Genetic Diversity and Selection Signatures in Ten Swiss Goat Breeds

Aggregating genotype data from the caprine 50k Illumina BeadChip for 10 local Swiss goat breeds. It was used to analyze genetic diversity, runs of homozygosity (ROH), and identify 384 putative selection signatures. The study was conducted by Alexander Burren and published in 2020.

Use Cases

• Compare genomic inbreeding coefficients (FROH) with pedigree-based inbreeding coefficients (FPED) across breeds like Saanen, Chamois, and Toggenburg.
• Identify genes associated with coat color variation (e.g., MITF, KIT, ASIP) from the 25 most significant selection signal windows.
• Analyze runs of homozygosity (ROH) patterns to assess genetic diversity within breeds such as Appenzell, Toggenburg, Valais, and Booted goats.
• Examine selection signatures for genes related to growth (e.g., IGF2, IGF2R) and milk composition (PITX2) between the 10 Swiss goat breeds.

Strengths

• Data is derived from the standardized caprine 50k Illumina BeadChip genotyping platform.
• Analysis includes 10 distinct local Swiss goat breeds, providing a comparative framework.
• The study reports 384 putative selection signals, offering specific genetic targets for investigation.

Limitations

• The specific sample size (number of individual goats genotyped) is not provided in the input.
• The dataset focuses exclusively on Swiss goat breeds, limiting generalizability to other populations.
• The raw genotype data files, column structure, and exact data format are unknown from the input.

Provenance

Source

Dryad digital repository.

Collection Method

Genotype data gathered using the caprine 50k Illumina BeadChip.

Freshness

Data was last updated in June 2020.

Geography

Switzerland.