Germplasm Menu

The following items of the Germplasm menu illustrate the order of dependency:

  1. Genus
  2. Genotype
  3. Specimen
  4. Specimen Lists
  5. Traits
  6. Trait Groups
  7. Treatment.

Genus

Genus refers to a logical grouping of genotypes which may optionally be botanically related. Once entered the Genus Name text may be altered if required.

The Add Genus window (select to zoom)

Genotype

Genotype records may either be entered manually or imported from file (see: Import Genotype). Synonym for genotype can be variety and should be used as a generic category.

This table describes the fields for the following illustration which allows manual addition or updating a Genotype:

Group Permissions - All fields are Mandatory
Field Description
Genotype Name The name of the Genotype.
Genus Select the Genus name.
Genotype Colour Can be used for Plant Variety Rights Information.
Species Name Latin name - common naming conventions should be established.
Genotype Acronym Abbreviated name of genotype.
OriginId Source Identifier - possible Part of Plant Variety Rights Information - could refer to organisation or contact.
Can be Published Indicate if Genotype is publicly available.
Note Any notes regarding the Genotype.
Access Fields Access Settings and Permissions.


The Add Genotype window (select to zoom)

Import Genotype

New Genotype records may be imported into KDDart and if required Specimens for the Genotype records can be automatically created within the process.

The following illustration and table describes the fields required in an input file to import Genotypes and create Specimens if required.

Note: Dialog window will match column names once users select file for import.

Import Genotype Fields
Field Mandatory Description
Genus M The Genus name for the Genotypes
Breeding Method   Select from the list of Breeding Methods (Use Default if not required/important)
Number of Specimens   A value must be selected from 0-9.
The value specified here applies to all Genotype records being imported unless overridden by the “Number of Specimen Column”. See example below.
Genotype File M Select the input file for the import.
Genotype Name Column M Column number for Genotype Name.
Species Name Column M Column number for the Species name.
Genotype Acronym Column   The Acronym column is optional.
Genotype Note Column M Column number for notes regarding the Genotype.
Number of Specimen Column   The column number which contains the ‘Number of Specimens’ to be created for a individual record. See example below.
Genpedigree start Column   The column number which begins a Genotype Name and Genotype Pedigree Type pairings. Use Genotype Names and Type Names.

Note

Access Fields (Refer to the Access Settings and Permissions topic) do not appear on the Import Genotype window.
These fields are automatically set with the owning group set to the group used to perform the import as follows:

Group Privileges
Group Privilege
Owner (Group used for import) Read & Write
Access Read & Link
Public Read & Link

When importing Genotypes from file, KDManage can optionally create Specimens for each or selected Genotypes if required. The following applies to the import window:

  • Number of ‘Specimens greater than zero’ - The specified number of Specimen records will be created for each Genotype record imported unless overridden by the individual record.
  • Numeric value in the ‘Number of Specimen Column’ - Directs the import to check that column in the file for each record and create the specified number of Specimens for the Genotype. Within the file where a:
    • Value for a record = blank - The ‘Number of Specimens’ value entered will apply for the Genotype
    • Value for a record = zero - No Specimen will be created for the Genotype
    • Zero < Value < 10 - This number (value) of Specimens will be created for the Genotype.

The following illustration shows the Import Genotype window:

The Import Genotype window (select to zoom)


Import Genotype Example

The following example shows a small Genotype input CSV file:

Example Genotype CSV import file (select to zoom)


The following illustration shows the completed import fields for this file.

The import file shown above will create six Genotype records and four Specimen records when imported using the following KDManage form settings.

Note: Those records in the file with a zero in the Specimen Number column will not have a specimen record created.

Import Genotype window with fields completed (select to zoom)


The following image illustrates the returned message for a successful import and shows the six newly imported Genotype records:

Successful Genotype import example for file shown above (select to zoom)

Successful Genotype import example for file shown above


The following window illustrates the automatically created Specimens based upon the input criteria above. Also notice how the specimen name was treated. When:

  • A single Specimen is created the Specimen name matches the Genotype name
  • Multiple Specimens are created for a Genotype, the Specimen name is given the Genotype name with a numeric suffix (eg for a Genus name ‘GenoA’, Specimen Names would be GenoA__1, GenoA__2, etc).
Automatically generated specimens (select to zoom)


Genpedigree entries can also been included in the CSV by including each Genpedigree pair following the column specified in dialog. See the example below:

Import Genotype with Genpedigree Example

Genotype CSV with Genpedigree example

Tip: Parents listed in CSV can either be Genotypes that are in the CSV or exisiting Genotypes that have already been added or imported.

This will result in the following Genpedigree being created for Genotype “Ge3”.

Genpedigree after import example

Import Genpedigree

New Genpedigree entries for existing Genotypes can be imported

Note: Dialog window will match column names once users select file for import.

Import Genpedigree
Field Mandatory Description
Genpedigree File M Select the input file for the import.
Genotype Id Column M Column number for Genotype Id. These are the “children” genotypes
Parent Genotype Id Column M Column number for Parent Genotype Id. These are the “parent” genotypes
Genotype Parent Type Id Column M Column number for Genotype Parent Type id

Genotype Alias

Genotypes may also have a Genotype Alias added to help with identifying. To add an alias to a genotype, click on the Add button add-btn.

Add Genotype Alias
Field Mandatory Description
Alias name M Alias name for Genotype
Type name   Alias type
Status   Status of Alias
Language   Language of Alias
Genotype Name?   Flag that alias is Genotype name or not

Genotype Page

The Genotype page is an improved interface when viewing Genotype data.

This can display the following entities related to the Genotype being viewed.

  1. Specimens associated with Genotype
  2. Phenotypic data (Trial data) associated with Genotype
  3. DNA and Marker data associated with Genotype
  4. Genpedigree of Genotype
Specimens associated with a Genotype (select to zoom)


Phenotypic data associated with a Genotype (select to zoom)


DNA and Marker data associated with a Genotype (select to zoom)


Genpedigree data of Genotype (select to zoom)

Specimen

Specimen is the physical representation of a genotype and this facilitates the recording of vital characteristics such as where and when it was grown.

Interestingly for example, in horticulture one specimen may be composed of two genotypes (rootstock and scion). The KDDart environment anticipates these scenarios and caters for this requirement.

The following table describes the fields for importing Specimens:

Specimen fields
Field Mandatory Description
Genus M Select an existing genus for all the specimens in the input file
Breeding Method M Select an existing breeding method for all the specimens in the input file.
Specimen File M Browse to locate the input Specimen CSV file.
Specimen Name Column M The specimen name column in the input file, numbered from zero.
Is Active Column   An indicator to show if the specimen is still ‘active’ (ie in production).
Pedigree Column   Could be a generated Purdy string from male and female parent ID (or some other than Purdy standard).
Selection History Column   Optionally siblings clones etc, where genotype name is the same.
Filial Generation Column   Level of specimens being ‘selfed’, required when full selection history is unavailable.
Genotype Start Column M The genotype name column in the input file, numbered from zero.
Genotype End Column   The second genotype name column in the input file, numbered from zero.

The Import Specimen window:

Import Specimen window (select to zoom)

Import Pedigree

New Pedigree entries for existing Specimens can be imported

Note: Dialog window will match column names once users select file for import.

Import Pedigree
Field Mandatory Description
Pedigree File M Select the input file for the import.
Specimen Id Column M Column number for Specimen Id. These are the “children” genotypes
Parent Specimen Id Column M Column number for Parent Specimen Id. These are the “parent” genotypes
Specimen Parent Type Id Column M Column number for Specimen Parent Type id

Specimen Lists

Specimens can be added to Specimens Lists. This allows specimens to be added in lists for convenience.


Add Specimen list window (select to zoom)


The following table describes the fields for importing Specimens lists:

Specimen list fields
Field Mandatory Description
Name M Name of Specimen List
Type M Type of Specimen List (see Types in Administrative Settings)
Status M Status of Specimen List (see Types in Administrative Settings)
Date Created M Date that Specimen list is created
Note/Description   Notes of Specimen List
Access Fields M Access Settings and Permissions

Traits

Traits are important descriptors of what is to be measured and what the permissible values are in those measurements. The Trait/Measurement window enables the definition and quantification of a trait or characteristic of the trial/experiment.

This includes a description and notes, the datatype, units of measurement, maximum value and validation rule.

Note: Traits need to be defined before they can be assigned to a Trial. Once Traits are added here they will appear in the selection list for Add Traits to a Trial.

The Add Trait window:

Add traits window (select to zoom)


The following table describes the fields appearing on the above Add Trait window:

Field Mandatory Description
Trait/Measurement Name M The name to identify the trait or measurement.
Caption M An abbreviated or shortened trait name (e.g. name without spaces). Could be used for display.
Description/Note M A description or note about the trait.
Data Type M The trait’s data type. Selection from class “Trait Data Type” in Types (see Types section in Administrative Settings)
Max Length M The maximum length of the value (e.g. 12).
Unit M Unit of measurement for the trait (e.g. kg/h, colour, etc).
Used for Analysis M May be used as an indicator (e.g export all traits need analysis).
Type of Validation Rule _ Indicator for the type of validation rule (either a Boolean, Regular, Range or a Choice expression). Upon selecting a rule, a helper will appear that you can use to make sure you use the correct format.
Validation Rule M A validation rule for the value of the trait.
Validation Error Message M An error message to display, when the validation rule criteria is not met.
Access Fields M Access Settings and Permissions

For Access Settings and Permissions fields refer to the Access Settings and Permissions topic.

Trait Groups

Traits can be added to Trait Groups. This allows traits to be added in groups for convenience.

Add Trait Group window (select to zoom)

Treatment

Treatment describes or quantifies an action performed on a trial unit in order to induce a measurable response, such as to a certain level of fertilisation (e.g. ‘Adding Nitrogen’) quantity of irrigation, etc.

The Treatment window illustrated consists of a single text field to capture the treatment performed:

Add Trait Group window (select to zoom)