GMT Tutorial Exercise 23 - Workflow 1 - Step 1

Choose MRT^TMmarkers for the genetic analysis

Selecting markers with a "pre-screening" experiment

A pre-screening experiment can be useful to identify e.g. polymorphic markers for the parents of a cross, before carrying out a genetic analysis of their descendents. This will reduce the number of markers that need to be screened, and allow determining the allele sizes that will be observed in the population. Often, markers can then be "packed" more closely in the electrophoretic separation step than would be possible without this "population-specific" information, reducing the cost of the genetic analysis.

• To select polymorphic markers from a custom marker list, carry out a marker pre-screening experiment following the instructions for the Automated Designer for Marker Screening.

OR

• To select polymorphic markers from one of the pre-fabricated Whole Genome Scan marker kits, carry out a marker pre-screening experiment following the instructions for the Automated Designer for Whole Genome Scan.

Selecting markers without a "pre-screening" experiment

• To carry out a genetic analysis without first pre-screening markers for polymorphism, select MRT^TM markers with your preferred method. Below are explanations for how markers can be chosen with the help of the Polymorphism Viewer macros or with GENica Marker Tools.

Select Markers with the "Polymorphism Viewers"

• The "Polymorphism Viewers" display genetic maps and highlight all the markers on these maps that are available in the MRT^TM format.
• Select markers, e.g. in a particular chromosome region, by following these steps:

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.
6. Prepare a BINNER input file. This file is required for the next step in the workflow.

Select Markers in the Multiplex-Ready^TM Marker Database

1. Login to GENica Marker Tools at https://www.genica.net.au/gmt/.
2. Select MARKERS and then select SEARCH.
3. From the "Marker Set" drop-down box, select the applicable data set (for either wheat or barley markers) under heading "MRT MARKERS":
   • "Wheat (MPBCRC:public)" to search all MRT^® wheat markers
   • "Barley (MPBCRC:public)" to search all MRT^® barley markers
4. To see all the available markers in the Marker Set, type the wildcard character '%' in the Search text box (immediately next to the Search button).
5. Click on Search.
6. Sort the results table as desired by clicking on different column headers.
7. The data set can be further filtered with the different available options (drop-down boxes to filter for Type, Prefix, Quality, etc.)
8. If desired, you can change the fields that are displayed for the dataset by switching between views. Fields for the 'Custom view' can be selected in the Marker Custom Fields tab, available in the OPTIONS mode of function (Select OPTIONS in the main menu bar).
9. Click on the CMAP link next to a marker of interest to search the MPBCRC CMAP Live installation for maps where a particular marker has been located.
10. Mark markers of interest for your study for the BINNER step (the next step in this workflow):
    • Tick the box next to all the markers you want to select for marker screening, then click on the Tag button, with --- New Tag ----- in the tagging drop-down box. Enter a new tag name and click Save.
    • To add further markers to this tag, select the newly created tag from the tagging drop-down box before hitting Tag.
    • To remove markers from a tag, select TAGS, then MARKERS. Click on the [Edit Markers] link next to the tag to be altered. Click on [Untag] next to every marker that needs to be removed.

• Tip: Refer to the GMT online help on the MARKERS»SEARCH interface for detailed information on the MRT markers database.

The MARKERS»SEARCH interface, showing marker information for markers tagged in Exercise 10.