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1.
Figure 8

Figure 8. ECA17 haplotype frequency and position in the Thoroughbred and Puerto Rican Paso Fino.. From: Genome-Wide Analysis Reveals Selection for Important Traits in Domestic Horse Breeds.

Position, size and frequency of extended haplotypes found under significant windows in the Puerto Rican Paso Fino and the Thoroughbred on ECA17. The haplotype in the Thoroughbred is shown as a solid, horizontal bar, while the alternate haplotype in the Puerto Rican Paso Fino is a dashed bar. Genes found within the Thoroughbred haplotype are listed in Table S2. No genes or genomic features are annotated within the haplotype found in the Puerto Rican Paso Fino.

Jessica L. Petersen, et al. PLoS Genet. 2013 January;9(1):e1003211.
2.
Figure 7

Figure 7. Frequency and location of extended haplotypes of gaited breeds on ECA23.. From: Genome-Wide Analysis Reveals Selection for Important Traits in Domestic Horse Breeds.

ECA23 haplotype sharing in breeds that are gaited or bred to race at a trot. The common haplotype within each breed is shown as a solid, horizontal bar. di windows are shown as double-sided arrows and SNPs used in phasing are noted as dots on the x-axis. All genes within the region shared across all breeds are noted.

Jessica L. Petersen, et al. PLoS Genet. 2013 January;9(1):e1003211.
3.
Figure 2

Figure 2. Genome-wide di values for the Thoroughbred, Paint, and Quarter Horse.. From: Genome-Wide Analysis Reveals Selection for Important Traits in Domestic Horse Breeds.

Output of the di calculation for the Thoroughbred, Paint, and Quarter Horse. The di 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 99th percentile of the empirical distribution of di for each breed.

Jessica L. Petersen, et al. PLoS Genet. 2013 January;9(1):e1003211.
4.
Figure 5

Figure 5. Effect of the MSTN SINE insertion and intron 1 “C” allele on fiber type proportions.. From: Genome-Wide Analysis Reveals Selection for Important Traits in Domestic Horse Breeds.

Mean additive effect and 95% confidence intervals of the MSTN SINE insertion or “C” allele of the intron 1 SNP on Type 1 and Type 2B fiber type proportions.

Jessica L. Petersen, et al. PLoS Genet. 2013 January;9(1):e1003211.
5.
Figure 6

Figure 6. Genome-wide di values displaying significance of ECA23 across gaited breeds.. From: Genome-Wide Analysis Reveals Selection for Important Traits in Domestic Horse Breeds.

Output of the di calculation for gaited breeds as well as those bred to race at a trot. The di 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 99th percentile of the empirical distribution of di for each breed.

Jessica L. Petersen, et al. PLoS Genet. 2013 January;9(1):e1003211.
6.
Figure 9

Figure 9. Genome-wide di values displaying significance of ECA11 across draft breeds and the Miniature Horse.. From: Genome-Wide Analysis Reveals Selection for Important Traits in Domestic Horse Breeds.

Output of the di calculation for draft breeds and the Miniature Horse. The di 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 99th percentile of the empirical distribution of di for each breed.

Jessica L. Petersen, et al. PLoS Genet. 2013 January;9(1):e1003211.
7.
Figure 11

Figure 11. Frequency and location of extended haplotypes near LCORL and NCAPG in the draft breeds.. From: Genome-Wide Analysis Reveals Selection for Important Traits in Domestic Horse Breeds.

Haplotype conservation and frequency across ECA3 near LCORL and NCAPG, candidate loci for size. SNPs on the Equine SNP50 Beadchip are designated on the x-axis as dots and windows where di was calculated are shown with arrows. The common haplotype within each breed is shown as a solid, horizontal bar. The positions of candidate genes LCORL and NCAPG are shown; all genes found within the haplotype of interest are given in Table S2.

Jessica L. Petersen, et al. PLoS Genet. 2013 January;9(1):e1003211.
8.
Figure 3

Figure 3. Significant signature of selection and associated haplotypes on ECA18 surrounding MSTN.. From: Genome-Wide Analysis Reveals Selection for Important Traits in Domestic Horse Breeds.

(top) Haplotype size, position, and frequency for the minimal, shared and extended haplotypes (solid, horizontal bars) on ECA18 in the Thoroughbred, Quarter Horse, and Paint. Significant di windows are shown as double-sided arrows. The position of the MSTN gene is shown. The identities of all genes found within the 0.78 Mb haplotype are given in Table S2. (bottom) di values for each window in the region of MSTN for the three breeds.

Jessica L. Petersen, et al. PLoS Genet. 2013 January;9(1):e1003211.
9.
Figure 10

Figure 10. Frequency and location of extended haplotypes on ECA11 in draft breeds and the Miniature.. From: Genome-Wide Analysis Reveals Selection for Important Traits in Domestic Horse Breeds.

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 di 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 Table S2.

Jessica L. Petersen, et al. PLoS Genet. 2013 January;9(1):e1003211.
10.
Figure 1

Figure 1. Haplotypes surrounding the MC1R locus in the Morgan and Belgian.. From: Genome-Wide Analysis Reveals Selection for Important Traits in Domestic Horse Breeds.

Extended haplotypes surrounding the MC1R 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 di 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 di statistic identified the signature of selection around MC1R in the Morgan, but not in the Belgian due to poor polymorphic SNP coverage resulting in no calculation of di over this region.

Jessica L. Petersen, et al. PLoS Genet. 2013 January;9(1):e1003211.
11.
Figure 4

Figure 4. Gluteal fiber type proportions observed based upon MSTN SINE and intron 1 SNP genotype.. From: Genome-Wide Analysis Reveals Selection for Important Traits in Domestic Horse Breeds.

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.

Jessica L. Petersen, et al. PLoS Genet. 2013 January;9(1):e1003211.

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