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Verification of Meat from Traditional Cattle and Pig Breeds using SNP DNA Markers - FA0101

The Food Standards Agency originally commissioned the research into the development of meat breed verification methods to authenticate premium beef and pork products. Some UK animal breeds are highly valued for their quality of meat and meat from these breeds can be sold at premium prices in the retail market. This provides an opportunity for fraudulent traders to gain financial advantage by deliberately mislabelling meat as originating from a traditional breed. There is therefore need for a method to authenticate meat being sold as having been derived from a particular breed.

This project aimed to develop a method for the genetic identification of meat labelled as originating from traditional breeds within the UK. Assays were developed for the following target breeds of cattle and pig: Aberdeen Angus, Welsh Black, Red Poll, Hereford (cattle) and Berkshire, Hampshire, Gloucester Old Spot, Welsh and Wild Boar (pig).
Objective No. Objective Description

01 To assemble a complete set of SNP genotype data for cattle and pigs that includes the key target breeds and relevant comparative breeds, with at least 40 representative samples of each. This will involve additional sample collection and genotyping where reference material and data are not already available. The data set will be used as the basis for subsequent bioinformatic analysis.

02 To conduct bioinformatic analysis of the SNP/breed dataset to identify the individual SNP markers that are responsible for breed differentiation. Genotype data will be used to calculate the discriminatory power of individual markers. Markers will be ranked according to their utility for different levels of breed identification. This will allow marker panels to be selected containing the minimum number of SNPs for verifying authenticity of claimed breed, or identification of unknown samples.

03 To transfer the SNP panels onto a suitable genotyping platform. The platform chosen will depend on the number of SNPs required to reliably identify breeds. The aim will be to minimize the number of SNPs and thereby transfer the panel onto the most cost-effective, accurate and widely available platform. Possible systems include the Agilent 2100 BioAnalyser, real-time PCR thermocyclers (e.g. TaqMan), multiplex SNP genotyping genetic analysers (e.g. SNPlex) and SNP-array platforms (e.g. Illumina). This will lead to the production of breed identification assays and related draft Standard Operating Procedures.

04 To establish a suitable analytical method for assigning a test sample genotype to its breed of origin. The method selected will produce a quantitative statistical likelihood that a test sample originates from each of the candidate breeds. This will not only allow the most likely source breed to be identified, but also enable the formulation of a likelihood ratio, required to evaluate the strength of evidence for any subsequent enforcement application.

05 Internal validation. To design and implement a validation protocol for the initial assessment of methods and SOPs. The work will deliver quantitative estimates of assignment accuracy, prior to undertaking further applied validation (Objective #06)

06 External validation. The sample type and DNA extraction technique used will be investigated to assess test stability across a range of varibales, including cooking methods, sample size, sample preparation and sample matrix. A trial of the draft SOP using a series of unknown samples to confirm the utility of the tests for breed identification will be undertaken either by a single project partner or organised as a multi-laboratory ring-trial. The results will be collated into a formal validation report to accompany an updated final version of the Standard Operating Procedures.

Project Documents
• FRP - Final Report : Q01130 Final Project Report-Published version-12mar12   (1671k)
• EXE - Executive Summary : Executive Summary one-page updated 30-06-11   (16k)
Time-Scale and Cost
From: 2008

To: 2011

Cost: £46,500
Contractor / Funded Organisations
Gen-probe Life Sciences Limited
Agro Food Quality              
Food and Drink              
Rare Breeds              
Regional Foods