Gramene: Genetic Diversity Database

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.

HOW TO SEARCH:

On the Diversity home page, use the search text field to retrieve allele data.

What search keywords to use:
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.

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.
Select the species of your interest from the species pull-down menu before you press "submit".

SEARCH RESULTS:

A: Search by germplasm accession name or accession numbers will provide the following information.

Passport description:

Accession name: common name of the germplasm
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.
Institute(s) holding accession: Sources of germplasm and link(s) to their online germplasm request forms.
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.

Name: title of the paper used as a data source or name of the experiment.
Description:Design, design, polymorhphism type, allele scoring protocol, originator, and comments 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.
Allele data table:

Locus name lists all the marker/loci assayed for a germplasm in a specific experiment.
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.
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 on the bottom of the page.

B: Search by marker/locus name

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.
For description of the columns in the allele data table, please refer to allele data table section above.
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 on its accession name or number.

For help on how to use the Germplasm Search, Molecular Diversity Search, Gene/Locus Search, Phenotype Search, and Advanced Search tools click on the their respective links.

FEEDBACK:

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