Two-way Hierarchical Cluster Analysis (HCA) of the 45 animals and 660 gene-set (A) and AF QTL analyses (B). (A) HCA color matrix display obtained with the 660 genes (Y axis) and the 45 chickens (X axis). Dark/light blue bars indicate the 20 fattest chickens (dark bars correspond to the extreme fat chickens (F1 to F10), light bars the next (F11 to F20)); dark/light orange bars indicate the 20 leanest chickens (dark bars correspond to the extreme lean chickens (L1 to L10), light bars the next L11 to L20); colorless bars correspond to the 5 intermediate chickens (I). The two final letters of the animal labels, indicate the Q or q haplotype inherited from the sire, with a probability > 95% for the QTL at 102 cM (first letter) or the QTL at 175 cM (second letter); × indicates a probability < 95%. For the two QTL, animals with discrepant AF values and q/Q haplotype are indicated by arrows. Long arrows indicate the 10 most extreme animals with AF value in discordance with q/Q haplotype. Short arrows indicate the 10 lowest extreme animals (F11 to F20 and L11 to L20). (B) Interval mapping for the AF trait on chromosome 5, with the whole family (blue) and without one or two subgroups observed by HCA (other colors). The chromosome-wide significance thresholds at the 5% level (-) are displayed. The 10% level (- -) obtained for analysis without subgroups 1 (light blue), 4 (yellow) or 1 and 4 (green) are also displayed. The genetic distances (cM) and likelihood ratio test (LRT) are shown on the X-axis and Y-axis, respectively.