Fig. 1
Association analyses in GSDs and LRCAD breeds revealed candidate variants located in tissue-specific enhancers. Association analyses including 104 fine-map SNPs located within the PKP2 locus on CFA27 were performed separately in GSDs and in GSDs combined with LRCAD breeds. a. The GSD association analysis defined a ~209 kb associated region by associated SNPs displaying high linkage (r2 > 0.95) with the two top SNPs 27:19,086,778 (blue and index SNP) and 27:19,140,837 (index SNP). b. The combined association analysis including LRCAD breeds revealed the highly significant top SNP 27:19,086,778 (blue), and SNP 27: 19,135,677 (index SNP) in high LD (r2 > 0.95) with seven SNPs forming a ~48 kb risk haplotype. c. The ~48 kb risk haplotype (pink bar) stretched from PKP2 intron 6 to the downstream region of the gene and was present in GSD, LR, and GR. A 21 kb risk haplotype (red bar) stretching from intron 6–10 was shared with WHWT. Asterisks and SNP positions mark the nine SNPs included in further analyses: purple and light blue SNPs were top SNPs in the GSD association and green SNPs were part of the ~48 kb risk haplotype. d. Positions of the SNPs in the human UCSC browser, where SNP 27:19,112,169 and 27:19,135,677 were not mapped from dog to human due to loss of conservation around the SNPs, and SNP 27: 27:19,124,996 (light blue) was not included in the luciferase experiments due to its location in a repetitive region. e. When matching the ~48 kb haplotype plus the SNP 27:19,086,778, to human ENCODE data, H3K4Me1 enhancer-associated histone modification marks were detected in normal human epidermal keratinocytes (NHEK) and human mammary epithelial cells (HMEC) (purple and green, respectively). f. The regulatory potential within the region is indicated by the tracks from the human UCSC browser (hg18): Transcription Factor ChIPSeq, HMR Conserved transcription factor binding sites, ESPERR and Regulatory Potential and conservation scores by PhyloP across placental mammals (https://genome.ucsc.edu/cgi-bin/hgGateway?db=hg18)