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. FST 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.

Prehistoric genomes reveal the genetic foundation and cost of horse domestication

“…By comparing genetic information of ancient and modern domesticated horses, we could pinpoint the genetic changes associated with domestication shared by all modern breeds. This methodology contrasts with scans for outlier genomic regions among modern breeds (35), which can, at best, identify genes that are specific to breeds, in the absence of knowledge of the predomesticated genetic background and sources of variation.…”

Genetic Susceptibility to Rhodococcus equi

“…Our laboratory conducted a CNV‐based GWAS by applying the aforementioned equine exon tilling array71 to the 72 foals studied in our SNP GWAS 48. Although similar lengths and numbers of CNVs were observed in these foals as in the previous report using this array, no CNVs were significantly associated with R. equi pneumonia in these foals.…”

“…Furthermore, the longer the LD of the species the fewer SNPs are necessary to identify significant associations. Estimates of LD for breeds of horses are markedly longer than those for humans 48, 49. Thus, one might expect to need fewer SNPs on an equine array to have the same discriminatory power as a human array or to have greater power in a GWAS for horses than humans for an array of the same size or density of SNPs.…”

Diversity and effective population size of four horse breeds from microsatellite DNA markers in South-Central Mexico

“…Petersen et al (2013), using whole-genome single-nucleotide polymorphism data, suggested that horse breeds with low within-breed diversity, such as Thoroughbred and Quarter Horse, may be related to population bottlenecks, intense selective pressure or closed conditions due to their long breed histories. For the Thoroughbred breed, they reported a high mean individual inbreeding coefficient (larger than 10 %) (Petersen et al, 2013). In the present study, high heterozygosis showed no current inbreeding risk.…”