GMT Tutorial Exercise 20

The Automated Designers - How to use the Polymorphism Viewers

• The Polymorphism Viewer macros can be used for different purposes, accordingly, the workflow to follow will vary according to your interests.
• Below are several example workflows showing how the Polymorphism Viewers can be used.
• Click on the step you would like to find out more about. Move between instructions for the different steps forming a workflow with the [previous step] and [next step] links in the top right-hand corner of each step-wise instruction.

Workflow 1: Find MRT^TM markers in a map location of interest

1. Download the Polymorphism Viewer macro for wheat or barley (as applicable) from GMT.
2. Open the macro and enable the macro functions.
3. Check the macro's version number.
4. Browse the worksheets where several genetic maps have been aligned to view the distribution of markers.
5. Select markers in map regions of interest by copy / pasting them into a marker list for your work.

Workflow 2: Find the locations of the "Whole Genome Scan" pre-selected markers

1. Download the Polymorphism Viewer macro for wheat or barley (as applicable) from GMT.
2. Open the macro and enable the macro functions.
3. Check the macro's version number.
4. Select the "Whole Genome Scan" build(s) of interest from the drop-down box.
5. Browse the worksheets where several genetic maps have been aligned to view the distribution of markers. Markers in the selected "Whole Genome Scan" marker kit are highlighted in grey.

Workflow 3: Find where MRT^TM markers are located on different genetic maps

1. Download the Polymorphism Viewer macro for wheat or barley (as applicable) from GMT.
2. Open the macro and enable the macro functions.
3. Check the macro's version number.
4. Enter the names of MRT^TM markers that you would like to see highlighted on the main page.
5. Browse the worksheets where genetic maps have been aligned. Markers that were entered on the main page are highlighted in grey.

Workflow 4: Display the location and polymorphism status of markers that have been pre-screened with the Automated Designer for Marker Screening

1. Use one of the Marker Screening macros to carry out an experiment identifying markers that are polymorphic between a set of samples.
2. Create a GenMAP file for the polymorphic markers with the Marker Screening macro.
   • For a user-selected list of markers, please refer to the instructions for the Automated Designer for Marker Screening macro for how to do these two steps.
   • For the "Whole Genome Scan" pre-fabricated marker kits, please refer to the instructions for the Automated Designer for Whole Genome Scan macros for how to do these two steps.
3. Download the Polymorphism Viewer macro for wheat or barley (as applicable) from GMT.
4. Open the macro and enable the macro functions.
5. Check the macro's version number.
6. On the Main Page, enter the required experimental data according to instructions 1) to 3) on the worksheet.
7. Browse the worksheets where genetic maps have been aligned. Markers that were entered on the Main Page are highlighted in different colours, depending on whether they were identified as polymorphic or monomorphic. See the Help page for colour-coding details.