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Fig. 7 | Genome Biology

Fig. 7

From: Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays

Fig. 7

Dissection of a major QTL for GY. In panel a GY shows a major QTL on the short arm of Chr 6 (pleiotropic on PH and EH). Green line and red line represent strong (P <0.01) and suggestive (P <0.63) thresholds. Panel b magnifies the QTL region and shows that the QTL has a flat and wide top, suggesting the involvement of a series of cis causal variants. The founder effect plot shows that at this locus the W153R and Mo17 alleles are associated with low GY. Panel c shows that 21 genes have differential expression between these and the remaining founders in a region spanning 2.5 Mb (red dots; black dots for not significant differential expression tests). Also in panel c, normalized sequencing read counts of founders in 0.1 Mb bins in the same region reveal substantially less reads for Mo17 and W153R, confirming the extant SV. Note that downstream this region the read counts for Mo17 and W153R are similar to that of other founders, ceasing the differential expression. In panel d are reported genes differentially expressed in the SV region

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