1. www.panzea.org Panzea Graphical Map Viewer Tutorial With the Panzea graphical map viewer you can construct custom graphical displays of the map positions of any of the maize or teosinte genes and markers used in our project that have known or estimated map positions Both physical and genetic maps can be viewed The Panzea graphical map viewer is a highly simplified access point to the full CMap viewer interface  CMap viewer = “comparative map” viewer Once inside CMap, you can use its powerful features to further customize your map, including building a comparative physical vs. genetic (or maize vs. teosinte) map

2. www.panzea.org Tutorial Outline How to view a genetic map of a chromosome or segment How to view physical maps of a maize contigs How to use the CMap interface to:  construct a comparative genetic vs. physical map of a maize chromosomal segment  construct a comparative genetic map between maize and teosinte

3. www.panzea.org View a genetic map of a maize chromosome... Step 1: Choose “Genetic Map” view (then click “Submit”)

4. www.panzea.org View a genetic map of a maize chromosome... Step 2: Choose the “IBM2” map (then click “Submit”)

5. www.panzea.org View a genetic map of a maize chromosome... Step 3: Choose the chromosome of interest -- say Chr 9 (then click “Submit”)

6. www.panzea.org View a genetic map of a maize chromosome Step 4: The “Region of genetic map” fields will automatically fill in with the full extent of the chosen chromosome You can zoom into a particular segment by narrowing this range (we will leave it as is) Step 5: Choose the features that you want displayed on your map. (Choosing all features will result in a cluttered map with considerable overlap, since almost all SNPs have a corresponding sequence feature, all SSRs are also considered marker loci, etc.) Then click “Display Map”

7. www.panzea.org Et voila! Here is your map Because of space limitations, not all of the selected features are shown. To be sure to not miss anything, you can zoom in the maximum amount by scrolling down the window and then...

8. www.panzea.org...changing the Magnification from “Original” to “20” and then clicking on “Redraw”

9. www.panzea.org Now you will need to use the scrollbar of your web browser to see the whole map But there will now be room on the display for all of the map features and their labels etc...

10. www.panzea.org View physical maps of maize contigs Step 1: Choose “Physical Map” view (then click “Submit”)

11. www.panzea.org View physical maps of maize contigs... Step 2: Choose the chromosome of interest -- say Chr 9 again then click “Submit”

12. www.panzea.org View physical maps of maize contigs Step 3: The “Contig on physical map” list will automatically be populated with all of the contigs anchored to the chosen chromosome. Contigs are numbered according to their physical order along the chromsome. You can select multiple contigs using the Shift or Ctrl keys, but we will choose only ctg373. Step 4: Choose the features that you want displayed on your map. (Choosing all features will likely result in a cluttered map with considerable overlap, since all Sequences are also classified as either a Candidate or Random gene, all SSRs are also considered marker loci, etc.) Then click “Display Map”

13. www.panzea.org Et voila de nouveau! Here is the CMap display of your physical map This time I have changed the CMap magnification option to 2X For most of the random genes ( purple labels ), the Genbank accession number identifies the gene – click on any of the labels for more info (same thing for any of the feature labels, and in the genetic map view as well) The physical map units are in “contig bands”, each of which are roughly 5 kb wide..etc...

14. www.panzea.org Compare maize genetic vs. physical maps First obtain a CMap view of Chr 9, as before  adjust the magnification to 20X Then use the CMap “Map Set” option to “Add maps right”  see illustration on next slide

15. www.panzea.org Click here to add a comparative map to the right of the current map

16. www.panzea.org Choose “ Physical : Zea mays - Panzea Genes&Markers on FPC ” from this drop down list

17. www.panzea.org Scroll down this list of available physical contig maps and choose “ Chr. 9–ctg373 ” Then click on “ Add Maps ”

18. www.panzea.org And here is your comparative genetic vs. physical map! (After adjusting the magnification of the ctg373 map to 2X and scrolling to the appropriate place in your web browser window) Corresponding features are shown with red labels There is generally very good correspondence between the map of this contig and the genetic map of this portion of Chr 9. Note that the physical map provides higher resolution map order of loci.

19. www.panzea.org Compare maize vs. teosinte genetic maps First obtain a CMap view of maize Chr 6, as before  but Chr 6 this time!  this time display IBM2 core markers, Panzea SNPs and Panzea SSRs (and set the magnification to 20X) Again use the CMap “Map Set” option to “Add maps right”  this time choosing the map set: “ Genetic : Zea mays – TeoMaizeBC1 ”  then choose chromosome “6” from the list below  and adjust the magnification of the added map to 20X

20. www.panzea.org And here is a portion of your comparison of the maize vs. teosinte genetic maps of chromosome 6 More accurately, a comparison of the maize map for Chr6 vs. that for a maize/teosinte hybrid (but that is a lot more typing!!) Again, there is excellent correspondence (synteny) between the two maps (scroll up and down in your browser to confirm that this is so)

21. www.panzea.org CMap: a powerful interface with many options Hence the need for a simplified Panzea access page that is less daunting to the novice user One purpose of this tutorial is to give you a feel for modifying a few of the options directly in CMap  e.g., controlling magnification, adding comparative maps Do go ahead and play around further in the CMap viewer to explore its many other options  We won’t cover those here, but there is a CMap help page: