Population structure and genetic diversity of 25 Russian sheep breeds based on whole-genome genotyping

Abstract

BackgroundRussia has a diverse variety of native and locally developed sheep breeds with coarse, fine, and semi-fine wool, which inhabit different 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 contributions from foreign breeds in Russian sheep, a set of 58 worldwide breeds from publicly available genotypes was added to our data.ResultsWe 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 effective population sizes estimated from linkage disequilibrium five generations ago ranged from 65 to 543. Multi-dimensional scaling, admixture, and neighbor-net analyses consistently identified a two-step subdivision of the Russian local sheep breeds. A first split clustered the Russian sheep populations according to their wool type (fine wool, semi-fine wool and coarse wool). The Dagestan Mountain and Baikal fine-fleeced breeds differ from the other Merino-derived local breeds. The semi-fine 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).ConclusionsIn 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.Electronic supplementary materialThe online version of this article (10.1186/s12711-018-0399-5) contains supplementary material, which is available to authorized users.

Population Structure and Genetic Diversity of Sheep Breeds in the Kyrgyzstan

“…One of the points of this study was to evaluate the genetic diversity of the popular sheep breeds of the Kyrgyzstan. Our results showed that the level of genetic variability in the Kyrgyz breeds was comparable to that demonstrated in other worldwide populations (Kijas et al, 2012;Beynon et al, 2015;Ciani et al, 2015;Deniskova et al, 2018).…”

“…In general, the studied populations of the Kyrgyz breeds were characterized by high historical effective population sizes (Table 1, Supplementary Figures 1 and 2). Even the smallest values of the effective population sizes estimated for five generations ago for the Kyrgyz coarse wool and Alai breeds, for example, were higher than those reported by Purfield et al (2017) for the Beltex breed (Ne 5 = 115) and by Deniskova et al (2018) for the Kuchugur breed (Ne 5 = 65). Effective population sizes estimated for 50 generations ago for the studied populations were higher (for example, Ne 50 = 467 in the Spanish Churra breed (García-Gámez et al, 2012) or Ne 50 = 2171 in the Russian Karakul breed (Deniskova et al, 2018)) or in agreement with the observations reported by the SheepHapMap project (Kijas et al, 2012).…”

“…Analyzing the combined dataset of the SNP genotypes of the Kyrgyz, Russian, and worldwide breeds, the genetic background present in sheep from Iran (Moghani, Qezel, Afshari) and China (Changthangi, Tibetan) as well as in Indian Deccani was found in the Alai, Gissar, Aykol, and Kyrgyz coarse wool breeds (Figures 5-8). In our previous study, we detected that Russian local coarse wool breeds were characterized by a similar genetic pattern of admixture with the same listed breeds of Asian and Southwestern Asian origin (Deniskova et al, 2018). We assumed that this probably resulted from the nomad expansions (Yunusbayev et al, 2015), Mongol invasions (Zhao et al, 2017) as well as the trade routes defined as the Great Silk Road.…”

“…To infer the genetic relationships of the Kyrgyz sheep breeds and to study their historical admixture patterns in the context of the worldwide gene pool, we combined our data set with SNP genotypes of 61 global sheep populations, including 22 Russian, four Central European, 23 South-West European, three Asian, three Southwest Asian, and one American breeds. The sheep data made available by the International Sheep Genomics Consortium (Kijas et al, 2012) and were obtained from other publicly available sources (Ciani et al, 2015;Deniskova et al, 2018). Description of 61 sheep breeds used in the study is provided in Supplementary Table 1.…”

“…), the vast exchange of domestic animals was inevitable (Boivin, 2017;Taylor et al, 2018). To date, large amounts of SNP genotyping data have been generated from worldwide popular sheep breeds (Kijas et al, 2012;Ciani et al, 2015) and local populations including Welsh (Beynon et al, 2015), Ethiopian (Edea et al, 2017), Chinese (Zhao et al, 2017), and Russian sheep (Deniskova et al, 2018). Analysis of whole genome data on the Kyrgyz sheep breeds including available SNP profiles of the European and Asian sheep populations might be useful to establish probable admixture patterns that resulted from ancient trade interactions.…”