As cis-acting regulatory elements are usually located within a few kilobases of a gene's coding sequence [59], we used the cis-QTLs as an internal metric of mapping precision by measuring the offset distance between a cis-QTL (position of peak QTL marker) and the parent gene (figure 3). For cis-QTLs with LOD scores between 3–4 (genome-wide p-value of 0.1–0.01) the mean gene-to-QTL peak distance is 900 kb. The offset decreases to a mean of 640 kb for cis-QTLs with LOD scores greater than 4 (p-value<0.001). Very strong cis-QTLs with LOD scores greater than 11 (p-value<10−6) have a mean gene-to-QTL peak distance of only 450 kb. In all, 60% of cis-QTLs we examined have peak linkage on markers located precisely in the same non-recombinant segment as the parent gene, and 30% have peak linkage on markers in a segment adjacent to the parent gene (dataset S1). These cis-QTLs provide an empirical metric of mapping precision within Qrr1.
