Success Rates of Commercial SNP Based Parentage Assignment in Sheep

Abstract

Single nucleotide polymorphism (SNP) based parentage assignment is attractive as SNP are abundant in the sheep genome and amenable to high throughput and therefore lower cost genotyping. To examine the minimum number of SNP required to obtain high accuracy parentage assignment, blood samples were collected from 4 industry flocks and genotyping was undertaken. A maximum likelihood approach was applied to the genotypes to predict sire, dam and progeny within 3 of the sampled flocks, and dams within 1 sampled flock. A SNP based, flock specific methodology utilizing differing numbers and types of SNPs for estimating assignment rates was developed. Rates of assignment ranged from 99.5% to 77.7% across 3 flocks, with 0% incorrect assignments, with the exception of one panel in one flock for sire assignment, where the incorrect assignment rate was 0.1%. Rates of assignment varied from 62.2% to 28.3% with 0% incorrect assignments in the fourth flock, with the exception of one panel for dam assignment where the incorrect assignment rate was 0.1%, but only 60% of dams and 50% of sires within this flock were genotyped. Using 2 out of a potential 6 multiplexed panels of SNP markers gave high rates of correct paternity, but using 3 panels provided higher confidence and is recommended. This maximum likelihood approach using SNPs provides the basis for delivering highly accurate parentage determination for under AUD20, increasing the affordability of this as a powerful tool for industry.