Food Control and Legislation Farm to Fork Traceability through DNA Technology

Ronan Loftus, IdentiGEN Ltd, Dublin, Ireland Paul Laronde, Ontario Ministry of Agriculture and Food Ontario, Canada


In the wake of the BSE crisis traceability has become a dominant theme in the meat chain. Its importance is underscored by growing concerns over food safety, biosecurity and the demand for products with specific attributes such as breed, aged or organic. Notwithstanding the lack of consensus as to what traceability actually means in practice, achieving and maintaining effective traceability within a meat production environment can be problematic due to supply chain complexity.

DNA technology has the potential to avoid this complexity by overcoming the need for external batch labelling systems. This is achieved using an animal’s DNA code to identify it and products derived from it, enabling meat to be traced to the individual with 100% precision. Developments in the area of DNA technology, particularly in relation to the cost and throughput of analysis are leading to the uptake of DNA traceability concepts in a number of countries. Aside from its use as a crisis management tool, DNA traceability is also being used as a consumer marketing proposition or a means of authenticating specific product claims.


Recent years have seen a growing demand for greater transparency and integrity within the food chain, largely precipitated by the BSE crisis. Ongoing food scares, biosecurity concerns and consumer desire for products with specific attributes such as organic, GMO free or welfare friendly are also fuelling demand. As a consequence there has been an explosion in the number of traceability systems developed as part of both the private and public sector initiatives. Not surprisingly, as such systems have sought to address different needs, different concepts and technology solutions have evolved.

ISO 8402 defines traceability as ‘…The capacity for establishing a product’s origin, process history, use and provenance by reference to written records…..” yet doesn’t define what parameters are to be measured and how history or origin should be determined. In their report on traceability systems Golan et al1 outline three key parameters, breadth, depth, and precision which can be used to characterise traceability systems. The breadth of a system describes the amount of information it records (e.g. details on an animals veterinary care, feed regime or pedigree). The depth of a system indicates how far back or forward the system tracks (to a grain elevator, farm or field) in many cases, the depth of a system is determined by its breadth or attributes of interest. Precision reflects the degree of assurance with which the tracing system can pinpoint a particular product’s movement and is described with reference to an acceptable error rate or what would happen if we got it wrong. In practice the shape of any particular traceability system represents a dynamic interplay between costs and benefits, which are likely to be determined by the sector and specific supply chain needs – a ‘one size fits all’ system is unlikely to meet the requirements of all stakeholders.


Within the meat industry in particular the need for traceability has been most sharply felt, principally due to BSE and the difficulties encountered in locating infected animals or meat derived from them. As a direct consequence beef traceability has become mandatory in many regions of the world, including the European Union2, Quebec3 and Japan4 with systems under development in other regions such as the United States5 and Australia6. Although the specifications of particular systems vary from region to region, traceability within the beef sector is typically achieved through animal eartags, meat labels and bar-codes, which identify a meat product and enable it to be tracked back to a production batch or group of animals of origin (Figure 1). Similar systems are being developed for the sheep meat sector, whereas within the pork and poultry sectors the group or lot is more commonly defined as the primary unit of identification.

While such systems have led to significant improvements in the ability to track and trace animals they have not been without their problems. A report commissioned following an outbreak of foot & mouth disease in the Irish Republic found that despite having mandated a traceability system for movement between jurisdictions ‘It was recognised that tags were often removed to facilitate free movement (of animals) within the island (between the Republic and Northern Ireland’7.

A summary report on animal identification and beef labelling within the European Union found discrepancies in its implementation and enforcement8. The report found that whilst live animal systems were largely in place and working effectively within member states, serious difficulties arose in maintaining traceability information post-slaughter. These difficulties may be attributed to complexity within the meat processing environment, i.e. large number of meat cuts from an individual animal; segregation of individuals based on quality characteristics; different target markets for specific cuts; and differential processing. Maintaining effective information flow within this environment, particularly in larger processing plants, has been found challenging at best and practically impossible for some of the more complex supply chains.


Unlike the non-biometric identification systems described above, DNA based traceability uses an animal’s DNA code to identify it and products derived from it the product acts as its own label. This code is permanent, unique to the individual (except identical twins) and remains intact throughout the animals/products life history. As a consequence DNA taken from any point along the agri-food continuum can be matched with the original animal’s record.

In practice implementation of DNA based traceability requires the collection of DNA samples (reference samples) from animals/carcasses. Samples can either be archived for subsequent analysis, or analysed, and their resultant DNA profiles stored in a database, along with information on animal origins. Storing samples or their associated DNA profiles does not in itself constitute a traceability system, rather it provides traceback capability, which could potentially be used to locate the source of a product should a particular food crisis arise – this model has become popular in Australia9. DNA Traceability is effected through combining reference sampling with DNA sampling at a further point in the supply chain (verification sampling). Both reference and verification samples are DNA profiled and compared to determine the source of a particular cut of meat (Figure 2). Through the development of a routine programme of verification sampling and DNA analysis/matching the ability of a supply chain to provide traceable products can be monitored. This approach has been used in Ireland and the UK since the late nineties where it is marketed to consumers and has led to significant increases in beef sales10.

The ability of DNA based systems to span the full supply chain, their lack of associated capital infrastructure and capacity to deliver traceable product is leading to the broader uptake of DNA traceability concepts. Maple Leaf Foods in Canada recently announced its intention to implement a DNA traceability system for its fresh pork11. The Japanese government have also indicated that they are going to use DNA technology as a means of monitoring the efficacy of beef Food Control and Legislation labelling12. The Japanese industry suffered a serious crisis of confidence following revelations of wide-scale meat mis-labelling13.


Underpinning DNA based traceability concepts are a number of key technologies, namely DNA sampling and DNA analysis. These are integrated through information technology (IT) infrastructure which can also store product related information (e.g. feeding regime, welfare, breed, process history) and incorporate data algorithms to enable the matching of meat cuts with source animals/carcasses.

DNA samples can in theory be collected from any biological tissue. In practice the DNA sampling function must be low-cost, relatively easy to perform and produce samples in a format suitable for laboratory analysis. There have been a number of innovations in the area of DNA sampling, most notably the integration of live animal identification with DNA sampling through DNA sampling eartags. Additionally systems are being developed which enable the integration of low-cost DNA sampling with conventional abattoir infrastructure to facilitate sample collection in high line speeds encountered in larger slaughter plants.

Probably the most critical technology impacting on the broader uptake of DNA traceability concepts is DNA analysis. Radical improvements are being realised through research conducted in the human healthcare and pharmaceutical industries. These improvements are focusing on a type of DNA marker called Single Nucleotide Polymorphism or SNP. SNPs are more amenable to automation and high throughput screening than traditional DNA identification technologies, which are based on DNA markers called simple tandem repeats (STRs) or microsatellites.

Each of the principal livestock species has literally hundreds of thousands of SNPs, although in practice relatively few are required for identity purposes. Key innovations in terms of how SNPs are detected (assay chemistries) and the platforms on which they are detected are leading to significant cost reductions and capacity increases – for a more detailed review of developments here see Jenkins & Gibson14. A critical feature of the DNA traceability application is the ability to screen large numbers of individuals with a relatively small number of SNP markers – typically 30-50. Consequently platforms which integrate multiple high-throughput approaches for sample handling, DNA preparation and DNA analysis are more suitable for this application than ones with large parallel processing power, where the focus is on detecting large numbers of SNP markers from fewer individuals.

Within the information technology sector Moore’s law predicts a doubling of micro-processing power every 2 years. Similar rates of improvement are being seen in relation to SNP genotyping, ultimately reducing the costs of DNA traceability – current platforms are capable of conducting 500,000 analyses per day at approximately 7-10c for DNA traceability applications. In reviewing the technology it is also important to note that like any technology DNA has its limitations. Principal amongst these are the inability to read the DNA code in real time which makes trace forward applications, or the monitoring of product movements more difficult. As a consequence it is likely that the integration of DNA with other identification technologies such as RFID is likely to lead to the most effective traceability solutions in the longer term – one such example of technology integration was recently completed in Ontario and is described in the next section.


As part of its ongoing work on traceability and animal identification, the Ontario Ministry of Agriculture and Food (OMAF) in conjunction with Beef Improvement Ontario (BIO) and the Canadian Food Inspection Agency, have recently completed pilot trial work that integrated RFID with DNA technology.

The trial included approximately 125 bovine and 350 ovine weanlings. The animals were tagged with an RFID tag and a DNA tissue collection tag. Ownership information and date of birth were reported to a central database collated to the tag number. As animals moved off the farm and through the marketing system, pre-installed RFID readers at abattoirs and auction barns read the RFID tags. All movement information was recorded via a network connection to the central database, indicating the value of RFID tags at collecting movement data up to the point of slaughter. As demonstrated in Figure 1, post slaughter individual ID is lost to a batch number. As product is disseminated to retail, the batch number becomes further diluted and consequently the information in the central database, including date of birth and movement information, is lost.

As described earlier the labelling systems used to connect retail sample to the original animal can contain errors due to quantity of meat cuts and complexity of processing and retail operations. Through DNA sampling and analysis we have been able to provide a link back to the RFID tag. By making this connection, all of the recorded data can be linked to a retail sample and, more generally any cut of meat, at any point in the chain linked contiguously, farm to fork (Figure 2).

As part of the pilot study DNA technology was also used to provide some value added components to the ID process. Genetic markers that detect Scrapie resistance were screened as part of the same process as screening for animal ID, providing information on the Scrapie status of individual animals. Such marker tests can prove very valuable for producers and breeders in providing decision making tools with the potential to impact production. The cost of running these types of tests in isolation can be prohibitive and time consuming. Traditionally, blood samples are required adding to overall cost. Integrating this function with animal ID through biotagging greatly reduces such costs. Large scale ID projects utilising DNA identification can be enhanced by adding selected marker tests which can be run simultaneously at a lower cost.


  1. Golan E., Krissoff B., Kuchler F., Nelson K. and Price G. (2004) Traceability in the U.S. Food Supply: Economic Theory and Industry Studies. Agricultural Economic Report No. (AER830) March
  2. European Parliament and Council Regulation (EC) No.1760/2000 establishing a system for the identification and registration of bovine animals and regarding the labelling of beef and beef products and repealing Council Regulation (EC) No 820/97. REGULATION 1760/2000 OF THE EUROPEAN PARLIAMENT AND OF THE COUNCIL of 17 July 2000. (OJ L 204, 11.8.2000, p.11) Article 4 and 7.
  3. Quebec (2002) Regulation respecting the identification and traceability of certain animals Animal Health Protection Act P-42, r.1.1
  4. Gain Report JA3040 (2003) Japan Mandates Traceability for Beef. USDA Foreign Agricultural Service Gain Report
  5. United States National Animal Identification Plan (USAIP) (
  6. National Livestock Identification System (NLIS) (
  7. Clarke P. (2002) The Foot & Mouth Disease Crisis and the Irish Border. Report commissioned by the Centre for Cross-Border Studies
  8. Federal Veterinary Office (FVO) Report (2003) Overview report of a series of missions carried out in all member states during 2002 in order to evaluate the operation of controls over the traceability and labelling of beef and minced beef FVO EU. Federal Veterinary Office Report 9505/2003
  9. Lawrence J.D. (2002) Quality Assurance “Down Under”: Market Access and Product Differentiation briefing paper of the Midwest Agribusiness Trade Research and Information Centre (MATRIC)
  10. Ó hAnluain D. (2001) Moo Tech Fingerprints Mad Cows Wired News; Nov. 06, 2001 (,1286,48005,00.html)
  11. McCain M. (2004) Food Safety: Our Maple Leaf Perspective World Meat Congress Winnipeg, Manitoba June 16, 2004
  12. Asahi Shimbun (2004) DNA list to verify beef label The Asahi Shimbun August 30th 2004
  13. Asahi Shimbun (2002) Shops filled with fake meat labels The Asahi Shimbun February 19th 2002
  14. Jenkins S. and Gibson N. (2002) High-throughput SNP genotyping. Comparative & Functional Genomics 3: 57-66

Ronan Loftus graduated from Trinity College Dublin in 1992 with a PhD in molecular genetics. Following three years as officer responsible for the characterisation of global animal genetic resources with the Food and Agriculture Organisation (UN), Ronan returned to Trinity College as a Research Fellow. In 1997 he became a Co-founder and Director of IdentiGEN, a biotechnology company focused on the development of DNA based technologies for the agri-food industry. His responsibilities with IdentiGEN include commercial and strategic development in addition to building the company’s traceability and food diagnostics offerings.

Paul Laronde is currently employed as the Coordinator for Traceability with the provincial government in Ontario, Canada. The role of the coordinator is to work with both industry and government groups to promote and develop traceability systems for food safety, emergency management and market differentiation. Additionally, the coordinator provides input for policy development, technical support and industry updates in various areas including animal identification. Paul has worked in various capacities in the animal health, veterinary and animal identification sectors over the previous 15 years.


Ronan Loftus
Address: IdentiGEN Ltd, Unit 9,
Trinity Enterprise Centre, Pearse St,
Dublin 02, Ireland.

Paul Laronde
Address: Ontario Ministry of Agricul
ture and Food, 1 Stone Road,
Guelph, Ontario, Canada.