Targeted resequencing of the Grey haplotype. (A) Depth of coverage given by sequences obtained from targeted resequencing experiment aligned to horse genome reference sequence (EquCab2) confirms the Grey duplication in STX17; the region presented is the one that is essentially identical-by-descent among all Grey horses tested so far. Upper graph: Grey horse (ID L147, G/G). Middle: Chromosomal coordinates, with genes and the Grey duplication indicated. SNPs investigated in detail are marked by numbers 1–7. Lower graph: Non-Grey horse (ID 800, g/g). Data derived from 75 bp non-sliding windows. (B) SNPs detected by targeted resequencing and found to be unique to the homozygous Grey Lipizzaner horse L147, or homozygous for a non-reference allele in all six non-Greys, including individual 800 having a haplotype closely related to the Grey haplotype. The Grey genotype is based on the genotype of the Lipizzaner horse L147. The non-Grey genotype is based on the genotype of all sequenced non-Grey horses. SNPs were selected for further analysis based on Sanger sequencing of Twilight (the Grey heterozygote used to generate the horse reference sequence), one additional Grey homozygote and one horse homozygous non-Grey carrying a haplotype closely related to Grey. Abbreviations: NT: Not tested for technical reasons, SEL: Selected for further analysis, SS: Sanger sequencing, NE: Not exclusive to Grey.