BINNER»MRT TAGS

Description

• Use BINNER to create panels of MRT^TM markers that can be analysed together on a sequencer to reduce genotyping costs.
• BINNER»MRT TAGS allows to use markers that were "tagged" in MARKERS»SEARCH or in GEMDB»SEARCH as input.
• Use BINNER»MRT UPLOAD to use lists of markers saved as *.txt files as BINNER input.
• All users have access to allele size data for barley and wheat markers that are published in the MARKERS database (marker sets barley and wheat). This allele size data was generated using eight genetically diverse varieties.
  • The varieties used for barley were Alexis, Chebec, Clipper, Harrington, Haruna Nijo, Sahara 3771, Sloop and WI3408;
  • The varieties used for wheat were Barunga, VPM Cook, Chinese Spring, Gabo, WI7984 (a synthetic hexaploid), Norin10, Olympic and Opata85.
  • In our experience, the allele size range reported for each published marker is generally sufficient to avoid allele overlap in domesticated germplasm. However, it should be realized that some markers may have allele sizes outside the expected range in certain genetic backgrounds, which may results in marker allele overlap.
• Alternatively, users can upload and manage their own marker allele size ranges, see the section on MARKERS»IMPORT.

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How to use this option

1. "TAG" the markers to be binned in MARKERS»SEARCH (find out how) or in GEMDB»SEARCH (find out how).
   • There is no limit to the number of markers you can tag and submit for binning.
   • In GEMDB»SEARCH, be sure to select a "GEMDB tag", not a "Sample tag" (what's this?).
   • You can view and delete markers that have been tagged in TAGS»MARKERS or in TAGS»GEMDB.
2. Go to BINNER»MRT TAGS and locate the tag created in step 1 from the "GEMDB Tags" drop-down box.
3. From the "Marker Set" drop-down menu, select the marker set with the allele size data you want to use to bin the markers.
   • The marker sets Barley and Wheat contain the default allele size data for all the multiplex-ready markers. These allele size data should be used when conducting parental polymorphism screens, genetic diversity analysis, or whenever allele size data for the germplasm of interest is unknown.
   • Customised marker sets can be used when the allele size ranges for the studied germplasm is known, e.g. in genetic mapping when the parental allele sizes are known. Please refer to the section on MARKERS»IMPORT for explanations on how a binnable marker set can be created and imported.
4. From the "Padding" drop-down menu, choose the minimum amount of distance in base pairs (bp) that BINNER must leave between markers when building a marker panel. It is recommended that a minimum padding of 10 bp is used for marker polymorphism screening unless the allele size range for each marker is known for the germplasm of interest. For genetic mapping, a minimum padding of 5 bp is recommended.
5. Select the algorithm that BINNER should use to construct the marker panels from the "Sort Order" drop-down menu. It may be worth testing several algorithms to achieve the best packing arrangement for the markers of interest.
6. Start the binning process by clicking on the UPLOAD button.
7. Download the BINNER result with the [Download results file] button.
   Alternatively, the table can be selected and copied straight from the webpage; in Excel, use the "Paste Special..." option and paste as "text".

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The BINNER output

• BINNER creates panels of MRT^TM markers that have correct spatial separation to avoid allele overlap when separated on an automated DNA fragment analyser.
• 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. 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

• The BINNER input parameters are displayed above the results table.
• The BINNER results table can be used directly as input for the "Automated Designer" macros. (See also the section on FILES»LIST for details on how to download the macros and related instruction manuals.) Simply copy / paste the marker panels created by BINNER directly from the web-page into the Microsoft Excel macros.
• Alternatively, a text file with the marker panels can be downloaded from BINNER using the [Download results file] button. (Files can be exported as a tab-delimited *.txt file or as a comma-delimited *.csv file; please refer to the section on OPTIONS for details on how to choose your preferred format.)
• Markers for which BINNER could not identify binning information are listed as "Rejects", see the example below.
  Note:
  If all the markers in your list have been rejected, verify that the correct marker set has been selected, e.g. the default marker set for "ta" markers is Wheat, the default marker set for "hv" markers is Barley.

Rejects
 
ta0094
ta0134
ta0063
ta0121
ta0011
ta0015

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Links to other user manual pages

I'd rather try the tutorial...

• Get started with the GMT Tutorial
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