Comparison of the density of functionally characterized genes and RAP loci and the number of QTLs. The density of functionally characterized genes or RAP loci at each point in the genome is expressed as the proportion of the total number of genes (loci) contained within the surrounding 1-Mb block, calculated by using a window size of 2 Mb. The number of QTLs was counted within every 1-Mb block along the genome sequence. Red and blue lines indicate densities of functionally characterized genes and RAP loci, respectively. Yellow bars indicate the number of QTLs in each 1-Mb block. Green vertical bars on the x-axis indicate the position of genes categorized as "natural variation" in the method of isolation. Positions of QTL clusters are indicated by purple lines on the x-axis and are based on Yonemaru et al. (2010).