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Open Access Highly Accessed Research article

A comparison of SNP and STR loci for delineating population structure and performing individual genetic assignment

Kevin A Glover1*, Michael M Hansen2, Sigbjørn Lien3, Thomas D Als4, Bjørn Høyheim5 and Øystein Skaala1

Author Affiliations

1 Institute of Marine Research, PO Box 1870, Nordnes N- 5817 Bergen, Norway

2 Department of Biological Sciences, Aarhus University, Ny Munkegade 114, DK-8000 Aarhus C, Denmark

3 Norwegian University of Life Science, Centre of Integrative Genetics and Department of Animal and Aquacultural Sciences, PO Box 5003, 1430 Ås, Norway

4 Technical University of Denmark, National Institute of Aquatic Resources, Section for Population Genetics, Vejlsøvej 39, DK-8600, Silkeborg, Denmark

5 Norwegian School of Veterinary Science, BasAM-Genetics, PO Box 8146, 0033 Oslo, Norway

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BMC Genetics 2010, 11:2  doi:10.1186/1471-2156-11-2

Published: 6 January 2010

Abstract

Background

Technological advances have lead to the rapid increase in availability of single nucleotide polymorphisms (SNPs) in a range of organisms, and there is a general optimism that SNPs will become the marker of choice for a range of evolutionary applications. Here, comparisons between 300 polymorphic SNPs and 14 short tandem repeats (STRs) were conducted on a data set consisting of approximately 500 Atlantic salmon arranged in 10 samples/populations.

Results

Global FST ranged from 0.033-0.115 and -0.002-0.316 for the 14 STR and 300 SNP loci respectively. Global FST was similar among 28 linkage groups when averaging data from mapped SNPs. With the exception of selecting a panel of SNPs taking the locus displaying the highest global FST for each of the 28 linkage groups, which inflated estimation of genetic differentiation among the samples, inferred genetic relationships were highly similar between SNP and STR data sets and variants thereof. The best 15 SNPs (30 alleles) gave a similar level of self-assignment to the best 4 STR loci (83 alleles), however, addition of further STR loci did not lead to a notable increase assignment whereas addition of up to 100 SNP loci increased assignment.

Conclusion

Whilst the optimal combinations of SNPs identified in this study are linked to the samples from which they were selected, this study demonstrates that identification of highly informative SNP loci from larger panels will provide researchers with a powerful approach to delineate genetic relationships at the individual and population levels.