Quantitative trait locus (QTL) mapping was performed for the saline and ethanol treated RMA datasets, as well as the saline vs ethanol S-score dataset, using a subset of informative microsatellite and SNP markers that have been used to genotype the BXD family [37], [38], and are available from GeneNetwork (genenetwork.org/genotypes/BXD.geno). Linkage between genotypes and expression phenotypes was assessed by performing Haley-Knott regression using R/qtl [39]. Genome-wide adjusted p-values were derived using distributions of maximum LOD scores obtained from 1,000 permutations of each probe-set's expression data. We classified the significance of an expression QTL (eQTL) using guidelines put forth by the Complex Trait Consortium for mapping traditional QTL [40]; where ‘significant’ refers to genome-wide corrected p-values≤0.01 and ‘suggestive’ refers to p-values≤0.63. Estimates of true QTL location were obtained using R/qtl's to calculate 1.5 LOD score drops, as recommended by Manichaikul [41]. Expression QTL were considered cis eQTL if their peak chromosomal location was less than 5 Mb upstream or downstream of the regulated gene; all others were considered trans eQTL.
