Association plots for tests of association between Egfr and shape parameter C1. Each plot shows the negative logarithm of the p-value for the test statistic at each polymorphic SNP from 5' to 3 along the Egfr locus. (A) Association profile from the whole NC inbred panel (N = 121, solid line) and the Kenyan chromosomes (N = 26, broken line). (B) The association profile for the RR experiment (outcrossed, N = 71, broken line) and the subset of NC lines (in inbred condition, N = 71, solid line) used for the outcrossing scheme. (C) Similarly the profiles for the BC panel (backcrossed to NC025 and NC144, N = 79, broken line) and the corresponding NC set (N = 79, solid line). The X scale is broken to indicate gaps between contigs with the gene structure represented below (exons as boxes in three contigs of non-coding sequence). Site T30200C (indicated) is located at the 5' most end of contig 2. Lines corresponding to single site significance levels α = 0.05 (negative log p: 1.30) and more conservative gene wide α = 0.0001 (negative log p: 4.0). Trait values for all lines and crosses come from data that were processed jointly in TPSrelw .