**1. Introduction**

Caucasian tur (*Capra caucasica*) is an ungulate species from the subfamily Caprinae (Figure 1). Its habitat is limited to Greater Caucasus Mountain Chain from Azerbaijan and Georgia in the East to Krasnodar region of Russia in the West (Figure 2). Its range is one of the smallest habitats of all ungulates—around 770 km in length and 80 km in width [1]. Taxonomically, the species is divided into two subspecies: West-Caucasian tur (*C. c. severtzovi*) and East-Caucasian tur (*C. c. cylindricornis*). Some authors even considered these populations as different species [2–5]. The areas of these subspecies are united, and

**Citation:** Dotsev, A.V.; Rodionov, A.N.; Kharzinova, V.R.; Petrov, S.N.; Medvedev, D.G.; Bagirov, V.A.; Brem, G.; Zinovieva, N.A. An Assessment of Applicability of SNP Chip Developed for Domestic Goats in Genetic Studies of Caucasian Tur (*Capra caucasica*) . *Diversity* **2021**, *13*, 312. https:// doi.org/10.3390/d13070312

Academic Editor: Michael Wink

Received: 23 June 2021 Accepted: 6 July 2021 Published: 8 July 2021

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in the territory between them a hybrid form, which is referred to as a Mid-Caucasian tur, is distinguished [6].

**Figure 1.** Caucasian tur in its natural habitat. Photo by M. Andreev and A. Andreeva (http:// mountaindreams.ru, accessed on 17 June 2021).

**Figure 2.** Map with sampling sites of Caucasian tur used in this study and the area of the species habitat. W\_TUR = West-Caucasian tur, E\_TUR = East-Caucasian tur, M\_TUR = Mid-Caucasian tur.

The International Union for Conservation of Nature (IUCN) has listed East-Caucasian tur with the total numbers of about 31,000–32,000 animals as near threatened [7] and West-Caucasian tur with census size only around 5000 animals as endangered [8]. Of particular concern is an increasing anthropogenic pressure (poaching, habitat destruction, grazing competition with livestock, etc.,), resulting in migrations to higher mountains and adaptation to nocturnal behavior in some populations.

Little is known about the genetic diversity and evolutionary history of this animal. Only several studies based on Y-chromosome SRY gene and mitochondrial cytochrome b and control region were conducted [9–12]. To clarify the taxonomy of Caucasian tur and investigate the diversity of its populations molecular genetic studies based on nuclear DNA are needed.

Currently, one of the most effective technologies for molecular genetic research is the genome-wide analysis of single-nucleotide polymorphisms (SNPs). Recent advances in the development of high-throughput genotyping platforms (SNP chips) have turned SNPs into a powerful tool for genetic studies of domestic animals [13,14]. Although such chips are not available for most of the wild animals, the use of the SNP chips developed for their domestic relatives were found to be suitable.

Tokarska et al. [15] used the BovineSNP50 BeadChip created for cattle (*Bos taurus*) to infer the population structure of European bison (*Bos bonasus*). Kasarda et al. [16] have demonstrated suitability of the above-mentioned SNP microarray for the evaluation of the Cervidae family diversity. Kharzinova et al. [17,18] have shown the applicability of the BovineSNP50 BeadChip and BovineHD BeadChip for genome-wide studies of reindeer (*Rangifer tarandus*). The OvineSNP50 BeadChip, created for domestic sheep, was successfully used to study wild Ovis species: bighorn (*Ovis canadensis*), thinhorn (*Ovis dalli*) [19,20] and snow sheep (*Ovis nivicola*) [21].

The first SNP chip for domestic goats—Goat SNP50 BeadChip, containing more than 50,000 markers was developed by the International Goat Genome Consortium in 2011 [22]. In terms of wild species, Goat SNP50 BeadChip, so far was only used for genotyping of Bezoar goat (*Capra aegagrus*) which is considered the ancestor of domestic goats [23].

It should be noted that for non-model species the genotyping call-rate decreases approximately 1.5% per each million years of divergence time between species and the number of polymorphic sites decline exponentially leveling off after about 5 million years of divergence [20]. Therefore, this approach is not suitable for some analyses, i.e., based on linkage disequilibrium (LD), but meanwhile could be successfully used for investigation of phylogenetic relationships, genetic diversity, admixture, and introgression.

According to the web resource TimeTree (http://www.timetree.org, accessed on 15 May 2021) [24] the estimated median time of Caucasian tur and domestic goat divergence is 1.36 million years ago, which is much less than for the majority of other non-model animals. It gives a great opportunity to investigate phylogeny and genetic characteristics of *Capra caucasica*.

In this regard, the aim of our study was to assess the applicability of Illumina Goat SNP50 Bead-Chip, developed for domestic goats, for genetic studies of Caucasian tur (*Capra caucasica*).
