Open Access Open Badges Research article

Development of a genetic tool for product regulation in the diverse British pig breed market

Samantha Wilkinson15, Alan L Archibald1, Chris S Haley12, Hendrik-Jan Megens3, Richard PMA Crooijmans3, Martien AM Groenen3, Pamela Wiener1* and Rob Ogden4*

Author Affiliations

1 The Roslin Institute and (Royal) Dick School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK

2 MRC Human Genetics Unit, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK

3 Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands

4 Wildgenes Laboratory, Royal Zoological Society of Scotland, Edinburgh EH12 6TS, Scotland, UK

5 Scotland's Rural College, The Roslin Institute Building, , Easter Bush, Midlothian, EH25 9RG, UK

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BMC Genomics 2012, 13:580  doi:10.1186/1471-2164-13-580

Published: 15 November 2012



The application of DNA markers for the identification of biological samples from both human and non-human species is widespread and includes use in food authentication. In the food industry the financial incentive to substituting the true name of a food product with a higher value alternative is driving food fraud. This applies to British pork products where products derived from traditional pig breeds are of premium value. The objective of this study was to develop a genetic assay for regulatory authentication of traditional pig breed-labelled products in the porcine food industry in the United Kingdom.


The dataset comprised of a comprehensive coverage of breed types present in Britain: 460 individuals from 7 traditional breeds, 5 commercial purebreds, 1 imported European breed and 1 imported Asian breed were genotyped using the PorcineSNP60 beadchip. Following breed-informative SNP selection, assignment power was calculated for increasing SNP panel size. A 96-plex assay created using the most informative SNPs revealed remarkably high genetic differentiation between the British pig breeds, with an average FST of 0.54 and Bayesian clustering analysis also indicated that they were distinct homogenous populations. The posterior probability of assignment of any individual of a presumed origin actually originating from that breed given an alternative breed origin was > 99.5% in 174 out of 182 contrasts, at a test value of log(LR) > 0. Validation of the 96-plex assay using independent test samples of known origin was successful; a subsequent survey of market samples revealed a high level of breed label conformity.


The newly created 96-plex assay using selected markers from the PorcineSNP60 beadchip enables powerful assignment of samples to traditional breed origin and can effectively identify mislabelling, providing a highly effective tool for DNA analysis in food forensics.