Some methods to look for candidate genes using qtlTools

Simulation of cis-trans test performance

Workflow from ASE counts to joinmap input file

Basic, 1-way QTL mapping for Maize P experiment

Intro for niche modeling script. For Martin

First try at heritability of variance

full qtl, gene expression and covariate analysis

Basic QTL analysis without epistasis. Generates a table of statistics for each QTL*trait combination

This script conducts simple statistics looking for differential gene expression between alleles along a QTL interval. This provides a way to narrow down the number of potential genes underlying a QTL by comparing the patterns of gene expression with phenotypic responses to the different environments

Full QTL analysis in one script, all automated

All analyses of qgen and ssr gen so far. Basically plotting everything.

We did two separate drydowns because there was very poor germination of a few genotypes in our first try and we did not have enough seed to re-do the drydown for a few of the genotypes. So, genotypes are nested within experiments... that is, all genotypes are represented in only 1 experiment. This is not an ideal design, especially since we see an "experiment" effect. Lets discuss.

Some comparisons of water-use-efficiency (d13C), treatments (wet/dry), populations and mating systems

New analyses of molecular and quantitative genetic diversity showing all data (without means)