To the editor

Verification of identity and parentage of animals is essential for the efficient management of animal populations and for assessing animal food safety. Recently, DNA-based tests, specifically the analysis of microsatellites, have been introduced for identity verification and parentage control of livestock. In this context, we propose that a standardized set of single nucleotide polymorphisms (SNPs) be adopted as an alternative to microsatellite analyses. To facilitate this approach, we have established a database (http://www.SNPZoo.de) that can serve as a depository of SNP information in livestock species.

The main advantages of SNPs are the low mutation rate, the suitability for standardization, and that they do not require a specific typing platform. Standardization consists of the selection of appropriate SNP loci and establishment of the order in which the genotypes are presented. For a given species, each SNP of this standardized set is unambiguously identified by its unique flanking nucleotide sequence. Each SNP position is queried for the presence or absence of a specific base, resulting in a string of binary answers (10, homozygous allele number 1; 01, homozygous allele number 2; 11, heterozygous; and 00, assay failure) that we term a digital DNA signature.

We hope that establishment of the database will facilitate the standardization process. It contains information on the SNP loci themselves as well as corresponding allele frequency data in a standardized fashion. It is possible to submit information on new variant sites or population data for previously identified SNPs. The goal is to compile, from a large collection of SNPs, a set of SNPs that would allow exclusion powers of >99.99% for parentage control and probabilities of identity of <10−11 for individual identification in each population. Forty SNPs with an average frequency of the minor allele of 20% will yield an exclusion power of 0.99994 and a probability of identity of 2.66073 ¥ 10−12 (ref. 1). There are numerous SNPs with a frequency of the minor allele >20% in several populations and probably even throughout a species, resulting in overlapping sets of SNPs, each set optimal for a different population.

We propose to define 96 SNP positions for the bovine species. Similar standards may also be established for other species. For analyses in a given population, single-nucleotide queries can be restricted to the most polymorphic sites for this population. For each signature, the associated probability of identity and the exclusion probabilities should be indicated to qualify exclusion in parentage control or a signature match in identity control. The first position of the signature will be reserved for the result of a gender query. The standardized format of SNP data will facilitate the maintenance of the allele frequency databases that will be necessary for calculating the exclusion powers and probabilities of identities. Such frequency databases will be an excellent tool for genetic diversity analyses. The proposed standard and the independence from a specific typing platform will be essential to ensure competition on the market for genotyping services and thus low-cost digital DNA signatures. Cost-efficient typing of entire animal populations for the consequent tracing of animals and animal products will become realistic.