About GrainGenes

    Last update Nov 1999
    GrainGenes--wheat, barley, rye, oat, sugarcane and relatives

    Coordinator: Olin Anderson / oandersn@pw.usda.gov

    GrainGenes is a genetic database for Triticeae, oats, and sugarcane, being assembled as part of the United States Department of Agriculture, National Agricultural Library's Plant Genome Program, initiated by Jerome P. Miksche and currently directed by Henry L. Shands. Additional support is provided by ITMI, the International Triticeae Mapping Initiative, through a grant from the USDA/DOE/NSF Joint Program on Collaborative Research in Plant Biology.

    The GrainGenes project is coordinated by Olin Anderson (USDA, Albany, CA). The master database is at Cornell University, administered by Dave Matthews. Kinds of information include:

    • genetic and cytogenetic maps,
    • genomic probes, nucleotide sequences,
    • genes, alleles and gene products,
    • associated phenotypes, quantitative traits and QTLs,
    • genotypes and pedigrees of cultivars, genetic stocks, and other germplasms,
    • pathologies and the corresponding pathogens, insects, and abiotic stresses,
    • a taxonomy of the Triticeae and Avena,
    • addresses and research interests of colleagues,
    • relevant bibliographic citations.

    Data Coordinators

    Needless to say, compiling and curating all this information is a very large project. We have identified specific areas that require data assembly and organization, and have formed a committee of coordinators. As is inherent in such databases many areas are overlapping and will require input from several areas of expertise. As the need becomes apparent, 'subcommittees' will form around broad topics. The following individuals have agreed to serve as the coordination committee for the database. 
    Database coord.,   Olin Anderson, USDA, ARS, WRRC, 800 Buchanan, Albany, CA
probe repository   94710, Tel: 510-559-5773  FAX: 510-559-5777
                   Email: oandersn@pw.usda.gov

Cytogenetics,      Bikram Gill, Department of Plant Pathology,
stocks, mapping    Kansas State University, Throckmorton Hall, Manhattan, KS
                   66506, Tel: 913-532-6176 FAX: 913-532-5692,
                   Email: raupp@ksu.edu

Proteins, gel      Bob Graybosch, USDA, ARS, Department of Agronomy, 322
patterns, wheat    Keim Hall, University of Nebraska, Lincoln, Nebraska,
quality            Tel: 402-472-1563 FAX: 402-437-5234,
                   Email: agro100@unlvm.unl.edu

Genetic stocks     Perry Gustafson, USDA, ARS, Department of Agronomy,
                   University of Missouri, Columbia, MO 65211, Tel:
                   314-882-7318   FAX: 314-875-5359,
                   Email: pgus@showme.missouri.edu

Genetics,          Gary Hart, Department of Soil & Crop ciences, Texas A&M
nomenclature       University, College Station, TX 77843, Tel: 409-845-8293
                   FAX: 409-845-0456, Email: ghart@acs.tamu.edu

Germplasm,         Ken Kephart, 214 Waters Hall, University of Missouri,
pathology (temp.), Columbia, MO 65211. Tel: 314-882-2001   FAX: 314-884-4317 
traits             Email: kephart@montana.edu

Data entry,        Gerry Lazo, USDA, ARS, WRRC, 800 Buchanan, Albany, CA
coord., maint.,    94710, Tel: 510-559-5640  FAX: 510-559-5777
database design    Email: lazo@pw.usda.gov

Genetics,          Udda Lundqvist, Svalof Weibull AB, Svalov, S268 81,
nomenclature       Sweden, Tel: +46 418 667010 FAX: +46 418 667109
                   Email: udda@ngb.se

Data entry,        David Matthews, Dept. of Plant Breeding & Biometry,
coord., maint.,    Cornell Univ., Ithaca, NY 14853, Tel: 607-255-9951 FAX:
database design    607-255-6683, Email: matthews@greengenes.cit.cornell.edu

Taxonomy           Pat McGuire, Genetic Resources Conservation Program,
                   UC Davis, Davis, CA 95616, Tel: 916-757-8923  FAX:
                   916-757-8755, Email: pemcguire@ucdavis.edu

Data entry,        Mark Sorrells, Dept. of Plant Breeding & Biometry,
coordination       Cornell Univ., Ithaca, NY 14853, Tel: 607-255-1665  FAX:
                   607-255-6683, Email: mes12@cornell.edu
    Anyone with interests in participating in database design, data contributions, data assembly in any of these or other specific areas should contact the appropriate coordinator or Olin Anderson.

    GrainGenes Database

    The GrainGenes Database is maintained and accessed via the software ACEDB, by Richard Durbin and Jean Thierry-Mieg. An overview of the data available in the Database as of Dec 1995 is given below.

         Data class  Number of records
  -------------  -----------------
       Map_Data  31      Wheat, T. tauschii, barley, oat, sugarcane, rice
            Map  328 
          Locus  7400 
          Probe  4000 
   Polymorphism  1600    With images of autoradiograms
       Sequence  200     End sequences of probes
           Gene  660 
         Allele  990 
    Gene_Product 60      HMW glutenin subunits
      Germplasm  11000   Unique wheat, rye, triticale germplasms 
        Species  1400    Including plants, pathogens and insects
   Trait_Scores  14000   24th International Spring Wheat Yield Nursery
            QTL  4 
      Pathology  450     With images of symptoms
          Image  1400
      Colleague  1100 
      Reference  1500
    The current downloadable version of GrainGenes is updated daily, as are the online versions at this WWW gateway and the GrainGenes Gopher server.

    A log of additions and updates to the database is maintained in the What's new? file on the GrainGenes Gopher server, and in the What's New page on the GrainGenes Webserver.

    GrainGenes Associated Datasets

    In addition to the core GrainGenes dataset, the GrainGenes Webserver and GrainGenes Gopher server purvey an equally large amount of information that is in non-ACEDB formats, including HTML and free text. Many of these additional datasets are searchable online, and some are also available for downloading in their entirety. They include

    • Annual Wheat Newsletter
    • Catalogue of Gene Symbols for Wheat
    • Commercial Wheat Cultivars of the US, an electronic monograph by Ken Kephart
    • HMW-glutenin subunit data for 1900 wheat cultivars, from Bob Graybosch
    • Wheat quality evaluations, from Bob Graybosch
    • CIMMYT list of abbreviations for 8700 wheat cultivars, from Bent Skovmand

    Long-Term Considerations

    Although the USDA is supporting the initial stages of database development, the success of this program will depend greatly on the cooperation and participation of laboratories throughout the research community world-wide. We are particularly interested in cooperating with members of international community who are recognized, officially or unofficially, as curators of data. The USDA will concentrate on hardware, software, assembly of combined databases, database access, and will only perform minor curatorial functions; each plant community will be called on to organize and update the data for its own plant system.

    All laboratories possessing relevant data are urged to deposit their data with the database. Any laboratory interested in accessing the databases or running the databases locally can contact Olin Anderson or David Matthews. Users are reminded that this is a developing database effort, therefore gaps in data should be expected. However, all users are encouraged to make both suggestions on improvements and new sources of data.

    Access Methods

    The most convenient access to the GrainGenes Database for many people will be via the ACEDB-WWW Gateway. Both this and the other GrainGenes services are mirrored at multiple Internet sites, for faster international access times and to avoid unavailability due to (rare but inevitable) local network outrages.

    • ACEDB-WWW Database Gateway

      • Demeter's Genomes, Cornell University, USA
      • WWW GRAIN, Jouy-en-Josas, France

    • ACEDB stand-alone Database

      Copies of the latest release of the ACEDB version of GrainGenes, for running on your own Unix, Windows95/NT or Macintosh computer, can be downloaded by anonymous ftp from
      • Demeter's Genomes
      • WWW GRAIN

      The Windows and Macintosh versions are also available on CD-ROM from the Korea Rice Genome Database Network. Please send requests to Dr. Baek Hie Nahm, Myongji University, Yongin, Korea.

      For those who wish to maintain a more up-to-date copy of GrainGenes, the software package Mirror can be downloaded. This package, for Unix or Windows, includes instructions for mirroring the anonymous ftp directory graingenes.current, which is updated daily from the master copy at Cornell University.

      Users who have no computer suitable for maintaining a local copy of the database but do have direct Internet access (TCP, PPP, ISDN etc.) and X11 software for their personal computer may request a GrainGenes ACEDB account from Olin Anderson or Dave Matthews.

    • GrainGenes Webserver

      • USDA Western Regional Research Center, Albany, CA, USA
      • WWW GRAIN, Jouy-en-Josas, FR

    • GrainGenes Gopher

      • Cornell University
      • WWW GRAIN
    - Dave Matthews