TDM Breeder's Training Lesson 18

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Contents

Using BROWSE to Manage Germplasm Records and Analyse Pedigrees

Introduction

Note: This chapter is for advanced users.

Objectives: At the end of this tutorial, the user should know how to manage germplasm records, i.e., edit or delete a record using BROWSE.

Use BROWSE to perform the following processes:

  • Generate a germplasm list;
  • Generate trees and mendelgrams;
  • Correct germplasm records; and
  • Calculate the coefficient of parentage between two lines.

Practice Set: A study whose entries consist of the following lines:

Lines for BROWSE Exercise
Name GID
PSB RC 80 879295
SIGADIS 386533
IR 78869-7 -110
PSB RC 12 447323

The corresponding germplasm identifiers (GIDs) appear in the second column.

GENERATING a LIST

  • 1. Start BROWSE from the launcher. The BROWSE application console window appears (see TDM GMS Browse).
If ‘ENTER VALID DIRECTORY PATH FOR LOG FILE’ appears at the bottom of the console, enter the full pathname of where ICIS is installed, e.g., if ICIS is installed in drive C, enter C:\ICIS.
  • 2. Add an entry to a germplasm list by entering the BROWSE command: .LST gidno
where ‘.LST’ is the command to add a germplasm record with GID = gidno to a list.
A list is automatically generated with the following characteristics:
    • NAME : BROWSE LIST
    • TYPE : BROWSE
    • DATE : <current date>
    • TITLE : BROWSE<current date>:<current time>
For the first entry of this tutorial, enter the command ‘.LST 879295’. The germplasm record with GID = 879295 (PSB RC 80) is added to BROWSE LIST.
  • 3. Add the remaining entries in the practice set of this tutorial. For each entry, repeat the step above.
NOTE: Each entry added to the list is automatically saved.

VIEWING TREES and MENDELGRAMS

The pedigree tree and/or mendelgram of any desired existing germplasm can be generated.

  • 4. Generate a Pedigree Tree. Generate a germplasm tree by entering the BROWSE command: .TRE gidno,nlevel
where ‘.TRE’ is the command to generate a pedigree tree of a germplasm with GID = gidno; and nlevel specifies the number of levels to generate. This value is optional. If no value is specified, this value defaults to seven.
For the first entry of this tutorial, enter the command ‘.TRE 879295’. A pedigree tree with seven levels is generated.
  • 5. Generate pedigree trees for the remaining entries of the practice set. For each entry, repeat step 4.
NOTE: Outputs generated in a session is saved to the BROWSE.LOG file. It can be found in the \ICIS directory.
  • 6. Generate a Mendelgram. Generate a mendelgram by entering the BROWSE command: .MGM gidno
where ‘.MGM’ is the command to generate a mendelgram of a germplasm with GID = gidno.
For this tutorial, enter the command ‘.MGM 879295’.
  • 7. Generate mendelgrams for the remaining entries of the practice set. For each entry, repeat step 6.

EDITING CHARACTERISTICS

The cross TB 165 E (GID = -10671) exists in the local tutorial database with the following characteristics:

    • METHOD : Unknown generative method (METHN = 1)
    • N PROGENITOS : 0
    • DATE : <unknown>
    • LOCATION : <unknown>
Suppose that it was recently discovered that the above cross was made in 1998 at the Ubon-Ratchathani Rice Research Center (URRC) as a single cross between KDML 105 (female parent) and IR 50401-77-2-1-3 (male parent). Edit germplasm characteristics of TB 165 E accordingly.
  • 8. Find a Location ID. Find the corresponding location ID (LOCID) of a location by entering the BROWSE command: .LOC locstr
where ‘.LOC’ is the command to search for locations whose name is the same as or starts with locstr. The locstr value may or may not contain wildcard (‘_’ or ‘%’) characters.
For this tutorial, to search for locations whose name starts with UBON, enter the command ‘.LOC UBON%’. All locations and their corresponding LOCIDs are displayed on the console.  :Look for the desired location name and note down its LOCID. Note that the LOCID corresponding to URRC is 10298.
  • 9. Edit a Germplasm Field. Edit a germplasm field by entering the BROWSE command: .SET fldname=newval IN gidno
where ‘.SET .. IN’ is the command for editing a germplasm record with GID = gidno; fldname corresponds to a germplasm field to edit. Fldname can be any of the following fields: GPIDn, GLOCN, GDATE, METHN, or GREFN. To edit a specific progenitor (GPIDn), replace n with the progenitor number, newval corresponds to the new value to change fldname to.
For this tutorial, the location where TH 98 was made is to be changed to URRC (LOCID = 10298). Enter the command ‘.SET GLOCN=10298 IN –10671’.
  • 10. To edit a germplasm date to another value, enter the BROWSE command: .SET GDATE=newval IN gidno
For this tutorial, to change the date to another value, enter the command: .SET GDATE=19980000 IN –10671.
  • 11. To edit a germplasm method to another value, enter the BROWSE command: .SET METHN=newval IN gidno
For this tutorial, to change the method from unknown generative method (METHN = 1) to single cross (METHN = 101), enter the command ‘.SET METHN=101 IN –10671’.
NOTE Corresponding method numbers must be known in order to use this command.
  • 12. Perform a Name Search. To perform a name search using BROWSE, simply enter the desired name (with or without wildcard characters). A name search is performed and the results displayed on the console. To view characteristics of a desired germplasm, enter the BROWSE command: .n where n corresponds to the nth record displayed in the list. This also corresponds to the value displayed in the first column of the console (the NO. column).
For this tutorial, enter the name ‘KDML 105’. Only one name is returned from the name search. To display its characteristics, enter the command ‘.1’. Note that the corresponding GERMPLASM_ID (GID) is 1709.
  • 13. To edit the female parent (GPID1) to another value, enter the BROWSE command: .SET GPID1=newval IN gidno
Similarly, to edit the male parent (GPID2) to another value, enter the BROWSE command: .SET GPID2=newval IN gidno
For this tutorial, to change the female parent to KDML 105 (GID = 1709), enter the command:.SET GPID1=1709 IN –10671.
  • 14. To edit the male parent to another value, repeat steps 12-13.

CALCULATING COEFFICIENT of PARENTAGE

  • 15. Calculate COP Interactively. To calculate the COP between two germplasm records in interactive mode, enter the BROWSE command: .COP gidno1 gidno2
where ‘.COP’ is the command to compute for coefficient of parentage; and gidno1 and gidno2 are the corresponding GIDs of germplasm records whose COP is to be calculated for.
For this tutorial, calculate COP between PSB RC 80 (GID = 879295) and SIGADIS (GID = 386333).  :Enter the command ‘.COP 879295 386333’. The COP value between the two records is 0.0478.
Calculating COP values between many pairs of germplasm records can be performed in batch mode as well. Suppose that COP values are to be computed for the following pairs of germplasm records:
    • PSB RC 80 (GID = 879295) and IR 78869-7 (GID = -110)
    • PSB RC 80 and PSB RC 12 (GID = 447323)
    • SIGADIS (GID = 386533) and IR 78869-7
    • SIGADIS and PSB RC 12
    • IR 78869-7and PSB RC 12
COP values can be calculated between all pairs of entries in a List by opening the list and entering the command .COP LST. To open a list, enter the command: .OPT LIST and then type the number of the list you want to open. Follow this by .COP LST to calculate COPs for all pairs.

PROCESSING COMMANDS IN BATCH MODE

  • 16. Any BROWSE commands can be processed in batch mode by entering the commands into a text file and then submitting that file to BROWSE. For example a series of TRE commands can be executed in Batch Mode. Create a text file named LIST1.TXT in the \ICIS folder.
  • 17. Enter the following in LIST1.TXT: 
.TRE 879295, 50
.MGM 879295
.TRE 386333, 50
.MGM 386333
.TRE –110, 50
.MGM -110
After entering the above lines, save the file.
  • 18. Enter the BROWSE command: .INP filename
where ‘.INP’ is the command to process the contents of text file = filename. The text file must exist in the same directory as BROWSE.LOG.
For this tutorial, to process the contents of LIST1.TXT, enter the command ‘.INP LIST1.TXT’.  :Each line is assumed to contain one command for processing. The outputs are appended to the BROWSE.LOG file.
  • 19. To exit BROWSE and close the console window, enter the BROWSE command: ./
  • 20. Open the \ICIS\BROWSE.LOG file and view its contents. Note that all outputs that were generated in the session appear in the file. If desired, edit and/or print the contents of the file.
NOTE: When a new BROWSE session is run, the existing BROWSE.LOG file is overwritten.
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