**1. Introduction**

The introduction of high throughput arrays for single nucleotide polymorphisms genotyping has led to the development of new bioinformatic approaches, which allow evaluation of genetic diversity more fully and address demographic history of the mammalian species. For example, estimation of genomic inbreeding and the analysis of patterns of distribution of runs of homozygosity regions in the genome are gaining popularity among the geneticists and are used in addition to classical methods to assess genetic processes in the populations.

Runs of homozygosity are contiguous stretches of homozygous loci that inbred offspring inherit from both parents originated from a common ancestor [1,2]. The number and length of ROH reflect individual demographic history and evaluate the homozygosity burden [3,4]. The length of ROH indicates whether inbreeding was recent or ancient in a population [1,2].

Nonetheless, livestock breeding practices often use selection schemes involving inbreeding as a tool to stabilize useful traits in farm animals. Thus, to trace the inbreeding events, the genome scanning for ROH segments was performed in various livestock species including cattle [5] (for example, Angus, Charolais, Hereford, Holstein, Simmental [6],

**Citation:** Deniskova, T.; Dotsev, A.; Selionova, M.; Brem, G.; Zinovieva, N. Biodiversity of Russian Local Sheep Breeds Based on Pattern of Runs of Homozygosity. *Diversity* **2021**, *13*, 360. https://doi.org/10.3390/d13080360

Academic Editor: Michael Wink

Received: 18 July 2021 Accepted: 3 August 2021 Published: 4 August 2021

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Russian Kholmogory and Yaroslavl breeds [7]) and small ruminant species (for example, German White-headed Mutton sheep [8] and African native goats [9]).

The patterns of ROH distribution were analyzed in local and commercial sheep breeds which were selected for various purposes, inhabit different environments, and are kept under diverse production systems. Al-Mamun et al. [10] performed a search for ROH segments in Australian populations of Border Leicester, Merino, Poll Dorset, and their crosses and found that Border Leicester sheep were characterized by a higher genome coverage by ROH. In addition, analysis of ROH distribution was used to elucidate the demographic history of the six commercial meat breeds including Belclare, Beltex, Charollais, Suffolk, Texel, and Vendeen [11]. Based on estimation of the genomic inbreeding coefficient based on ROH (FROH), He et al. [12] suggested that Chinese Merino had the lowest levels of inbreeding.

However, more precise attention was paid to estimation of genomic inbreeding based on ROH in populations of local sheep. Such populations often lack reliable pedigree information, and according to Purfield et al. [11], ROH might be recommended as a predictor of the pedigree inbreeding coefficient (correlation 0.62). Mastrangelo et al. [13] investigated the occurrence of ROH in 21 Italian sheep breeds using medium-density SNP genotypes and found that Barbaresca, Leccese and Valle del Belice breeds have been affected by recent inbreeding events. Signer-Hasler et al. [14] found a high correlation (0.95) between genomic inbreeding coefficients based on ROH (FROH) estimates from mediumdensity data and HD data in eight local Swiss sheep breeds. Low genomic inbreeding was observed in the Kyrgyz local sheep breeds including Alai, Aykol, Gissar, and Tien-Shan [15]. Abied et al. [16] suggested that some animals have experienced recent inbreeding events in Chinese indigenous sheep breeds. Using Illumina OvineSNP50 BeadChip, Dzomba et al. [17] analyzed ROH distribution in 400 animals from South African sheep populations representing mutton, pelt and mutton and wool dual-purpose breeds, as well as indigenous non-descript breeds and contributed to the better understanding of the genomic landscape of African sheep breeds.

After the severe crisis caused by the USSR collapse, Russian sheep breeding, which has been focused mainly on wool production for several decades, became unprofitable due to weak demand and low prices [18]. Thus, over the eighteen-year period, the share of fine wool sheep breeds decreased by 20.9%, the population number of semi-fine wool breeds reduced by 2.3 times, and the share of coarse wool breeds increased by 5.4 times [19].

Besides an increase in the population number of unproductive sheep may lead to drastic consequences in sheep farming by financial ruining of farmers and smallholders because sale prices for wool and mutton do not cover the costs for keeping sheep [18]. Considering that majority of sheep rearing farms are in the geographical areas of underdeveloped or risky farming [20], the recessions in the regional sheep industry have notable negative consequences for local people. In this regard, along with the economic aspect, sheep farming is of significant social and cultural importance in Russia.

Summarizing, contemporary Russian sheep breeding should be focused on increasing the meat production and using low-cost technologies. The import of commercial meat breeds was not beneficial because the specific harsh feeding and keeping conditions did not allow these sheep to realize full genetic potential. In addition, development of new hybrid breeds was expected to have a positive effect on the sheep rearing industry; however, this prediction did not come true [21].

Sustainable use and management of existing local breeds is a topic priority for the rising national sheep industry. Genetic resources of Russian local sheep include breeds, which were specifically selected for wool and dual-purpose production (wool and meat), and autochthonous breeds, which are adapted to extreme environments and from which all types of sheep products are used by local smallholders [22,23].

However, the levels of genetic diversity of local breeds, including the addressing of inbreeding events, should precede the changes in the selection direction to design scientificbased breeding programs. The evaluation of genetic diversity by calculating heterozygosity

and effective population sizes in the most popular Russian local breeds was not a very informative tool [24].

In this regard, the aim of our present study is to address the distribution of the runs of homozygosity and to estimate genome inbreeding in Russian local sheep breeds based on SNP-genotyping data for better understanding of current levels of genetic diversity in these valuable livestock resources.
