Figure 3.

Regional Association and Critical Interval Determination of the CFA1 Viscerocranium QTL

(A) SNP associations with viscerocranium PC1 are shown for ∼1 Mb on either side of significant SNPs on CFA1. SNPs are colored depending on the degree of LD (r²) with the index SNP (BICF2P250912; 1.91 × 10⁻²⁰).

(B) Ten-SNP sliding window haplotype association.

(C) Genotypes between 55,881,672 and 56,020,217 (including ∼500 kb of flanking sequence) were phased and ranked by their viscerocranium PC1 value. Only haplotypes from brachycephalic dogs (viscerocranium PC1 ≤ −0.2; see Figure S3) were considered. Haplotypes are paired by subject and ranked by viscerocranium PC1 value. Alleles colored light gray match the consensus haplotype; dark gray alleles are variant. A 187.7-kb critical interval is defined by at least three meiotic recombinations (indicated above by black bar). The 12 SNPs that constitute the associated haplotype (red bar) are distributed within or up to ∼44 kb downstream of SMOC2. Black arrows indicate 3 of 37 dogs that have a homozygous variant haplotype. These dogs are registered as two Dogues de Bordeaux and a Chihuahua. The red arrow indicates a Japanese Chin that is homozygosed for a recombinant haplotype within the critical interval.

See also Figures S2 and S6 and Table S3.