One of the key advantages of using the BMS is that it facilitates the unique identification of germplasm and pedigree tracking. To start using the BMS, however, lists of current germplasm from your breeding program should be entered into the database. These lists are ideally imported with complete pedigrees. However, for this exercise, we will consider the simple import of existing lists without pedigrees.
Once germplasm are imported into the database it is often necessary to make lists of germplasm for different purposes such as planting, shipment, and testing. These germplasm lists are created by selecting entries from previous lists and adding the imported lines. Other new lists are made from harvest actions from nurseries and trials.

Objectives

At the end of this chapter, the user should be able to:

1. Complete a template with germplasm names to be imported.

2. Import germplasm into the database from a template (without pedigrees).

3. Add inventory for imported germplasm

4. Select lines from an existing list and add them to a new list of germplasm.

Importing a list of germplasm from a template file.

Creating a basic germplasm list in Excel
Lists of germplasm can be entered into the system using an Excel file. This file must follow a specific format so a template has been provided. Users with appropriate permission will see the action Import Germplasm on the ACTIONS menu of the Germplasm Manager main menu. If you click on this item you will see that you can download a template.

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The template has two sheets, an observation sheet where the germplasm details are supplied and a Codes sheet where some metadata codes are available.
Use Excel to modify the germplasm import template and create a file with the following format and minimum content.
The Observation sheet has a number of proposed columns covering all the characteristics of a germplasm record, but the minimum data required is just a consecutive entry number and a germplasm name. There are still more columns beyond column I which we will ignore for now.
A minimum entry would look as follows:

Fill the first two columns of a template file exactly as shown in the image above and save it as <Your Initials>21GI.xls (CGM21GI.xls for me). The correct germplasm names are given below. Notice the typo in Entry 15 – include that in your file.

To save typing you may be able to copy the names from the above table.
Once the template is completed select Import Germplasm form from the Actions Menu of the Germplasm Manager again and browse for the file just created.

Click Open.

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Then click Next.

The Specify Germplasm Details form appears. This form allows you to specify some germplasm information such as the breeding method, the germplasm location, the creation date, and the preferred name type. These details can also be specified on the Germplasm Import Template, and this allows them to be different for every entry. If they are specified on the Germplasm Details form then the values specified there are used for all cases where they are not specified on the template.
For this exercise, we will specify all the items on the form, and leave all the columns for those items blank on the template. On the form:

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   1. The first item is the method by which the lines were produced in their last generation. Set this to Unknown derivative method by starting to type "unknown " in the box and selecting the result. You will need to uncheck the Show only favorites button.

   2. The second is the location where the germplasm was obtained or harvested, start to type "Int Rice " and select International Rice Research Institute. You will need to uncheck the Show only favorites button.

   3. The third is a date that the germplasm was harvested or acquired which you can set to today's date.

   4. And finally you can enter a text which will be stored as a reference for the germplasm.

   5. You will see what columns have been found for alternative names and attributes attributes, in the default case just Derivative name and Notes, but you cannot set values for these on the Basic Details form, they must be supplied via the template.

Click Next.
Since the template has columns for inventory and some data has not been entered, you are asked to supply inventory details:

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You can just click Next, since we do not want to specify inventory.
A preview of the germplasm you intend to import follows next:

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An important feature of this review form is that it allows you to see which names were found in the database, and which have not been found. Pull down the Show Matches pick list and select New records only.

You will see just one entry which corresponds to our typo YINLX NO 28 instead of YUNU NO 28

Since we are expecting all entries to be found we can identify the typo in this way. Click the x at the top right of the Review panel to cancel the import process. Return and edit the template.
Fix the typo – change the X to U for entry 15, save the template again, and process from the Import Germplasm item on the actions menu of the Germplasm Manager again. When you get to the review form again you will see there are no New Records.

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Since we expect the germplasm entries to existing in the database already, and since we want to select those existing entries we select the Creation option "Select existing germplasm whenever found".
You should almost always choose Select existing germplasm whenever found unless you know the germplasm to be new to the system. Failure to make this selection can result in many duplicate entries being created for a single germplasm and this makes data integration for that line very difficult.
Once you have made this selection, click 'Save'.
There is a checkbox to select single hits whenever found and this is checked by default, all you have to do is click next for each match with a single hit. If there are multiple matches the user must select the most appropriate. For this example select the existing germplasms in the database where the Location is International Rice Testing Program and IRTP {number} as one of its names. Click to highlight the germplasm and click Next.

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The below example, describes a scenario where there are some duplicate germplasm names in the import file e.g. germplasm name: CML202 even though its written with some typo errors. During the import process, the system identifies that CML 202 matches to 2 germplasm names in the database already assigned to GID 34221 and GID 351815. As mentioned above, when there are multiple matches, the user has to manually select the appropriate match and CLICK NEXT to proceed with the import process.

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Also, When there are 2 or more matches are found during the Import Germplasm process, the user can choose from available Options as described below:

Option 1: Use the same match for all remaining occurrences: Used when there are repeated germplasm names in the import file (e.g CML 202 in the above example is repeated 3 times) and If “Use same match” is ticked for the first occurrence of the germplasm name found, the user will not be prompted again for the succeeding occurrences of the same germplasm name in the import file.

Option 2: Ignore matches and add a new entry: the found matches will be ignored and a new GID will be assigned to the entry.

Option 3: Ignore remaining matches and add new entries: All entries in the import file will be added as new entries.

NB: Users should be cautious when choosing Options 2 and 3, as they create duplicate germplasm names with different GIDs which makes data integration very difficult for that germplasm name.

GID Creation options

The BMS assigns numeric identifiers, called GIDs* to every new germplasm imported to the database. See more about germplasm Germplam and Geneology in BMS. New germplasm names are assigned a GID number and when the import file has already existing germplasm in the BMS, they are mapped to GIDs of similar germplasm name matches in the database to allow continuity of data relationships. Users with permissions have an option to ‘force BMS create new records’ by ignoring the germplasm name matches identified. The user permission(s) are usually defined when user accounts are created.

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When all the entries have been processed BMS will show you a summary of found and new records. This is a second chance to catch any typos (if there should be no new records) and you can cancel to return to the Review form and see which entries are now with the filter.

Since we have no new records, which is what we expect, we click Confirm and this opens the Save List page.
You can make a folder for your current lists (if the right one does not exist already) by clicking on the + symbol and enter <Your initials> 2021 Lists for example. Again use your initials to keep your lists separate from other students. Then click the tick and the folder will be created.

Highlight the newly created folder and fill in the list name and description. The List name should also have your initials so that it is different from list stored by other students.

Then click Save.
A message appears that the list has been saved. After which, the newly created list is opened. Click the Germplasm List Data to view the entries.

Exercise – Importing New Germplasm

The Germplasm Import Template is very versatile for supplying a lot of information about newly imported germplasm. It is also useful for assembling germplasm, whether new or existing in the database into lists and can be used to add inventory for new or existing entries. However, if the Germplasm exists in the BMS, germplasm information will not be changed. To change or add information about existing germplasm you must use the Germplasm Editing features of the Germplasm Details forms or the Germplasm Update template from the Germplasm Manager Actions menu.
Use the following example to fill a Germplasm Import template with some germplasm information about some new germplasm that will not be in the database (pick some distinct names with your initials included).

Part 1. - Names and locations – will not be modified for existing germplasm records

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Columns A to G.

• A. Entry_NO must be filled with a sequential integer 1,2,3 …

• B & C. You can have columns for different name types. By default two name types are listed, LNAME (Line name) and DRVNM (Derivative name) you can add more name types from the Codes sheet (under the heading NAMES). At least one name is required. We will keep the default ones and fill them both with invented names as above. Use your own initials to make your names unique.

  • LNAME is a line name. DRVNM is a derivative name. You must have one name but can give more. All given names are added for new germplasm but new names are not added for existing germplasm, that must be done with the Germplasm Update template.

• D. PREFERRED_NAME - Enter the name type column heading that you want to be the preferred name for each new germplasm entry. If this is blank, the first name supplied is preferred.

• E. ENTRY_CODE is just a code name for the entry in the list. It is local to the list.

• F. LOCATION_ABBR is the abbreviation of the location where the germplasm was produced. You can look up some location abbreviations in the Codes sheet, but this is not a complete list and you can look up others in the BMS Manage Locations page. We will select BKE which is the abbreviation for Africa Rice-Bouake as you can see in the Codes sheet. This may not be available in your Codes sheet so select one that is there.

• G. REFERENCE you can provide text that will be added as a reference for new germplasm.

Part 2. Pedigree information and attributes – affects new entries only

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Columns H to L.

• H. CREATION_DATE You can enter the date the germplasm was created, collected or received according to your convention.

• I. BREEDING_METHOD You can fill the column with the code of the breeding method finally used to produce the entry You can see the codes on the Codes sheet. UDM is an Unknown Derivative Method, and DSP is Single Plant Selection.

• J. PROGENITOR1 and PROGENITOR2 can be used to capture pedigree information for the line. They need to be filled with GIDs of progenitors, the progenitors must already exist in the BMS (You must import the parents first if necessary). If the entry is a cross (an F1) then PROGENITOR1 should contain the GID of the female parent and PROGENITOR2 the GID of the male parent.

• K. If the entry is a derived line (not F1) then PROGENITOR2 should contain the GID of the immediate source of the entry. PROGENITOR1 should be set to zero. However if the immediate source is not known, but the cross from which the entry was derived is known then PROGEITOR2 should be zero and PROGENITOR1 should be set to the cross from which the entry was derived.

• L. You can add attributes for the entries being imported by adding columns with headings obtained from the Codes sheet. A column for NOTES has be added by default. Add some notes.

Part 3. – Inventory and unique identifiers – inventory can be supplied for new or existing entries

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Columns M to Q.

• M. STORAGE LOCATION ABBR is for the abbreviation of the seed storage location where you will store the seeds associated with this import list. These seed storage location abbreviations are looked up on the Codes sheet. New ones must be entered through the Location Manager.

• N. UNITS contains the name of the storage units for each entry from the list on the Codes sheet.

• O. This contains the amount of seed going into storage for new or existing entries.

• P. STOCK ID is a short unique ID for the seed lot. It is better to let the BMS assign these codes since they must be unique.

• Q. GUID can contain Germplasm Universal Identifies for the entries. If left blank the BMS will assign a unique code, but if a suitable global identifier exists you can enter it here and it will be used for new germplasm. If germplasm exists in BMS with that GUID it will be selected as the imported entry irrespective of any name matching or otherwise.

Now select Germplasm Import from the Actions menu of the Germplasm Manager and select the file you have saved to see the effect of the settings.

Viewing Lists

To view any list of germplasm, such as the one just imported, click on Germplasm Lists under the LISTS main menu.

Then click on Browse navigate to the folder where your list is located and highlight the list you want to view. (You can navigate and highlight several lists). Then click the X at the top right of the navigation box to clear it and you will see the lists you highlighted in separate tabs.

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Adding Inventory for Imported Germplasm

Although seed inventory can be added to the seed inventory system by filling the inventory columns on the germplasm import template, it is better to use the inventory functions for the Manage Germplasm and the Inventory Manager to do this since this offers more control of how inventory is stored and provides access to a unique LotID which can be used to bar code the seed packets.

To add inventory for the imported list, open the list in the Manage Germplasm by selecting "Germplasm List" in the Search by pulldown list, select all entries in the list, and then select Actions > Create inventory lots:

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On the create lots form you must enter a stock ID prefix which should identify the 'owner' or project to which the seed lot belongs. This will be extended by adding a batch number for the seed batch and an entry number for the particular line. It is useful to store the seed packets in order of stockID at the seed storage location for easy retrieval. Enter your initials for this example to keep track of your seed stocks.

Next, select the storage location – we only have a location called the Default Seed Store, but of course, other locations can be added as appropriate. Choose the scale in which the seed will be managed and enter a note if desired.

Now we can also add an initial deposit at this time, and if, for example, the sender had sent the same amount of seed for each entry you can enter that here and confirm the transactions directly.

Click save and you will get a message that the lots have been created.

Manipulating Germplasm Lists in the List Manager

View existing Program Lists
From LISTS go to Germplasm Lists, Browse for Lists, Program lists><your initials>2021 Lists, and highlight the list just entered <your initials>GI21 (CGMGI21 for me).

Clear the Browse for Lists panel by clicking on the x in the upper right corner and you will see the list just entered.  Click Columns > CROSS > Apply button.

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Click on the header of the Cross column and enter cross expansion level 1. Because all the entries were selected from the database, they do have pedigrees which are displayed in the Cross column:

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If no cross information is available, the Designation is simply displayed in the cross column.

Using Crop Lists to share germplasm between programs

Click on Browse below the heading List Details and expand the Crop Lists section.
Lists saved to or moved to the Crop Lists section are visible to all programs in the crop.

Navigate to INGER NURSERIES>IRLYN-E and highlight list IRLYN-E-1993. You can see this list because it is in the Crop Lists section even though it was not made in the current program. You cannot do much with this list until you copy it into your Program Lists.

The list contains 17 entries:

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Highlight all the entries by clicking on select all.  Click Actions > Clone List
 

Save the list in your folder with name :<your initials>21PVT (CGM21PVT for me).

Now in Browse Lists Program Lists> <Your initials>2021 Lists we have a second list:

Adding Entries to an existing list

Suppose I wish to add two entries from my import list (<your initials>21GI) to my PVT list to be check entries for example.

From Browse Lists open the PVT list and select Actions > Add Entries.  The germplasm search box appears.  Type FARO 41 and click Apply.

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Type FARO 41 and click Apply.

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Select the entry.

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Type UPL RI 5.  Choose the entry with the inventory amount and click Select.

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You will see that the selected entries have been added to the end of the list. 

Adding Entries from the Germplasm Search to a list

You can also add germplasm to lists using the Actions menu items from the Germplasm Search Application:

If you highlight entries in the filter list and click the Create new list action item you will be asked to save a new list with those entries added. If you click the Add to existing list item, you will be asked to choose a list and the checked entries will be added to lat list. Try the exercise below.

Exercise on Germplasm Manager

1. Use the Actions Menu on the Germplasm List Browser to try exporting your list to an Excel file.

2. Use the Germplasm Search App to search for the entry of IR 64 with GID 50533. Use the Action menu of the Germplasm Search App to add it to a new list called <your initials>Checks in your 2021 Lists folder, then search for IR 72 (GID 70125) and add that to the same list, finally search for NERICA 4 (GID 765439) and add that to the list. (Note you could search for all three GIDS at the same time and add all three to the new list).

3. In the Manage Germplasm, open your checks list, select all three entries and add inventory lots from the actions menu. Specify the location Bulk Seed Store, units KG, and add initial deposits of 5 kg for all entries. Confirm the transactions.

4. Use the   icon on the top right of the workbench to go to the help system or the latest BMS MANUAL section. Scroll into the MANAGE GERMPLASM and look through the manual section for other things you can do with this application. Can you list some new things?

5. Additional reading re. Germplasm and Genealogy and how BMS manages germplasm in a breeding program:  https://bmspro.io/2187/training/breeding-management-system-manual-50/germplasm-genealogy

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