1. Gramene V. 221 Gramene Diversity Gramene 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.

2. Gramene V. 22 2 Tutorial Help 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.

3. Gramene V. 22 3 From either of the search or quick start menus, click on Diversity. Gramene Home www.gramene.org

4. Gramene V. 22 4 1. Enter germplasm name, accession number or marker name to view allelic data. Diversity Home: Search (by Germplasm name) Example searches Click for database species summaries (see Slide 13) 3. Click “Submit” General search does NOT search Diversity 2. Select species optional

5. Gramene V. 22 5 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

6. Gramene V. 22 6 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)

7. Gramene V. 22 7 Allele Data (by Germplasm Accession #) Return to Germplasm Data (Previous Slide) Click for all allele data on this marker from this experiment (see Slide10) Click for allele data on this marker from all experiments (Slide 8 & 9) Markers assayed for a germplasm Allele(s) for the corresponding loci

8. Gramene V. 22 8 Marker See Slide 6 for more information on details of this page. Click to view marker details in Gramene Marker DB. (See Slide 9) Click to view allele data for marker from experiment. (Slide 10)

9. Gramene V. 22 9 Marker Detail Marker Data in Gramene Marker DB. See Markers Tutorial Markers menu indicates you are not in Diversity database anymore

10. Gramene V. 22 10 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 Germplasm Data – as in slide 6.

11. Gramene V. 22 11 Click for database summary by species (see Slide 12) Search result is the same as slides 8-10. Search by Marker Enter Marker name.

12. Gramene V. 22 12 Data Summary Summary of information in the current release of Gramene.

13. Gramene V. 22 13 Germplasm search Select options and click submit Options are based on species

14. Gramene V. 22 14 Molecular Diversity Search Options are based on species Select options and click submit

15. Gramene V. 22 15 Gene/Locus Search Options are based on species Select options and click submit

16. Gramene V. 22 16 Phenotype Search Options are based on species Select options and click submit

17. Gramene V. 22 17 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.

18. Gramene V. 22 18 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.

19. Gramene V. 22 19 Tutorials Tutorials are available in PDF or Powerpoint All Gramene Tutorials listed here. Click for other help documents

20. Gramene V. 22 20 FAQ’s Select a module to view it’s FAQs Search FAQ Submit a question to Gramene

21. Gramene V. 22 21 Release Notes

22. Gramene V. 22 22 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