Figure 5

Sequence gap in the physical map masks probe homology sites. A Schematic of selected maize chromosomes. A "master regulating" trans-eQTL residing on chromosome 2, BAC AC207404 (blue diamond) regulates expression of two iron superoxide dismutase genes on the long arms of chromosomes 1 (BAC AC221053) and 6 (BAC AC187242), as measured by unique microarray probes (red and cyan, respectively); centromeres = black circles. B Re-sequencing analysis of the eQTL interval on chromosome 2 revealed a 2 kb gap (gray dotted line) in the known sequence (gray bars). Probe homology sites for both regulated genes were discovered within the gap negating a trans-acting master regulator effect, therefore suggesting a strong cis-acting eQTL in the vicinity of the newly identified third iron superoxide dismutase gene.