home and abroad and the management system of the medium-term storage in Beijing.
- Dale Bumpers National Rice Research Center (DBNRRC) Genetic Stocks - Oryza (GSOR) Collection
- International Rice Information System (IRIS) offers germplasm pedigrees
- Pedigrees of Oat Lines (POOL) A Curated Internet Database of Oat Pedigrees, from Eastern Cereal and Oilseed Research Center
Wheat Genetic and Genomic Resources Center The WGGRC has established a national and international network to conduct and coordinate genetic studies in wheat. The WGGRC maintains a gene bank, along with evaluation and passport data, on 2,500 wheat species accessions. In addition, the WGGRC houses 2,200 cytogenetic stocks, the genetic treasures produced by a lifetime of work by wheat scientists.- Wheat genetic stocks, from Graingenes
- Genetic Resources Center - a wealth of information about the conservation and utilization of rice biodiversity. Tells about the International Rice Genebank and its management, how you can obtain seed, the taxonomy of Oryza, and many other things. You can find details about a major rice biodiversity project and see many images of the project activities in Asia, sub-Saharan Africa, and Costa Rica.
TOP Pathology
- Plant Pathology Online (apsnet)
- Plant Pathology at Cornell, include photos, a glossary, and the Northeast Plant Dignostic Network
- International Rice Blast Genome Consortium
- Extension Plant Pathology, Kansas State University
- Plant Pathology, University of Nebraska
Taxonomy
- NCBI Taxonomy home page privdes links to taxonomy for grasses, including rice, wheat, maize, oats, barley, sorghum, sugarcane
- Plants Database
- Integrated Taxonomic Information System (ITIS)
Bibliography
- IRRI Library
- Citations for rice in PubMed
- Agricola, National Agricultural Library and Article Citation Database
- Literature Database at Gramene
TOP Learn about Rice
- 2004 International Year of Rice - "All about Rice"
- The Asia Rice Foundation - "Learn about Rice"
- USA Rice Federation - "Everything a rice consumer needs to know"
- US Rice Producers Association Rice Romp - K-12 Lesson plans for teachers and games for students
- Cooperative Research Centre for Sustainable Rice Production - Interactive educational resource on the science of rice
- International Rice Research Institute - Frequently Asked Questions
- Gramene - Rice Resource Links
- The Washington Post's Photo Voyage - "Rice - a global grain"
- Genetic Resources Center - a wealth of information about the conservation and utilization of rice biodiversity. Tells about the International Rice Genebank and its management, how you can obtain seed, the taxonomy of Oryza, and many other things. You can find details about a major rice biodiversity project and see many images of the project activities in Asia, sub-Saharan Africa, and Costa Rica.
- Rice Knowledge Bank Provides information and support for farmers (such as NGOs), as well as an ever-increasing wealth of information on training and rice production.
- Rice growth staging system
- Riceworld - a compendium of facts and figures from the world of rice (under construction as of 7/22/05)
- When Rice Was King
- Georgetown's Rice Museum
- Plant Genome Research Outreach Portal
- American Association of Cereal Chemists a resource cereal specialists for timely technical information, significant research findings, industry trends and career development.
- Facts about Rice from Lotus Foods
- Rice Facts from the Asia Rice Foundation
- All about Rice
- USA Rice Federation - info for consumers.
- Graindell - Learn, explore and discover the colorful world of rice
TOP Agriculture
- United States Department of Agriculture, Agricultural Research Service
- USDA National Agricultural Statistics Service
- Food and Agriculture Organization of the United Nations
- Med Rice Network - The objective of MED-RICE is to promote scientific exchanges among rice scientists working in the mediterranean area and in the other world regions with mediterranean climate
- Agricultural Biotechnology International Conference (ABIC)
Other (non-cereal) Genome Projects
- Worm Genome Database
- Mouse Genome Database
- Saccharomyces Genome Database (yeast)
- Flybase: A Database of the Drosophila Genome
- TAIR - The Arabidopsis Information Resource
- Rat Genome Database
- E-coli Genome Database
- AgBase is a curated, open-source, Web-accessible resource for functional analysis of agricultural plant and animal gene products. Our long-term goal is to serve the needs of the agricultural research communities by facilitating post-genome biology for agriculture researchers and for those researchers primarily using agricultural species as biomedical models.
- PAMGO - plant-associated microbes
Other Plant Databases
Plants Database from NRCS. New World Grasses Catalogue, Smithsonian Institution Grass Manual on the Web Grass Genera of the World TOP
