GenXplore - Overview

Note

This Module Is In Alpha. Check back here or contact us at kdxplore@diversityarrays.com for more information.

GenXplore is the KDXplore plug-in that enables users to search though specimen and pedigree data for genotypes.

From GenXplore, the database can be queried on the basis of different search criteria for certain individuals (genotypes).

After completing a search, the genotype pedigree, detailed parentage information, cross information and phenotypic information can be viewed.

GenXplore is also aimed at cross design which can be performed after a list of individuals is created. When a cross is designed in GenXplore the user will be warned if the cross has already been made.

Main Window

To access GenXplore, navigate to the KDXplore Main Window and then select the gen_explore_btn GenXplore Button. This will open the GenXplore Plug-in which will look like the image below:

Navigating the GenXplore Main Window

Connecting to a database
Number Component Description
circle1 Search Panel Contains options for searching for genotypes and the Entries List where results are displayed.
circle2 Genotype Information Panel Provides information on selected genotypes (after being selected from the Entries List).
circle3 Genealogy Tree/Crosses/Trait Values Tabs Provides visualisations for genealogy trees, crosses, and trait values.
circle4 Discover/Make Crosses Tabs The Discover Tab (as in the above image) contains information and visualisations. The Make Crosses Tabs opens the Crosses Panel contains tools for crossing genotypes (see the below image).

Crosses Panel


Connecting to the KDDart Database - refer to the one on the index page

When the laptop/pc has a network connection KDXplore can login to KDDart. Login requires:

  • The URL for the database;
  • A valid username and password; and
  • The Group Name, if applicable.

The following image shows the GenXplore window and the login steps are described below:

Connect to a database from the GenXplore

Connecting to a Database
Step Action
1. To connect to a database in GenXplore click the Connect Button seen at circle1.
2. This will open the Login Window seen at circle2.
3. Enter the database URL in the first field (or select from the drop down of previous database URLs), then the username and password.
Choose a login group (if applicable) from the fourth field drop down menu.
4. Select the Login Button at circle3 to login.

Searching for Genotypes

Users can search for genotypes once GenXplore is connected to the KDDart Database. The following instructions explain how to search for genotypes with various criteria:

Searching Genotypes with GenXplore

Searching for Genotypes
Step Action
1. Select the genus to search for from the drop down menu at circle1. This will populate with all genera available when a database is connected.
2. Select the search criteria from the drop down menu circle2.
3. Select the search modifier for the criteria chosen from the drop down circle3. In this example, there are no other options so choose so the area is disabled.
4. Enter the search term in the field at circle4. Using the example, the search is for the genotype ID ‘424856’.
5. Filial generation of results shown can be adjusted at circle5.
6. Once search parameters have been set, select the Search button (at circle6) or press enter to start the search. Results (such as the entry 424856 in the above image) will be displayed in the in a list below the search parameters.

Genotype Table

All genotypes can be searched in the Search Panel. The instructions below demonstrate how to search for a genotype by genotype ID:

GenXplore Genotype Table showing search results

Displaying Search Results
Step Action
1 The Search Panel displays the search results. The columns appearing are user configurable with the default display showing: ID, name, acronym, note, filial generation (F), and alias (“Also known as”).
2 Navigation of search results is by page using the controls in area circle2 where the Results per page setting can be adjusted.
3 Search results can be accumulated by selecting the Add to Previous Results Checkbox at circle1.
4 Selecting a search result circle3 will display Genotype Information in the right panel.
Selecting the search result with a right mouse button click will reveal a menu as illustrated. Results may be removed from the displayed table; selected rows can be exported to CSV file; or collected to prepare for seed preparation or trial design.

Making a new Germplasm list

The GenXplore Plug-in has the ability to collate genotypes into lists that can be created and edited by the user. These lists allow for easier and more efficient analysis of specific genotypes. The below instructions detail how to use search results to create a new germplasm list:

Creating a New Germplasm list

Creating A New Germplasm List
Step Action
1 To create a new germplasm list, select the Tools Menu at circle1 and choose the Entry List Editor option. This will open up the Entry List Editor.
2 Select entries such as the ones selected in circle2 and click and drag the selected entries to the Entry List Editor’s Specimen List panel in circle3.
3 Select the Save Button at circle4 which will bring up the Enter Details Window at circle5.
4 Enter the details and select Save to create a new germplasm list.

Note

After a new list is prepared it, can be saved as a specimen group, used in the Trial Design Plug-in, or exported.

Genotype Information

Genotype information for the selected search result, from the Genotype Table is displayed in the fields at circle1 in the below image:

Viewing genotype information

The Tool Bar, appears below the Genotype information fields which operate as follows:

Buttons
Button Response
tree_btn Genealogy Tree Build Collects the parentage, cross and phenotypic data for the selected genotype.
undo_btn Previous Navigate to the previous genotype.
redo_btn Next Navigate to the next genotype.
backspace_btn Clear Clears the selected entry.
helium_btn Export to Helium Exports or imports data with helium.
export_btn Export Exports data.
expand_btn Expand Opens the Genotype Information Panel in a separate window.

Exporting to CSV

The following steps will demonstrate how to export genotype information to a CSV file:

Exporting Genotype Parentage Information To CSV
Step Action
1 Select the Collect Genotype Information Button tree_btn to collect information for the selected genotype.
2 Next, select the CSV Export/Import Button export_btn and select the Export option.
3 Select the file location and select Save.

Exporting to Helium

The following steps will demonstrate how to export Genotype Information to Helium:

Exporting Genotype Parentage Information To Helium
Step Action
1 Select the Collect Genotype Information Button tree_btn to collect information for the selected genotype.
2 Next select the Helium Export/Import Button helium_btn and select the Export option.
3 Select the file location then select Save. The subsequent file can then be opened in Helium for viewing.

Genotype Genealogy Tree

The GenXplore Plug-in can create a genealogy tree for any selected genotype ID. The following instructions outline how to do this:

Generating a Genealogy Tree for Selected Genotypes

Generating a Genealogy tree for Selected Genotypes 1/2
Step Action
1. By selecting a Genotype from the Genotype table and selecting the tree_btn button at circle1, the panel below will be populated with the Genealogy tree structure or ancestry of the selected genotype appearing in area circle2.
2. Undocking the panel, by selecting the expand_btn button seen in area circle3, provides a closer view.

Generating a Genealogy Tree for Selected Genotypes

Generating a Genealogy Tree for Selected Genotypes 2/2
Step Action
3. Controls for the genealogy tree can be seen in area circle4 and area circle5. The controls in area circle4 have zoom control, whether to pan when dragged or select nodes, display the tree in radial format and save the tree to PNG file. The top controls also contain a legend for what the shape of nodes in the tree represent, and the colour. The shape of the nodes and the colour in this instance represent the known (or unknown) sex of the nodes of the tree, when they were used to create progeny (also seen) in the tree.
4. Controls at the bottom of the panel seen in area circle5 allow the user to set what criteria, size and colour should be represented as. E.g. the size of each node in the tree could be representative of the # of crosses it was involved in, or maybe how many ancestors it has (length of line). The controls in area circle5 also contain options for the naming of nodes, e.g. whether to display ID, name of genotype or acronym.
5. To the furthest left of the controls in circle5 is a selector for what level of ancestry to show. In the instance shown here the tree is very large. This can be reduced by only showing 5 generations (as seen below).

Changing Genealogy Tree Depth

The genealogy tree that is generated will automatically show 10 levels of depth. The image and steps below outline how to change the depth of the tree.

Changing Genealogy Tree Depth

Changing Genealogy Tree Depth
Step Action
1. Enter the desired amount of tree depth such as the level of ‘5’ as shown in circle1. Nodes can also be selected and dragged manually around the panel area.
2. Select the Choose option in circle2.

Genealogy Tree Options

Once genotypes are selected, right-clicking anywhere will present a number of options as seen below:

Genealogy Tree Options

From the options the user can:

  • Export selected genotypes to CSV format
  • Add selected genotypes to the list in the genotype table
  • Collect genotypes for trial/nursery design.
  • Cross genotypes as female (Automatically adds to crossing table - see section 12.)
  • Cross genotypes as male (Automatically adds to crossing table - see section 12.)
  • Change the colour scheme used for node rendered (When a numeric genotype info is chosen for node colour, the colour scheme used to display it is set here).

Genotype Cross Information

The genealogical history of any Genotype crosses can be shown in the Cross Information Panel as seen below:

Genotype Cross Information

  • circle1 Crosses Tab displays the overall cross information for the selected genotype.
  • circle2 Cross Information Panel displays the overall cross information including total crosses and total back/test crosses.
  • circle3 Crosses Panel is a list of crosses that the selected genotype has been involved in. The resulting genotypes (By name and ID) can also be seen here.
  • circle4 Back/Test Crosses Panel is a list of back/test crosses for the selected genotype. Note that the Crosses Panel will not contain these entries.

Genotype Trait Information

Some genotypes may have trait information attached to them. To display the trait information, the user will need to search for, and select a trait, and then follow the instructions below:

Genotype Trait Information

Displaying Trait Information
Step Action
1. To display phenotypic data for the selected genotype select the Trait Values Tab in area circle1.
2. The Traits and respective values for the selected genotype will display in area circle2. Selections from this table will display the trait description in area circle3.
3. Trial information for the selected genotype will be visible from this screen also in the panel in area circle4.

Cross Designer

The GenXplore Plug-in gives users the ability to design crosses between various genotypes. After searching for, and selecting genotypes in the Search Panel, genotypes can be dragged into the Crossing Panel. After selecting genotypes for crossing, the below instructions will demonstrate how to create the cross.

Designing Crosses In GenXplore

Designing Crosses In GenXplore
Step Action
1. Navigate to the Make Crosses tab by selecting at circle1.
2. The genotypes selected for crossing can will be visible at area circle2 and circle3 after being dragged to those locations. Genotypes to-be-crossed as female are displayed in the left table and male genotypes are in the right table.
3. The cross_btn at circle4, when selected checks each cross has not been previously made and generate the names for subsequent intermediate child entries in the lower area circle5.
4. Attempting a cross that has already been made will display a warning dialog that can be seen in the image below. Crosses made previously will also display in the table in area circle5.

Duplicate Crosses

Rank and Expected Crosses

The concept of rank and expected crosses are that the genotypes chosen for crossing have an intended rank or importance.

For each parent genotype, crosses will be performed with each corresponding genotype of the opposite sex with the same rank, if expected crosses is larger than 0. Expected crosses then corresponds to how many ranks below the genotype will cross with genotypes of the corresponding sex.

Rank and Expected Crosses Cross Designer

Rank and Expected Crosses Cross Designer
Step Action
1. Rank of genotypes for crossing can be adjusted by selecting a genotype in either parent list and using the arrows seen in area circle1.
2. Expected crosses for genotypes can be adjusted by selecting a genotype in either parent list and entering the expected crosses values in area circle2.
3. Preset values for Diallel and Half-Diallel can be set by selecting the check boxes in area circle3.
4. Once parameters are set, the cross_btn Cross Button seen in area circle4 can be selected to perform the crosses.

Note

For a less advanced crossing setup see the following section.

Punnet Square Crosser

The Punnet View allows the users to cross genotypes but has a simpler display to choose male and females to cross. The below instructions outline how to use this view.

Punnet Square Crosser

Crossing with Punnet View
Step Action
1. Selecting the button with the filter_btn Filter Button seen in area circle1 of the crossing panel will open the Cross Editor Window at circle2.
2. Inside this dialog seen in area circle3 are the selected genotypes for crossing. X-axis is female entries. Y-axis is male entries. By selecting cells in this matrix, you are selecting crosses to be performed.
3. In area circle4 the options for including a back cross and test cross can be checked.
4. Once crosses have been designed, the Cross Button seen in area circle5 can be selected to perform the crosses.

What To Do With Generated Progeny

Generated progeny can be used in the Trial Design Plug-in.