QTL co-localization of significantly regulated genes and polymorphic transcriptional landscape between B73 and Mo17. QTL confidence intervals are indicated for corresponding traits (Fe = iron content in the shoot; SP5 = SPAD values of the 5th leaf; SP5 = SPAD values of the 6h leaf, RL = root length; RW = root weight; SL = shoot length; SDW = shoot dry weight) as orange boxes for the 10 μM iron regime and in dark green for the 300 μM iron regime as identified by Benke et al., (unpublished). Genetic distances are given in cM and were retrieved from marker information available at http://www.maizegdb.org for the IBM population. For projection of differentially regulated genes within specific two-way comparisons (Table 1) the available physical transcription start site positions (http://www.maizegdb.org) were converted into putative genetic positions by interference from adjacent marker positions. Candidate genes for Chromosome (Chr.) 1 (A), 4 (C) and 8 (E) were projected onto the genetic map. The equivalent polymorphic and transcriptional landscape is displayed for Chr.1 (B), 4 (D) and 8 (F). The number of polymorphisms (SNPs and INDELs) is given for artificial bins of a size of 4Mbps. The median log2FC for transcripts detected across all statistical approaches is given for specific two-way comparisons (Comp. 1 = blue; Comp. 2 = green; Comp. 3 = orange; Comp. 4 = purple) at the relative physical position, represented by the transcriptional start site. In the case of absent/present expression data, log2FC of ±∞ were exchanged by ±20 (the highest log2FC across the experiment). QTLs confidence intervals for iron content in the shoot (red) and SPAD values of the 5th (turquoise) and the 6th leaf (light cyan) are indicated at their interpolated physical position for the 10 (Fe10) and 300 μM iron (Fe300) regime.