QTL modified by Shawn Yates

Shawn Yates — Wed, 22 Jul 2026 19:07:18 -0000

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

 ## Open the QTL screen
+
+![](https://sourceforge.net/p/ciera/wiki/QTL/attachment/QTL.png)
+*CIERA - Quantitative Trait Locus*


 1. Open CIERA.
 2. From the main menu, select **Manage Data > Manage Genotypic Data > Quantitative Trait Locus**.

QTL modified by Shawn Yates

Shawn Yates — Wed, 22 Jul 2026 19:06:22 -0000

QTL modified by Shawn Yates

Shawn Yates — Wed, 22 Jul 2026 18:52:38 -0000

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+# 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
+
+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.

QTL modified by Shawn Yates

Shawn Yates — Wed, 22 Jul 2026 18:49:11 -0000

Recent changes to QTL

QTL modified by Shawn Yates

QTL modified by Shawn Yates

QTL modified by Shawn Yates

QTL modified by Shawn Yates