title: Use of bovine single nucleotide polymorphism markers to verify sample tracking in beef processing.
abstract: OBJECTIVE
  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.
  
  
  METHODS
  Prospective, blinded validation study.
  
  
  METHODS
  165 cows and 3 bulls from 18 states (82% Holstein, 8% other dairy breeds, and 10% beef breeds).
  
  
  METHODS
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: USDA, Agricultural Research Service, US Meat Animal Research Center, State Spur 18D, PO Box 166, Clay Center, NE 68933-0166, USA.
authors.forename: Michael P
authors.initials: MP
authors.lastname: Heaton
authors.forename: James E
authors.initials: JE
authors.lastname: Keen
authors.forename: Michael L
authors.initials: ML
authors.lastname: Clawson
authors.forename: Gregory P
authors.initials: GP
authors.lastname: Harhay
authors.forename: Nathan
authors.initials: N
authors.lastname: Bauer
authors.forename: Craig
authors.initials: C
authors.lastname: Shultz
authors.forename: Benedict T
authors.initials: BT
authors.lastname: Green
authors.forename: Lisa
authors.initials: L
authors.lastname: Durso
authors.forename: Carol G
authors.initials: CG
authors.lastname: Chitko-McKown
authors.forename: William W
authors.initials: WW
authors.lastname: Laegreid
mesh_terms: D000823:Animal Identification Systems / Q000379:methods / Q000592:standards / Q000662:veterinary*; D000818:Animals; D001483:Base Sequence; D002417:Cattle / Q000235:genetics*; D004247:DNA / Q000097:blood / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification; D005260:Female; D005525:Food-Processing Industry / Q000379:methods / Q000592:standards; D005787:Gene Frequency; D005819:Genetic Markers / Q000235:genetics; D005838:Genotype; D008099:Liver / Q000737:chemistry; D008297:Male; D008460:Meat; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction / Q000662:veterinary; D020641:Polymorphism, Single Nucleotide; D011446:Prospective Studies; D017422:Sequence Analysis, DNA / Q000662:veterinary
chemical_list: D005819:Genetic Markers; D004247:DNA