QTL mapping for 4 RIL sets, 3 traits and 2 conditions.

QTL maps obtained from four RIL sets (BlaxCol in black; CvixCol in red; BurxCol in blue; YoxCol in green) using three phenotypes (PRA29, RER16-29 and Compactness29), generated independently in two conditions (top panels: WW; middle panels: WD) and from the genotype x environment interaction term in the model (bottom panels: Interaction term). LOD score values above (below) zero indicate that the Col allele increases (decreases) trait value with respect to the other parental allele. Significance threshold (LOD = 2.4) is shown as dotted lines. The x-axis indicates consensus markers along the genetic map (scale is shown for 20cM). The parameters of the significant QTLs detected are listed in S3 Table.