Additional file 2: Table S2. of Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds

SNP50 breed informativeness. Impact of breed on SNP50 informativeness. Table shows informativeness (MAF ≥ 0.05) of the legacy, SNP50 SNP set for light, draft, and pony breeds described by McCue et al. [1, 2]. Mean number of informative SNPs per breed was ~42,000 (~77%). 19,427 SNPs were informative in all 14 breeds. (XLSX 8 kb

Number of samples (N), effective population size (N_e), individual inbreeding estimates (f), inbreeding coefficient (F_IS), and expected heterozygosity (H_e) from four SNP sets pruned based upon varying levels of LD.

a<p>Individuals from this breed also included in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054997#pone.0054997-McCue1" target="_blank">[41]</a>;</p>b<p>20 of these individuals were also reported in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054997#pone.0054997-McCue1" target="_blank">[41]</a>;</p>c<p>17 of these individuals were also reported in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054997#pone.0054997-McCue1" target="_blank">[41]</a>;</p>d<p>21 of these individuals were also reported in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054997#pone.0054997-McCue1" target="_blank">[41]</a>;</p>e<p>19 of these individuals were also reported in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054997#pone.0054997-McCue1" target="_blank">[41]</a>.</p><p>F_IS and f were calculated based upon the primary SNP set (10,536 loci). Samples also used in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054997#pone.0054997-McCue1" target="_blank">[41]</a> are indicated in the footnotes.</p>*<p>indicates significance at α<0.05 determined by 10,000 permutations.</p

Individual and breed relationships among 814 horses illustrated by parsimony.

<p>Parsimony tree created from 10,066 SNPs and rooted by the domestic ass. Breeds are listed in the legend in order starting from the root and working counterclockwise. Individual outliers with respect to their breeds are noted with arrows. Bootstrap support calculated from 1,000 replicates is shown for major branches when greater than 50%.</p

Pairwise F_ST values based upon 10,536 SNPs in 37 horse populations.

<p>Pairwise F_ST values as calculated in Arlequin using 10,536 autosomal SNPs and significance tested using 20,000 permutations. All pairwise values are significantly different from zero. (individual outliers were removed from this analysis).</p

Populations (breeds) included in the study, region of breed origin and sampling location, notes on population history relevant to diversity statistics, and breed classification based upon use and phenotype.

<p>Populations (breeds) included in the study, region of breed origin and sampling location, notes on population history relevant to diversity statistics, and breed classification based upon use and phenotype.</p

Frequency and location of extended haplotypes near <i>LCORL</i> and <i>NCAPG</i> in the draft breeds.

<p>Haplotype conservation and frequency across ECA3 near <i>LCORL</i> and <i>NCAPG,</i> candidate loci for size. SNPs on the Equine SNP50 Beadchip are designated on the x-axis as dots and windows where <i>d_i</i> was calculated are shown with arrows. The common haplotype within each breed is shown as a solid, horizontal bar. The positions of candidate genes <i>LCORL</i> and <i>NCAPG</i> are shown; all genes found within the haplotype of interest are given in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003211#pgen.1003211.s003" target="_blank">Table S2</a>.</p

Genome-wide <i>d_i</i> values displaying significance of ECA23 across gaited breeds.

<p>Output of the <i>d_i</i> calculation for gaited breeds as well as those bred to race at a trot. The <i>d_i</i> value is plotted on the y axis and each autosome is shown in the x axis in alternating colors. Each dot represents one 500 kb window. The dashed horizontal line represents the 99^th percentile of the empirical distribution of <i>d_i</i> for each breed.</p

Gluteal fiber type proportions observed based upon <i>MSTN</i> SINE and intron 1 SNP genotype.

<p>Gluteal muscle fiber type proportions in 79 Quarter Horses based upon myostatin genotypes, not accounting for age and sex. The top panel shows the SINE (N = wild-type allele, S = SINE insertion) and bottom panel the intron 1 SNP genotypes. Each grey circle indicates fiber type proportion in one horse (y-axis). The mean is shown with a black dot and the error bars represent 95% confidence intervals around the mean. The SINE and SNP are each significantly associated with a lower proportion of Type 1 and higher proportion of Type 2B muscle fibers.</p

Haplotypes surrounding the <i>MC1R</i> locus in the Morgan and Belgian.

<p>Extended haplotypes surrounding the <i>MC1R</i> locus on ECA3 in Morgan and Belgian horses. SNPs on the Equine SNP50 Beadchip are designated on the x-axis as dots and windows where <i>d_i</i> was calculated are shown with double-sided arrows. The common haplotype is shown as a solid, horizontal bar. As the result of haplotype length in each breed, the <i>d_i</i> statistic identified the signature of selection around <i>MC1R</i> in the Morgan, but not in the Belgian due to poor polymorphic SNP coverage resulting in no calculation of <i>d_i</i> over this region.</p

Frequency and location of extended haplotypes on ECA11 in draft breeds and the Miniature.

<p>Haplotype frequencies on ECA11 for the draft breeds, Miniature horse, Shetland and Caspian ponies, and the Tennessee Walking Horse. The common haplotype within each breed is shown as horizontal bars. The solid bars represent the haplotype similar across draft breeds while the dashed bars represent the haplotype common to the Miniature horse and related breeds. Significant <i>d_i</i> windows are shown as double-sided arrows and SNPs used in phasing are noted as dots on the x-axis. All genes within the haplotype shared across draft breeds, including the region shared with the Miniature horse are listed in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003211#pgen.1003211.s003" target="_blank">Table S2</a>.</p