ISGC SNP50 HapMap and Sheep Breed Diversity Genotypes
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 r... moreeady 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. less
Evolutionary Biology not elsewhere classified, Genomics
06 Jul 2009
06 Jan 2010
Sheep, breeds, DNA, SNP
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).
The collection was generated under the auspices of the International Sheep Genomics Consortium (ISGC) in a project coordinated by CSIRO. DNA samples were made available by ISGC participants for the benefit of the sheep research community. SNP genotyping was performed by Illumina as part of the development of the ovine SNP50 BeadChip. Quality filtering was performed by James Kijas at CSIRO. Analysis of the dataset was performed by a collection of scientists within the ISGC, and published in the February 2012 issue of PLoS Biology (Kijas et al., PLoS Biol: e1001258).
CSIRO Data Licence
CSIRO (Australia), Illumina (United States)
Kijas, James (2013): ISGC SNP50 HapMap and Sheep Breed Diversity Genotypes. v1. CSIRO. Data Collection.
All Rights Reserved (including copyright) CSIRO Australia 2013.
The metadata and files are available to the public.
CLSD 1206.1 NextGenBreedOpt C2012/5905
The project collected SNP genotypes from a diverse collection of teh world's sheep breeds, before performing analysis to reveal high levels of historic mixture and strong recent selection.