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ISGC SNP50 HapMap and Sheep Breed Diversity Genotypes

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About this Collection

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... more


Evolutionary Biology not elsewhere classified, Genomics


http://doi.org/10.4225/08/51870B1E8EE56


06 Jul 2009


06 Jan 2010


CSIRO Enquiries
CSIROEnquiries@csiro.au
1300 363 400

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. http://doi.org/10.4225/08/51870B1E8EE56


All Rights Reserved (including copyright) CSIRO Australia 2013.


The metadata and files are available to the public.

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About this Project

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.


James Kijas


SNP genotyping


SNP genotyping


Experiment


James Kijas


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