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Gramene DiversityGramene Genetic Diversity database contains SSR and SNP allelic data and passport descriptions for rice, maize and wheat germplasms. It also holds

phenotypic data for maize.

The ultimate goal is to make this database a source of rice, maize, and wheat bio-information from/for

evolutionary, domestication, association, and genetic diversity studies. It also could potentially be useful for applications such as germplasm management, marker

assisted selection and DNA-based variety identification.

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Search by Germplasm

Passport DataAccession data

SynonymsHolding Institute

Stock SourceGermplasm

Taxonomy dtaCollection Data

Collector, LocationExperiment Data

TitleDesign

Polymorphism typeScoring Protocol

ProducerOriginatorCommentsAllele data

Marker and Allele DataAccession #

Accession nameLocus name

GenotypeAll genotypes on a marker/

germplasms

Search by Marker

Literature DB Markers DB

External germplasm DBs

Diversity Data Map

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Tutorial HelpThe hand icon indicates a link that allows you to go to the same page

in your web browser.

If you are viewing this tutorial with Adobe Acrobat Reader, click the "bookmarks" on the left hand side of the Reader for easier navigation.

Action Options are noted in this type of font.

Notes or comments use this style font.

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From either of the search or quick start menus, click on Diversity.

Gramene Home www.gramene.org

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1. Enter germplasm name, accession number or marker name to view allelic data. 2. Select species

Diversity Home: Search (by Germplasm name)

Example searches

Click for database species summaries (see Slide 13)

3. Click “Submit”

optional

General search does NOT search Diversity

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Error messages?

For accession numbers with IRGC

prefix, use quotations : “IRGC

3575“.

For small names (<3 letters/word) with a space, remove the

space : IR36

For small names (<3 letters) double the

name : T1T1

Error message gives hint

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Link(s) to external

databases

Link(s) to germplasm

request form(s)

Links to abstract

Click to view allele data on germplasm(see

Slide 8)

Click to view marker type details

Click to view taxonomic details (See Gramene Ontology

tutorial)

Search Results (Germplasm Name)

Passport Description

Collection Information

Experiment Information

Click to begin new search (home page)

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Allele Data (by Germplasm Accession #)

Return to Germplasm Data (Previous Slide)

Click for all allele data on this marker

(see Slide11)

Click for Marker Information

(Slide 9 & 10)

Markers assayed for a germplasm Allele(s) for the

corresponding loci

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See Slide 7 for more information on

details of this page.

Click to view marker details in Gramene

Marker DB. (See Slide 10)

Click to view allele data for marker from

experiment.(Slide 11)

Marker

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Marker Detail

Marker Data in Gramene Marker

DB. See Markers Tutorial

Markers menu indicates you are not in Diversity

database anymore

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Germplasm Data – as in slide 7.

All alleles for marker on all germplasms in an

experiment

Click to view all allele

data on all markers/loci

on a germplasm.

Allele Data for Marker

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Enter Marker name.

Click for database summary by species (see Slide 13)

Search result is the same as slides 9-11.

Search by Marker

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Data Summary

Summary of information in this

release of Gramene.

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Germplasm searchOptions are

based on species

Select options and click submit

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Molecular Diverisity Search

Options are based on species

Select options and click submit

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Gene/Locus Search

Options are based on species

Select options and click submit

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Phenotype Search

Options are based on species

Select options and click submit

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GDPC Browser

For more complex queries, you can use The Genomic Diversity and Phenotype Connection (GDPC) Browser. Here you can download and get documentation how to use the GDPC Browser.

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Use Feedback to ask questions or make

comments to Gramene

Help

Help documents assist in how to conduct a search and to define

your results.

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Tutorials

Tutorials are available in PDF or Powerpoint

All Gramene Tutorials listed here.

Click for other help documents

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FAQ’s

Select a module to view it’s FAQs

Search FAQ

Submit a question to Gramene

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Contact Gramene

Use the feedback button, located at the top of every page, to provide feedback or to ask questions about Gramene.

Email Gramene at gramene@gramene.org

or