Contents - Index

Find traits associated with a single locus (Pleiotropic effect)

This function is applicable to a QTL mapping dataset, i.e., a genotype-by-(marker+trait) two-way table

• Under Association, click Find Associated Testers of…, 
• An input box will appear, asking for the probability level for a trait to be considered as 'associated' with the target marker. Put a number between 0 and 0.5, and click OK. A panel will appear above the biplot.
• Click the drop-down arrow by the textbox, and select the target marker, and then click Find.
• An input box will appear, asking if you want to use any of the markers or traits as covariates. Take the default value ('no') and click OK.
• The biplot will be transformed to the following:
• The target marker is indicated by a larger and underlined font;
• Only marker/trait labels are shown in the biplot to focus on the relationships among the markers and traits (the genotypes are hidden and can be called back by clicking Show Both from menu View);
• Vectors (lines from biplot origin to the trait labels) are drawn for all retained markers and traits.
• A set of concentric circles will appear to facilitate visualizing the relative length of the vectors of the markers/traits. Short-vectored markers/traits may not be adequately represented in the biplot.
• Unwanted markers can be deleted from the biplot using the function Data/Run a Subset by…/Removing any Testers. 

Interpretations:

• Traits that have longer vectors and smaller angles (close to 0° or 180°) with the target marker are more strongly associated with the target marker. An acute angle means positive association and an obtuse angle negative association.
• Traits with short vectors may have a weak association with the target trait or other traits.
• Traits that have shorter vectors or a close to 90° angle with the target marker are less associated with the target marker. 
• Clustered traits are similarly associated with the target marker.