Viewing Genetic Maps with MapViewer in CottonGen Katheryn Buble, Jing Yu, Sook Jung, Ping Zheng, Jodi Humann, Taein Lee, Chun-Huai Cheng Morgan Frank, Deah McGaughey, Amita Mohan, Heidi Hough, Josh Udall, Don Jones and Dorrie Main Hi, my name is Katheryn and I am the developer of the MapViewer on the CottonGen website. Thank you for attending this presentation. Today, I would like to show you how to use MapViewer to view genetic maps in the CottonGen website and introduce several of MapViewer’s features. 2018 International Cotton Genomics Initiative Conference May 28 – June 1, 2018 Edinburgh, Scotland

Access to MapViewer on CottonGen Mapviewer is a tool for viewing and comparing genetic maps. MapViewer is accessible from several different locations in CottonGen. It can be used from the Tools menu in the header, the Crop Overview page or the Map Overview page. The Map Overview page displays a summary graphic of all linkage groups and clicking a linkage group opens a more detailed view in MapViewer. B

Linkage Group Zoom and Marker Detail C MapViewer displays the complete linkage group on the left (A), and zoomed-in region (B) on the right. The zoom scaling can be adjusted by dragging and resizing a window on the linkage group on the left side. A legend with marker colors is drawn below the linkage group figure. To view more information about each marker, hover over the marker name with the pointer for the marker summary which will appear on the right side zoomed graph to see a tooltip, or click on the marker to open the Marker Overview details page (C). Here in the Marker Overview, in the Map Positions table the MapViewer column will link back to the linkage group in the MapViewer for each marker. B

MapViewer Control Panel B The MapViewer Control Panel is located at the bottom of the MapViewer page below the linkage group(s) display. The Control Panel is used to configure which linkage groups are displayed as well as their viewing options. A,B: Using the “Select Reference Map” and “Select Comparison Map” controls, the species, maps and linkage groups for viewing can be selected.  C: The color of the markers and which markers are displayed can be changed. These changes in the marker colors are also reflected in the legend, located below the linkage groups. D: Markers can be hidden by selecting on the specific marker type in the Marker visibility selector field. E: The ruler and marker positions can be toggled on or off. In the on position, each marker displays its own specific marker position label.   Then to display the changes after updating any of these parameter sections, press the Submit button. C D E

Marker Correspondences B CottonGen Data Overview 84 Markers Genetic Maps QTLs Traits 119,778 1,336 23,120 Here, marker correspondences between linkage groups from different maps are displayed. We can zoom in on the region where correspondences exist, using the zoom scroll, specifically on the left reference linkage group (A) or the right comparison linkage group (B). This enables detailed viewing of all markers in common between the two linkage groups. The Mapviewer in CottonGen can be used to access 84 genetic maps containing 119,778 markers and 1,336 QTLs, for 23,120 traits (9,979 +13,141), with more data being added from publications on a regular basis.

Acknowledged with thanks I would like to thank the following organizations for providing funding support to CottonGen. If you have any questions or suggestions, please contact us with the CottonGen webform or reach out to us directly during the conference. We are looking forward to answering any questions. Are there any questions about MapViewer or its use on the CottonGen website? Contact us: https://www.cottongen.org/contact Cite us: Yu et al., 2014