FIGURE 7.

(A) Principal component analysis (PCA) using the NN regularity ratio, VD regularity ratio, and packing factor traits as variables, revealed a first principal component that accounted for over 80% of the total variance across these traits. (B) The value for each recombinant inbred strain along this first component was used to create a new trait that could be mapped. Notice that the two parental strains are located near the extremes of the distribution. (C) Whole genome map for the association between this first component with genotype across the strains, with conventions as in Figure 5A. Both previously identified QTL, on Chrs 1 and 14, have high LRS scores, with the former passing the significant threshold and the latter closely approaching it. (D,E) Haplotype maps of the 25 recombinant inbred strains and two parental strains through a 10 Mb region centered at the QTL on Chrs 1 and 14, with the A haplotype indicated in green, and the B haplotype in red. A single strain (AXB18) is heterozygous for A and B alleles at the Chr 1 locus, and is indicated in blue. The strains are ordered, from bottom to top, by their increasing value of the first component. Three genes (colored rectangles below each LRS trace) reside at the narrow genomic locus on Chr 1, while 25 genes are present at the locus on Chr 14, which were narrowed down to six top candidate genes based on bioinformatic analysis.