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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 (how to get themlinkID=840}) may not be exactly visualized from the angles.