Genome-wide SNP data show little differentiation between the Appaloosa and other American stock horse breeds

The Appaloosa, American Quarter Horse (QH) and American Paint Horse (Paint) breeds are commonly referred to as stock horses, as each is used, to some extent, when managing livestock. QHs and Paint horses are genetically similar, which is predicted based on phenotype, ancestry and admixture allowed between the registries and with the Thoroughbred. In the Appaloosa, admixture is also allowed with the Thoroughbred, QH and Arabian. The Appaloosa is similar in conformation to the other stock breeds but has a unique leopard-spotting coat color pattern as well as mottled skin, white sclera of the eye and striped hooves. The goal of this study was to examine the relationship of the Appaloosa to the other stock breeds and determine whether genomic regions unique to the breed could be identified. This work will inform future clinical and genetic work of inherited phenotypes. The horses studied were sampled for other purposes and, as much as possible, represented a random sample of each breed. Second-order relationships (shared grandsire/dam) within each breed were excluded based on pedigree. The Appaloosas (n = 24) included 20 in the regular registry (had Appaloosa characteristics), two non-characteristic and two non-characteristic but with a completed certified pedigree option. Six Appaloosas had a QH parent, whereas 11 others had a QH or Thoroughbred grandsire/dam. Twenty-five QHs and 18 Paint horses were included. Diversity and F-statistics were calculated from 12 013 autosomal SNPs genotyped on the Illumina SNP50 or SNP70 BeadArray; these SNPs were selected after eliminating loci with minor allele frequency 0.2) in PLINK. The Appaloosas studied had higher diversity (expected heterozygosity) than did the QH and Paint as anticipated by pedigree. This greater degree of diversity was also noted in the number of fixed loci (of 40 281 total) within each breed (QH = 728, Paint = 1347, Appaloosa = 567). FIS did not indicate inbreeding (Table S1). Across breeds, cluster analysis (STRUCTURE) was unable to support clustering beyond K = 1 (Fig. S1). Principal component (PC) analysis in SNPRELATE revealed that PCs 1 and 2 accounted for 4.15% of the total variation. PCs 1 and 3 failed to separate the breeds, whereas PC 2 showed a trend of clustering the Appaloosas apart from the intermingled Paint and QHs (Fig. 1). Pairwise FST values were low [0.001 (Paint-QH) to 0.005 (QH-Appaloosa)] (Table S1) but significantly different from zero as determined by 15 000 permutations in ARLEQUIN; however, an exact test of population differentiation, assuming the null hypothesis that all alleles are drawn from the same pool/population, was not significant. The highest single-locus FST across populations was on ECA1 at 108.9 Mb, which also was the highest pairwise value between the Appaloosa and Paint and ranked second when comparing Appaloosa to the QH (Table S1); this SNP is 574.5 kb from the 5’ end of TRPM1, the gene implicated in Appaloosa coat color. Another SNP on ECA1, 62.5 kb from TRPM1, also had a high FST in pairwise comparisons including the Appaloosa. Therefore, although the divergence between breeds is low, these results are evidence that genomic signatures of selection for major, breed-defining phenotypes in the Appaloosa can be detected.