QTL Genome Scan

This menu can be used to perform a genome-wide scans for QTL effects (Simple and Composite Interval Mapping) in single- or multi-environment trials. The phenotypic data required is one value for each genotype from a single environment trial, and one value for each genotype-environment combination from a set of multi-environment trials. These values will usually be predicted means obtained from a preliminary analysis of each trial (see the PSEA menu). When data structures have been stored within the QTL workbook then the names of these structures will be automatically entered in the relevant input fields.

The menu is designed to provide step-by-step determination of a model to estimate QTL effects. The menu allows for the following steps:

An initial genome-wide scan by simple interval mapping (SIM) to obtain candidate QTL positions. These can be used as cofactors in subsequent scans (composite interval mapping).
One or more rounds of composite interval mapping (CIM), ie. a genome-wide scan for QTL effects in the presence of cofactors, which are usually potential QTL positions detected at previous steps.
Fit a final QTL model, usually following back-selection from a set of candidate QTLS, to get a final set of estimated QTL effects.

In the case of multi-environment trials, the scans test for both QTL main effects and QTL by environment interactions.

Type of QTL scan

This specifies whether the QTL scan is for a single environment or multi-environment. When the multi-environment option is selected some additional input fields for specifying the environments and across environment variance-covariance model are enabled.

Available Data

This lists data structures appropriate to the current input field. Double-click on a name to copy it to the current input field; alternatively, you can type the name directly into the input field. When data has been stored in a QTL workbook then by default the available data will display only the data structures present within that workbook. You can right-click on the available data list to switch between displaying data only within the QTL workbook and all data within GenStat. If the QTL workbook has not been used, then all current data structures within GenStat will be displayed.

Quantitative trait means

A variate specifying the quantitative trait (phenotypic) means for each genotype (single-environment analysis) or genotype by environment combination (multi-environment analysis).

Genotype factor

A factor specifying the genotype for each mean.

Genetic predictors

A pointer to a set of variates specifying the additive genetic predictors.

Linkage groups

A factor specifying the linkage groups for each additive genetic predictor.

Position within linkage group

A variate specifying the positions within linkage group for each additive genetic predictor.

Multi-environment

These options are enabled when the multi-environment option is selected.

Environment factor

A factor specifying the environment for each mean.

Variance-covariance model

This allows you to select the variance-covariance model to use across the set of environments. For more details about the models see the help on the "Select best variance-covariance model" menu.

Action Buttons

Initial scan	Performs an initial genome-wide scan by simple interval mapping (SIM).
Scan with cofactors	Opens a dialog to perform composite interval mapping using cofactors. A default set of cofactors selected by SIM is provided and can be changed.
Select final model	Opens a dialog where you can establish a final model from a set of QTL candidates using backward selection and get estimates of QTL effects from this joint model.
Cancel	Close the menu without further changes.
Options	Opens a dialog where additional options and settings can be specified.
Defaults	Set the menu settings back to the default settings. Clicking the right mouse on this button produces a shortcut menu where you can choose to set the menu using the currently stored defaults or the GenStat default settings.