**1. Introduction**

Nomadic cattle husbandry across the vast territory of the south steppe has been undertaken since ancient times. The harsh climate conditions of short dry summers and cold winters have resulted in herders moving across large areas to seek better pastures for livestock [1–4]. During the short period of a plant's vegetation, cattle can restructure their

**Citation:** Abdelmanova, A.S.; Kharzinova, V.R.; Volkova, V.V.; Dotsev, A.V.; Sermyagin, A.A.; Boronetskaya, O.I.; Chinarov, R.Y.; Lutshikhina, E.M.; Sölkner, J.; Brem, G.; et al. Comparative Study of the Genetic Diversity of Local Steppe Cattle Breeds from Russia, Kazakhstan and Kyrgyzstan by Microsatellite Analysis of Museum and Modern Samples. *Diversity* **2021**, *13*, 351. https://doi.org/10.3390/ d13080351

Academic Editor: Michael Wink

Received: 3 July 2021 Accepted: 27 July 2021 Published: 30 July 2021

**Publisher's Note:** MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations.

**Copyright:** © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/).

body and create enough fat reserves to survive the long winters. Historically, poorly fleshed, weak livestock that are unable to find forage under the snow have died during the winter– spring period [5,6]. The similar way of life of nomadic tribes across the different parts of the south steppes over the centuries has resulted in their cattle having similar phenotypic characteristics. These animals are very hardy, of small to medium size, approximately 110–128 cm in stature, and are able to survive under poor forage conditions and be quickly fattened up with improved feeding [7–9]. Initial attempts to survey cattle inhabiting the south steppe of Russia were undertaken in the last decade of 19th century and the first decade of the 20th century, but the reports mainly described the number of cattle owned by different families and their movement routes [10]. Clear data on the exterior and particular properties of cattle of that time are not available. A comprehensive survey of the steppe cattle of Russia and the neighboring republic of former USSR countries was carried out in the first quarter of the 20th century, which resulted in the division of the entire cattle population into two groups (breeds), with a description of their properties, including coat color, exterior characteristics, and productivity [11]. The medium-sized, compact red cattle with a small head, long face, and short horns distributed in the southern regions of the European part of Russia (i.e., the Kalmykia, Rostov, Volgograd, and Astrakhan regions) and East Siberia were known as Kalmyk cattle (Supplementary Materials, Figure S1a). The origin of these cattle, officially recognized as a separate breed in 1934, was traced back to the 16th–17th centuries, when the Oirats tribe migrated from western Mongolia to the lower Volga through the territory of modern Kazakhstan, founding the Kalmyk Khanate [12,13]. At the end of the 18th century, because of disagreements with the government of the Russian Empire, part of the Oirats—now called Kalmyks—moved back to Dzungaria (the modern territories of northwest China) [14,15]. The small-sized cattle of different colors (red, black, brown, gray, white, pied, or tiger) with a relatively large head and well-developed horns that inhabited the territory of Kazakhstan and Kyrgyzstan were recognized as Kazakh or Kyrgyz cattle depending on the region of their distribution (Supplementary Materials, Figure S1b). It is well documented that the Kazakh and Kyrgyz tribes attacked Kalmyk caravans on their way to Dzungaria, capturing cattle as trophies [14,15]. This forms a basis for the suggestion that the ancient Kalmyk cattle have possibly contributed to the development of the gene pool of Kyrgyz (Kazakh) cattle. According to the cattle breeding plan of the USSR (1934), Kalmyk and Kyrgyz (Kazakh) cattle were chosen as the target breeds for further breeding in the steppe regions of the former USSR (Supplementary Materials, Figure S2) [16]. In the 1930–1940s, local steppe cattle were crossed with highproducing transboundary breeds to improve their growth capacity, meat, and carcass traits [17]. Kalmyk cattle were crossed with Brown Swiss and Simmental bulls, but most authors consider that these breeds only represent a small contribution to the development of the modern gene pool of Kalmyk cattle [8,16–19]. In Kyrgyzstan, major part of the local cattle population was crossed with Brown Swiss and Holland breeds that resulted in developing during the Soviet time several novel synthetic breeds [8,9]. The small remaining part of native Kyrgyz cattle was further developed without contribution of other breeds. The populations inhabiting the northern and western territories of Kazakhstan were crossed with Herefords followed by backcrossing of hybrid Kazakh-Hereford females with Hereford bulls over a number of generations, which resulted in the development of the Kazakh white-headed breed [17]. Additional crossing of Kazakh white-headed cows with Hereford bulls was regularly carried out during subsequent periods of breed development. Currently, the Kalmyk and Kazakh white-headed breeds are the main breeds used for meat production in the south steppe regions of Russia, Kazakhstan, and Kyrgyzstan. In Russia, the ratio of these breeds to the total number of beef cattle (2020) account for 36.6% and 11.7%, respectively [20]. Only a small number of purebred native Kyrgyz cattle are still kept by private owners in Kyrgyzstan. Because the pedigree records of modern Kyrgyz cattle are lacking, the decision on the assignment of an animal as native Kyrgyz cattle is made in most cases based on exterior characteristics and verbal information got from the

owners. The origin of modern Kyrgyz cattle and its relationship with ancestral Kyrgyz cattle should be elucidated.

Native cattle breeds are an invaluable source of genetic diversity, which is necessary to ensure the sustainability of animal production systems in local geoclimatic conditions [18,21–23]. However, a drastic decline in the population size of most of the native breeds, as well as the active use of crossbreeding with high-producing commercial breeds, can lead to the irreversible loss of genetic diversity [24]. Conservation of genetic diversity is an important task in order to ensure the sustainability of the animal production system [25]. Successful conservation of local populations and breeds requires the selection of animals that are carriers of breed-specific genetic components, mostly reflecting the breeds' origin and trajectories of development and artificial selection.

A method with great potential for reconstructing breeds' origins and maintaining the ancestral genetic components in the modern populations of animal breeds is the analysis of specimens stored in museum collections [26–29]. Over the last decades, the field of ancient DNA (aDNA) heavily relied on mitochondrial DNA (mtDNA) markers. This is due to the low copy number and general difficulties associated with the recovery of nuclear DNA from archaeozoological materials [30]. However, the maternal inheritance characteristic of mtDNA has limited the ability to trace the history of cattle breeds with complex genetic background or breeds that were developed by crossing with bulls of other genetic origins. One of the most powerful tools for inferring genetic patterns of populations is microsatellite analysis [31–33]. During application of microsatellites for molecular genetic studies of farm animals over long time scales, reliable methods for analysis of these types of DNA markers have been developed [34]. Moreover, the data derived from different laboratories or different experiments can be standardized according to the Guidelines of the International Society of Animal Genetics (ISAG) [35].

The aim of our work was to compare the genetic diversity of Kalmyk, Kyrgyz, and Kazakh cattle inhabiting the steppe region of southern Russia and the neighboring republics of the former USSR in the first quarter of the 20th century with the current gene pool of the above breeds based on the analysis of microsatellite genotypes of museum and modern samples.
