Updating germplasm records

Owned by Clarissa Pimentel
Last updated: 01 Jul, 2022

Updating germplasm records

There are two ways to update Germplasm Records in BMS if you have the correct privileges to do so (e.g. 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 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.

You complete the template as follows:

I could also change the pedigree of the germplasm using columns C,D,E. See following exercise.

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:

Exercise on Pedigree Editing

There are two ways to edit the pedigree of Germplasm Records in BMS if you have the correct privileges 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 in this exercise.

Currently there is a restriction on which germplasm can have pedigrees changes – they should not have any descendants. This restriction will be reduced in subsequent releases of BMS.

Considering our previous exercise on Importing New Germplasm where we imported new entries CGMLine1 and CGMLine2 for me. Use your own entries for this exercise.

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 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.

Columns A to K.

  • A. GID – Fill the GID colum 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

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Before Updates

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Before Updates

After Updates