Population structure of five native sheep breeds of Sweden estimated with high density SNP genotypes ...
Background Native Swedish sheep breeds are part of the North European short-tailed sheep group; characterized in part by their genetic uniqueness. Our objective was to study the population structure of native Swedish sheep. Five breeds were genotyped using the 600 K SNP array. Dalapäls and Klövsjö s...
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| Format: | Dataset |
| Language: | English |
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Dryad
2020
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| Online Access: | https://dx.doi.org/10.5061/dryad.34tmpg4gj https://datadryad.org/stash/dataset/doi:10.5061/dryad.34tmpg4gj |
| Summary: | Background Native Swedish sheep breeds are part of the North European short-tailed sheep group; characterized in part by their genetic uniqueness. Our objective was to study the population structure of native Swedish sheep. Five breeds were genotyped using the 600 K SNP array. Dalapäls and Klövsjö sheep are from the middle of Sweden; Gotland and Gute sheep from Gotland, an island in the Baltic Sea; and Fjällnäs sheep from northern Sweden. We studied population structure by: principal component analysis (PCA), cluster-based analysis of admixture, and an estimated population tree. Results The analyses of the five Swedish breeds revealed that these breeds are five distinct breeds, while Gute and Gotland are more closely related to each other as seen in all analyses. All breeds had long branch lengths in the population tree indicating they’ve been subjected to drift. We repeated our analyses using 39 K SNP and including 50 K SNP genotypes from other European and southwestern Asian breeds from the Sheep HapMap ... : From the methods of Rochus et al. 2020 (for full details please see: http://dx.doi.org/10.1186/s12863-020-0827-8): "Blood samples were collected from native Swedish sheep. Ethical permission was obtained prior to the collection of blood samples. Genomic DNA used in this study was extracted from fresh blood samples using a QIAsymphony® DSP DNA extraction robot and DSP DNA Midi Kit (QIAGEN). For this study 21 Dalapäls, 10 Fjällnäs, 19 Gotland, 22 Gute and 21 Klövsjö sheep were genotyped for 653,305 autosomal SNPs (Ovine Infinium® HD SNP BeadChip) at Labogena, INRA, Paris, France. Quality control and filtering of SNPs included removing SNPs with a minor allele frequency of zero, removing SNPs with a missing rate greater than 0.01 and removing sheep with a missing genotype rate greater than 0.15 using PLINK 1.9 [18, 19]. All of the 93 sheep, and a total of 502,144 SNPs passed quality control and filtering steps." ... |
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