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.

The Genetic Diversity of Horse Native Breeds in Russia

“…The Akhal-Teke breed, along with the Arabian horse, has had a minimum effective population size for many generations, which is consistent with our results of significant homozygosity in both breeds. Moreover, our results are consistent with earlier studies that were conducted using Axiom™ Equine Genotyping Array on Russian horse breeds [8]. Other studies involving Arabian and Akhal-Teke breeds have also found high levels of homozygosity; however, given that they studied five individuals of each breed, it cannot be stated that the obtained data are sufficient for a general breed characterization [22,23].…”

“…Both ADMIXTURE and PCA analysis revealed the similarity of Don horse with the Kabardin breed, and for some animals with the Arabian breed. Earlier studies revealed traces of Thoroughbreds in Don stallions [8].…”

“…ADMIXTURE and PCA results revealed differences between individuals in riding horses (particularly Kabardin and Don breeds), which may be the result of introgression from other breeds. Other studies emphasize that the loss of local breeds' genetic uniqueness is due to the improvement of their sports performance by purebreds [8,24,25].…”

“…As a result of this crossing, the level of heterozygosity of the population increased, without causing significant changes in the number of alleles found in the Oryol trotting breed [27]. Our early research [8] on ADMIXTURE found traces of Thoroughbred and Standardbred breeds. To date, purebred breeding of the Orlov Trotter is under strict control, and the infusion of blood from other breeds is forbidden.…”

“…However, the Russian Federation, with its vast territory, diverse natural conditions, and rich equine breeding history, owns numerous horse breeds of indigenous origin [7]. Recently, there have been efforts to evaluate the genetic variation of breeds bred within Russia's borders [8], but these were Stud breeds that showed a reduction in the uniqueness of some breeds, though there is still no clear picture of all the genetic variability in native horse breeds.…”