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

Speed-genotyping

Source: Lai, C-Q., Leips, J., Zou, W., Roberts, J.F., Wollenberg, K.R., Parnell, L.D., Zeng, Z-B., Ordovas, J.M., and Mackay, T.F.C. Speed-mapping quantitative trait loci using microarrays. 2007. Nature Methods, 4(10): 839-41

The authors used microarrays to genotype a large number of individuals for a QTL study into longevity. Instead of individually genotyping and measuring the phenotype, the authors instead selected a subset of the population based on their phenotype (longevity). Then they pooled this subset’s DNA and ran it across a microarray that had oligos from both parents. They compared each marker hybridization with a young group that should be equally mixed for the alleles at each marker. A simple t-test was computed for each marker (with FDR correcting) to determine whether that marker had a skewed allele ratio between samples. Multiple QTLs were found, more so than using previous genotyping methods.