Data from: Genetic diversity analyses reveal first insights into breed-specific selection signatures within Swiss goat breeds

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 FROH and FPED was confirmed for goats by including
samples from the three main breeds (Saanen, Chamois and Toggenburg goats).
FROH appears 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.