Data from: Runs of homozygosity and signatures of selection: a comparison among eight local Swiss sheep breeds

A dataset consisting of 787 animals with high density SNP chip genotypes
(346,774 SNP) and 939 animals with medium density SNP chip genotypes
(33,828 SNP) from a total of 8 indigenous Swiss sheep breeds was analyzed
to characterize population structures, quantify genomic inbreeding based
on runs of homozygosity and identify selection signatures. In concordance
with the recent known history of these breeds, the highest genetic
diversity was observed in Engadine Red sheep and the lowest in Valais
Blacknose sheep. Correlation between FPED and FROH was around 0.50 and
thereby lower than that found in similar studies in cattle. Mean FROH
estimates from medium density data and HD data were highly correlated
(0.95). Signatures of selection and candidate gene analysis revealed that
the most prominent signatures of selection were found in the proximity of
genes associated with body size (NCAPG, LCORL, LAP3, SPP1, PLAG1, ALOX12,
TP53), litter size (SPP1), milk production (ABCG2, SPP1), coat color (KIT,
ASIP, TBX3) and horn status (RXFP2). For the Valais Blacknose sheep the
private signatures in proximity of genes/QTL influencing body size, coat
color and fatty acid composition were confirmed based on runs of
homozygosity analysis. These private signatures underline the genetic
uniqueness of the Valais Blacknose sheep breed. In conclusion we
identified differences in the genetic make-up of Swiss sheep breeds and we
present relevant candidate genes responsible for breed differentiation in
locally adapted breeds.