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

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.

Downloads

Title Size Date published
4.0MB 01/09/2014

Contracts

Contract No. Title Start date End date Funding type
B.BSC.0097
Maddox - SNP selection and pre-commercial development of a high accuracy parentage assay for sheep industry use
15/06/2010 30/11/2012
Industry
B.BSC.0113
Genotyping Services Agreement for ovine SNP parentage
01/01/2012 18/04/2012
Industry
B.BSC.0095
CSIRO - SNP selection and pre-commercial development of a high accuracy parentage assay for sheep industry use
15/06/2010 07/06/2012
Industry
B.BSC.0098
Development and evaluation of SNP multiplexes using Platinum IPLEX and MassArray technology for pre-commercial use in the determination of ovine parentage.
21/06/2010 29/11/2011
Industry
B.BSC.0101
CMA: Purchase of SNP multiplex reagent pools for ovine parentage assay
25/11/2011 28/02/2012
Industry CMA

This page was last updated on 03/08/2018

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