Marker Groups

Definitions

Field Descriptions

• Marker Group name: Mandatory field describing the marker group. This can include a description of the marker groups function (e.g., purity analysis, disease resistance, etc.) as well as the germplasm group in which the marker group functions.
• Germplasm Group: Optional field describing the germplasm group that the marker set can be used for e.g., a marker group and set of favorable alleles that is used to detect disease resistance may only be relevant to a particular germplasm group. Note that an entry here is not validated against any germplasm fields in the system.
• Markers: This shows a list of the markers associated with the Marker Group name. Marker names cannot be entered directly in this window but need to be uploaded from a file using the Import Markers button. N.B. New marker names cannot be created here, but need to have previously been uploaded into the system and associated with a platform using the Marker Wizard. 
  • The Marker Group file should consist of the following:
    • a Header row with minimum of 2 columns
      •  if  header row is not included, your first marker row will not be loaded to the marker group
    • Column 1: Marker name
      • Marker name must be previously loaded to the system
    • Column 2: Platform
      • Platform must be previously defined in the system
    • Column 3: optional - used to describe Favorable alleles 
      • The favorable allele column can contain more than one allele and each allele must be comma separated
      • Allowed characters must be in the following set: {A,C,G,T,+,-,0,1,2,Any 4 digit number (for SSR alleles) (0000 <= x <= 1000)}
    • Number of markers in the file is limited to 200
  • The file being loaded must be a .txt file 
    
    
    

Add New Marker Group

1. Create your marker group file. This should consist of at least 2 columns; Marker name and Platform. An optional 3rd column is allowed to describe Favorable alleles. The Marker name and Platform need to have already been loaded to the system. Headers need to be included or else your first marker will not be loaded to the marker group. The file must be a .txt file.  The favorable allele column can contain more than one allele and each allele should be comma separated. 
2. From the menu bar, select Create | Marker Groups. A list of existing Marker Groups display on the left-hand side of the page. Clicking Export exports a text file of the Marker Groups listed.
3. Enter a Marker Group name in the Marker Group Name field. Ensure that it is unique - otherwise, you will receive an error message.
4. Add a Germplasm description in the Germplasm group field - an optional field.
5. Click Import Markers. Browse to the location where your marker group file is stored. Click Open. Your markers will appear in the Markers window.
6. Click Add New Marker Group. The new Marker Group name displays on the left-hand side of the page and is associated with the marker names that you loaded.
7. Click on Export Markers to export the list of markers, platforms and favorable alleles contained within the marker group. This can be used as a template for other marker groups or to edit the markers in the marker group.
   
   

Update Marker Group Information

1. From the menu bar, select Create | Marker Groups. A list of existing Marker Groups display on the left-hand side of the page.
2. Select the Marker Group that you want to update. Details relating to the Marker Group display on the right-hand side of the page. Edit any applicable fields. Even if you change the Marker Groups name, any associated entities remain associated.
3. If you wish to update or append the markers associated with the Marker Group, click on Import Markers, browse your updated Marker Group file, select Open, you will then be promoted to Update or Append the marker list. Click on Update if you want the existing list to be replaced with the markers in the new file, or Append to add only new markers from the file. 
4. Click Update. The requested changes are made. 
5. Click on Export Markers to export the list of markers, platforms and favorable alleles contained within the marker group. This can be used as a template for other marker groups or to edit the markers in the marker group.