GMT Tutorial Exercise 22 - Workflow 1 - Step 2

Use BINNER to develop marker panels for the selected markers

• BINNER creates panels of markers that have correct spatial separation to avoid allele overlap when separated on an automated DNA fragment analyser.
• BINNER can use two different types of input: Marker names can either be uploaded as a list file or "tagged" for binning within GENica Marker Tools, see below.

1. Login to GENica Marker Tools (https://www.genica.net.au/gmt/).
2. Go to BINNER and submit markers to be binned:
   • If marker names have been saved in a list file... (The preparation of the marker list file is described here)
     1. Select BINNER, then UPLOAD.
     2. Browse for the file with markers to be binned, then click Open.
   • If markers have been "tagged" with GENica Marker Tools... (Tagging markers in GMT is explained in the [previous step] of this workflow.)
     1. Select BINNER, then TAGS.
     2. Choose the tag with markers to be binned from the Tags drop-down box.
3. Select the applicable marker set from the Marker Set drop-down box:
   • "Wheat (MPBCRC:public)" for MRT^® wheat markers (names beginning with "ta")
   • "Barley (MPBCRC:public)" for MRT^® barley markers (names beginning with "hv")
4. Select a minimum padding of "10 bp" from the Padding drop-down box, unless the allele size range for each marker is known for the germplasm of interest.
5. Leave the Sort order setting unchanged ("Sort by longest loci range before binning").
6. Click Bin Markers.
7. When binning results have been prepared, click [Download results file] and save binned markers to your computer, e.g. to a folder for the "Marker Screening" experiment.
8. Repeat the binning process, but this time change the Sort order input option ("Sort by highest loci midpoint before binning").
9. Compare the two different outputs (downloaded files can be opened with Microsoft Excel or similar).
   

The BINNER results interface displays a table with the panel number in the first column, the marker name in the second column, followed by up to 8 columns, indicating the minimum and maximum allele sizes of up to 4 allele size ranges for the marker. Markers that have the same panel number (i.e. the same number in the first column) can be analysed together in one capillary of the ABI3730. An example of the BINNER results table is shown below:

1	ta0094	214	252	
1	ta0121	256	280	
1	ta0134	146	164	
2	ta0011	232	241	
2	ta0063	153	162	
3	ta0015	148	154

10. Select the binning result with:
    • Fewer bins (the highest number in the first column gives the total number of bins) and / or
    • More even distribution of markers per bin.