ISGC SNP Loci for Parentage Assignment

The International Sheep Genomics Consortium (ISGC) has performed technical evaluation of SNP suitable for assignment of parentage in sheep. The consortium recognised the need for a set of technically robust SNP that have high levels of polymorphism across a diverse collection of breeds.

The objectives of the work have been to:

• evaluate SNP using multiple genotyping platform
• identify SNP with high minor allele frequency across many breeds
• ensure all data is made public to encourage use of a common set of technically robust SNP

ISGC Core Panel

The ISGC has proposed a model whereby a ‘core panel’ of 89 SNP could be used by groups interested to deliver SNP based parentage. This set of markers has undergone extensive characterisation. First, SNP were tested using Golden Gate technology across 22 breeds from Africa, Asia and Europe as described by Kijas et al 2009. Subsequently, SNP were tested using the Infinium technology across an expanded set of 70 breeds as described by Kijas et al 2012. Subsets of the SNP have also been evaluated using both Fluidigm and Sequenom as described in presentations to the 2012 Plant and Animal Genome conference as well as the 2012 Internataional Society of Animal Genetics conference. The resulting core panel has been promoted to the ISAG Sheep and Goat Parentage Testing committee for comparison testing from 2012 onwards. A copy of the talk promoting the SNP to ISAG can be downloaded here.

The following files are available for download:

• SNP Identifiers for the Core Panel of 89 Loci
• SNP Identifiers for an expanded set of 383 Loci used in Australian Flocks

The ISGC Parentage SNP Project Acknowledges:

James Kijas, John Henshall and Amy Bell (CSIRO)
John McEwan and Shannon Clarke (AgResearch)
Felice Driver and Terry Longhurst (Meat and Livestock Australia)
Julius van der Werf (Sheep CRC)
Sam Gill (Sheep Genetics)
Jill Maddox (University of Melbourne)
Mike Heaton (USDA)
Our partners in Sequenom, Fluidigm, GeneSeek and Illumina.