Cubillos et al. BMC Genomics 2012, 13:117 http://www.biomedcentral.com/1471-2164/13/117 Page 4 of 12 Figure 1 Genetic landscape for transcript accumulation variation. a. eQTL heatmap for CviCol population significant at a 5% FDR. Each horizontal bar represents an eQTL mapped on the x-axis and controlling the accumulation of a transcript expressed from the locus indicated on the y-axis. The colour of the bar indicates the direction and strength of the eQTL additive effect, and its length along the x axis encompasses the eQTL support interval. Local eQTLs form the diagonal, while distant eQTLs fall elsewhere in the map. b. eQTL heatmap for BurCol as described in a. c. Bar plot indicating the proportion of local and distant eQTLs for increasing LOD value intervals in CviCol set. d. Bar plot as in c. for BurCol set. between the BurCol and CviCol populations. We found that 564 transcripts mapped to an overlapping local eQTL interval in the populations, corresponding to 26.3% of all local eQTLs in the CviCol set (Additional file 3: Figure S4). The direction of the allelic effect for these potentially shared eQTLs was consistent in 88.4% of the cases. Moreover, within this subset, we observed a strong correlation between populations for the strength of the additive effect associated with the eQTLs (R2 = 0.82; Figure 2) and for the explained phenotypic variance (Spearman correlation test, P < 0.01). We also compared the distribution of local eQTLs along the gen- ome between crosses. For this, we divided the genome into 1Mb windows (bin) and estimated the fraction of transcripts with local eQTLs on every bin per chromo- some. A spearman test detected a significant correlation between both distributions (P < 0.01), suggesting major structural genomic aspects. We determined whether dense eQTL regions were enriched for SNP polymorph- isms or were gene-dense regions. A genome-wide regression analysis did not detect a significant correla- tion between the number of SNPs and eQTLs within intervals for CviCol, however a marginally significant association was found for BurCol (P = 0.15 in CviCol, P = 0.07 in BurCol). In contrast, an expected significant correlation was found with gene density in both cases (P