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

Signer-Hasler, Heidi; Burren, Alexander; Ammann, P.; Drögemüller, C.; Flury, Christine (2019). Runs of homozygosity and signatures of selection: a comparison among eight local Swiss sheep breeds Animal Genetics, 50(5), pp. 512-525. Wiley-Blackwell 10.1111/age.12828

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A dataset consisting of 787 animals with high-density SNP chip genotypes (346 774 SNPs) and 939 animals with medium-density SNP chip genotypes (33 828 SNPs) from eight indigenous Swiss sheep breeds was analyzed to characterize population structure, 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 F PED and F ROH was around 0.50 and thereby lower than that found in similar studies in cattle. Mean F ROH 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.

Item Type:

Journal Article (Original Article)


School of Agricultural, Forest and Food Sciences HAFL > Resource-efficient agricultural production systems
School of Agricultural, Forest and Food Sciences HAFL > Agriculture


Signer-Hasler, Heidi0000-0001-5193-5306;
Burren, Alexander0000-0001-9948-7039;
Ammann, P.;
Drögemüller, C. and
Flury, Christine


S Agriculture > S Agriculture (General)
S Agriculture > SF Animal culture








Nadine Werndli

Date Deposited:

24 Sep 2019 11:08

Last Modified:

18 Dec 2020 13:29

Publisher DOI:





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