Detection and characterization of SNPs useful for identity control and parentage testing in major European dairy breeds

Abstract

We propose the use of single nucleotide polymorphisms (SNPs) instead of polymorphic microsatellite markers for individual identification and parentage control in cattle. To this end, we present an initial set of 37 SNP markers together with a gender-specific SNP for identity control and parentage testing in the Holstein, Fleckvieh and Braunvieh breeds. To obtain suitable SNPs, a total of 91.13 kb of random genomic DNA was screened yielding 531 SNPs. These, and 43 previously identified SNPs, were subjected to the following selection criteria: (1) the frequency of the minor allele must be larger than 0.1 in at least two of the three examined breeds, and (2) markers should not be linked closely. Allele frequencies were estimated by analysing sequencing traces of pooled DNA or by genotyping individual DNA samples. The selected SNP loci were physically mapped by radiation hybrid mapping or by fluorescence in situ hybridization, and tested against the neutral mutation hypothesis. The presented marker set theoretically allows probabilities of identity less than 10(-13) for individual verification and exclusion powers exceeding 99.99% for parentage testing.

Compilation of a panel of informative single nucleotide polymorphisms for bovine identification in the Northern Irish cattle population

“…Some of the best characterised SNPs at the inception of this work were those described by Werner et al . and Heaton et al ., [18,22]. However unlike the Stockmarks STR based system, these SNPs were not well characterised across a variety of cattle breeds from different countries.…”

“…As a result, single SNPs don't discriminate between individuals very well. However, genotyping of multiple SNPs can overcome this problem [18]. …”

“…Owing to their smaller size, they are less prone to gametic mutation and therefore do not suffer from the same non-identical by descent problems that can affect STRs as they mutate between generations [18]. SNPs are also more robust in their interpretation/analysis than STRs [19] and can be genotyped by a variety of high throughput methods on various platforms, many of which can be automated with economy of scale savings [20].…”

“…With the advent of ever-improving genotyping technologies [21], it has recently become attractive to develop a SNP-based DNA profiling system for the identification of cattle. Two SNP panels have recently been assembled for this purpose [18,22]. …”

“…SNP panels previously identified by Heaton et al, 2002 and Werner et al ., 2004 [18,22] were characterised in our cattle population to determine which would uniquely identify bovine animals. An allele frequency study was carried out in representative breed panels of the most common breeds used in Northern Ireland.…”