Genome-wide analysis reveals selection for important traits in domestic horse breeds

Abstract

Intense selective pressures applied over short evolutionary time have resulted in homogeneity within, but substantial variation among, horse breeds. Utilizing this population structure, 744 individuals from 33 breeds, and a 54,000 SNP genotyping array, breed-specific targets of selection were identified using an F(ST)-based statistic calculated in 500-kb windows across the genome. A 5.5-Mb region of ECA18, in which the myostatin (MSTN) gene was centered, contained the highest signature of selection in both the Paint and Quarter Horse. Gene sequencing and histological analysis of gluteal muscle biopsies showed a promoter variant and intronic SNP of MSTN were each significantly associated with higher Type 2B and lower Type 1 muscle fiber proportions in the Quarter Horse, demonstrating a functional consequence of selection at this locus. Signatures of selection on ECA23 in all gaited breeds in the sample led to the identification of a shared, 186-kb haplotype including two doublesex related mab transcription factor genes (DMRT2 and 3). The recent identification of a DMRT3 mutation within this haplotype, which appears necessary for the ability to perform alternative gaits, provides further evidence for selection at this locus. Finally, putative loci for the determination of size were identified in the draft breeds and the Miniature horse on ECA11, as well as when signatures of selection surrounding candidate genes at other loci were examined. This work provides further evidence of the importance of MSTN in racing breeds, provides strong evidence for selection upon gait and size, and illustrates the potential for population-based techniques to find genomic regions driving important phenotypes in the modern horse.

Figure 1. Haplotypes surrounding the MC1R locus in the Morgan and Belgian.

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 d_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 d_i 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 d_i over this region.

Figure 2. Genome-wide d_i values for the Thoroughbred, Paint, and Quarter Horse.

Output of the d_i calculation for the Thoroughbred, Paint, and Quarter Horse. The d_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 d_i for each breed.

Figure 3. Significant signature of selection and associated haplotypes on ECA18 surrounding MSTN.

(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 d_i 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) d_i values for each window in the region of MSTN for the three breeds.

Figure 4. Gluteal fiber type proportions observed based upon MSTN SINE and intron 1 SNP genotype.

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.

Figure 5. Effect of the MSTN SINE insertion and intron 1 “C” allele on fiber type proportions.

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.

Figure 6. Genome-wide d_i values displaying significance of ECA23 across gaited breeds.

Output of the d_i calculation for gaited breeds as well as those bred to race at a trot. The d_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 d_i for each breed.

Figure 7. Frequency and location of extended haplotypes of gaited breeds on ECA23.

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. d_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 region shared across all breeds are noted.

Figure 8. ECA17 haplotype frequency and position in the Thoroughbred and Puerto Rican Paso Fino.

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.

Figure 9. Genome-wide d_i values displaying significance of ECA11 across draft breeds and the Miniature Horse.

Output of the d_i calculation for draft breeds and the Miniature Horse. The d_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 d_i for each breed.

Figure 10. Frequency and location of extended haplotypes on ECA11 in draft breeds and the Miniature.

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 d_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 Table S2.

Figure 11. Frequency and location of extended haplotypes near LCORL and NCAPG in the draft 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 d_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 LCORL and NCAPG are shown; all genes found within the haplotype of interest are given in Table S2.