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

Kevin A Glover,Michael M Hansen,Thomas D Als,Sigbjørn Lien,Øystein Skaala,Bjørn Høyheim

doi:10.1186/1471-2156-11-2

Abstract

BackgroundTechnological 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.ResultsGlobal 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.ConclusionWhilst 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.

Highlights

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
Genotyping quality DNA was isolated from a total of 512 salmon that were analysed for 15 short tandem repeats (STRs) loci at Institute of Marine Research (IMR) and 388 SNP loci at CIGENE
Individuals failing to yield PCR products for the STR loci were spread among samples, whereas all complete amplification failures in the SNP data set were observed within the sample of escapees

Summary

Introduction

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. The characterisation and availability of single nucleotide polymorphisms (SNPs) in non-model organisms is increasing rapidly [1,2], and within the field of population genetics, growing attention is being given to this class of marker to address a broad range of evolutionary questions (reviewed by [3,4]). Polymorphic short tandem repeat loci (STR), commonly known as microsatellites, have been the primary molecular tool of choice for addressing evolutionary questions for nearly two decades. These markers display several negative characteristics including size homoplasy [5], complex mutational patterns, and are prone to genotyping errors [6]. The implementation of SNPs to delineate population genetic structure is still in its infancy outside the field of human genetics (but see SNPs in cattle e.g., [9,10,11]) for example where they have been demonstrated to out-perform microsatellites for specific questions such as individual ancestry [8]

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