Gramene User Help

Is there a tutorial or help document for using the Diversity module?

Yes. The tutorial and help documents are available at http://www.gramene.org/tutorials/diversity.html and http://www.gramene.org/diversity/help.html, respectively.

What kind of data is in the Diversity database?

Gramene Genetic Diversity database contains SSR, RFLP and SNP allelic data and passport descriptions for rice, maize and wheat germplasms. It also holds phenotypic data for rice and maize (from QTL studies). The database can be searched by germplasm accession number, accession name and marker/locus name.

Why is the allele value for some rice SSR loci one and others two?

If you see one allele value for a SSR locus in rice, then it means the primer set amplified one fragment. If there are two values, then the primer set amplified two fragments. In Maize, if a primer set amplifies one fragment, then it is assumed the locus is homozygous and hence two identical allele values.

What sources does Gramene use to curate the Genetic Diversity database?

Currently rice data is from studies published in peer-reviewed journals only. Maize and wheat data is obtained from the "Molecular and Functional Diversity of the Maize Genome" and "Haplotype Polymorphism in Polyploid Wheats and Their Diploid Ancestors" projects, respectively .

Where can I find information about the history of a germplasm accession "RA####"?

Please refer to the Gramene Diversity database to find the germplasm information (country of origin, collection date etc...) Gramene has for the accessions. The RA- numbers are stock numbers assigned to the accessions in Dr. Susan McCouch's lab; you will find more identification including their common names, accession numbers assigned to them at IRRI/IRIS and NSGC/GRIN. For additional information the IRIS and GRIN databases may have about the germplasms, click the "search at IRRI" or "search at GRIN" links.

How can I search for phenotype data?

The search capability of the database for phenotype data is under development. However, if you are interested for phenotype data from a particular population study or germplasm, you can search by the germplasm or population name.

Where can I find a primer set and/or map location(s) of a marker of interest?

From the diversity pages, click on the marker name and you will see on the top of the next page a link with "primer sequences....". Follow the link and you will find the details of the marker in the marker database. Another option is to directly search the marker database using the marker name.

Where can I find a detailed description of the methodology used to generate the allele or phenotype data?

There is a link to the abstract of the paper used to curate rice data. For maize and wheat data, you may need to directly contact the personnels at http://www.panzea.org/ and http://wheat.pw.usda.gov/SNP/project.html, respectively.