SNPs for Parentage Testing and Traceability in Globally Diverse Breeds of Sheep

Authors

Michael P. Heaton, U.S. Meat Animal Research CenterFollow
Kreg A. Leymaster, U.S. Meat Animal Research Center
Theodore S. Kalbfleisch, University of Louisville
James W. Kijas, CSIRO
Shannon M. Clarke, Invermay Agricultural Center
John McEwan, Invermay Agricultural Center
Jillian F. Maddox, Meat and Livestock Australia
Veronica Basnayake, GeneSeek
Dustin T. Petrik, GeneSeek
Barry Simpson, GeneSeek
Timothy P. L. Smith, U.S. Meat Animal Research CenterFollow
Carol G. Chitko-Mckown, U.S. Meat Animal Research CenterFollow
International Sheep Genomics Consortium

Date of this Version

2014

Document Type

Article

Citation

Published in PLoS One (2014) 9(4): e94851. DOI:10.1371/journal.pone.0094851

Abstract

DNA-based parentage determination accelerates genetic improvement in sheep by increasing pedigree accuracy. Single nucleotide polymorphism (SNP) markers can be used for determining parentage and to provide unique molecular identifiers for tracing sheep products to their source. However, the utility of a particular ‘‘parentage SNP’’ varies by breed depending on its minor allele frequency (MAF) and its sequence context. Our aims were to identify parentage SNPs with exceptional qualities for use in globally diverse breeds and to develop a subset for use in North American sheep. Starting with genotypes from 2,915 sheep and 74 breed groups provided by the International Sheep Genomics Consortium (ISGC), we analyzed 47,693 autosomal SNPs by multiple criteria and selected 163 with desirable properties for parentage testing. On average, each of the 163 SNPs was highly informative (MAF≥0.3) in 48±5 breed groups. Nearby polymorphisms that could otherwise confound genetic testing were identified by whole genome and Sanger sequencing of 166 sheep from 54 breed groups. A genetic test with 109 of the 163 parentage SNPs was developed for matrix-assisted laser desorption/ionization– time-of-flight mass spectrometry. The scoring rates and accuracies for these 109 SNPs were greater than 99% in a panel of North American sheep. In a blinded set of 96 families (sire, dam, and non-identical twin lambs), each parent of every lamb was identified without using the other parent’s genotype. In 74 ISGC breed groups, the median estimates for probability of a coincidental match between two animals (P_I), and the fraction of potential adults excluded from parentage (P_E) were 1.1×10(-39) and 0.999987, respectively, for the 109 SNPs combined. The availability of a well-characterized set of 163 parentage SNPs facilitates the development of high-throughput genetic technologies for implementing accurate and economical parentage testing and traceability in many of the world’s sheep breeds.