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Introduction

The Germplasm Manager allows you to:

• Filter germplasm by a variety of parameters

• Create a new germplasm list

• Add germplasm to an existing list

• Import germplasm or germplasm updates

• Group and ungroup germplasm

• Apply code names to germplasm

• Create inventory lots for germplasm

  Open

  

Filter germplasm

• Filter germplasm by variety of mix and match data types.

Example: Germplasm List Filter

• Choose the Germplasm List filter.

Open

• Select the germplasm list filter (teal button).

• Choose the list of interest. Ok.

The selected entries are now available to:

• Create a new list

• Add to an existing list

• Import germplasm updates

Basic Details for GID 356865: The preferred name is CML578. The germplasm was created in the BMS January 1, 2019 by an unknown derivative breeding method at the International Center for Maize and Wheat Improvement. The germplasm isn't grouped, so there is not a group ID for this germplasm and its descendants. The germplasm UUID is a unique identifier with a statistically unlikely chance of being duplicated in another BMS database.

Attributes

Attributes are non-heritable descriptors of germplasm. For example, a line can be deemed “drought tolerant” after characterization in a multi-location study. See below for more on editing attributes.

Attribute Example: "ETRC" indicates that CML578 is E. turcicum resistant.

Attributes can be edited via import germplasm updates.

Pedigree

The BMS database keeps a record of pedigree connections throughout the process of crossing and nursery advancement.

• Expand Pedigree Tree and select View Pedigree Graph. The default view shows only generative steps in the pedigree.

IB1F is the result of backcrossing. The recurrent parent, Bambey21:201710, is female.

• Select include derivative and maintenance lines to view steps, like seed increase.

The recurrent female parent, Bambey21:201710, is derived by seed increase from Bambey 21.

Inventory Information

Reveal details about inventory lots, storage locations and availability. See more

• Click LOT_ID hyperlink to reveal details about associated lot(s).

Lot 3990: 1194.0g of Augustus KWS seed can be found in IBP Storage 1A. The lot is active and there are two pending withdrawals, leaving an available balance of 1044.0g.

Create new list

• Using filters, select germplasm of interest. Select "Create New List" from the Actions menu.

• Select or create a folder to house the new list. Name the germplasm list and Save. The germplasm list will then be available from the germplasm list filter and the Germplasm Lists module of the BMS.

Add to existing list

• Using filters, select germplasm of interest. Select "Add to an existing list" from the Actions menu.

• Specify the list to which the selected germplasm will be added. Add. The germplasm will then be added to the specified germplasm list.

Import germplasm

From the Germplasm Manager Actions menu select Import Germplasm. A Germplasm Import form will open and you can download an excel template from that form.

The Germplasm Import Template is very versatile for supplying a lot of information about new 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 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.

The following example shows how to fill a Germplasm Import template with some germplasm information about some new germplasm that is not yet in the database.

Part 1. - Names and location

Column Effect

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

B.     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 of the template (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.

C.      CRSNM: We will also add Cross name (CRSNM) and fill that with some invented names for two new crosses. 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.     DRVNM: Fill with derivative names if you have them.

E.      PREFERRED_NAME enter the name type column heading that you want to be the preferred name for each new germplasm entry. If you leave it blank, the first name will be preferred.

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

G.     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 for the lines which is the abbreviation for Bouake as in our example of the Codes sheet. We will select CNRRI for the crosses. These abbreviations may not be available in your Codes sheet so select ones that are there.

H.     REFERENCE you can provide text which will be added as a reference new germplasm.

 Part 2. Pedigree information and attributes

Column Effect

I.       CREATION_DATE You can enter the date the germplasm was created, collected or received according to your convention. Format YYYYMMDD.

J.       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 Unknown Derivative Method, DSP is Single Plant Selection, C2W is a two-way cross and UGM is Unknown Generative Method.

K.      PROGENITOR1 and PROGENITOR2 can be used to capture pedigree information for the line or the cross. 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 like entries 3 and 4 in the example) then PROGENITOR1 should contain the GID of the female parent and PROGENITOR2 the GID of the male parent if they are known.

L.      If the entry is a derived line (not F1) then PROGENITOR2 should contain the GID of the immediate source of the entry, in this case 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.

M.    You can add attributes for the entries being imported by adding columns with headings obtained from the Passport or Attributes sheets of the Template. If the attribute you want is not there you must add it first through the ontology manager. A column for NOTES has be added by default. Add some notes.

Part 3. – Inventory and unique identifiers

Column Effect

N.     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.

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

P.      This contains the amount of seed going into storage for new or existing entries. If some inventory entries are blank BMS will ask if you want those left blank of filled with set values at the time of importing.

Q.     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.

R.     PUI can contain Public Universal Identifiers for the entries. The BMS will assign a unique code, the GUID, but if a suitable global public identifier exists you can enter it in the PUI column and it will be stored as a name for the new germplasm, the GUID will also be created.

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.

 Update/edit germplasm

Automatic list creation

After new distinct germplasm have been imported in the BMS, the v19 Import Germplasm tool can be used a second time to automatically create a list of germplasm ready for use in a study.

In the following example, a list of parents needs to be created for use in a crossing block nursery. The same steps apply when preparing a germplasm list for a trial.

Step 1. Import distinct new germplasm (no repeats)

Step 2. Import list of existing germplasm (with repeats)

Manage Studies : Design crosses

Edit germplasm

Update a single GID: Germplasm details

Clicking on blue hyperlink text containing a GID or germplasm name anywhere in the BMS reveals germplasm details.

The pencil button is visible and enabled for a user with Edit Germplasm permission. Germplasm basic details, names, descriptors (eg. passport information, attributes), pedigree, and files can be modified.

The trashcan button is visible and enabled for a user with Delete Germplasm permission.

The bulletpoints button is visible and enabled for a user with View Change History permission.

Update a batch of GIDs: Import germplasm updates

There are two ways to update Germplasm Records in BMS if you have the correct privilege to do so (eg Crop Admin). The first way is to use the edit features on the Germplasm Details forms – one GID at a time as described in the previous section. A second way is to use the Germplasm Update template from the Germplasm Manager to update a batch of GIDs in a single pass. We will demonstrate the second way here.

Click on Import germplasm updates from the Actions menu of Germplasm Manager.

You can download a Germplasm Update template by clicking on the “here” link:

Now suppose I want add accession numbers and make them the preferred name for germplasm BALAJAN with GID 3780217 and germplasm SINYARUE with GID 3781237. (If you are trying this in a classroom setting, pick some different GIDs for your own exercise by looking in the Germplasm Filter list).

First I have to define the germplasm I want to change by entering their GIDs in column A of the template. I can also look up their unique identifiers on the Germplasm Details page and enter them in column B (instead of GID or as well as GID if I want). Then I look up in the Codes sheet the code for Name Type Accession number – ACCNO and I replace the heading in column J (DRVNM) with this code (ACCNO). Then, since I want the accession number to be the preferred name, I add the same code in column F of the template.

I can also change the germplasm location by entering a location abbreviation in column G. (I can look up location abbreviations in the Codes sheet or in the Location Manager of the BMS).

I can change the germplasm date by adding a valid date (YYYYMMDD) in column H,  I can add a germplasm reference by adding a reference text in column I.

Finally, I can add any attributes I want. For example I can add some notes in column K and I can add columns after that with attribute codes from the Passport or Attributes sheets of the template. For example I can add a column headed STATUS_ACC_AP_text  (accession status) to column L and fill it with AV for available.

Your completed template appears as above.

I could also change the pedigree of the germplasm using columns C,D,E as will be described below.

Once the template is complete, select Import germplasm updates form the Actions menu of the Germplasm Manager and browse to the file and click Import. The updates will be applied and can be viewed in the germplasm details form:

Pedigree Editing

There are two ways to edit the pedigree of Germplasm Records in BMS if you have the correct privilege to do so (eg Crop Admin). The first way is to use the edit features on the Germplasm Details forms – one GID at a time. A second way is to use the Germplasm Update template from the Germplasm Manager to update a batch of GIDs in a single pass. We will demonstrate the second way below.

Let us consider our example on Importing New Germplasm described in a previous section where we imported new entries CGMLine1 and CGMLine2.

CGMLine1 has GID 8016348 and CGMLine2 GID 8016349.

Suppose we later discover that CGMLine1 is a purification from NERICA 4  (GID 765439) and that CGMLine2 is an unknown derivative line from the cross IR 1234 (GID 1903) made at IRRI in 19950101.

Suppose also that we discover that the unknown cross IR 56279 (GID 68722) is a three-way cross between NERICA 4 (GID 765439) and the F1 IR 1234 (GID 1903) and that we would like to make the alternative name CP 135, which is a cultivar name, the preferred name.

Click on Import germplasm updates from the Actions menu of Germplasm Manager and download a template.

Column Effect

A.     GID – Fill the GID column with the GIDs of the germplasm for which you wish to change the pedigree information.

B.     GUID – you can enter the Germplasm unique identifiers in the GUID column instead of the GIDs or as well as the GIDs if you like.

C.      BREEDING METHOD – look up in the Codes sheet the codes for the breeding methods you want for the germplasm: DPR for Purification, UDM for unknown derivative method, and C3W for three-way cross. If you don’t want to change the method for a line leave the cell blank.

D.     PROGENITOR1 – If the subject germplasm is derivative (like an inbred line) and you want to connect it to a known immediate source set PROGENITOR1=0 and PROGENITOR2 to the GID of the known source. If the subject germplasm is derivative from a known cross, but you don’t know the immediate source, set PROGENITOR1 to the GID of the known cross and PROGENITOR2=0.

E.      PROGENITOR2 – If the subject germplasm is generative (like a cross) set PROGENITOR1 to the GID of the female parent and PROGENITOR2 to the GID of the male parent.

F.      PREFERRED NAME – If you want to change the preferred name of the subject germplasm to one of a different type, look up the code for the type in the Codes sheet and enter it in the PREFERRED NAME column. The name could exist for the germplasm already or it could be added in a column of the template having the name type code as column heading.

G.     LOCATION ABBR – If you want to change the germplasm location for the subject germplasm, look up the abbreviation in the Codes sheet or in the Location Manager of the BMS and enter it in the LOCATION ABBR column.

H.     CREATION DATE – If you want to change the creation date of the subject germplasm, enter a valid date (YYYYMMDD) in the CREATION DATE column.

I.       REFERENCE – If you want to add or change the reference relating to the subject germplasm enter the text of the reference in the REFERENCE column.

J.       DRVNM – If you want to a add new names for the subject germplasm, enter the names in column(s) headed by the name type code for the type of name you want. Derivative name (DRVNM) has been added as a column for example, but you can look up other name types in the Codes sheet and add columns for those name types as well as DRVNM or instead of DRVNM.

K.      NOTES_AA_text – If you want to add attributes for the subject germplasm, enter the values in column(s) headed by the attribute code(s) which you can look up on the Passport or Attributes  sheets of the template. The attribute NOTE_AA_text has been added to the template as an example.

Before Updates

After Updates

 Before Updates

After Updates

Before Updates

After Updates

Delete germplasm

Germplasm created in the system erroneously can be deleted. Once deleted, the designation and GID will not appear in germplasm searches. The GID is not available for reuse after deletion.

The system will prevent deletion of germplasm:

• if the germplasm has inventory

• if the germplasm exists in multiple lists

• if the germplasm is associated with a nursery or trial

• if the germplasm is fixed

• if the germplasm has descendants

Confirm deletion.

Export data and labels

You can export data and labels based on the current label printing features in Manage Germplasm.

• Select the germplasm of your interest- You can use a filter, the checkbox, or the current page.

• From the Actions menu select Export data and labels

You will be presented with options to select the Output format (Formatted PDF Label Sheets, Excel, CSV)

And an option to select an existing configuration preset

Also, you can select: i) GID,  ii) Preferred Name), iii) GroupID, or iv) Creation Date for sorting the data to be exported

Available Fields

The available fields are Germplasm Details, Pedigree, Names and germplasm Attributes.

Export Option - PDF

• Select the PDF output format, and Preferred Name in Sort label by.

• Specify the label stock parameters: Size of label sheet and the number of rows per page

You will see two sections where to allocate the available fields.

When the PDF format is selected, also are presented the options to include barcodes in the export.

• Do you want to use automatically generated unique barcodes: No

• Select the First, Second and Third barcode field

NOTE: the GUID is the barcode field if you select Yes to "automatically generate barcodes"

You can save the fields specified in a preset to be used in the future.

• In Save settings, add a preset name.

• Save Preset, a success message is displayed: SUCCESS - Successfully saved preset. The preset is now available for selection when checking the "Load saved settings" option.

• Export. The file exported should have germplasm-labels_ [USERNAME] _ [yyyymmdd]_[hhmmss], truncating the file name if it is needed

Predefined template for Excel format

You can use the existing preloaded preset ticking the Load saved settings checkbox and selecting the Excel template default

The preloaded preset has the following fields available by default under Selected Fields section:

GID, GUID, Location Abbr, Breeding Method Name, Preferred Name, Reference, and Creation Date 

You can modify the fields selected by default adding or removing fields

And the exported file will have all the fields and their values populated correctly

Export option - CSV

• Select CSV as the format option

• Select the option for sorting labels

• Select the fields of your interest in Germplasm Details, Pedigree, Names, and germplasm Attributes.

• Export labels, remember you can save a new preset or use an existing one.

Group and ungroup germplasm

In the BMS, a 'group' is a set of germplasm with a shared ancestry. Grouping is useful when working with inbred lines in hybrid breeding or varieties of a self-pollinating species. In a typical hybrid breeding program when a line is considered homozygous (fixed), either by inbreeding or doubled haploid formation, it is set as the founder of a new group and given a code name. Grouping and coding can also be useful to track families and to indicate when germplasm has passed through a breeding phase, such as disease resistance selections.

A group is created by selecting a germplasm that is to be the founder of a new group and using the 'Group' action in the List view of the Germplasm Management module. This creates a group identity -- a Group ID.  When Germplasm with a group identity is propagated using breeding methods that refine or preserve genetic variation (derivative or maintenance methods) the resulting descendants will inherit the group identity.

Inbred Lines

Group ID can be used to identify a fixed inbred line and all descendants. A line that has reached fixation is expected to give rise to genetically identical offspring through maintenance breeding methods. When an inbred line is deemed "fixed" it can be grouped, so that all descendants, even those with different breeding histories and GIDs, can be retrieved by searching Group ID. At any point in the breeding process, descendants can be re-grouped or un-grouped. For example, inbred lines resulting from pedigree breeding will not be 100% homozygous. Offspring with off-type phenotypes can be regrouped to distinguish from non-segregating lines.   

Scenario: A breeder considers some F4 lines sufficiently inbred (fixed) and wants to group them.

GERBB020-1-RB-1 is an F4, which has homozygosity estimated at ~87.5%. This estimate can be presumed higher for traits of interest if the selection was applied during line development. A breeder might consider F4 lines as fixed and want to keep track of descendants.

Group

To create a group, one or more germplasm records are selected in Germplasm Search in the Manage Germplasm module and the Group action is selected from the Actions menu. For each germplasm record, the BMS will create a new group with that germplasm record as the founder of the group. Note that if you select multiple germplasm records, they will not belong to the same group unless they are related by descent.

• From Germplasm Search, select lines to group. Select Group from Actions options.

20 F4s are selected for grouping.

Options

Preserve existing group

Preserve existing group will preserve the existing Group ID. In other words, if the germplasm is already a part of a germplasm group, that group ID will be preserved.

Include descendants

Include descendants in the grouping to ensure that all descendants from these lines can be tracked for inbred line development. This is useful in cases where the line has already been advanced. For example, a line may have been advanced to the F6, but the breeder considers the F5 to have been sufficiently homozygous and homogeneous to be considered the founder of an inbred lineage. The breeder would then open a list containing the F5, select the individual for grouping, and check 'Include descendants'.  The F5 and any F6s derived from that F5 would then belong to the same group.

• To assign a new Group Id to selected germplasm and their offspring, do not select 'Preserve existing group' and select 'Include descendants'.

The descendants by maintenance and derivative breeding methods will inherit the same GroupID as these selected F4s. Preserve existing group is not relevant in this example, because these lines are ungrouped.

• Review the grouping results and select OK.

All entries received a new Group ID that will be inherited by the descendants.

The germplasm is now updated with a new Group ID.

Notice that the founder of a group's GID matches the Group ID. Subsequent advancement of the founder and its descendants will share this same Group ID, but will receive unique GIDs.

This table shows a list of seed increases from the previously grouped F4s. Notice that the newly created germplasm receives new GIDs, but shares the Group IDs of their progenitors (see F4 list in the example above).

• Selection of individual germplasm reveals that this germplasm is a grouped line, Group ID.

Ungroup

If grouped germplasm is found to be "off-type" or segregating it can be ungrouped and removed from the shared lineage designation (Group ID).

• Highlight germplasm and select ungroup from the Coding and Grouping Options of the Action menu.

• Confirm

The selected line is now ungrouped - there is no longer a group ID associated with this entry. Ungrouping only affects the selected line. Ungrouping does not retroactively apply to descendants.

Apply code names to germplasm

Codes are customizable names that can be assigned to grouped lines at different stages of line development, such as inbred line fixation and hybrid formation. Coded names become the preferred name for the lines, and are inherited as the preferred names of descendants in the same group. There are three levels of codes which can be assigned at different stages of development and each level supersedes the other as the preferred name for the group as it is assigned to any member of the group.

• From Manage Germplasm list view, assign codes to selected grouped lines from the Actions menu.

Coding Level

The BMS allows breeding programs to automatically name 3 different coding levels. For example, a program may want to update the name of germplasm after it successfully passes through a specific phase in the breeding process. Examples of breeding milestones that may be associated with code levels include:  'fixation' of inbred lines, successes after disease selection, creation of hybrids, line release.

Automatic name generation

Institutes can set automatic naming conventions through database customization. Please see your database administer for more information on your institution's coded naming conventions.

• To use your institution's coded naming conventions, select 'Automatic naming generation' and Apply Codes.

Specify Codes Manually

Users are able to customize coded names via UI options.

• Select 'Specify Codes Manually'. Enter the naming details and Apply Codes.

In this example the 20 selected F4s are going to be renamed with inbred line prefix "IL", a 3 digit sequence number, and a suffix "-18" to indicate the year of fixation.

• Review the code results and select OK. Notice that the specified prefix has been concatenated with a sequence number to produce the code names.

Notice that the coded name is applied to all members of the group. In the first entry or example, GID 379138 & 366641 share the same group ID, so both are assigned IL022-18 as their preferred name. Also notice that the final entry shows that 379142 and 366645 have previously been coded, so the new name will not apply. The new name will not apply to GID 366646 due to it is not part or a germplasm group.

Create inventory lots

Create lots allows you to create lot one at a time through the user interface (see Import Lots above for batch functionality). This function also provides the option to specify an initial deposit amount in Manage Germplasm. This action requires that germplasm already exists in the system with GIDs. (See related topics: Import Germplasm, Crossing, Selections )

• Select the germplasm desired, using a filter or using the checkbox. From the Actions menu select Create inventory lots option.

Fill the details. Stock ID prefix cannot end in a number. Save.

If the lot creation is successful, you will receive a confirmation message and the germplasm is now updated with a lot.