1. Introduction
Horses are one of the most important domesticated animals that have played a huge role in the history of mankind. Despite the fact that their domestication commenced much later than that of other domestic animals, the diversity of their breeds is remarkable [
1]. These variations are due to the different purposes for which horses have been intensively used in human life. As a result of strict selective breeding for certain traits, several types of equines have been formed. Conventionally, they are divided into three categories. The first includes horses primarily used for riding, the second includes horses used for draught [
2], and the third includes horses used for milk or meat. Certain indigenous breeds were utilised for both dairy and meat production [
3,
4]. The development of horse breeds was particularly influenced by the widespread settlement of people around the globe, and the ability of horses to adapt to different climates and conditions of use [
5]. Horses have been used in manufacturing, as a means of transport and communication between nations, in wars, and even as a symbol of wealth. Stallions possessing distinctive traits were highly valued and selectively bred within local communities through inbreeding among closely related individuals, leading to a substantial decrease in genetic variation among the breeds now recognized as thoroughbreds [
6]. These breeding methods have resulted in a loss of adaptive plasticity to husbandry conditions, making it challenging to implement breeds on a broad scale. There were indigenous breeds everywhere that were not efficient enough in a rapidly developing society that required a combination of high working qualities and external phenotypic characteristics. As the result of crossing, breeds with thoroughbred stallions in their pedigree have emerged. In contemporary times, enhancing tribal resources using such breeds has resulted in a considerable loss of breed differentiation. Reproduction of some horse breeds has almost eliminated genetic diversity, resulting in the loss of the unique quality of these breeds. Technological advancements have superseded horses, which had occupied a niche for centuries that had been exploited by humans. 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.
This study presents both Russian indigenous and production breeds, which have been inbreeding for centuries, avoiding the infusion of blood from other breeds. The evaluation of genetic diversity using a medium-density chip for indigenous and certain commercial equine varieties is important for the preservation of the world’s equine genetic resources.
4. Discussion
To date, horse breeding in Russia has four distinct directions of productivity including working purpose, food production, sports, and breeding. It is believed that breeds can be divided into coldblood (harness), warmblood (riding and trotting) breeds, and breeds for food production (milk, meat) [
2,
14,
15]. Our studies have confirmed similar differences at the genome level.
Draft and indigenous horse breeds serve a dual purpose, as they can be used for both working purpose and production, including milk and meat production. They are bred in local areas, often with extreme climatic conditions [
15,
16,
17]. In our study, they are represented by Vyatka, Tuva, and Yakut horse breeds, which are characterized by exceptional endurance, as well as high adaptability to the surrounding natural and climatic conditions. The body features of aboriginal horses include a medium-sized stature, broad body, elongated body, and relatively short legs. Scientific and technological advances have had a significant impact on the quantitative aspects of indigenous horse populations, and the decline in population size has led to a significant reduction in genetic diversity. However, all local breeds have a distinctive, and often unique, genetic structure, which in most cases is characterized by the presence of private alleles.
The Vyatka breed is an indigenous breed of northern forest type horses, established during the end of XVII—beginning of XVIII centuries in the modern Kirov region and Udmurtia territories [
17]. It is believed that the Vyatka breed history begins with the Livonian kleppers arrival to the Vyatka region first in 1374 and later, be the decree of Peter I, around 1720. However, the strong and energetic horse was already being used in postal troikas—a traditional Russian harness driving combination consisting of three horses abreast—by the end of the XVIII century; thus, the participation of Livonian kleppers has not been proven yet. A considerable damage to the Vyatka gene pool occurred in the middle of the XX century, when draft horses, as well as Orlov and Russian trotters, were used for breed improvement. The genomic analysis, conducted in our study, confirms the historical establishment of this population. Moreover, the Vyatka breed genome clearly shows traces of similarities with Russian and Soviet Heavy Draft breeds. In addition, genomic analysis revealed accumulation of homozygosity in certain individuals, and Admixture analysis showed genetic heterogeneity of the population.
The Yakut horse is one of the oldest local breeds. It was formed in the conditions of the Far North of Yakutia several thousand years ago. It is the most cold-resistant indigenous breed, which has been developed via popular breeding under the strong influence of natural selection. In Yakutia, horses are kept outdoors all year round (at temperatures up to +40 °C in summer and −60 °C in winter), and have to search for food on their own. Traditionally, these horses are used for meat and milk production, as well as for riding. Currently, there are several types of Yakut horses in the Republic of Yakutia, which vary in their habitat, as well as in the extent to which they have been crossbred with other breeds [
18]. Purebred animals from the central region of the Republic of Sakha (Yakutia) of the Russian Federation were used in our study. Genetic analysis revealed no traces of crossbreeding with other breeds (with the exception of one animal with low bloodlines from other breeds). We also identified low heterozygosity and high inbreeding levels in the studied population. The strong pressure of natural selection has significantly narrowed the genetic diversity, relatively to SNP pool, used in the analysis. Our results were also confirmed through the studies of other authors, in which 7 Yakut horses were studied using whole genome sequencing (WGS), and similar data were obtained, in particular, through FROH analysis.
The Tuva horse is another indigenous breed of the Russian Federation. This breed was also developed via popular breeding over many centuries in the Republic of Tuva territory. The unique climatic conditions of Tuva had a great influence on the development of the breed, which was formed without noticeable influence from other breeds until the mid-20th century. The Tuva horse is characterized as a highly efficient and enduring local breed, which easily withstands year-round grazing conditions. Moreover, this breed has a high working capacity, as well as good meat and milk productivity [
7].
With the emergence of large cities, the growth of trade and cargo turnover prompted the need for a large, massive horse capable of carrying large loads, and pulling heavy agricultural implements and machines. In the first half of the 19th century, a fairly large group of draft horses was created in the Voronezh province. This group of horses was called Bityug. However, in the middle of the 19th century, heavy draft horses from European countries began to be imported to Russia in large numbers. These were Ardennes, Clydesdales, Shires, Suffolks, Percherons and Brabançons.
Through crossing Brabançons with local draft horses of various origins, the Soviet draft breed was developed. Horses of this breed have versatile working qualities, speed, strength, and endurance. They acclimatize well in harsh conditions, and are not demanding in terms of maintenance. This is the largest breed of heavy draft horses of Russian selection.
Russian draft horses are intended for agricultural work. In addition, they have high meat quality, as well as high milk productivity. This makes this breed very promising in productive horse breeding. The history of the creation of the breed is associated with the arrival of mountain-type Ardennes from Belgium to Russia that occurred in the mid-19th century. To increase the number of Ardennes, they were crossed with draft mares of different breeds. The main breeds used were Brabançons and Percherons. As a result of many years of breeding work through complex interbreeding of Ardennes and their crosses, the Russian draft horse breed was created in the mid-20th century. Horses of this breed are not large, with well-defined draft forms, wide-bodied, and have a strong constitution, as well as a balanced temperament. Currently, the Russian draft breed is the most common draft breed in Russia.
The Vladimir breed of horses was bred in the Vladimir and Ivanovo regions of Russia. The bulk of the horse population in these areas was made up of small peasant horses of strong constitution. They were hardy, but weak in strength. At the end of the 19th century, crossing of local mares with stallions of the Percheron, Suffolk, and Ardennes breeds began. This led to the gradual replacement of outbred horses with improved crossbreds. At the beginning of the 20th century, Clydesdale stallions had a significant influence on the formation of the breed, which contributed to the further enlargement of horses, and gave them a draft type. The creation of the breed was completed in the mid-20th century. The horses of the Vladimir draft breed are distinguished by their large stature, well-developed muscles, strong constitution, and energetic temperament. These are strong and hardy horses that are well adapted to the climatic conditions of Central Russia.
According to the data we received, heavy horse breeds are the closest to aboriginal breeds (Yakut, Tuvan, and Vyatka breeds). In our study, three breeds were used: the Soviet heavy truck, the Russian heavy truck, and the Vladimir heavy truck. Although no significant differences were found between the draft breeds, these breeds constitute a separate block, distinct from other breeds. Other studies of draft breeds are represented only through studies of individual breeds or the mitochondrial genome [
19,
20,
21].
A number of horse breeds have a significantly lowered level of genetic diversity as a result of high selection pressure and purebred breeding. The Akhal-Teke horse, along with the Arabian and Thoroughbred, belongs to the purebred group of breeds. This horse breed was developed for riding, presumably about 5000 years ago, in the modern Turkmenistan territory (Ahkal-Teke), which explains its adaptation to dry and hot climates. Being the oldest of the purebred breeds, the Akhal-Teke horse has had a significant influence on the Arabian and Thoroughbred breeds. The limited use of stallions in breeding also significantly increased the population’s homozygosity level. 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].
Other authors have studied the origin of Akhal-Teke horses [
24]. The data obtained on ADMIXTURE and PCA of Syrian Arabian horses and Akhal-Teke horses are fully consistent with our data, and confirm the origin of the Akhal-Teke breed from eastern horses.
Riding horses are performance-oriented; therefore, these breeds are occasionally improved by thoroughbreds. 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].
The Kabardin breed is one of the oldest breeds, used both for riding and harness. A unique characteristic they possess is their adaptability to mountainous landscapes [
26]. It is believed that the breed is the result of complex and lengthy crossing of the horses of steppe breeds with eastern ones, and breeding in the specific mountain conditions of the North Caucasus. In the 16th century, horses of the Kabardian breed were already famous far beyond the Caucasus. Kabardian horses are very hardy, unusually brave, and careful when riding along mountain trails. Horses of this breed have a more advanced vestibular apparatus, and strong hoof horn, which is especially important for long rides in mountainous areas. They are characterized by a strong constitution, and a good ability to quickly restore body condition and maintain it in the winter when kept in herds. Our study identified unique genotypes that need to be conserved.
The Don breed is also an old breed, used both for riding and harness, which was developed during the XVIII-XIX centuries in the territory of the modern Rostov region. The first stud farm of the Don breed was established by the Cossack ataman M.I. Platov back in 1770, on the left bank of the Don River. The ancestor of this eastern steppe horse is the Kalmyk or Mongolian horse; for its improvement, stallions of Persian, Kabardin, Turkmen, Karabakh, Nogai, and Turkish selection were used, and from the beginning of the XIX century, the Arabian and Thoroughbred breeds as well. The Don breed was strictly selected for its cavalry qualities, endurance, and adaptability [
27]. Nature has endowed the Don breed with a very strong constitution, unpretentiousness, good distance abilities, undemanding conditions for keeping and feeding, and high performance. Modern horses of the Don breed are characterized by good conformation, dry strong limbs, and strong hooves. There are several intra-breed types in the Don breed, which expands the boundaries of the use of Don horses. Don horses, especially, had an impact on horse breeding in Kazakhstan and Kyrgyzstan. There is a significant proportion of Don blood in the Kushum, Kustanai, and Novokyrgyz breeds. As an improver of local horses, Don horses were widely used in the Lower Volga region, the Urals, the mountainous part of Altai, Tyva, Buryatia, the Chita region, and the North Caucasus. 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].
The Orlov Trotter formed a separate cluster in both structural and PCA analyses. According to the second ADMIXTURE vector, this breed differs significantly from the studied breeds. Orlov Trotter is a famous Russian light harness horse breed with the hereditary ability to trot. The breed was developed in Russia, in the second half of the XVIII—early XIX centuries in the Khrenovskoy stud farm in Voronezh province under the leadership of its owner Count A.G. Orlov through a complex crossbreeding method using Arabian, Danish, Dutch, Mecklenburg, and other breeds. However, at the end of the XIX century, mass mestization began, during which some of the Orlov mares were mated with American trotting stallions. In the 20th century, large losses in Russian horse breeding were associated with the Civil War. At this time, most of the breeding stock was lost. In this connection, the Orlov Trotter was on the verge of extinction. However, already in the middle of the 20th century, the Orlov Trotter became one of the most numerous breeds in Russia. In order to increase the trotter speed, and expand the genetic diversity in the breed, crossing of Orlov trotting mares with Thoroughbred horses, standardbred and Russian trotting stallions, was carried out in the second half of the 20th century (in the 1960s). 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. The Orlov Trotter is the pride of Russia, its national treasure and calling card. The Orlov Trotter breed in its modern form is the result of long-term breeding work of many generations of the breeders. However, due to the small population size of the breed, we found high FROH in all animals analyzed. However, in PCA we see high inter-animal variability in the second component. This may be due to small introductory crosses at some historical stages of breeding.