Germplasm lists are the best way to handle a collection of lines in the system. These collections can be a list of potential parents or the list of lines in a specific test. There is no limit to the number of lists that any specific line can belong to, but having a repository for saving these lists can be beneficial when loading data, retrieving data, checking pedigrees or following seed source of lines. In CIERA, we have a tool that is used to create and edit germplasm lists, import germplasm from excel sheets, assign Germplasm IDs (GID) to new lines and allow the user to make changes to pedigree information for individual lines.
The best way to ensure that accurate pedigrees, seed source, dates and locations are entered into the system is to gather all that information for a population ahead of time.

Creating a New Germplasm List

To create a list, click List>New>List and then enter a name for the list that makes sense to your workgroup. If you would like to create a folder to put the list in, you can choose List>New>Folder first.

Germplasm List Manager

Entering in a New Cross

Double-click on your list to open it. To add an entry to the list, click on the “+” button from the tool bar on the top.

Add a new entry to a list

Using the pedigree book, start by entering in the name of the cross into the “Designation” text box. Leave the GID empty, as this is only used for looking up germplasm by GID instead of name. In this case, we are creating a new cross so no GID had been assigned yet. Leave the “Entry Code” and “Source” text boxes blank as well. Press OK.
The system will search to see if that name has ever been entered in the database. If so, you will get a list of the germplasm that name matches.
If not, you will get a notification.

Name not found

The next window that pops up will allow you to enter more information about the crossing method, location, dates and name type.

Enter a new germplasm
Choose the appropriate method from the “Germplasm Method” drop down box. Anything with a “GEN” before the method is a Generative Method (creating a new germplasm), anything with a “DER” before the method is a Derivative Method (advancing a germplasm) and anything with a “MAN” is a Management Method (handling of a germplasm). For a cross, we need to choose the appropriate Generative Method. Use the pedigree book, or contact the breeder to choose the proper method (see Appendix I for a list of breeding methods).
The “Name Type” drop down box allows the user to give more information about the type of name you entered. For a cross, “CROSS NAME” should be chosen, but for Derivative lines, other name types for the synonyms, accession IDs, germplasm bank Ids, National testing number, etc. will have to be chosen.
Fill out the date the cross was made in the format yyyymmdd. The “Germplasm Date” refers to the date the cross was made. Then, to choose the proper location, click on “<Change” next to the “Location” text box, and find the appropriate location.
Do the same for the “Name Date and Location”. This refers to the date when the germplasm was named and where. For a cross this will usually be the same as the Germplasm Date, but not always. Double check with the pedigree book to ensure that cross names weren’t added after, or by another institution. For example, this happens regularly with CIMMYT material or other International Research Centres.
After clicking OK you will be moved to the “Add a GMS Germplasm Record” screen (which looks identical to the “Edit a Germplasm” Screen). Here you will see the choices you made entered for name, date and method. However, the “Female Parent” and “Male Parent” text fields will be blank.

Edit germplasm details

Checking with the pedigree book, enter the Female parent’s name into the text box next to “Female Parent”. If you know the GID of the female parent (unlikely, but possible), you could enter it instead. Press the “<Add/Change” Button on the right. The system will check the database for any matches in the name you supplied and either returns a GID, or if there are multiple hits, opens a window and allows you to choose the appropriate germplasm. This window looks identical to GMS Search, and allows the user to look at all information about the germplasm prior to making a choice (see Fig. 8). When looking for a registered variety, unless the seed source (i.e. the bag of seed used) is known, you should always choose the entry that has the method “VCR” or “Germ. Creation Method” field says “CULTIVAR RELEASE”, as this represents the original registered bag of seed for Released cultivars. When dealing with unregistered lines, a little more detective work will be required and you may need to ask the breeder which entry makes the most sense. For example, if DT xxx was used in a cross in 2015, choosing an increase from 2002 would not make much sense but an increase from the winter nursery in 2014 might. Again, talk to the breeder or technician for help on finding the proper entry for seed source, Follow the same steps above for the "Male Parent".
It is always good to add supporting information about the cross. In the “Attributes” section on the screen, click on “ADD” to add a new attribute. In the first text box, enter the name of the breeder, choose “BREEDER” from the drop down box, enter the current date for “Attribute Date”, and then choose the location of where the note is being added (usually the same location as the “Germplasm Location”). Do the same if the purpose of the cross has been entered in the pedigree book (Choose “Purpose of the Cross” from the Attribute Type drop down box). Any other notes could be added by selecting “Notes” as your attribute type . When you click “OK”, a new GID is assigned to that cross and it will show up in your list.

Entering in Lines

Entering a derivative line into SETGEN requires gathering of information ahead of time. You will need to try and find information about the name, location, seed source, cross, and any other supporting information you can get. If any of this information is unknown, you can still proceed but it is much easier to enter it right away, rather than trying to remember to go back afterwards.
To add an entry to your list, click on the “+” button on the tool bar at the top and the “Add a New List Entry” screen will appear.
Designation: enter the name of the germplasm you wish to add. Alternatively, if you know the actual GID (unlikely, but possible), you can enter the GID in the “GID” text box but normally this will be left blank.
Entry Code: If your germplasm list has entry codes listed (i.e. Codes from the winter nursery, or some kind of lab code) you can enter this in the “Entry Code” text box.
Source: If you have information about the seed source, you can enter it here. Note – this is only a note about the seed source, not a link to the seed source. For example, you might put “2013 Winter Nursery”, or “2013 Centre Farm” but it will not link to the actual GID of the seed source from this text box.
Click "OK" when done.
If the germplasm name is found in the database, a search window will open up which shows all the hits found in the database.
If the germplasm name is found in the database, a window will open up which displays all the hits found in the database.
- Carefully check through each entry, and use the information about the name, location, dates and any notes in the Attributes section to help you decide which entry to select. Tracking seed source is important in a breeding program, so choosing an incorrect entry may cause errors in future pedigrees.
- If you see the entry you want, highlight it and click on Select, otherwise click on the New button.
If the database does not find a hit on the name entered, or if you did not find your germplasm among the hits, a new window called Name Information for New Entry opens up:
- Germplasm Method: If the germplasm is being advanced in a nursery, then you will want to pay attention to any methods in the drop down box that start with DER for Derivative Methods. For germplasm being increased, stored or managed in a way that does not affect the filial generation, then look for any methods that start with MAN for Management Methods. The Method No. will change with your selection, automatically.
- Name Type: Look through all the choices for a "Name Type that best describes the name. In most cases, Derivative Name will be used for lines at your Research Centre until they hit the Cooperative Trials, in which the National Testing Name should be the name selected (i.e. BW xxx, DT xxx)
- Date and Location: if known, enter the dates (yyyy-mm-dd) in which the name was given and when the cultivar was harvested. Choose where the name was give and where the seed was harvested. Ex) Lines from a winter nursery may be harvested in New Zealand, but the name comes from your Research Centre.
- Click OK when done filling in the known information.
The Add a Germplasm Record window will open. The name, locations and dates information added in the previous step will be shown.
- Source Germplasm: If you know the seed source of the germplasm, start here and enter the name (or germplasm_id) of the cultivar that was harvested as seed source for your entry. Press the Add/Change button.
  - The system will do a search and look for the name you supplied in the database. If found, you will see a list of hits from the database, and you can select the correct one, following the same steps from the previous section.
  - Once the source is selected, it will automatically add the Cross Germplasm.
- Cross Germplasm: If the source is unknown, but the cross or cross name is known, enter it into this text box and press the Add/Change button.
  * Just as with Source Germplasm, a window will open with any hits from the database, so you can select the appropriate entry or add a new one.
Names: To add synonyms to the germplasm, click on the Add in the Names section.
- Choose a name type that is appropriate. If you are not sure, ask the system administrator for help. Note: some names types are specific to International Research Centres, such as CIMMYT, and may not be reflective of your breeding program's nomenclature.
Attributes: To add any notes or information about the cultivar, click on the Add button in the Attributes section.
- Choose an attribute type that classifies the note being added. Multiple notes can be added of different types.
Click OK to commit the entry to the list and to the database.

Exporting a Germplasm List to Excel or Text File

To export your list of germplasm to an Excel file, open the list by double-clicking on it, then choose List>Export As>.xlsx Excel File or List>Export As>Tab delimited text file.

Batch Importing of Germplasm From Excel

Entering in germplasm one-by-one can be a very time-consuming process, so there is a function to load a list of germplasm from an Excel file.

Basic Import

Basic importing of lines from Excel

For the basic import, you need to first create/open a germplasm list.
Make sure you have an Excel file, which has the column headers for Designation, Entrycode, and Source on row 1.
Make sure the name, entry code (if known) and source (if known) are starting on row 2. Take note of how many entries you have in the file.
Click on List>Import List>Basic, a new window will open, Basic Import of Germplasm List.
- Excel File Name: Click on the Browse button and find the Excel sheet you create above.
  - WorkSheet: Choose which tab on the Excel file has the germplasm information.
- ** Designation:** Select the column header from the Excel file that representst the name of the germplasm.
- Entry Code: Select the column header from the Excel file that represents the entry code.
- Source: Select the column header from the Excel file that represents the source of the seed.
- Cross: Leave this blank.
Click OK.
The system will go through each entry to ensure it is in proper format. When it is done processing the entries, you will get a pop-up window that says how many entries were processed and ask if you want to save. Click Yes to move forward, or No if you found there were problems (i.e. some entries did not process).
A Generate Germplasm Ids in Batch Mode For ... window will open.
- **Destination List: ** Leave this as the list you have open.
- Germplasm Location: Click on <Change button to choose a location where all the germplasm in the list were harvested. Leave blank if unknown, or if you need to edit this manually due to the entries being harvested at various locations.
- Germplasm Creation Date: Enter the date (yyyy-mm-dd) that the germplasm was harvested on. Leave blank if unknown, or if entries were harvested at different times.
- Name Location: Click on the <Change button to choose a location where all the entries in the list were named. Leave blank if unknown, or if the entries were named at different locations.
Name Date: Enter the date (yyyy-mm-dd) that the name was given to the entries. Leave blank if unknown, or if the entries were named at different times.
- Options:
  - **Treat entries as new germplasm: ** if your list is of existing germplasm, then leave this unchecked. This option is used to create new germplasm_ids for each entry, which is useful when advancing a nursery, or creating an increase.
  - **Parse unknown derivatives: ** this option will automatically try to parse the entries it does not recognize.
  - Exclude germplasm bank accessions (name type = 1) from hit list: This will remove any genebank accession names from the search.
  - Automatically commit processed entries: Check this to automatically save the list entries as they are found. Uncheck if you wish to check the list prior to saving (will have to save maunally).
  - Do not process entries not found: ** If you have already checked Treat entreies as new germplasm**, you do not need to worry about checking this box. Otherwise, this option will not create a GID for any entries it does not find. Instead, the GID = 0 and allows the user to manually handle these missing entries.
  - Set name type of new germplasm name as: Check this if you checked the Treat entries as new germplasm option, and then select the name type you wish all entries to have in the list.
  - ** Set creation method of new germplasm as: Check this if you checked the Treat entries as new germplasm option**, and then select the breeding method, derivative method or management method that applies to all the entries in the list.
Click START
At this point, the system will go through and look up each entry from the Excel file. When it finds multiple hits, you will be asked to select the correct entry, or create a new one if it does not exist in the choices, using the same procedure as above.
When processing is done, your new list will appear with the GIDs added. Save the list by clicking on List>Save.

Advanced Import

Advanced importing of germplasm from Excel

Same fields as the Basic Import but also includes more assignment columns to assist in creating new germplasm in CIERA.
The input excel sheet, in addition to having columns for DESIGNATION, ENTRYCODE, SOURCE, the following are also optional to include:
- METHOD ID - the breeding method ID for the type of generative, derivative and management method of the germplasm. Method IDs and descriptions can be found here
- Germ. Creatiion Date - the date where the germplasm was created (mm/dd/yyyy).
- Germ. Location ID - ID of the location where the germplasm was physically created.
- GID of the Source/Male - Germplasm ID of the source germplasm (Derivative and Management Methods) or Male Parent (Generative Methods).
- GID of Group/Female - Germplasm ID of the group (cross in Derivative and Management Methods) or Female Parent (Generative Methods).
- Name Type - ID of the name type.
- Name Date - the date when the germplasm was named (mm/dd/yyyy).
- Name Location ID - ID of the location where the organization that named the germplasm is situated.