Figure 4

False positive cis-eQTL. Relative expression levels determined by the microarray suggests that cis-acting factors regulate the expression of two example genes. In both cases (A,B) the B73 transcript abundance is far greater than that of Mo17 according to the microarray. Amplification of genomic and cDNA sequence from B73 and Mo17 reveals that actual expression in situ may be more similar than the microarray would suggest. Sequence analysis of the probe-hybridization loci reveal that the microarray probes (red highlight) would fail to hybridize efficiently to the Mo17 alleles, thus inappropriately suggesting extreme differential expression and strong cis-eQTL. Blue boxes show polymorphisms between the Mo17-derived sequences as compared to the reference probe and B73-derived sequences.