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Gramene Genetic Diversity Database Help Document

Gramene Genetic Diversity module is a repository for SSR and SNP allelic and phenotypic data for cereal crops. Currently, there is SSR data for rice, SNP and phenotypic data for maize, and SNP data for wheat. Please read the data summaries for more detail.

The Genetic Diversity module allows you to view allelic variation at particular loci across multiple germplasms from a specific experiment, as well as genome-wide allelic variation in particular germplasms.

Genetic Diversity search options

A. Search

• On the Diversity home page, use the search text field to retrieve allele data searching by keyword.
• Searches can be done using germplasm accession name, accession number,or marker/locus name. For example, for rice, enter IR36, "IRGC 3575", PI 385418, RA4969, RM22.
• Optionally, filter your search by type - marker or germplasm.
• Select the species of your interest from the species pull-down menu
• Click the search icon.
Tips:
• To improve the relevance of search results, especially when searching using an accession number or name with a space between the letters or numbers, insert the accession number or name between quotation marks. Eg. For IRGC 3575, use "IRGC 3575".
• If a germplasm name, especially a name with less than five letters, has a space between the letters, then try your search with out the space between the letters, eg. for IR 36 use IR36.
• If the accession name has only two letters, then double the name, eg. for germplasm T1 use T1T1.
• Different examples are given for each species. Select the species of interest in order to view examples.
• For help on how to use the Panzea searches: Germplasm Search, Molecular Diversity Search, Gene/Locus Search, Phenotype Search; see their respective pages, or go to the Panzea website for more information.

B. Panzea Searches

• These searches can be accessed from the Diversity Home Page. Panzea is updating the tutorials, so for help on how to use the Germplasm Search, Molecular Diversity Search, Gene/Locus Search, Phenotype Search, and Advanced Search tools go to their respective pages and follow the links.

C. Advanced Search

• For a brief tutorial, see Gramene's Diversity Advanced Search: Highly-Flexible User Front-End Built on GDPC Middleware.
• For information on installing and using the GDPC browser, see the GDPC website.

Genetic Diversity Search Results

A: Search by germplasm accession name or accession numbers.

• Passport description:
• Accession name: common name of the germplasm
• Institute(s) holding accession: Sources of germplasm and link(s) to their online germplasm request forms.
• Accession number: unique identifier number assigned to a germplasm when entered to into genebank collection or into a PI's laboratory
• Synonym(s): unique identifier numbers assigned to a germplasm when entered to into genebank collection. Link to IRIS or GRIN databases allows to view information on the germplasm on those databases.
• Stock Source
• Stock Number
• Germplasm type: biological status of a germplasm.
• Taxonomy data:Genus, species, subspecies, and subtaxa are taxonomic classes of a germplasm based on the genetic data analysis in an experiment.
• Taxonomy xref: link to Gramene Ontology database for more taxonomic information on a germplasm.
• Collection information: collector, collection date, latitude, etc. describe where a germplasm was collected.
• Experiments: List of experiments from which allele data on germplasm was generated.
  • Title: title of the paper used as a data source or name of the experiment. Links to experiment information
    • Detail: Title, Design, Polymorphism Type, Allele Scoring protocol, Pis and Comments
    • Markers: A list of markers used in the experiment, with links to allele data.
    • Germplasm: a list of germplasm used in experiment, Provides accession name and mumber, Type, Source, and links to allele data.
  • Details: Design, polymorhphism type, allele scoring protocol, and PIs, give detailed description of the experiment(s).
  • Comments: brief summary of the experimental protocol and a link to the abstract of the paper used as the data source.
  • Show allele data: a link to view the allele data for a germplasm from the experiment.
  • Germplasm Accession Name: To learn about the germplasm details, view genome-wide allelic variation on a germplasm, and to see if there is allele data on a germplasm from other experiments click here to return to Passport and experiment data.
  • Subspecies and subtaxa:
  • Country of Origin:
  • Accession Number:
  • Stock Number:
  • Locus name: lists all the marker/loci assayed for a germplasm in a specific experiment.
    • To view all allele data on a particular locus in all the germplasms from the experiment, click the marker/locus of interest or click the "view" link corresponding to the locus of interest in the "all allele data on locus"column.
    • To view information such as primers sequences, repeat motif, map position etc. on a marker, click on the marker name and on the next page click the "search for.. on Gramene Marker Database" link above the marker table.
  • Genotype columnn gives allele values (band length in base pairs for SSR loci, and single nucleotide variants for SNP loci) for the corresponding locus of the germplasm of interest.
  • Link to " View all genotypes on marker":

B: Search by marker/locus name

• Experiments: List of the experiment(s) the marker/locus of interest was assayed is provided. For details of the experiment information please refer to experiments section above.

Other Resources

Tutorial	More in-depth than the help pages, use the tutorial for an exaple of using the database, see how it integrates other datasets, and get tips to increase your data search efficiency.
FAQ	Frequently Asked Questions - see what questions users have asked, and get the developers answers.
Release Notes	For more information about the most recent release.

Feedback

• Please send comments, questions and suggestions to us using the "Feedback" link at the top of the Gramene pages or by going to the following URL: /db/feedback/send_feedback?refer_from=/diversity/index.html
• If you find any inconsistencies or mistakes, please communicate them to us by clicking on the "feedback" link. Your suggestions and feedback are highly appreciated by the Gramene staff.

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