Development of a 25‐plex SNP assay for traceability in cattle
- 12 May 2009
- journal article
- Published by Wiley in Animal Genetics
- Vol. 40 (3), 353-356
- https://doi.org/10.1111/j.1365-2052.2008.01846.x
Abstract
Single nucleotide polymorphisms (SNPs) are amenable to automation and therefore have become the marker of choice for DNA profiling. SNaPshot, a primer extension-based method, was used to multiplex 25 SNPs that have been previously validated as useful for identity control. Detection of extended products was based on four different fluorochromes and extension primers with oligonucleotide tails of differing lengths, thus controlling the concise length of the entire chromatogram to 81 bases. Allele frequencies for Holstein, Simmental, Limousin, Angus, Charolais and Tux Cattle were estimated and significant positive Pearson-correlation coefficients were obtained among the analysed breeds. The probability that two randomly unrelated individuals would share identical genotypes for all 25 loci varied from 10(-8) to 10(-10) for these breeds. For parentage control, the exclusion power was found to be 99.9% when the genotypes of both putative parents are known. A traceability test of duplicated samples indicated a high genotyping precision of >0.998. This was further corroborated by analysis of 60 cases of parent-sib pairs and trio families. The 25-plex SNaPshot assay is adapted for low- and high-throughput capacity and thus presents an alternative for DNA-based traceability in the major commercial cattle breeds.Keywords
This publication has 10 references indexed in Scilit:
- Genetic traceability of meat using microsatellite markersFood Research International, 2008
- Genetic traceability of livestock products: A reviewMeat Science, 2007
- Individual identification and genetic traceability in the pig using the SNPlexTM genotyping systemAnimal Genetics, 2007
- Matrix-Assisted Laser Desorption/Ionisation, Time-of-Flight Mass Spectrometry in Genomics ResearchPLoS Genetics, 2006
- Estimation of the number of genetic markers required for individual animal identification accounting for genotyping errorsAnimal Genetics, 2006
- A multiplex assay with 52 single nucleotide polymorphisms for human identificationElectrophoresis, 2006
- Detection and characterization of SNPs useful for identity control and parentage testing in major European dairy breedsAnimal Genetics, 2003
- A review on SNP and other types of molecular markers and their use in animal geneticsGenetics Selection Evolution, 2002
- Selection and use of SNP markers for animal identification and paternity analysis in U.S. beef cattleMammalian Genome, 2002
- Comparisons of three probability formulae for parentage exclusionAnimal Genetics, 1997