A 20-SNP Panel as a Tool for Genetic Authentication and Traceability of Pig Breeds.

Abstract

Simple SummaryGiven the high economic and qualitative values of local-breed meat products, it is not uncommon that substitution or mislabeling (either fraudulent or accidental) occurs at the market level. Therefore, to protect the interests of both producers and consumers, a reliable traceability tool should be developed. Nowadays, traceability usually relies on physical labeling systems (e.g., ear tags, tattoos, or electronic transponders). These systems do not, however, have good performances when dealing with carcasses or processed meat products. Molecular markers (i.e., based on the DNA sequence) can be a solution, since DNA is easily extracted from a wide variety of animal products and parts, and is not degraded during processing, even at the high temperatures involved. The aim of this study was to identify a small number of DNA mutations for breed-traceability purposes, in particular of the Italian Nero Siciliano pig and its derived products. A small panel of 12 DNA mutations was enough to discriminate Nero Siciliano pigs from other pig breeds and from wild boars.Food authentication in local breeds has important implications from both an economic and a qualitative point of view. Meat products from autochthonous breeds are of premium value, but can easily incur fraudulent or accidental substitution or mislabeling. The aim of this study was to identify a small number of SNPs using the Illumina PorcineSNP60 BeadChip for breed traceability, in particular of the Italian Nero Siciliano pig and its derived products. A panel of 12 SNPs was sufficient to discriminate Nero Siciliano pig from cosmopolitan breeds and wild boars. After adding 8 SNPs, the final panel of 20 SNPs allowed us to discriminate all the breeds involved in the study, to correctly assign each individual to its breed, and, moreover, to discriminate Nero Siciliano from first-generation hybrids. Almost all livestock breeds are being genotyped with medium- or high-density SNP panels, providing a large amount of information for many applications. Here, we proposed a method to select a reduced SNP panel to be used for the traceability of pig breeds.