SNP selection and pre-commercial development of a high accuracy parentage assay for sheep industry use

Summary

The ability to correctly assign parentage is important to producers. The advantages of DNA based methods are well known, however industry uptake has been limited due to cost. To reduce cost and increase accuracy, this project sought to develop and evaluate panels of SNP markers.
SNP were selected based on assay quality and allele frequency across breeds. Following three rounds of optimization, six marker panels were developed containing 383 SNP. This included markers for horn - poll, muscularity, pigmentation and a small number of inherited diseases. To determine the minimum number of panels required to obtain high accuracy assignment, blood cards were collected from industry flocks that contain differing levels of genetic relatedness between candidate sires.
Genotyping was performed using SEQUENOM, before a maximum likelihood based approach was developed and applied to examine parentage. Use of two panels (or 127 SNP) gave high rates of correct paternity and may be sufficient for many flocks. Use of three panels (or 191 SNP) provided higher confidence and is the recommendation for initial commercial application. The current reagent cost associated with genotyping 3 panels, using the US based GeneSeek company as a supplier, is approximately $10 per sample, opening the possibility to offer a DNA based parentage product for under $20.