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 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.