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

María E Fernández,Pilar Peral-García,María V Ripoli,Egle E Villegas-Castagnasso,Juan P Lirón,Mónica H Carino,Andrés Rogberg-Muñoz,Diego M Posik,Guillermo Giovambattista,Daniel E Goszczynski

doi:10.1590/s1415-47572013000200008

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).

Highlights

DNA markers are becoming increasingly important in animal breeding and have been successfully used in bovine identification, in parentage testing and to establish relationships between two or more individuals (GlowatzkiMullis et al, 1995; Heyen et al, 1997; Williams et al, 1997; Heaton et al, 2002)
These markers have been used to trace meat through the entire food chain (Arana et al, 2002) because of the reliable and accurate traceability they provide based on matching genetic marker profiles (Dalvit et al, 2007); the use of such markers has the potential to improve the rate of genetic progress (Van Eenennaam et al, 2007)
The allele frequencies for single nucleotide polymorphisms (SNPs) and short tandem repeats (STRs) are available from the corresponding author upon request

Summary

Introduction

DNA markers are becoming increasingly important in animal breeding and have been successfully used in bovine identification, in parentage testing and to establish relationships between two or more individuals (GlowatzkiMullis et al, 1995; Heyen et al, 1997; Williams et al, 1997; Heaton et al, 2002). These markers have been used to trace meat through the entire food chain (Arana et al, 2002) because of the reliable and accurate traceability they provide based on matching genetic marker profiles (Dalvit et al, 2007); the use of such markers has the potential to improve the rate of genetic progress (Van Eenennaam et al, 2007). SNPs have been successfully used in the discovery of quantitative trait loci (QTL) and the association of genes with specific productive traits (Chen and Abecasis 2007; Wollstein et al, 2007) and in the identification of individuals and breeds (Negrini et al, 2008)

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