ISGC SNP50 HapMap and Sheep Breed Diversity Genotypes

Brief description

The collection contains SNP genotypes from a diverse collection of the world’s sheep breeds. For each breed, a selection of sheep (20 – 100) were genotyped using the ovine SNP50 BeadChip. Following quality filtering, the final dataset contains 49,034 SNP genotyped from 2819 animals. Genotypes are made available in .PED and .MAP format ready for analysis in programs such as PLINK. To assist users with interpretation, a help file is included describing the data format along with additional information.
Lineage: DNA from 2819 animals were assembled to form the ISGC DNA Repository (separate DAP entry). DNA from each animal was genotyped using the ovine SNP50 BeadChip. The BeadChip returns bi-allelic data from 49,034 loci distributed evenly across the sheep genome. Raw genotypes were filtered to remove low quality information, before animals were removed with poor call rate. The genotypes were used by the ISGC to perform analysis of the genetic diversity present within a large collection of the world’s sheep. Analysis was also performed to detect chromosomal regions that have experienced recent positive selection. The results were published in the February 2012 issue of PLoS Biology (Kijas et al., PLoS Biol: e1001258).