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Population structure of five native sheep breeds of Sweden estimated with high density SNP genotypes

Citation

Rochus, Christina Marie; Jonas, Elisabeth; Johansson, Anna M. (2020), Population structure of five native sheep breeds of Sweden estimated with high density SNP genotypes, Dryad, Dataset, https://doi.org/10.5061/dryad.34tmpg4gj

Abstract

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 project and 600 K SNP genotypes from a dataset of French sheep. Results arranged breeds into five groups: south-west Asia, south-west Europe, central Europe, north Europe and north European short-tailed sheep. Within this last group, Norwegian and Icelandic breeds, Finn and Romanov sheep, Scottish breeds, and Gute and Gotland sheep were more closely related while the remaining Swedish breeds and Ouessant sheep were distinct from all breeds and had longer branches in the population tree.

Conclusions

We showed population structure of five Swedish breeds and their structure within European and southwestern Asian breeds. Swedish breeds are unique, distinct breeds that have been subjected to drift but group with other north European short-tailed sheep.

Methods

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 [1819]. All of the 93 sheep, and a total of 502,144 SNPs passed quality control and filtering steps."

Funding

Erik Philip-Sörensen foundation

Swedish board of Agriculture

European Commission and the Swedish University of Agricultural Sciences, within the framework of the Erasmus-Mundus joint doctorate “European Graduate School in Animal Breeding and Genetics”

Sveriges Lantbruksuniversitet

Erik Philip-Sörensen foundation

Swedish board of Agriculture