QTL

Quantitative Trait Locus (QTL) Tutorial

Use this tutorial to add, edit, search for, or delete Quantitative Trait Locus (QTL) information in CIERA.

Open the QTL screen

CIERA - Quantitative Trait Locus

1. Open CIERA.
2. From the main menu, select Manage Data > Manage Genotypic Data > Quantitative Trait Locus.
3. The Quantitative Trait Locus window opens.

Before you begin

Gather the QTL details you want to record. At minimum, be prepared to enter the QTL name, project, phenotypic trait, linkage group, QTL position, minimum position, maximum position, effect, score, and R2 value. Fields shown in red on the screen are the primary required fields.

If your QTL is associated with an existing genetic dataset, select that dataset before choosing flanking markers. CIERA uses the selected genetic dataset to populate the left and right flanking marker lists.

Add a new QTL

1. In Enter the QTL name, type the name of the QTL.
2. Complete the required fields and any optional fields that apply to your QTL. See Field reference below for an explanation of every field.
3. Select Add/Edit QTL.
4. CIERA saves the QTL information and displays a success message when the upload is complete.

Edit an existing QTL

1. In Enter the QTL name, type the existing QTL name.
2. Select Search (if existing).
3. If CIERA finds the QTL, the window is filled with the saved values.
4. Review and update the fields that need to change.
5. Select Add/Edit QTL to save the edits.

If CIERA cannot find the QTL name, it displays a message that the QTL is not in the system. You can then continue entering information and save it as a new QTL.

Delete an existing QTL

1. In Enter the QTL name, type the QTL name you want to remove.
2. Select Delete QTL.
3. CIERA deletes matching QTL records and clears the screen when deletion succeeds.

Use deletion carefully. Deleted QTL information is removed from the database.

Field reference

Field	Required?	What to enter	Notes
Enter the QTL name	Yes	The unique QTL name or identifier.	Use Search (if existing) after entering a name to load an existing record. Selecting this field clears the current form so you can start a new search or entry.
Project	Yes	The project associated with the QTL study.	Choose from the project list.
Phenotypic Trait	Yes	The trait associated with the QTL.	Choose the trait measured in the phenotypic study.
Map	No	The genetic map to which the QTL data can be projected.	Leave blank if no map is associated with the QTL.
Genetic Dataset	No	The genetic marker dataset associated with the QTL.	This field is editable. Selecting a genetic dataset loads marker names that can be used in the flanking marker fields.
Pheno. Dataset	No	The phenotypic study associated with the QTL.	This field is editable. Use it to link the QTL to the study where the phenotype was measured.
Linkage Group	Yes	The chromosome or linkage group where the QTL was mapped.	Examples: 1A, 2B, LG3.
Position of QTL	Yes	The numeric QTL position.	Enter the mapped QTL position, typically in centimorgans or the unit used by the selected map. Numeric values are expected.
Min. Position	Yes	The numeric lower bound of the QTL interval.	This is the minimum position for the QTL interval. Numeric values are expected.
Max. Position	Yes	The numeric upper bound of the QTL interval.	This is the maximum position for the QTL interval. Numeric values are expected.
Effect	Yes	The numeric effect of the QTL on the trait.	Enter the positive or negative effect value reported by the QTL analysis. Numeric values are expected.
Score	Yes	The numeric score value for the QTL.	The screen tooltip describes this as the log-base-10 ratio value. Depending on the analysis, this may correspond to a LOD or similar score. Numeric values are expected.
R2	Yes	The percent of total phenotypic variation explained.	Enter the R-squared value from the QTL analysis. Numeric values are expected.
Lf, Flank. Marker	No	The marker to the left of the QTL.	Choose from markers loaded from the selected genetic dataset, or type a marker name.
Rt, Flank. Marker	No	The marker to the right of the QTL.	Choose from markers loaded from the selected genetic dataset, or type a marker name.
CLEN	No	The numeric chromosome length value.	Leave blank or 0 if not available. Numeric values are expected.
SE Additive	No	The numeric standard error of the additive effect.	Leave blank or 0 if not available. Numeric values are expected.
HV Allele Prnt GID	No	The GID of the high-value allele parent.	Use pedigree tools to find the correct parent GID. Leave blank or 0 if not available. Numeric values are expected.
High Value Allele	No	The high-value allele.	Enter the allele associated with the higher trait value.
LV Allele Prnt GID	No	The GID of the low-value allele parent.	Use pedigree tools to find the correct parent GID. Leave blank or 0 if not available. Numeric values are expected.
Low Value Allele	No	The low-value allele.	Enter the allele associated with the lower trait value.
Interactions	No	Notes about interactions involving this QTL.	Use this for epistatic interactions or other interaction notes reported by the analysis.

Buttons

Button	What it does
Search (if existing)	Searches the database for the QTL name entered at the top of the screen. If found, the screen is populated with the existing QTL information. If not found, CIERA reports that the QTL is not in the system and treats the form as a new QTL entry.
Add/Edit QTL	Saves the information on the screen. If the QTL was found by search, this updates the existing QTL. Otherwise, it adds a new QTL.
Delete QTL	Deletes QTL records matching the entered QTL name.

Data entry tips

• Use the same units for Position of QTL, Min. Position, Max. Position, and CLEN that were used in the genetic map or QTL analysis.
• Ensure Min. Position is less than or equal to Position of QTL, and Position of QTL is less than or equal to Max. Position.
• Select Genetic Dataset before selecting flanking markers so the marker lists are populated from the associated dataset.
• For optional numeric fields, leave the field blank if the value is not available. CIERA treats blank or 0 values for CLEN, SE Additive, and allele parent GIDs as unavailable.
• If you are editing an existing QTL, always use Search (if existing) first so CIERA knows to update the existing record instead of adding a new one.