Selection and use of SNP markers for animal identification and paternity analysis in U.S. beef cattle

Abstract

DNA marker technology represents a promising means for determining the genetic identity and kinship of an animal. Compared with other types of DNA markers, single nucleotide polymorphisms (SNPs) are attractive because they are abundant, genetically stable, and amenable to high-throughput automated analysis. In cattle, the challenge has been to identify a minimal set of SNPs with sufficient power for use in a variety of popular breeds and crossbred populations. This report describes a set of 32 highly informative SNP markers distributed among 18 autosomes and both sex chromosomes. Informativity of these SNPs in U.S. beef cattle populations was estimated from the distribution of allele and genotype frequencies in two panels: one consisting of 96 purebred sires representing 17 popular breeds, and another with 154 purebred American Angus from six herds in four Midwestern states. Based on frequency data from these panels, the estimated probability that two randomly selected, unrelated individuals will possess identical genotypes for all 32 loci was 2.0 x 10(-13) for multi-breed composite populations and 1.9 x 10(-10) for purebred Angus populations. The probability that a randomly chosen candidate sire will be excluded from paternity was estimated to be 99.9% and 99.4% for the same respective populations. The DNA immediately surrounding the 32 target SNPs was sequenced in the 96 sires of the multi-breed panel and found to contain an additional 183 polymorphic sites. Knowledge of these additional sites, together with the 32 target SNPs, allows the design of robust, accurate genotype assays on a variety of high-throughput SNP genotyping platforms.

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.…”

“…Allelic association between SNPs would render one of a pair completely uninformative as an identifier. Whilst Werner et al and Heaton et al had positioned their respective panels on chromosomes using fluorescence in situ hybridisation and linkage mapping respectively, only Heaton et al [22] had calculated the LD between SNPs on the same chromosomes. Quantification of LD between SNPs from both of these panels had not been undertaken.…”

“…Amplification products were SNP genotyped by pyrosequencing [26]. Genbank accession numbers of sequences containing all SNPs and location of SNPs are available [18,22]. …”

“…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.…”