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

Abstract

During the last decade, microsatellites (short tandem repeats or STRs) have been successfully used for animal genetic identification, traceability and paternity, although in recent year single nucleotide polymorphisms (SNPs) have been increasingly used for this purpose. An efficient SNP identification system requires a marker set with enough power to identify individuals and their parents. Genetic diagnostics generally include the analysis of related animals. In this work, the degree of information provided by SNPs for a consanguineous herd of cattle was compared with that provided by STRs. Thirty-six closely related Angus cattle were genotyped for 18 STRs and 116 SNPs. Cumulative SNPs exclusion power values (Q) for paternity and sample matching probability (MP) yielded values greater than 0.9998 and 4.32E−42, respectively. Generally 2–3 SNPs per STR were needed to obtain an equivalent Q value. The MP showed that 24 SNPs were equivalent to the ISAG (International Society for Animal Genetics) minimal recommended set of 12 STRs (MP ∼ 10−11). These results provide valuable genetic data that support the consensus SNP panel for bovine genetic identification developed by the Parentage Recording Working Group of ICAR (International Committee for Animal Recording).

Genetic population structure in Greenland halibut (Reinhardtius hippoglossoides) and its relevance to fishery management

“…The second key benefit of using SNPs is their binary allelic nature, which simplifies analysis and comparison of results among studies (Smith and Seeb 2008;Morin et al 2009;Slate et al 2009). A disadvantage of binary scoring is the lower statistical power per locus compared with multiallelic markers, such as microsatellites (e.g., Fernandez et al 2013). Fortunately, SNPs are the most abundant genetic mutation within genomes, and it is possible to compensate for low power by increasing the number of loci (Willing et al 2012).…”

Subset of SNPs for parental identification in European bison Lowland-Białowieża line (Bison bonasus bonasus)

“…Because of the wide availability and high polymorphic information content (PIC), microsatellite markers (STRs) were used for this purpose (Glowatzki-Mullis et al 1995), but lower mutation and genotyping error rate, automation of genotyping, ease of data manipulation and calculation caused that panels of single nucleotide polymorphisms (SNPs) have displaced STRs (Heaton et al 2002;Werner et al 2004). Recently, the International Committee for Animal Recording (ICAR) developed a cattle consensus panel of 100 SNPs for routine parentage testing (Fernández et al 2013).…”

Lamb meat traceability: The case of Sambucana sheep

“…Third, the effectiveness of the set of markers might not be high enough to allow for the identification of the likely true father. In this respect it must be taken into account that the discriminatory power certainly is an intrinsic feature of the markers, but it is also depending on the inbreeding level of the breed, which decreases the genetic variability, hence increasing the similarities among individuals (Fernández et al, 2013). So the presence of related subjects among the putative fathers could negatively affect the discriminatory power of the markers used.…”