PMC

GWAS identifies a strong association on CFA28 with lack of an undercoat. (A) Manhattan plot of -log₁₀ transformed Wald p-values for the SNP association of single- versus double-coated dogs. Black horizontal line indicates genome-wide significance (5.0 × 10⁻⁸). Red line indicates Bonferroni-corrected genome-wide significance (3.3 × 10⁻⁷). Four loci surpass the significance threshold, with the most associated locus located on CFA28 and represented by a single SNP (arrow). (B) Manhattan plot of -log₁₀ transformed Wald p-values for the WGS association of single- versus double-coated dogs. Black horizontal line indicates genome-wide significance (5.0 × 10⁻⁸). Red line indicates Bonferroni-corrected genome-wide significance (3.4 × 10^-9). Three loci, two on CFA1 and one on CFA28, exceed both thresholds. Only SNPs with p-value ≤ 0.1 were included in this plot. (C) Regional Manhattan plot of CFA28 locus from the WGS GWAS. Pairwise linkage (r²) of each variant was calculated relative to the most significant variant: chr28:24,863,224 (purple). All strongly correlated variants (r² ≥ 0.6) with significant p-values reside within the intron of an uncharacterized lncRNA.

The CFA28 locus and variants effects on TF binding. (A) UCSC Genome Browser display centered around the CFA28 GWAS locus. The locus (black bar) is in the intron of ADRB1-AU1 (green) upstream of ADRB1 (blue). Both variants are indicated within the region. Also shown are the curated annotations from ORegAnno (orange). (B) In silico prediction of transcription factor binding surround the two derived alleles in wolf with low frequency. Transcription factor prediction was performed using AliBaba2 at the significant variant plus/minus 20bp in single- (derived) and double-coated (ancestral) alleles. Binding is denoted by a black line below target sequence. (C) The consensus sequence for each of the four transcription factors identified in (B) are shown. AP-1 is composed of a dimer of FOS and JUN. The two variant positions lie within well conserved regions of each transcription factor.