Use of bovine single nucleotide polymorphism markers to verify sample tracking in beef processing

USDA, Agricultural Research Service, US Meat Animal Research Center, State Spur 18D, PO Box 166, Clay Center, NE 68933-0166, USA.
Journal of the American Veterinary Medical Association (Impact Factor: 1.56). 04/2005; 226(8):1311-4. DOI: 10.2460/javma.2005.226.1311
Source: PubMed

ABSTRACT To determine whether a selected set of 20 single nucleotide polymorphism (SNP) markers derived from beef cattle populations can be used to verify sample tracking in a commercial slaughter facility that processes primarily market (ie, culled) dairy cows.
Prospective, blinded validation study.
165 cows and 3 bulls from 18 states (82% Holstein, 8% other dairy breeds, and 10% beef breeds).
Blood was collected by venipuncture from randomly chosen animals just prior to slaughter. The purported corresponding liver samples were collected during beef processing, and genotype profiles were obtained for each sample.
On the basis of SNP allele frequencies in these cattle, the mean probability that 2 randomly selected individuals would possess identical genotypes at all 20 loci was 4.3 x 10(-8). Thus, the chance of a coincidental genotype match between 2 animals was 1 in 23 million. Genotype profiles confirmed appropriate matching for 152 of the 168 (90.5%) purported blood-liver sample pairs and revealed mismatching for 16 (9.5%) pairs. For the 16 mismatched sample pairs, 33% to 76% of the 20 SNP genotypes did not match (mean, 52%). Discordance that could be attributed to genotyping error was estimated to be < 1% on the basis of results for split samples.
Results suggest that this selected set of 20 bovine SNP markers is sufficiently informative to verify accuracy of sample tracking in slaughter plants that process beef or dairy cattle. These or similar SNP markers may facilitate high-throughput, DNA-based, traceback programs designed to detect drug residues in tissues, control of animal diseases, and enhance food safety.

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Available from: Michael P. Heaton, Sep 26, 2015
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    • "Recent advances in high-throughput DNA sequencing, computer software and bioinformatics have made the use of SNPs more popular (Heaton et al., 2002). Although in terms of genetic information a biallelic marker may be considered as a step backwards, SNPs have some promising advantages, including greater abundance (Heaton et al., 2005), genetic stability in mammals (Markovtsova et al., 2000; Nielsen, 2000; Thomson et al., 2000), simpler nomenclature and suitability to automated analysis and data interpretation (Wang et al., 1998; Lindblad-Toh et al., 2000). Furthermore, SNPs have been successfully used in the discovery of quantitative trait loci (QTL) and the association of genes with specific "
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    ABSTRACT: During the last decade, microsatellites (short tandem repeats or STRs) have been successfully used for animal genetic identification, traceability and paternity, although in recent year single nucleotide polymorphisms (SNPs) have been increasingly used for this purpose. An efficient SNP identification system requires a marker set with enough power to identify individuals and their parents. Genetic diagnostics generally include the analysis of related animals. In this work, the degree of information provided by SNPs for a consanguineous herd of cattle was compared with that provided by STRs. Thirty-six closely related Angus cattle were genotyped for 18 STRs and 116 SNPs. Cumulative SNPs exclusion power values (Q) for paternity and sample matching probability (MP) yielded values greater than 0.9998 and 4.32E(-42), respectively. Generally 2-3 SNPs per STR were needed to obtain an equivalent Q value. The MP showed that 24 SNPs were equivalent to the ISAG (International Society for Animal Genetics) minimal recommended set of 12 STRs (MP ∼ 10(-11)). These results provide valuable genetic data that support the consensus SNP panel for bovine genetic identification developed by the Parentage Recording Working Group of ICAR (International Committee for Animal Recording).
    Genetics and Molecular Biology 07/2013; 36(2):185-91. DOI:10.1590/S1415-47572013000200008 · 1.20 Impact Factor
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    • "Genetic identification of single individual – the so called DNA fingerprinting – allows localizing and isolating farms with animals positive to contagious diseases or to trace back any contamination detected in food to the original source [7]. Individual DNA fingerprinting can also support the conventional paper-based traceability; at any point along the supply chain, the DNA profile of a carcass or a meat cut can be matched with the reference biological sample collected on the living animal. "
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    ABSTRACT: This review updates the available molecular techniques and technologies and discusses how they can be used for traceability, food control and enforcement activities. The review also provides examples on how molecular techniques succeeded to trace back unknowns to their breeds of origin, to fingerprint single individuals and to generate evidence in court cases. The examples demonstrate the potential of the DNA based traceability techniques and explore possibilities for translating the next generation genomics tools into a food and feed control and enforcement framework.
    01/2013; 5(1). DOI:10.2174/2212798411305010004
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    • "Recent advances in high-throughput DNA sequencing and bioinformatics have facilitated the identification and validation of large collections of Single Nucleotide Polymorphisms (SNPs) in a number of species (Hall, 2007). SNPs are the fundamental unit of genetic variation and are very useful molecular markers due to their abundance (Heaton et al., 2005), genetic stability (Markovtsova , Marjoram, & Tavaré, 2000) and suitability to automated analysis (Lindblad-Toh et al., 2000). SNPs have been successfully employed in association analysis as markers for a wide range of traits (Chen & Abecasis, 2007; Wollstein et al., 2007), to estimate linkage disequilibrium (Angius et al., 2008) and to identify genes by linkage studies (Hamada et al., 2005). "
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