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

Abstract

Background: Russia 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.

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 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).

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.

Fig. 1

Map of sampling locations for this study. Both maps illustrate the geographical points where the samples of the 25 Russian sheep breeds were collected for this study. The coarse wool breeds are in blue; the semi-fine and fine wool breeds are in red and green colors, respectively. The numbers for the breeds are as follows: 1. Andean Black, 2. Buubei, 3. Edilbai, 4. Kalmyk, 5. Karakul, 6. Karachaev, 7. Kuchugur, 8. Lezgin, 9. Romanov, 10. Tushin, 11. Tuva, 12. Altai Mountain, 13. Kuibyshev, 14. North-Caucasian, 15. Russian Longhaired, 16. Tsigai, 17. Baikal fine-fleeced, 18. Dagestan Mountain, 19. Groznensk, 20. Kulundin, 21. Manych Merino, 22. Salsk, 23. Soviet Merino, 24. Stavropol, 25. Volgograd. For a description of the sheep breeds (see Additional file 1: Table S1, Additional file 2: Table S2)

Fig. 2

Multi-dimensional scaling (MDS) analysis of the Russian sheep breeds. The analysis was performed for the first two components (C1 and C2) (a) and for the first and third components (C1 and C3) (b). The coarse wool breeds are indicated in blue; the semi-fine and fine wool breeds are in red and green colors, respectively. For a description of the sheep breeds (see Additional file 1: Table S1, Additional file 2: Table S2)

Fig. 3

Cluster structure of the 25 Russian sheep breeds revealed by admixture analysis. For a description of the sheep breeds (see Additional file 1: Table S1, Additional file 2: Table S2)

Fig. 4

Neighbor-net graph of 25 Russian sheep breeds based on pairwise Fst values. The branches corresponding to the Russian coarse wool, semi-fine and fine wool breeds are indicated in blue, red and green, respectively. For a description of the sheep breeds (see Additional file 1: Table S1, Additional file 2: Table S2)

Fig. 5

Historical effective population size (Ne) based on LD estimates. Ne values for 50–1000 generations ago are shown for the fine wool (a, d), semi-fine wool (b, e) and coarse wool (c, f) sheep breeds. For a description of the sheep breeds (see Additional file 1: Table S1, Additional file 2: Table S2)

Fig. 6

Neighbor-net graph of Russian and worldwide sheep breeds based on pairwise Fst values. The branches corresponding to the Russian coarse wool, semi-fine and fine wool breeds are indicated in blue, red and green, respectively. The colors of the branches of the worldwide breeds correspond to their ancestral geographic origin and are identical to the colors in Table S3 (see Additional file 3: Table S3): green for the British Isles, black for Northern Europe, pale pink for Central Europe, cyan for Southwestern Europe, orange for Asia, yellow for Southwestern Asia, purple for Africa and gray for the Americas. For a description of the sheep breeds (see Additional file 1: Table S1, Additional file 2: Table S2)

Fig. 7

Bar plot showing the extent of admixture of the Russian sheep breeds from worldwide breeds. Breed codes are indicated at the bottom of the bar plots. The breeds are grouped according to their ancestral geographic origin (Russia, the British Isles, Northern Europe, Central Europe, Southwestern Europe, Asia, Southwestern Asia, Africa and the Americas) and arranged in the order indicated in Table S2 (see Additional file 2: Table S2). For a description of the Russian sheep breeds (see Additional file 1: Table S1, Additional file 2: Table S2) and of the worldwide sheep breeds, (see Additional file 2: Table S2)