Leading into my work...

Source: Lisec, J., Meyer, R.C., Steinfath, M., Redestig, H., Becher, M., Witucka-Wall, H., Fiehn, O., Torjek, O., Selbig, J., Altmann, T., and Willmitzer, L. Identification of metabolic and biomass QTL in Arabidopsis thaliana in a parallel analysis of RIL and IL populations. 2008. The Plant Journal, 53: 960-72

The authors created a number of RIL and IL lines in Arabidopsis and then ran targeted GC-MS on them. They were able to measure 181 compounds and find QTLs for 84, for a total of 157 QTLs. The contribution of these loci was between 1.7 and 52.1%. They found that many of these metabolites co-mapped, and that in nearly all of them a good candidate gene could be found that might explain the effect. They defined a candidate gene as a gene within the support interval in the direct pathway of the metabolite. None of these metabolite linkages showed a strong ability to change biomass.



Other notes:
-permutation test for candidate gene: randomly assign linkage to metabolite, sort through interval and see if any genes overlap with metabolite in AraCyc
=most metabolites showed no significance
=only 13 metabolites showed a higher than permutation-average number of candidate genes
-near impossible to find epistasis, found it only explained 2.72% of phenotypic variation on average
-nonrandom distribution of mQTLs, does not correlate with distribution of metabolic genes