GMT Tutorial Exercise 18

Bin MRT^TM markers

To "bin" MRT^TM markers is to identify markers that can be analysed together in a sequencer capillary, as their expected allele size ranges do not overlap. BINNER uses information on allele size ranges for wheat and barley that have been determined by analysing diverse sets of varieties, and that are recorded in the MRT^TM markers database.

1. Select MARKERS and then select SEARCH.
2. Select and tag MRT^TM markers to be binned:
   1. Try using the search, sort and tag options. You can e.g. tick individual entries in a MARKERS search result and Tag these individual markers. Add more markers to this MARKER TAG to build up your list of markers.
   2. Alternatively, try copy / pasting this comma-separated list of markers to be binned in the search text box, click Search and then Tag all results: hv0001, hv0002, hv0003, hv0004, hv0005, hv0006, hv0008, hv0009, hv0010, hv0011, hv0013, hv0016, hv0020, hv0023, hv0024, hv0027, hv0029, hv0030
3. Select BINNER and then MRT TAGS, see the BINNER»MRT TAGS interface on the left screenshot below.
4. Select the MARKERS TAG with the markers to be binned
5. Select the MRT^TM Marker Set where allele size ranges for the markers to be binned are stored.
   1. For wheat markers (e.g. "ta1234"), this is Marker Set "Wheat".
   2. For barley markers ("hv1234"), this is Marker Set "Barley".
   3. You can equally create a marker set with custom allele size range data, refer to the GMT manual section on MARKERS»IMPORT.
6. Leave the default binner settings unchanged in this tutorial.
7. Select Bin Markers.

• Click on HELP to access the GMT online manual for information on how the different binning parameters should be used, and how to read the BINNER output (see the right screenshot below for an example of the BINNER output).

The BINNER»MRT TAGS interface.

An example for the BINNER output. Note the "bin number" in the first column. Markers with the same bin number can be analysed together on a capillary sequencer, as their alleles size ranges do not overlap. The binner output can be used directly to set up experiments and write panel files with the "Automated Designers" downloadable from FILES»LIST.