Marker Binner

The Marker Binner is an application for placing molecular markers into bins according to their product sizes.

Login to Marker Binner

Password required, contact Gregory Lott to receive a login.

This web site is developed and maintained by the Centre for Comparative Genomics (CCG) for the Molecular Plant Breeding Cooperative Research Centre (MPB-CRC).

Navigating the BINNER software

The BINNER software supports individual user accounts to enable users to upload and manage their own marker data. Following login, a list of markers is shown for which allele size data is available. All users have access to allele size data for barley and wheat markers that are published in the Multiplex-Ready Marker Database. 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; those 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.

The marker list displayed can be refined using the Group Selection dialog box, and individual markers searched for using the Search function. To move between BINNER modes of function, click on the appropriate Tab Button.

Uploading marker allele size data

Marker allele size data can be uploaded to BINNER and used to develop marker panels for specific germplasm. This function is particularly useful for genetic mapping when parental allele sizes are known. Described below is the process required to upload marker allele size data.

1. Generate a table for the marker allele size data using Microsoft Excel as shown below. The allele size range for each marker is defined by the minimum and maximum allele size in base-pairs. Each marker can have up to four allele size ranges. This feature allows markers amplifying multiple loci to be accurately described, and enables "noise"¿ regions (which are regions in an electrophoretic trace containing non-specific PCR fragments that might interfere with scoring if another marker was allowed to co-occupy the region ) to be indicated.

Note: The table does not contain a header row. It has also been found useful to subtract 2-bp from the minimum allele size and add 2-bp to the maximum allele size when describing the size range for each marker. This adjustment to the allele size range for each marker ensures that GeneMapper is able to automatically call a microsatellite allele when stutter bands are present.

2. Save the marker allele size data table as a tab-delimited text file (.txt) using the Save as type option in Microsoft Excel.
3. Click on the Marker Group tab in BINNER, and then the Add button in the dialog box. Enter a group name that describes the marker allele size data that you are about to upload, for example Sahara x Clipper. If the allele size data is to be added to an existing marker group then go directly to step (4).

4. Click on the Import tab in BINNER, and then the Browse button to locate the marker allele size data file that you want to upload. Select the marker group to which you would like to add the new allele size data using the Group dialog box, and click the Import button.

Creating marker panels

Marker panels for deployment on an automated DNA fragment analyser are constructed automatically by BINNER for a set of user-defined markers using either default or imported barley and wheat allele size data. Described below is the process required to create a set of marker panels.

1. Select markers of interest from the multiplex-ready marker database using the query functions, or by other means.
2. Create a text-delimited file containing a list of unique laboratory codes corresponding to each of the selected markers. This file can be created by pasting the query results from the multiplex-ready database into Microsoft Excel, Microsoft Word, or Windows Notepad. Ensure that the header row is deleted if a query result from the multiplex-ready database is used to generate the table of markers for binning. There is no limit to the number of markers that can be binned at a time. An example of a marker file is shown below.

ta0094
ta0134
ta0063
ta0121
ta0011
ta0015

3. Click on the Bin Markers tab in BINNER and then the Browse button to locate your file containing the list of markers to be binned.
4. Select the allele size data that should be used to construct the marker panels using the Group option. The group names barley and wheat contain the default allele size data for all markers published in the multiplex-ready database. 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.
5. Choose from the Padding option the minimum amount of distance (in base-pairs) 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.
6. Select the algorithm that BINNER should use to construct the marker panels from the Sort Order dialog box. It may be worth testing several algorithms to achieve the best packing arrangement for the markers of interest.
7. Start the binning process by clicking on the Upload button.

Marker panels created by BINNER can be copied directly from the web-page into Microsoft Excel using the Paste Special option. Each panel contains a list of markers that have correct spatial separation to avoid allele overlap when separated on an automated DNA fragment analyser. Alternatively, a text-delimited file for the marker panels created can be downloaded from BINNER using the Download tab delimited results file button.