Distribution of EBVs and dEBVs for conformation traits in FM horses.

a<p>Minimum and maximum estimated breeding values (EBV). The average estimated breeding value for animals born between 1998 and 2000 was set to 0.</p>b<p>Minimum and maximum deregressed breeding values (dEBV). Deregressed EBVs were used for association analysis.</p

Significantly associated SNPs with dEBV for height at withers using a mixed-model approach.

a<p>EquCab 2.0 assembly.</p>b<p>corresponding homologous human position, build 37.</p>c<p>trait-increasing allele/trait-decreasing allele; (frequency of the trait-increasing allele).</p>d<p>corresponding list of p-values of 1-d.f. (additive or allelic) test for association between SNP and trait; the Bonferroni-corrected threshold for a 5% genome-wide significance level is p_BONF = 1.31×10⁻⁶.</p>e<p>corresponding list of empirical p-values derived from permutations with 40,000 replicates.</p

Combined effect size of the two identified QTL on ECA 3 and ECA 9 on the dEBV for height at withers in the FM horse breed.

<p>The box plot indicates the median values, 25% and 75% quartiles and the outliers of the distribution. A total of 308, 513, 211, and 21 animals, respectively, represented the classes from zero to three trait-increasing alleles. The difference in the medians between horses with zero and three trait-increasing alleles, respectively, is 2.97 cm. None of the analyzed horses carried four trait-increasing alleles. The association between the number of trait increasing alleles and height at withers is highly significant (p = 8.4×10⁻¹³; Kruskal-Wallis test). Medians are significantly different between groups.</p

Effect of different QTL genotypes on the dEBV height at withers.

a<p>The mean dEBV for the homozygous trait-decreasing genotype was arbitrarily set to zero. The values correspond to centimeters.</p

The Franches-Montagnes horse belongs to the type of light draft horse breeds and has its origins in Switzerland (A).

<p>Height at withers is one of 28 conformation traits, for which breeding values are estimated once a year (B). The breed standard calls for horses between 150–160 cm in size. The stallion in the background was the tallest horse in our study with a phenotypic height at withers of 165 cm. (Picture: Swiss National Stud Farm).</p

Manhattan plot for height at withers based on dEBV.

<p>The red line indicates the Bonferroni-corrected significance level (p<1.31×10⁻⁶). The inset shows a quantile-quantile (qq) plot with the observed plotted against the expected p-values. The used mixed-model approach efficiently corrected for the stratification in the sample. The skew at the right edge indicates that these SNPs are stronger associated with height than would be expected by chance. This is consistent with a true association as opposed to a false positive signal due to population stratification.</p

SNPs associated with maxillary prognathism using a mixed-model approach.

a<p>frequency of the minor allele.</p>b<p>corresponding list of p-values of 1-d.f. (additive or allelic) test for association between SNP and trait; the Bonferroni-corrected threshold for a 5% genome-wide significance level is p_BONF = 1.31×10⁻⁶.</p>c<p>The two SNPs were in perfect linkage disequilibrium. The small differences in allele frequencies and p-values result from missing genotype calls in a few animals.</p

Genotype frequencies of the best associated SNP BIEC2-235929.

<p>The genotype distribution indicates a dominant or additive effect of the trait-associated variant.</p

Maxillary prognathism phenotype.

<p>(A) Unaffected phenotype with normal occlusion. (B) Affected phenotype: moderate maxillary prognathism with resulting malloclusion of the incisor teeth (Picture: ISME).</p

Phylogenetic relationship between haplotypes at <i>MITF</i> and <i>KIT</i>.

<p>Phylogenetic relationships between haplotypes at <i>MITF</i> (M1–M6) and <i>KIT</i> (K1–K7). Haplotype combinations (hap1 = haplotype 1, hap2 = haplotype 2) and individuals average total white markings score (aTSC = average Total Score) are shown on the right.</p