Select Final Model (Multi-environment)

Use this to select and fit a final QTL model to estimate QTL effects for multi-environment trials. QTLs are selected from a list of candidate QTLs (loci) in multi-environment trials by backward selection.

Display

This specifies which items of output are to be produced by the analysis.

Summary	A summary of the QTLs retained in the model
Model	Description of the model fitted by the analysis
Variance parameters	Estimates of variance parameters
Estimated effects	Estimates of QTL (and QTL x E) effects
Wald test	Wald tests for all QTL effects in model
Variance-covariance,/	Variance-covariance matrix of the estimated parameters
Monitoring	Monitoring output from the mixed model analysis

Run QTL backward selection

When selected backward selection is used to determine a set of QTLs from the candidate QTLs.

Significance level for backward selection

The significance level to use at each step of the backward selection process.

Model

A list of variance-covariance models for the set of environments that can be used for the selection and fitting of the QTL model. By default this will be set to the model used for the QTL scan. For more details about the models see the VGESELECT procedure.

Graphics

This specifies whether plots are to be produced by the analysis.

Plot QTL positions on genetic map	Plots the significant QTLs on a genetic map.
Bar charts of additive effects	Plots two bar charts. The first plots the QTL additive effects for each QTL within each environment. The second plots the QTL additive effects for each environment within the QTLs.

Save

These results can be saved when fitting the final QTL model. After selecting the appropriate boxes, you need to type the names for the identifiers of the data structures into the corresponding In: fields.

Effects	Variate	Saves the estimated QTL effects.
Standard error of effects	Pointer	Saves the standard errors of the QTL effects.
QTL positions	Pointer	Saves the index numbers of the selected QTLs. This option is only enabled when the run QTL backward selection option is selected.
QTL save structure	Pointer	Pointer to QTL save structure storing information and results for the significant effects. This structure cannot be displayed in a spreadsheet.

Display in spreadsheet

Select this to display the results in a new spreadsheet window.

Action buttons

Run	Select and fit the final QTL model.
Cancel	Close the dialog without further changes.
Candidate QTLs	Opens a dialog that lets you select or modify the set of candidate QTLs.

Action Icons

	Clear	Clear all fields and list boxes.
	Help	Open the Help topic for this dialog.