Application of Digital PCR to Perform Species Identification in Food

Introduction: The setting-up of new methods for species identification in food is a very important topic to avoid frauds. In fact, to verify foodstuffs compliance to labels and to discriminate accidental contamination from voluntary addition, it is necessary to quantify ingredients. To date, European legislation does not indicate how to achieve this goal, but several studies are in progress to develop and standardize new quantitative methods.

Purpose:  The aim of this work was to verify the applicability of Digital PCR for species identification in food; in particular, to quantify chicken after artificial contamination in raw meat.

Methods: Digital PCR (Quant Studio 3D^®) was applied to evaluate three topics: 1) Linearity between the spiking percentage of chicken (100% to 0.1%) and related observed genomic copies. 2) Correspondence between different targets (chicken, turkey, beef, pork) and a housekeeping gene (miostatin) to develop a ratio comparable with known target percentage. 3) Repeatability of 1% chicken in different meat categories.

Results: Linearity between target percentage in spiked material and related genomic copies value was verified (R²=0.9996). However, due to DNA extracts moot quantifications, several troubles were observed in attributing the exact copies value to each spiking level. Miostatin was confirmed as the housekeeping gene for chicken, while a discrepancy between target and miostatin copies was observed for the other tested species. Finally, chicken genomic copies in swine and bovine raw meat, were not comparable for each sample.

Significance:  These data suggest that the digital PCR system could be applied in species identification. However, further studies will be necessary to investigate the possibility of different housekeeping genes and to validate repeatability studies in order to verify the extraction efficiency.