Genetic Control of Conventional Labeling through the Bovine Meat Production Chain by Single Nucleotide Polymorphisms Using Real-Time PCR

Abstract

Since January 2002, the European Union has adopted precise guidelines aimed at protecting the safety of meat and controlling the production chain. To this purpose, the conventional traceability of livestock and meat represents the main tool, but verification of traceability requires genetic support. At present, single nucleotide polymorphisms (SNPs) represent the most innovative molecular markers in genotyping studies. The aim of this study was to verify correct labeling in a bovine meat production chain by a real-time PCR protocol based on SNP analysis. Reference hair samples from 5,000 animals were randomly collected from 22 farms. Twelve hundred meat samples were collected at different steps of the bovine meat production chain. In particular, 1,000 meat samples were collected at the slaughterhouse and 200 samples from the same animals directly at the butcher's shop. The protocol was optimized and validated by testing a set of 16 SNP markers on 95 DNA samples from bovine sires of different breeds. Thereafter, the genotyping of 2,200 samples was conducted with a set of 12 selected SNPs to verify traceability of the meat production chain at three different stages: farm, slaughterhouse, and butcher's shop. Irregularities in conventional traceability were evidenced directly in 1.87% of the samples at the slaughterhouse. This percentage increased to 3.25% when sampling was conducted at the butcher's shop. This study demonstrates that despite the precautions adopted over the meat production chain, some critical points still exist that cause the loss of a correct association between registration numbers and samples.

Tracing Cattle Breeds with Principal Components Analysis Ancestry Informative SNPs

“…Early studies of cattle genomic diversity mainly focused on the analysis of sparse data from microsatellite markers [6], [7], [8], [2], [9], [10], [11]. More recently, studies that evaluated bovine population structure have used Single Nucleotide Polymorphisms (SNPs) [12], [13], [14], [15]; however they focused on a small number of markers. The advent of modern high-throughput technologies is starting to produce genomewide data for thousands of markers across the bovine genome [16], [17], [18], [19], [20].…”

Compilation of a panel of informative single nucleotide polymorphisms for bovine identification in the Northern Irish cattle population

“…A recent study used DNA traceability to indicate that 2% of randomly selected samples from labelled carcases at the abattoir did not match the profiles of the animals they were purported to come from. This increased to 3% when sampling was conducted at the point of sale [12]. …”

Development and validation of a SNPs panel used for beef traceability throughout the food chain

“…In this sense, traceability is essential to avoid fraud. But in some occasions, conventional tracing techniques are susceptible to error through the loss of correspondence between a registration number and the related animal (Aung & Chang, 2014;Capoferri et al, 2006). It is therefore necessary to develop new methods of traceability that are not susceptible to any type of manipulation.…”

“…In a recent article, Zhao et al (2019) developed a PCR-capillary electrophoresis method based on the analysis of 12 SNPs for genetic traceability in China large-size beef company and distinguish individuals with a matching probability of 1.70 × 10 -5 . Similarly, Capoferri et al (2006) developed a method for genetic control of conventional beef labeling based in the analysis of 12 selected SNPs by real-time PCR. In this study, the probability that two random individuals presented the same genotype was 7.67 10 -5 .…”