Quick Queries

Expedited access to GrainGenes' most Frequently Asked Queries.
If you have a GrainGenes question you want to ask, please let us know using the feedback button on the top right corner of the page.
Click here for a video tutorial on GrainGenes queries.

Microsatellites and STS's

  • SSR primers and corresponding mapped loci.
    Improvements suggested by Christie Williams, Simon Berry and Tim Langdon.

     SSR set (* for all)   
      Map locations on chromosome (* for all)
      Mapping data: segregation scores for these SSRs in all populations for which we have the data.

  • STS primers
    "Sequence-Tagged Sites", primers designed to amplify specific sequences.
    Source species (* for all)  
  • Markers and Mapped Genes

    • Download a whole map (Map_Data)
      Linkage groups, Loci and positions, and the corresponding Probes.
      Suggested by Gramene.

      Map_Data name  
      List Map_Data names
    • Download mapping scores for a whole map (Map_Data)
      Suggested by Clare Nelson.

      Map_Data name 
      List Map_Data records that have scores
    • Download all mapping scores in GrainGenes
      Suggested by Matthieu Falque.
    • Nearby Loci
      All Loci within a specified distance of a specified Locus on any map.
      Suggested by Jim Anderson; improved by Yavuz Barbaros.

      Locus  List all Loci

      On map:
      Wheat Composite 
      • Nearby Genes
        A modification that shows only the Genes near the specified locus.
        Suggested by Angelo Karakousis and Victor Aguilar.

        Distance   List all Loci
      • Nearby QTLs
        A modification that shows the QTLs near the specified locus.

        Distance   List all Loci
      • Loci between two markers
        All Loci that are between two specified Loci on any map.
        Suggested by Molly Jahn and Gilly Sanchez.

        Locus 1
        Locus 2  List all Loci
      • Locus types
        Loci of a particular type from a particular species

      • Trait markers
        Linkages between useful genes and molecular markers.
        From Greg Penner's 2_Point_Data database.
      • All maps for a given Probe
        Suggested by Mark Sorrells.

          List all Probes
      • Genes by chromosome group
        Genes mapped to a specified chromosome group.
        Suggested by Angelo Karakousis.

      • Probes mapped to a specified chromosome
        Suggested by Jon Raupp.

      • Mapped Sequences

      • Sequenced probes that have been mapped in

        (* for any species) 
      • Mapped known-function probes
        Cloned genes that have been mapped in a particular species.
        Suggested by Peter Hedley; improved by Barbara Read.

      • Sequenced genes
        Listed by Gene Class. With map location if available.
        Suggested by Peter Mascia.
      • Mapped STS's
        FASTA sequence data only.
        Suggested by Philippe Leroy.
      • Loci for a specified sequence
        Suggested by Tim Close.

         GenBank Accession 
      • Loci homologous to a specified sequence

         GenBank Accession 
      • Probes homologous to a sequence of specified function
        Suggested by Jose Gonzalez-Hernandez.
        (wEST-SQL Database, mapped wheat ESTs from the NSF project.)

         (Don't use wildcard *s.) 
      • Sequences

      • Count of sequences by cultivar
        Suggested by Gerry Lazo.

      • EST contigs vs. libraries
        Compare treatments that produced ESTs in the same Contig.
        Suggested by Tim Close.

        Treatment 1
        Treatment 2  List all Treatments
      • QTLs

        • QTLs for a specified trait, or all.

          Trait (* for all)  List all QTL traits
        • Trait scores from a specified QTL mapping study

          Trait Study    List all QTL Trait Studies
        • Marker scores from a specified QTL mapping study

          Trait Study   List all QTL Trait Studies
        • Genes

          • Genes by class and chromosome
            Use '*' to specify a gene or gene prefix and a chromosome, group (5*) or genome (*B).
            Suggested by Bob Bowden.

          • Genes vs. germplasm lines
          • Alleles vs. germplasm lines
          • Barley genes
            Symbols, synonyms, chromosomes, and references for Hordeum genes.
            Most of these are from von Wettstein-Knowles (1993) and Barley Genetics Newsletter volume 26.
            Other major sources are the Wheat Gene Catalogue and Joergensen (1993)'s catalogue of Ml genes.


            • Allele differences (polymorphisms) between two germplasm lines

                List germplasms with allele data
            • Allele identities (monomorphisms) between two germplasm lines

              Suggested by Michael Wanous.


              • Search by Author, Keyword, and/or Date.
                (Author and Keyword can be left blank. "since" must be a number.)

                Keyword,    since
              • Search reference titles and keywords.
                Suggested by Victoria Carollo.
                • "OR" search

                  Keyword 1 Keyword 1 only
                  Keyword 2 Keyword 1 or 2
                  Keyword 3 Keyword 1 or 2 or 3
                  Keyword 4 Keyword 1 or 2 or 3 or 4
                  Keyword 5 Keyword 1 or 2 or 3 or 4 or 5

                • "AND" search
                  Keyword 1
                  Keyword 2 Keywords 1 and 2
                  Keyword 3 Keywords 1 and 2 and 3
                  Keyword 4 Keywords 1 and 2 and 3 and 4
                  Keyword 5 Keywords 1 and 2 and 3 and 4 and 5

                • Address Book

                  • Plant breeders
                    Colleagues whose position or research interest includes breeding.

                  • Colleagues
                    All colleagues for which GrainGenes has an email address and/or photograph.


                  • Resistant germplasm
                    Accessions rated as "Resistant" or "Immune" or "Low sporulation" from the Wheat Genetics Resource Center (WGRC).
                    (Note: not all of the WGRC collection is in the database yet.)
                    Suggested by Jon Raupp.
                  • ICARDA durums
                    Names, ICARDA accession numbers and pedigrees.