Contents - Index

Identify markers closely associated with a target marker

• Under the main menu Association, select Find Associated variables...

• You will be asked to set a probability threshold for an association to be considered as significant. Put a number between 0 and 0.5, exclusive.

• A variable selection tool will appear, allowing you to select the target variable (marker). Select one, click the Find button.

• A biplot will appear, with the target variable (with a larger font) plus those markers or traits that meet your criterion of being associated.

• Marker vectors are shown to facilitate visualization of the relationships among markers/variables.

• This biplot will be based on tester-focused SVP, which supports the interpretation that the cosine of the angle between two markers approximates the correlation between them. Under a perfect goodness of fit, 90 degree means independent, acute angles mean positive correlation (linked), and obtuse angles mean negative correlation (repulsively linked)

• A rough linear map can be invoked by clicking Linear Map of Testers. The range of 0-90 degree may roughly correspond to the range of 1-50 cent Morgan.

The following biplots provide two examples, in which the markers are in red and genotypes in blue: