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Parentage identification using SNP genotypes: application to product tracing

W. G. Hill^*, B. A. Salisbury and A. J. Webb^#

^* Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, West Mains Road, Edinburgh, EH9 3JT, UK , Clinical Data Inc., Five Science Park, New Haven, CT 06511, USA ^# Maple Leaf Foods Inc., 30 St. Clair Avenue West, Toronto, Ontario M4V 3A2, Canada

w.g.hill{at}ed.ac.uk

Abstract

Identification of relatives using SNP markers has many possible applications. One is as a route to tracing a food product such as a cut of meat back to its source of origin by identifying the parents of the animal from which the product was derived. We develop methods for using SNP markers with maximum likelihood, allowing for the possibility of genotyping errors that would cause false exclusions by simpler methods. We use expectations of likelihood ratios to consider how gene frequencies in the parental populations, numbers of loci, and error rates affect accuracy. This is further quantified as the ‘risk’, the probability that an incorrect sire is identified from a panel that contains many other putative sires including his relatives, using a breeding structure relevant to pig breeding. This appears to be a straightforward and potentially effective means of product tracing.

Key Words: genetic markers • genotyping errors • parentage identification • pigs • product tracing • SNPs

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