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

Abstract

Background Animal identification is pivotal in governmental agricultural policy, enabling the management of subsidy payments, movement of livestock, test scheduling and control of disease. Advances in bovine genomics have made it possible to utilise inherent genetic variability to uniquely identify individual animals by DNA profiling, much as has been achieved with humans over the past 20 years. A DNA profiling test based on bi-allelic single nucleotide polymorphism (SNP) markers would offer considerable advantages over current short tandem repeat (STR) based industry standard tests, in that it would be easier to analyse and interpret. In this study, a panel of 51 genome-wide SNPs were genotyped across panels of semen DNA from 6 common breeds for the purposes of ascertaining allelic frequency. For SNPs on the same chromosome, the extent of linkage disequilbrium was determined from genotype data by Expectation Maximization (EM) algorithm. Minimum probabilities of unique identification were determined for each breed panel. The usefulness of this SNP panel was ascertained by comparison to the current bovine STR Stockmarks II assay. A statistically representative random sampling of bovine animals from across Northern Ireland was assembled for the purposes of determining the population allele frequency for these STR loci and subsequently, the minimal probability of unique identification they conferred in sampled bovine animals from Northern Ireland. Results 6 SNPs exhibiting a minor allele frequency of less than 0.2 in more than 3 of the breed panels were excluded. 2 Further SNPs were found to reside in coding areas of the cattle genome and were excluded from the final panel. The remaining 43 SNPs exhibited genotype frequencies which were in Hardy Weinberg Equilibrium. SNPs on the same chromosome were observed to have no significant linkage disequilibrium/allelic association. Minimal probabilities of uniquely identifying individual animals from each of the breeds were obtained and were observed to be superior to those conferred by the industry standard STR assay. Conclusions The 43 SNPs characterised herein may constitute a starting point for the development of a SNP based DNA identification test for European cattle.

Penalized classification for optimal statistical selection of markers from high-throughput genotyping: application in sheep breeds

“…These systems usually include a first step in which SNPs are preselected and a second step in which different assignment methods are applied (Bertolini et al, 2015). For example, Allen et al (2010) in a study on Irish cattle, reported a set of 43 SNPs for breed identification on the basis of allele frequency. Heaton et al (2014) identified 163 SNPs for use in parentage testing and traceability in sheep, using the minor allele frequency (>0.3).…”

“…The main result was the selection of 48 SNPs from a whole set of 48 068 and these contained sufficient genetic information to produce sufficient power for individuals' breed assignment, using a relatively low number of individuals for breed and closely related breeds. The majority of the SNPs are in non-coding/intergenic regions of the sheep genome (Supplementary Material Table S1) which is ideal for identification and assignment purpose since these regions/ SNPs should be less influenced by natural or artificial selection (Allen et al, 2010).…”

Comparison of the effectiveness of microsatellites and SNP panels for genetic identification, traceability and assessment of parentage in an inbred Angus herd

“…Previous studies designed strategies to sample the entire genetic diversity in beef cattle or purebred populations and simulated populations of purebred gene frequencies have been used to estimate the resolution and sensitivity of these methods in identifying individuals and in parental analysis (Table S7) (Heaton et al , 2002; Werner et al , 2004; López Herráez et al , 2005; Van Eenennaam et al , 2007; Baruch and Weller, 2008; Karniol et al , 2009; Allen et al , 2010; Hara et al , 2010a,b). …”

Imputation of microsatellite alleles from dense SNP genotypes for parentage verification across multiple Bos taurus and Bos indicus breeds

“…Recent work by Fernández et al (2013) showed that even in a Brazilian inbred Angus herd that only 24 SNP were needed to obtain the equivalent matching probability (MP) for parental verification as 18 microsatellites. Similarly, 43 SNP provided 2–4 orders of magnitude grater MP than 11 MS in 6 Northern Ireland cattle breeds (Aberdeen Angus, Belgian Blue, Charolais, Holstein, Limousin, and Simmental) (Allen et al, 2010). …”