title: Genetic diversity analyses reveal first insights into breed-specific selection signatures within Swiss goat breeds.
abstract: We used genotype data from the caprine 50k Illumina BeadChip for the assessment of genetic diversity within and between 10 local Swiss goat breeds. Three different cluster methods allowed the goat samples to be assigned to the respective breed groups, whilst the samples of Nera Verzasca and Tessin Grey goats could not be differentiated from each other. The results of the different genetic diversity measures show that Appenzell, Toggenburg, Valais and Booted goats should be prioritized in future conservation activities. Furthermore, we examined runs of homozygosity (ROH) and compared genomic inbreeding coefficients based on ROH (FROH) with pedigree-based inbreeding coefficients (FPED). The linear relationship between FROHand FPEDwas confirmed for goats by including samples from the three main breeds (Saanen, Chamois and Toggenburg goats). FROHappears to be a suitable measure for describing levels of inbreeding in goat breeds with missing pedigree information. Finally, we derived selection signatures between the breeds. We report a total of 384 putative selection signals. The 25 most significant windows contained genes known for traits such as: coat color variation (MITF, KIT, ASIP), growth (IGF2, IGF2R, HRAS, FGFR3) and milk composition (PITX2). Several other putative genes involved in the formation of populations, which might have been selected for adaptation to the alpine environment, are highlighted. The results provide a contemporary background for the management of genetic diversity in local Swiss goat breeds.
authors.affiliation: School of Agricultural, Forest and Food Sciences HAFL, Bern University of Applied Sciences, Länggasse 85, 3052, Zollikofen, Switzerland. alexander.burren@bfh.ch.
authors.forename: A
authors.initials: A
authors.lastname: Burren
authors.affiliation: Swiss National Stud Farm, Agroscope Research Station, Les Longs-Prés, 1580, Avenches, Switzerland.
authors.forename: M
authors.initials: M
authors.lastname: Neuditschko
authors.affiliation: School of Agricultural, Forest and Food Sciences HAFL, Bern University of Applied Sciences, Länggasse 85, 3052, Zollikofen, Switzerland.
authors.forename: H
authors.initials: H
authors.lastname: Signer-Hasler
authors.affiliation: School of Agricultural, Forest and Food Sciences HAFL, Bern University of Applied Sciences, Länggasse 85, 3052, Zollikofen, Switzerland.
authors.forename: M
authors.initials: M
authors.lastname: Frischknecht
authors.affiliation: Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109, 3001, Bern, Switzerland.
authors.forename: I
authors.initials: I
authors.lastname: Reber
authors.affiliation: Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109, 3001, Bern, Switzerland.
authors.forename: F
authors.initials: F
authors.lastname: Menzi
authors.affiliation: Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109, 3001, Bern, Switzerland.
authors.forename: C
authors.initials: C
authors.lastname: Drögemüller
authors.affiliation: School of Agricultural, Forest and Food Sciences HAFL, Bern University of Applied Sciences, Länggasse 85, 3052, Zollikofen, Switzerland.
authors.forename: C
authors.initials: C
authors.lastname: Flury
mesh_terms: D000818:Animals; D001947:Breeding; D014644:Genetic Variation; D005828:Genetics, Population; D005838:Genotype; D006041:Goats / Q000235:genetics*; D006720:Homozygote; D007178:Inbreeding; D010375:Pedigree; D012641:Selection, Genetic; D013557:Switzerland
keywords: 
  SNP
  ; inbreeding coefficient; pedigree; runs of homozygosity; selection signals