Traceability of four European Protected Geographic Indication (PGI) beef products using Single Nucleotide Polymorphisms (SNP) and Bayesian statistics

Abstract

The use of SNPs in combination with Bayesian statistics for the geographic traceability of cattle was evaluated using a dataset comprising 24 breeds from Italy, France, Spain, Denmark, the Netherlands, Switzerland and UK genotyped with 90 polymorphic markers. The percentage of correct assignment of the individuals to their Country of origin was 90%, with an average assignment probability of 93% and an average specificity of 92%. The higher value was observed for UK breeds (97% of correct assignment) while Swiss animals were the most difficult to allocate (77% of correct assignment). Tracing of Protected Geographic Indication (PGI) products, the approach correctly assigned 100% of Guaranteed Pure Highland Beef; 97% of "Vitellone dell'Appennino Centrale" breeds; 84% of Ternera de Navarra, and 80% of Boeuf de Chalosse. Methods to verify Products of Designated Origin (PDO) and Protected Geographic Indication (PGI) products will help to protect regional foods and promote the economic growth of marginal rural areas by encouraging the production of high quality niche market foods.

On the way to functional agro biodiversity: coat colour gene variability in goats

“…This result can be partially explained by the high degree of genetic originality of this breed, already observed by Ajmone-Marsan et al (2001) and by Pariset et al (2006). In fact, as pointed out by several authors (Negrini et al, 2008 and, the assignment ability of a set of markers is proportional to the genetic differentiation among the individuals/breeds to be allocated.…”

“…Of course, the validity of the methods is confined to the set of reference breed analyses. Unfortunately, the high degree of admixture and the low genetic differentiation between livestock breeds (Luikart et al, 2001;Negrini et al, 2008 and) make the screening process of a universally applicable SNP panel for breed identification a very difficult task. Therefore, to be effective, all DNA-based assignment tests should be customized, identifying the target breeds or products to be authenticated and properly selecting the local or cosmopolite breeds' potential market competitors to use as references.…”

“…Several breed assignment methods have been tested, mainly in cattle and pigs, using the classic multiallelic simple sequence repeat molecular markers or, more recently, small and high SNP panels (Ballester et al, 2007;Negrini et al, 2008 andBovine HapMap Consortium, 2009).…”

Tracing the origin and species identity of Quercus robur and Quercus petraea in Europe: a review

“…Although genetic differentiation within species was not higher than with microsatellites, the move towards the use of SNPs for traceability is underway, as shown by the use of Blanc-Jolivet et. al.·Silvae Genetica (2015) [182][183][184][185][186][187][188][189][190][191][192][193] DOI:10.1515/sg-2015-0017 edited by Thünen Institute of Forest Genetics this marker type in several animal species (BEKKEVOLD et al, 2015;NEGRINI et al, 2008;OGDEN and LINACRE, 2015), and even in human (O'DUSHLAINE et al, 2010). Screening of large amount of loci, followed by selection of loci showing high genetic differentiation and/or outliers (BEKKEVOLD et al, 2015;GLOVER et al, 2010;OGDEN and LINACRE, 2015) might be a good strategy to develop cost-effective marker sets for genetic traceability.…”

“…The second step is to find the most likely population among the stands exhibiting non-significant exclusion probability (JOLIVET and DEGEN, 2012). Although many studies pro- vided results on genetic assignment, only a subset used this two-step procedure (DEGEN et al, 2013;FRANTZ et al, 2006;HONJO et al, 2008;HOWARD et al, 2009;JOLIVET and DEGEN, 2012;MAUDET et al, 2002;NEGRINI et al, 2008), which provides high security in forensic applications, as the true origin might have not been sampled (MANEL et al, 2002). Other methods for exclusion testing include calculation of likelihood ratios (BEKKEVOLD et al, 2015;OGDEN and LINACRE, 2015).…”