Extended Data Fig. 2. Dog haplotypes across the ASIP locus with comparison to previously associated variants for color patterns.

Dog coat pattern phenotypes are listed on the left. The genomic organization of the ASIP gene with its alternative promoters is illustrated at the top. Yellow indicates a homozygous match to the reference genome, grey deleted, white heterozygous and blue homozygous alternate allele. The black rectangles highlight the promoter regions. Green triangles represent the location of variants that were previously identified to distinguish different alleles for coat color patterns: (i) The previously identified intronic duplication, “RALY dup”, associated with BS vs. BB haplotypes in some breeds, lies 86 kb to the left of the VP, but recombinants (Supplementary Table 7) exclude a causal role for ASIP pattern variation¹⁶. Similarly, (ii), a SINE insertion associated with BB and BS haplotypes in some breeds, and, (iii)³², missense variants in exon 4 associated with DY haplotypes¹⁷, are also excluded from a causal role in ASIP pattern variation by rare recombinants (Supplementary Table 7). In the samples presented here, the dominant yellow haplotype extends through the coding sequence where the missense variants associated with this haplotype were previously identified10. The results shown here will allow more accurate genetic testing in the future. Samples used are listed in Supplementary Table 3. Raw genotyping results are in Supplementary Table 4 and summary results comparing previously identified variants are in Table 1 and Supplementary Table 7.