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The QTL menus provide easy access to QTL analysis within Genstat. Two sources of data are required: phenotypic data (measurements of trait values) and genotypic/map data (evaluation of genotyping at markers and positions of markers on a genetic map). The description below gives a step-by-step approach to a QTL analysis for a single environment trial with trait means.
| Step 1. | Put trait means with genotypes (factor) into a Genstat spreadsheet. |
| Step 2. | Load the phenotypic (trait) means into the QTL data space using the Stats | QTLs (Linkage/Association) | Data Import/Export | Load Phenotypic data menu item. Select the option for Trait means and load the trait data and genotype factor. The QTL data space, found under Stats | QTLs (Linkage/Association) | View QTL Data Space should now show these variables under the Phenotypic means folder. |
| Step 3. | Load genetic marker and map data using the Stats | QTLs (Linkage/Association) | Data Import/Export | Load Genotypic (Marker and Map) data menu item. Choose the file type that contains the data (Flapjack text genotype/map, R/QTL csvsr/csvs and MapQTL loc/map file formats) and load the data. |
| Step 4. | Check marker and map data using the display genetic map and genotype data plots menus (opened by selecting Stats | QTLs (Linkage/Association) | Data Exploration | Genotypic Data | Display Genetic Map and Stats | QTLs (Linkage/Association) | Data Exploration | Genotypic Data | Genotype Data Plots respectively). |
| Step 5. | Calculate genetic predictors for use in QTL interval mapping using the calculate genetic predictors menu opened using the menu Stats | QTLs (Linkage/Association) | Genotypic Analysis | Calculate Genetic Predictors. The QTL data space will now show these data structures under the Genetic predictors folder. Using the calculate genetic predictors menu:
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| Step 6. | Run simple interval mapping using the Initial scan button on the Single Trait Linkage Analysis (Single Environment) menu (opened using the Stats | QTLs (Linkage/Association) | QTL Analysis | Single Trait Linkage Analysis (Single Environment) menu item). This does an initial scan for candidate QTLs, which are saved for further analysis. By default, the results of the scan are plotted and the candidates are displayed in the output.
Using the Single Trait Linkage Analysis (Single Environment) menu:
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| Step 7. | Run composite interval mapping using the Scan with cofactors button on the Single Trait Linkage Analysis (Single Environment) menu. By default, the cofactors are set as the candidate QTLs from the previous scan. This does a scan for additional candidate QTLs in the presence of the cofactors, although cofactors within a set window (see Options) are ignored to avoid problems of collinearity. A modified set of candidate QTLs is saved. By default, the results of the scan are plotted and the candidates are displayed in the output.
Using the Single Trait Linkage Analysis (Single Environment) menu:
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| Step 8. | Run composite interval mapping final model selection using the Select final QTL model button on the Single Trait Linkage Analysis (Single Environment) menu. By default, the full set of candidate QTLs are the set selected from the previous scan. The default first step is backwards selection from this candidate step, followed by estimation of the QTL effects for all QTLs retained in the selected model.
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