Contents - Index
Pleiotropic effects of a marker
This functions requires a genotype by marker + trait table.
Under the main menu Association, click Find Associated Variables. An input box will appear, asking for a probability level to be considered as associated. Input a number, say, 0.001, and click OK.
The variable selection penal will appear on the top of the biplot. Select a marker (represent a QTL or gene) from the drop-down box, say, 7MWG502, and click Find.
The following biplot, or plot rather, as the genotypes were hidden, will appear:
Under the main menu Data, click Run Any Subset..., and select By Deleting Testers. A tester selection device will appear. Remove all markers except 7MWG502 and click the Find button again, the biplot will become:
The biplot shows that the marker 7MWG502 is associated, at the 0.001 level, with four more or less independent groups of traits:
The Pleiotropic effect of genes represented by this marker is therefore very obvious.
Note: Some trait relations in the two biplots on this page are not consistent. This is because the biplot explains only 50% of the total variation. In such cases, the relationships seen from the biplot are only qualitatively correct (positive vs. negative and strong vs. loose), but the correlations among traits (
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