The Genetic Diversity of Stallions of Different Breeds in Russia

Abstract

The specifics of breeding and selection significantly affect genetic diversity and variability within a breed. We present the data obtained from the genetic analysis of 21 thoroughbred and warmblood horse breeds. The most detailed information is described from the following breeds: Arabian, Trakehner, French Trotter, Standardbred, and Soviet Heavy Horse. The analysis of 509,617 SNP variants in 87 stallions from 21 populations made it possible to estimate the genetic diversity at the genome-wide level and distinguish the studied horse breeds from each other. In this study, we searched for heterozygous and homozygous ROH regions, evaluated inbreeding using FROH analysis, and generated a population structure using Admixture 1.3 software. Our findings indicate that the Arabian breed is an ancestor of many horse breeds. The study of the full-genome architectonics of breeds is of great practical importance for preserving the genetic characteristics of breeds and managing breeding. Studies were carried out to determine homozygous regions in individual breeds and search for candidate genes in these regions. Fifty-six candidate genes for the influence of selection pressure were identified. Our research reveals genetic diversity consistent with breeding directions and the breeds' history of origin.

Keywords: Equus caballus; breeds; genetic diversity; runs of homozygosity; single-nucleotide polymorphisms (SNPs).

Figure 1

Examples of individual stallions used in the present study: (A) Kvantum, of the American Standardbred Trotter; (B) Volf, of the Trakehner breed; (C) Forvard Loc, of the French Trotter; (D) Ecspirien, of the Arabian breed and (E) Rasstrel, of the Soviet Draft.

Figure 2

Graph obtained when calculating the number of ancestral clusters (K) from 2 to 6 based on cross-validation errors (CV% error).

Figure 3

Comparative structure of horse populations calculated using the program Admixture 1.3 with the number of ancestral clusters K from 2 to 6. Each bar represents an individual animal for each terminal breed and the six colors represent each K population cluster.

Figure 4

Plot of mean, quartiles, and frequency (plot width) based on the ROH of the coefficient of inbreeding (FROH) for each breed group. Breed designations: 2—Arabian (AR); 5—Trakehner (TR); 13—French Trotter (FR); 14—Standardbred (AMST); 21—Soviet Heavy Draft (SH).

Figure 5

Inbreeding calculated from FROH for five horse populations by chromosome. Breed designations: 2—Arabian (AR); 5—Trakehner (TR); 13—French Trotter (FR); 14—Standardbred (AMST); 21—Soviet Heavy Draft (SH).