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


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
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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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