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Population Structure and Genetic Diversity of 25 Russian Sheep Breeds Based on Whole-Genome Genotyping Tatiana E

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Population Structure and Genetic Diversity of 25 Russian Sheep Breeds Based on Whole-Genome Genotyping Tatiana E Population structure and genetic diversity of 25 Russian sheep breeds based on whole-genome genotyping Tatiana E. Deniskova, Arsen V. Dotsev, Marina I. Selionova, Elisabeth Kunz, Ivica Medugorac, Henry Reyer, Klaus Wimmers, Mario Barbato, Alexei A. Traspov, Gottfried Brem, et al. To cite this version: Tatiana E. Deniskova, Arsen V. Dotsev, Marina I. Selionova, Elisabeth Kunz, Ivica Medugorac, et al.. Population structure and genetic diversity of 25 Russian sheep breeds based on whole-genome genotyping. Genetics Selection Evolution, BioMed Central, 2018, 50 (1), pp.29. 10.1186/s12711-018- 0399-5. hal-02405241 HAL Id: hal-02405241 https://hal.archives-ouvertes.fr/hal-02405241 Submitted on 11 Dec 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License Deniskova et al. Genet Sel Evol (2018) 50:29 https://doi.org/10.1186/s12711-018-0399-5 Genetics Selection Evolution RESEARCH ARTICLE Open Access Population structure and genetic diversity of 25 Russian sheep breeds based on whole‑genome genotyping Tatiana E. Deniskova1*†, Arsen V. Dotsev1†, Marina I. Selionova2, Elisabeth Kunz3, Ivica Medugorac3, Henry Reyer4, Klaus Wimmers4, Mario Barbato5, Alexei A. Traspov1, Gottfried Brem1,6 and Natalia A. Zinovieva1* Abstract Background: Russia has a diverse variety of native and locally developed sheep breeds with coarse, fne, and semi-fne wool, which inhabit diferent climate zones and landscapes that range from hot deserts to harsh northern areas. To date, no genome-wide information has been used to investigate the history and genetic characteristics of the extant local Russian sheep populations. To infer the population structure and genome-wide diversity of Russian sheep, 25 local breeds were genotyped with the OvineSNP50 BeadChip. Furthermore, to evaluate admixture contri- butions from foreign breeds in Russian sheep, a set of 58 worldwide breeds from publicly available genotypes was added to our data. Results: We recorded similar observed heterozygosity (0.354–0.395) and allelic richness (1.890–1.955) levels across the analyzed breeds and they are comparable with those observed in the worldwide breeds. Recent efective popula- tion sizes estimated from linkage disequilibrium fve generations ago ranged from 65 to 543. Multi-dimensional scal- ing, admixture, and neighbor-net analyses consistently identifed a two-step subdivision of the Russian local sheep breeds. A frst split clustered the Russian sheep populations according to their wool type (fne wool, semi-fne wool and coarse wool). The Dagestan Mountain and Baikal fne-feeced breeds difer from the other Merino-derived local breeds. The semi-fne wool cluster combined a breed of Romanian origin, Tsigai, with its derivative Altai Mountain, the two Romney-introgressed breeds Kuibyshev and North Caucasian, and the Lincoln-introgressed Russian longhaired breed. The coarse-wool group comprised the Nordic short-tailed Romanov, the long-fat-tailed outlier Kuchugur and two clusters of fat-tailed sheep: the Caucasian Mountain breeds and the Buubei, Karakul, Edilbai, Kalmyk and Tuva breeds. The Russian fat-tailed breeds shared co-ancestry with sheep from China and Southwestern Asia (Iran). Conclusions: In this study, we derived the genetic characteristics of the major Russian local sheep breeds, which are moderately diverse and have a strong population structure. Pooling our data with a worldwide genotyping set gave deeper insight into the history and origin of the Russian sheep populations. *Correspondence: [email protected]; [email protected] †Tatiana E. Deniskova and Arsen V. Dotsev contributed equally to this work 1 L.K. Ernst Federal Science Center for Animal Husbandry, Dubrovitzy Estate 60, Podolia, Russia 142132 Full list of author information is available at the end of the article © The Author(s) 2018. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creat​iveco​mmons​.org/licen​ses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creat​iveco​mmons​.org/ publi​cdoma​in/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Deniskova et al. Genet Sel Evol (2018) 50:29 Page 2 of 16 Background Romney and Lincoln breeds [10, 11]. Most of the Russian Te sheep (Ovis aries) is one of the economically most fne wool breeds were developed during the Soviet period important agricultural species and produces a wide range by improving local breeds with low productivity, mainly of valuable products including food (meat, milk) and raw through crossbreeding with Merino-derived breeds such materials (wool, sheepskin) [1]. Since their domestication as Rambouillet and Australian Merino sheep. approximately 11,000 years ago (YA) [2, 3], sheep have Te development of high-throughput arrays for geno- spread to all continents where they were reared under typing of multiple single nucleotide polymorphisms diferent environmental, management, and selection con- (SNPs) has revolutionized modern genetic studies [12, ditions. Consequently, diverse local breeds with a unique 13]. Tis technology allows unambiguous scoring and the composition of various traits were developed. combination of standardized data from diferent labora- Sheep breeding has always been an important branch tories [14–16], thus providing a powerful tool to address of animal husbandry in Russia. Te harsh climate condi- a number of genetic issues [17, 18] including the suc- tions, which are characterized by low temperatures and cessful application for studies on population structure 120 to 240 windy days per year, dictate a steady pub- in farm animals. During the last decade, detailed studies lic demand for wool, sheepskins and felt products. Fur- of the biodiversity and admixture levels in sheep breeds thermore, Russia ofers more than 75 million hectares from Asia, Africa, America, Europe, Australia and New of natural grasslands and pastures that are suitable for Zealand were performed using SNPs [19–23]. To date, sheep rearing. Until 1990, Russia, along with Australia, only a few Russian sheep breeds have been genotyped China and New Zealand, was one of the world leaders in using the OvineSNP50K BeadChip [24], whereas most of wool sheep production. However, the radical reforma- them have been analyzed using mitochondrial [25] and tion of the economy reduced the number of sheep from microsatellite markers exclusively [26–28]. 58 million in 1990, to 24.7 million in 2014 [4]. Tis trend In this work, we investigated the patterns of whole- was partly associated with a worldwide reduction of the genome diversity and the population structure of 25 local demand of wool. Currently, sheep breeding is recover- Russian sheep breeds using genome-wide genotype data. ing and turning its production to meat instead of wool. Furthermore, we determined the genetic relationship of Tus, the proportion of wool breeds has decreased from the studied breeds with other breeds worldwide to eluci- 90% in 1990 to 56% in 2014, while that of meat types date the origin of the Russian sheep breeds. has increased from 10 to 44% [5]. Tese developments threaten many wool breeds and they have even abol- Methods ished several of them [6]. From the 45 breeds that were Sample collection recorded in 1990, only 28 are still maintained [7]. Wool Tree hundred and ninety-six tissue samples were col- breeds comprise breeds with coarse wool and breeds lected from 25 local Russian sheep breeds. Tese breeds with fne and semi-fne wool. Te Russian coarse wool included nine fne wool breeds (Baikal fne-feeced, Dag- breeds originated from local sheep that were well adapted estan Mountain, Groznensk, Kulundin, Manych Merino, to the local environmental conditions of certain regions, Salsk, Soviet Merino, Stavropol, and Volgograd), fve such as the Edilbai and Kalmyk fat-rumped breeds in the semi-fne wool breeds (Altai Mountain, Kuibyshev, North hot dry steppe regions in the south of Russia, the Tuva Caucasian, Russian Longhaired, and Tsigai), and 11 short-fat-tailed breed in the Trans-Baikal area with a coarse wool breeds. Te latter comprised the short-thin- harsh continental climate, the Andean and Lezgin breeds tailed Romanov, the fat-tailed Andean Black, Buubei, in the mountain areas of the North Caucasus with poor Karakul, Karachaev, Kuchugur, Lezgin, Tushin, Tuva forage resources, and Romanov sheep in the Central Rus- breeds, and the fat-rumped Edilbai and Kalmyk breeds sia with cold winters. Te coarse wool breeds were cre- (Table 1), (Fig. 1) and (see Additional fle 1: Table S1). ated mainly by folk selection practices and were only Tissue samples were collected by trained personnel under slightly improved by crossbreeding with high-producing strict veterinary rules. foreign breeds
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