SNP-based parentage assignment in sheep: Application in Australian Flocks

Abstract

The ability to correctly assign parentage is important to producers. The advantages of DNA based methods are well known, but industry uptake is conditional on cost effectiveness. We sought to develop and evaluate multiplexed SNP sets for their power to deliver parentage. 383 SNP were formatted into 6 multiplexes for Sequenom genotyping. We included SNP from the parentage panel developed by the International Sheep Genomics Consortium and markers for polled / horn. Blood cards were collected from 7 industry flocks (~2000 sheep). All animals were genotyped for each multiplex, before analysis sought to determine the minimum number of SNP sets capable of returning high accuracy assignment. A maximum likelihood based approach was applied and thresholds for assignment were defined using simulation within each flock. Under stringent thresholds (low type 1 error) the percentage of parent – offspring pairs correctly assigned using 3 multiplexes gave a high assignment rate. The results demonstrate that as few as 150 SNP can deliver accurate parentage within Australian flocks. Given the SNP have high minor allele frequency within international breeds, the results are likely to be replicated within other populations. The genomic location and identifier for each SNP is given to promote the uptake of a standardized test and encourage high volume and low unit cost genotyping.