DNA integrity ‘critical factor’ for approach in origin testing

By Joseph James Whitworth contact

- Last updated on GMT

©iStock/stevanovicigor
©iStock/stevanovicigor

Related tags: Dna

Molecular biology approaches that target DNA are being increasingly used for geographical traceability due to their speed, accuracy and reliability, according to review.

However, DNA integrity is a critical factor in predicting the probability of a successful outcome, which becomes more of an issue when working with highly degraded DNA, such as that isolated from highly processed foods.

The review of DNA-based methodologies to determine geographical point of origin​ was by Timothy Wilkes, Gavin Nixon and Malcolm Burns of LGC.

Although existing paper traceability and tagging systems may help provide consumer confidence in the geographical origin of foods, they have been shown to be subject to fraud, said the authors.

Due to the widespread transportation of food across international borders, numerous opportunities exist for the unscrupulous relabelling of products, they added.

Traceability of the geographical origin for food relies on a variety of chemical and isotopic measurement techniques.

These have included analysis of mineral composition, of elemental isotope ratio’s; nuclear magnetic resonance spectroscopy (NMR); Near and Infrared Spectroscopy (NIR); and analysis of nucleic acid sequence composition.

Wilkes, Nixon and Burns said alternative methodologies will be required to assist authorities with enforcement of labelling requirements and for Government Chemist referee cases.

Pros and cons of DNA based techniques

DNA based approaches for country of origin labelling include Cleaved Amplified Polymorphisms (CAPS), microsatellites, species specific PCR amplification, Single Nucleotide Polymorphisms (SNPs), and DNA sequencing (e.g. targeting the nuclear genome or the metagenome).

CAPS requires prior DNA sequence knowledge of the target species genome and suffers from problems associated with incomplete amplicon restriction which can result in ambiguous fingerprints.

Microsatellite analysis is highly reproducible and informative but throughput can be limiting compared to more modern DNA approaches, it can be technically challenging and needs a number of consumables in the laboratory.

Species specific PCR amplification is rapid, robust and cost effective and can be adapted to provide quantitative estimates of target abundance when using quantitative real-time PCR (qPCR).

However, it is dependent upon the availability of prior accurate DNA sequence information of the species of interest.

Next Generation Sequencing (NGS) technology is currently too expensive and time consuming for use in routine testing of food samples.

However, adoption of sequencing strategies which include analysis at single or multiple loci (DNA Barcoding) or of microbial communities on the surfaces of food samples could prove valuable in determination of a samples geographical point of origin.

DNA Barcoding and metagenomics

DNA Barcoding is rapid and cost effective to implement and has been broadly accepted by the scientific community as being the definitive method for species identification.

However, it requires extensive prior knowledge of the target sequence, and selection of an appropriate target needs to be on a case by case basis.

Surfaces of food and feedstuffs are populated by microorganisms or their fragments. The variety and abundance of these microbes is dependent upon environmental factors (e.g. climate, soil ecology, spoilage, insects, disease etc.), as well as man and animals, and are indicative of a sample’s origin.

Sequencing the entire or specific regions of these microbial genomes (often referred to as metagenomics sequencing) can give an indication of the likely origin.

However, adoption of the technique would require a global microbial distribution database as well as extensive use of NGS technology.

Chemical and isotopic measurement techniques are likely to remain the methods of choice for determining the geographical point of origin of biological and non-biological substances, said the authors.

These are limited by the availability of appropriate databases describing the global distribution of minerals and isotopic elements.

“The major limitation of all of the methods reviewed here, with the exception of microfloral sequencing, is that they infer geographical origin from identifying those individuals, particularly with respect to elite cultivars and breeds, most likely to be genetically suited to exist at a particular geographical location (adapted to local environmental conditions, resistant to disease etc.).

“This does not take into account the practicing of modern day methods where domesticated animals or plants are frequently reared at a considerable geographical distance from their natural point of origin.”

Related topics: Science, Food Safety & Quality

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