Association with size at the <i>HMGA2</i> locus.

<p>(A) Haplotypes spanning <i>HMGA2</i> were inferred with PHASE for a set of nine SNPs that included all size-associated SNPs at the locus. (B) The haplotype counts differ in the set of all little breed horses (American Miniature to Puerto Rican Paso Fino) vs. all big breed horses (Friesian to Shire). (C) For each breed, the count of chromosomes inferred to be carrying that haplotype. (D) Size-associated SNPs occur within and adjacent to <i>HMGA2</i>. SNP associations from the 16-breed GWA scan are plotted above the genes in this locus. These SNPs were discovered and genotyped by capillary sequencing (see main text). Each gene’s exons (vertical bars), introns (horizontal lines) and direction of transcription (arrow) are indicated.</p

Haplotypes at the <i>LCORL</i> locus on horse chromosome 3 are associated with size.

<p>(A) Haplotypes for five SNPs were inferred with PHASE and (B) have different counts in the set of all little breed horses (American Miniature to Puerto Rican Paso Fino) vs. all big breed horses (Friesian to Shire). (C) For each breed, the count of chromosomes inferred to be carrying each haplotype. (D) Size-associated SNPs on chromosome 3 are adjacent to the <i>LCORL</i> gene. SNP associations from the 16-breed GWA scan are plotted above the genes in this locus. Each gene’s exons (vertical bars), introns (horizontal lines) and direction of transcription (arrow) are indicated. (E) The size of each horse was quantified via a principal components analysis of 33 measurements from the head, neck, trunk and limbs. For each horse, breed membership is plotted vs. PC1-size score.</p

Two genome-wide association scans for size identify five significantly associated loci.

<p>(A) Horse breed phylogenetic relationships were inferred using a principal components analysis of SNP genotypes collected from 48 horses from 16 extreme size breeds plus 48 Thoroughbreds. Thoroughbreds (filled green circles) and other breeds have distinct genetic signatures. Large breeds (blue points) are genetically clustered in PC-space as are small breeds (red points). The first four PCs are plotted: PC1 (9.7% of variance explained) and PC2 (2.7%) and in (B) PC3 (2.4%) and PC4 (2.0%). Breeds in size order: American Miniature  =  filled red squares, Falabella  =  filled red circles, Caspian  =  filled red triangles, Shetland Pony  =  filled red diamonds, Welsh Mountain Pony  =  unfilled red squares, Welsh Pony  =  unfilled red circles, Dartmoor Pony  =  unfilled red triangles, Puerto Rican Paso Fino  =  unfilled red diamonds, Friesian  =  filled blue squares, Suffolk Punch  =  filled blue circles, Ardennais  =  filled blue triangles, Brabant  =  filled blue diamonds, Belgian  =  unfilled blue squares, Percheron  =  unfilled blue circles, Clydesdale  =  unfilled blue triangles, and Shire  =  unfilled blue diamonds. (C) Quantile-quantile plot for the GWA scans. The p-values for the 16 breed scan are plotted in red and have a genomic inflation factor of 1.189. The p-values for the Thoroughbred scan are plotted in blue and have a genomic inflation factor of 1.114. (D) Manhattan plot for the GWA scan of 48 horses from 16 breeds of extreme size and (E) 48 Thoroughbreds. The horizontal line in each indicates genome-wide significance with an alpha  = 0.05 and Bonferroni correction for multiple hypothesis testing.</p

plink files for cornell canine dataset

chromosome, name, location, alleles for each SN

plink files for cornell canine dataset

genotypes for each dog at each SN

plink files for cornell canine dataset

ID and sex information for each do

phenotypes

phenotypes for each do

Sample file for merged Illumina and Affymetrix array data (fam)

Sample file for merged Illumina and Affymetrix array data (fam

Genotype file for Canine HD semi custom array (bed)

Genotype file for Canine HD semi custom array (bed

Y haplotype calls for indviduals

Y haplotype calls for indvidual