HCA and linkage analysis using subtype combination. (A) Heatmap using the 688 genes (Y axis) and the 45 chickens (X axis). (B) Interval mapping for the AF trait on chromosome 5, with the whole family (blue) and without one subgroup observed by HCA (other colors). The graph gives the statistical test (Likelihood Ratio Test) related to the test "no QTL" versus "one QTL" (y-axis") for every tested location on the chromosome (centiMorgan, x-axis). The chromosome-wide significance threshold at the 5% level obtained for the analysis including all animals (blue) and for analysis without one of the five subgroups: fat1 (green), fat2 (yellow), lean1 (light blue), mixed (red) or lean2 (brown) are displayed. The genetic distances (cM) and likelihood ratio test (LRT) are shown on the X-axis and Y-axis, respectively. (C) The two letters indicate the Q or q haplotype inherited from the sire, with a probability > 99% for the proximal QTL (first letter) or the distal QTL (second letter); × indicates a probability < 99%. The probability of inheriting the paternal Q versus q haplotype was calculated only on the basis of marker information in the region of interest.