Genetic diversity in the modern horse illustrated from genome-wide SNP data

Abstract

Horses were domesticated from the Eurasian steppes 5,000-6,000 years ago. Since then, the use of horses for transportation, warfare, and agriculture, as well as selection for desired traits and fitness, has resulted in diverse populations distributed across the world, many of which have become or are in the process of becoming formally organized into closed, breeding populations (breeds). This report describes the use of a genome-wide set of autosomal SNPs and 814 horses from 36 breeds to provide the first detailed description of equine breed diversity. F(ST) calculations, parsimony, and distance analysis demonstrated relationships among the breeds that largely reflect geographic origins and known breed histories. Low levels of population divergence were observed between breeds that are relatively early on in the process of breed development, and between those with high levels of within-breed diversity, whether due to large population size, ongoing outcrossing, or large within-breed phenotypic diversity. Populations with low within-breed diversity included those which have experienced population bottlenecks, have been under intense selective pressure, or are closed populations with long breed histories. These results provide new insights into the relationships among and the diversity within breeds of horses. In addition these results will facilitate future genome-wide association studies and investigations into genomic targets of selection.

Figure 1. Individual and breed relationships among 814 horses illustrated by parsimony.

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%.

Figure 2. Distance based, neighbor joining tree calculated from SNP frequencies in 38 horse populations.

Majority rule, neighbor joining tree created from 10,536 SNP makers using Nei’s genetic distance and allele frequencies within each population. Percent bootstrap support for all branches calculated from 1,000 replicates is shown.

Figure 3. Bayesian clustering output for five values of K in 814 horses of 38 populations.

Structure output for five values of K investigated. Each individual is represented by one vertical line with the proportion of assignment to each cluster shown on the y axis and colored by cluster. Other values of K are shown in Figure S1 and a summary of assignment of each breed in Tables S1 and S2.

Figure 4. Pairwise F_ST values based upon 10,536 SNPs in 37 horse populations.

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).